@article{monte_nethery_berman_keelara_lincopan_fedorka-cray_barrangou_landgraf_2022, title={Clustered Regularly Interspaced Short Palindromic Repeats Genotyping of Multidrug-Resistant Salmonella Heidelberg Strains Isolated From the Poultry Production Chain Across Brazil}, volume={13}, ISSN={["1664-302X"]}, DOI={10.3389/fmicb.2022.867278}, abstractNote={Salmonella enterica subsp. enterica serovar Heidelberg has been associated with a broad host range, such as poultry, dairy calves, swine, wild birds, environment, and humans. The continuous evolution of S. Heidelberg raises a public health concern since there is a global dispersal of lineages harboring a wide resistome and virulome on a global scale. Here, we characterized the resistome, phylogenetic structure and clustered regularly interspaced short palindromic repeats (CRISPR) array composition of 81 S. Heidelberg strains isolated from broiler farms (n = 16), transport and lairage (n = 5), slaughterhouse (n = 22), and retail market (n = 38) of the poultry production chain in Brazil, between 2015 and 2016 using high-resolution approaches including whole-genome sequencing (WGS) and WGS-derived CRISPR genotyping. More than 91% of the S. Heidelberg strains were multidrug-resistant. The total antimicrobial resistance (AMR) gene abundances did not vary significantly across regions and sources suggesting the widespread distribution of antibiotic-resistant strains from farm to market. The highest AMR gene abundance was observed for fosA7, aac(6')-Iaa, sul2, tet(A), gyrA, and parC for 100% of the isolates, followed by 88.8% for blaCMY-2. The β-lactam resistance was essentially driven by the presence of the plasmid-mediated AmpC (pAmpC) blaCMY-2 gene, given the isolates which did not carry this gene were susceptible to cefoxitin (FOX). Most S. Heidelberg strains were classified within international lineages, which were phylogenetically nested with Salmonella strains from European countries; while CRISPR genotyping analysis revealed that the spacer content was overall highly conserved, but distributed into 13 distinct groups. In summary, our findings underscore the potential role of S. Heidelberg as a key pathogen disseminated from farm to fork in Brazil and reinforce the importance of CRISPR-based genotyping for salmonellae. Hence, we emphasized the need for continuous mitigation programs to monitor the dissemination of this high-priority pathogen.}, journal={FRONTIERS IN MICROBIOLOGY}, author={Monte, Daniel F. M. and Nethery, Matthew A. and Berman, Hanna and Keelara, Shivaramu and Lincopan, Nilton and Fedorka-Cray, Paula J. and Barrangou, Rodolphe and Landgraf, Mariza}, year={2022}, month={Jun} }
 @article{hempstead_gensler_keelara_brennan_urie_wiedenheft_marshall_morningstar-shaw_lantz_fedorka-cray_et al._2022, title={Detection and molecular characterization of Salmonella species on US goat operations}, volume={208}, ISSN={["1873-1716"]}, DOI={10.1016/j.prevetmed.2022.105766}, abstractNote={Salmonella species are an important cause of gastrointestinal disease in animals, including goats. Additionally, Salmonella species are among the top five U.S. foodborne pathogens causing illness to humans. The goat industry is rapidly expanding in the U.S. yet estimates of Salmonella prevalence within these populations is lacking. The aim of this study was to investigate the fecal prevalence, antimicrobial resistance (AMR), biofilm potential, and virulence profile of Salmonella species isolated from goat feces as part of the United States Department of Agriculture (USDA) National Animal Health Monitoring System (NAHMS) Goat 2019 study, enteric microbe component. A total of 4917 fecal samples were collected from 332 operations, from September 2019-March 2020. Salmonella were isolated using standard enrichment and culture methods; antimicrobial susceptibility was determined by broth microdilution. Biofilm production was assessed using a crystal violet assay and normalized to a positive control strain, and PCR was used to detect virulence genes. Overall, we detected a low prevalence (0.7%, n = 35/4917) of Salmonella in goat feces and identified a broad range of serotypes including S. Bareilly (35%) and a single rare S. Sharon. All isolates were pansusceptible to 14 antimicrobials except one, which was resistant to only tetracycline (MIC ≥ 32 µg/mL). All strains were found to possess the majority of virulence determinants screened, and 40% (14 of 35) formed weak, moderate, or strong biofilm. We found a low prevalence of Salmonella, and characteristics of Salmonella in the U.S. goat population informs ongoing public health efforts to manage risk of animal food products and animal interactions.}, journal={PREVENTIVE VETERINARY MEDICINE}, author={Hempstead, Stephanie C. and Gensler, Catherine A. and Keelara, Shivaramu and Brennan, Matthew and Urie, Natalie J. and Wiedenheft, Alyson M. and Marshall, Katherine L. and Morningstar-Shaw, Brenda and Lantz, Kristina and Fedorka-Cray, Paula J. and et al.}, year={2022}, month={Nov} }
 @article{atlaw_keelara_correa_foster_gebreyes_aidara-kane_harden_thakur_fedorka-cray_2022, title={Evidence of sheep and abattoir environment as important reservoirs of multidrug-resistant Salmonella and extended-spectrum beta-lactamase Escherichia coli}, volume={363}, ISSN={["1879-3460"]}, url={http://dx.doi.org/10.1016/j.ijfoodmicro.2021.109516}, DOI={10.1016/j.ijfoodmicro.2021.109516}, abstractNote={The increase in antimicrobial-resistant (AMR) foodborne pathogens, including E. coli and Salmonella in animals, humans, and the environment, is a growing public health concern. Among animals, cattle, pigs, and chicken are reservoirs of these pathogens worldwide. There is a knowledge gap on the prevalence and AMR of foodborne pathogens in small ruminants (i.e., sheep and goats). This study investigates the prevalence and antimicrobial resistance of extended-spectrum beta-lactamase (ESBL) E. coli and Salmonella from sheep and their abattoir environment in North Carolina. We conducted a year-round serial cross-sectional study and collected a total of 1128 samples from sheep (n = 780) and their abattoir environment (n = 348). Sheep samples consisted of feces, cecal contents, carcass swabs, and abattoir resting area feces. Environmental samples consisted of soil samples, lairage swab, animal feed, and drinking water for animals. We used CHROMAgar EEC with 4 μg/ml of Cefotaxime for isolating ESBL E. coli, and ESBL production was confirmed by double-disk diffusion test. Salmonella was isolated and confirmed using standard methods. All of the confirmed isolates were tested against a panel of 14 antimicrobials to elucidate susceptibility profiles. The prevalence of ESBL E. coli and Salmonella was significantly higher in environmental samples (47.7% and 65.5%) compared to the sheep samples (19.5% and 17.9%), respectively (P < 0.0001). We recovered 318 ESBL E. coli and 368 Salmonella isolates from sheep and environmental samples. More than 97% (310/318) of ESBL E. coli were multidrug-resistant (MDR; resistant to ≥3 classes of antimicrobials). Most Salmonella isolates (77.2%, 284/368) were pansusceptible, and 10.1% (37/368) were MDR. We identified a total of 24 different Salmonella serotypes by whole genome sequencing (WGS). The most common serotypes were Agona (19.8%), Typhimurium (16.2%), Cannstatt (13.2%), Reading (13.2%), and Anatum (9.6%). Prevalence and percent resistance of ESBL E. coli and Salmonella isolates varied significantly by season and sample type (P < 0.0001). The co-existence of ESBL E. coli in the same sample was associated with increased percent resistance of Salmonella to Ampicillin, Chloramphenicol, Sulfisoxazole, Streptomycin, and Tetracycline. We presumed that the abattoir environment might have played a great role in the persistence and dissemination of resistant bacteria to sheep as they arrive at the abattoir. In conclusion, our study reaffirms that sheep and their abattoir environment act as important reservoirs of AMR ESBL E. coli and MDR Salmonella in the U.S. Further studies are required to determine associated public health risks.}, journal={International Journal of Food Microbiology}, publisher={Elsevier BV}, author={Atlaw, N.A. and Keelara, S. and Correa, M. and Foster, D. and Gebreyes, W. and Aidara-Kane, A. and Harden, L. and Thakur, S. and Fedorka-Cray, P.J.}, year={2022}, month={Feb}, pages={109516} }
 @article{dieye_hull_wane_harden_fall_sambe-ba_seck_fedorka-cray_thakur_2022, title={Genomics of human and chicken Salmonella isolates in Senegal: Broilers as a source of antimicrobial resistance and potentially invasive nontyphoidal salmonellosis infections}, volume={17}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0266025}, abstractNote={Salmonella enterica is the most common foodborne pathogen worldwide. It causes two types of diseases, a self-limiting gastroenteritis and an invasive, more threatening, infection. Salmonella gastroenteritis is caused by several serotypes and is common worldwide. In contrast, invasive salmonellosis is rare in high-income countries (HIC) while frequent in low- and middle-income countries (LMIC), especially in sub-Saharan Africa (sSA). Invasive Nontyphoidal Salmonella (iNTS), corresponding to serotypes other than Typhi and Paratyphi, have emerged in sSA and pose a significant risk to public health. We conducted a whole-genome sequence (WGS) analysis of 72 strains of Salmonella isolated from diarrheic human patients and chicken meat sold in multipurpose markets in Dakar, Senegal. Antimicrobial susceptibility testing combined with WGS data analysis revealed frequent resistance to fluoroquinolones and the sulfamethoxazole-trimethoprim combination that are among the most used treatments for invasive Salmonella. In contrast, resistance to the historical first-line drugs chloramphenicol and ampicillin, and to cephalosporins was rare. Antimicrobial resistance (AMR) was lower in clinical isolates compared to chicken strains pointing to the concern posed by the excessive use of antimicrobials in farming. Phylogenetic analysis suggested possible transmission of the emerging multidrug resistant (MDR) Kentucky ST198 and serotype Schwarzengrund from chicken to human. These results stress the need for active surveillance of Salmonella and AMR in order to address invasive salmonellosis caused by nontyphoidal Salmonella strains and other important bacterial diseases in sSA.}, number={3}, journal={PLOS ONE}, author={Dieye, Yakhya and Hull, Dawn M. and Wane, Abdoul Aziz and Harden, Lyndy and Fall, Cheikh and Sambe-Ba, Bissoume and Seck, Abdoulaye and Fedorka-Cray, Paula J. and Thakur, Siddhartha}, year={2022}, month={Mar} }
 @article{atlaw_keelara_correa_foster_gebreyes_aidara-kane_harden_thakur_fedorka-cray_2021, title={Identification of CTX-M type ESBL E. coli from sheep and their abattoir environment using whole-genome sequencing}, volume={10}, ISSN={["2076-0817"]}, url={https://doi.org/10.3390/pathogens10111480}, DOI={10.3390/pathogens10111480}, abstractNote={Widespread dissemination of extended-spectrum beta-lactamase (ESBL) Escherichia coli (E. coli) in animals, retail meats, and patients has been reported worldwide except for limited information on small ruminants. Our study focused on the genotypic characterization of ESBL E. coli from healthy sheep and their abattoir environment in North Carolina, USA. A total of 113 ESBL E. coli isolates from sheep (n = 65) and their abattoir environment (n = 48) were subjected to whole-genome sequencing (WGS). Bioinformatics tools were used to analyze the WGS data. Multiple CTX-M-type beta-lactamase genes were detected, namely blaCTX-M-1, blaCTX-M-14, blaCTX-M-15, blaCTX-M-27, blaCTX-M-32, blaCTX-M-55, and blaCTX-M-65. Other beta-lactamase genes detected included blaCMY-2, blaTEM-1A/B/C, and blaCARB-2. In addition, antimicrobial resistance (AMR) genes and/or point mutations that confer resistance to quinolones, aminoglycosides, phenicols, tetracyclines, macrolides, lincosamides, and folate-pathway antagonists were identified. The majority of the detected plasmids were shared between isolates from sheep and the abattoir environment. Sequence types were more clustered around seasonal sampling but dispersed across sample types. In conclusion, our study reported wide dissemination of ESBL E. coli in sheep and the abattoir environment and associated AMR genes, point mutations, and plasmids. This is the first comprehensive AMR and WGS report on ESBL E. coli from sheep and abattoir environments in the United States.}, number={11}, journal={Pathogens}, publisher={MDPI AG}, author={Atlaw, N.A. and Keelara, S. and Correa, M. and Foster, D. and Gebreyes, W. and Aidara-Kane, A. and Harden, L. and Thakur, S. and Fedorka-Cray, P.J.}, year={2021}, pages={1480} }
 @article{king_schmidt_thakur_fedorka-cray_keelara_harden_essack_2021, title={Resistome of a carbapenemase-producing novel ST232 Klebsiella michiganensis isolate from urban hospital effluent in South Africa}, volume={24}, ISSN={["2213-7173"]}, DOI={10.1016/j.jgar.2021.01.004}, abstractNote={Klebsiella michiganensis is an emerging pathogen implicated in nosocomial infections. Here we report on the resistome, virulome and mobilome of a carbapenemase-producing K. michiganensis isolate from urban hospital effluent in Pietermaritzburg, KwaZulu-Natal, South Africa. Klebsiella sp. isolate KP124 was originally isolated from the final effluent of an urban tertiary hospital in Pietermaritzburg, KwaZulu-Natal.Following phenotypic characterisation and antibiotic susceptibility testing, the genome of carbapenemase-producing isolate KP124 was sequenced using an Illumina MiSeq platform, de novo assembled and analysed using established bioinformatics tools.The draft genome of strain KP124 was 6 544 586 bp in length, comprising 203 contigs >200 bp. Following confirmation of isolate KP124 as K. michiganensis using reference genomes, the blaOXA-181 carbapenemase gene as well as 11 additional genes encoding resistance against β-lactams, aminoglycosides, fluoroquinolones and sulfonamides were detected. Virulence factors enabling iron acquisition and cell adherence, capsule locus type and plasmid replicon types were identified.This study represents the first report of an OXA-181 carbapenemase-producing K. michiganensis isolate from hospital effluent in South Africa. The presence of such a strain in the environment owing to the absence of hospital effluent treatment presents a potential risk to informal communities that may use contaminated surface water domestically.}, journal={JOURNAL OF GLOBAL ANTIMICROBIAL RESISTANCE}, author={King, T. L. and Schmidt, S. and Thakur, S. and Fedorka-Cray, P. and Keelara, S. and Harden, L. and Essack, S. Y.}, year={2021}, month={Mar}, pages={321–324} }
 @misc{cray_sheahan_dekaney_2021, title={Secretory Sorcery: Paneth Cell Control of Intestinal Repair and Homeostasis}, volume={12}, ISSN={["2352-345X"]}, DOI={10.1016/j.jcmgh.2021.06.006}, abstractNote={Paneth cells are professional secretory cells that classically play a role in the innate immune system by secreting antimicrobial factors into the lumen to control enteric bacteria. In this role, Paneth cells are able to sense cues from luminal bacteria and respond by changing production of these factors to protect the epithelial barrier. Paneth cells rely on autophagy to regulate their secretory capability and capacity. Disruption of this pathway through mutation of genes, such as Atg16L1, results in decreased Paneth cell function, dysregulated enteric microbiota, decreased barrier integrity, and increased risk of diseases such as Crohn's disease in humans. Upon differentiation Paneth cells migrate downward and intercalate among active intestinal stem cells at the base of small intestinal crypts. This localization puts them in a unique position to interact with active intestinal stem cells, and recent work shows that Paneth cells play a critical role in influencing the intestinal stem cell niche. This review discusses the numerous ways Paneth cells can influence intestinal stem cells and their niche. We also highlight the ways in which Paneth cells can alter cells and other organ systems.}, number={4}, journal={CELLULAR AND MOLECULAR GASTROENTEROLOGY AND HEPATOLOGY}, author={Cray, Paul and Sheahan, Breanna J. and Dekaney, Christopher M.}, year={2021}, pages={1239–1250} }
 @article{cray_sheahan_cortes_dekaney_2020, title={Doxorubicin increases permeability of murine small intestinal epithelium and cultured T84 monolayers}, volume={10}, ISSN={["2045-2322"]}, DOI={10.1038/s41598-020-78473-1}, abstractNote={Abstract Enteric bacteria and/or their products are necessary for doxorubicin (DXR)-induced small intestine mucosal damage. While DXR does not induce gross loss of epithelium, others have shown elevated serum endotoxin after DXR administration. However, the mechanism of movement is unknown. We hypothesized that DXR treatment resulted in increased paracellular translocation of bacteria or bacterial products through the small intestinal epithelium. We measured permeability after DXR administration using transepithelial resistance and macromolecular flux and assessed tight junctional gene expression and protein localization both in vitro using T84 cells and ex vivo using murine jejunum. DXR treatment increased flux of 4 kDa dextrans in mouse jejenum, but increased flux of 4, 10 and 20 kDa dextrans in T84 cells. Following DXR, we observed increased permeability, both in vitro and ex vivo, independent of bacteria. DXR induced increased expression of Cldn2 and Cldn4 in murine small intestine but increased only CLDN2 expression in T84 cells. DXR treatment induced disorganization of tight junctional proteins. We conclude that DXR increases paracellular transit of small macromolecules, including bacterial products, through the epithelium, by altering expression of tight junctional components and dynamic loosening of cellular tight junctions.}, number={1}, journal={SCIENTIFIC REPORTS}, author={Cray, Paul and Sheahan, Breanna J. and Cortes, Jocsa E. and Dekaney, Christopher M.}, year={2020}, month={Dec} }
 @article{ball_monte_aidara-kane_matheu_ru_thakur_ejobi_fedorka-cray_2020, title={International lineages of Salmonella enterica serovars isolated from chicken farms, Wakiso District, Uganda}, volume={15}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0220484}, abstractNote={The growing occurrence of multidrug-resistant (MDR) Salmonella enterica in poultry has been reported with public health concern worldwide. We reported, recently, the occurrence of Escherichia coli and Salmonella enterica serovars carrying clinically relevant resistance genes in dairy cattle farms in the Wakiso District, Uganda, highlighting an urgent need to monitor food-producing animal environments. Here, we present the prevalence, antimicrobial resistance, and sequence type of 51 Salmonella isolates recovered from 379 environmental samples from chicken farms in Uganda. Among the Salmonella isolates, 32/51 (62.7%) were resistant to at least one antimicrobial, and 10/51 (19.6%) displayed multiple drug resistance. Through PCR, five replicon plasmids were identified among chicken Salmonella isolates including IncFIIS 17/51 (33.3%), IncI1α 12/51 (23.5%), IncP 8/51 (15.7%), IncX1 8/51 (15.7%), and IncX2 1/51 (2.0%). In addition, we identified two additional replicons through WGS (Whole Genome Sequencing; ColpVC and IncFIB). A significant seasonal difference between chicken sampling periods was observed (p = 0.0017). We conclude that MDR Salmonella highlights the risks posed to animals and humans. Implementing a robust, integrated surveillance system will aid in monitoring MDR zoonotic threats.}, number={1}, journal={PLOS ONE}, author={Ball, Takiyah and Monte, Daniel and Aidara-Kane, Awa and Matheu, Jorge and Ru, Hongyu and Thakur, Siddhartha and Ejobi, Francis and Fedorka-Cray, Paula}, year={2020}, month={Jan} }
 @article{jacob_keelara_aidara-kane_alvarez_fedorka-cray_2020, title={Optimizing a Screening Protocol for Potential Extended-Spectrum beta-Lactamase Escherichia coli on MacConkey Agar for Use in a Global Surveillance Program}, volume={58}, ISSN={["1098-660X"]}, DOI={10.1128/JCM.01039-19}, abstractNote={The increasing prevalence of extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli is worrisome. Coordinated efforts to better understand global prevalence and risk factors are needed. Developing lower- and middle-income countries need reliable, readily available, and cost-effective solutions for detecting ESBL E. coli to contribute to global surveillance. We evaluated MacConkey agar supplemented with ceftriaxone or cefotaxime as a screening method for accurately detecting and quantifying potential ESBL E. coli .}, number={9}, journal={JOURNAL OF CLINICAL MICROBIOLOGY}, author={Jacob, Megan E. and Keelara, Shivaramu and Aidara-Kane, Awa and Alvarez, Jorge R. Matheu and Fedorka-Cray, Paula J.}, year={2020}, month={Sep} }
 @article{monte_lincopan_fedorka-cray_landgraf_2019, title={Current insights on high priority antibiotic-resistant Salmonella enterica in food and foodstuffs: a review}, volume={26}, ISSN={2214-7993}, url={http://dx.doi.org/10.1016/j.cofs.2019.03.004}, DOI={10.1016/j.cofs.2019.03.004}, abstractNote={Multi-drug resistant Salmonella enterica remains one of the most pressing global concerns. The use of antimicrobials in food chain has contributed to the selection of resistant strains and their dissemination through vectors contributes to persistence in the environment. Further, the emergence of international clones could be favored by the versatility of Salmonella through host adaptability, ubiquity, and persistence along the food chain. Mobile genetic elements are likely a key vector, which propagates resistant clones. In this regard, Salmonella isolates displaying resistance, especially to the last resort antibiotics raises a public health concern as treatment options become limited. This review aims to provide insights on our current understanding of the antibiotic-resistant S. enterica and of their persistence along food chain.}, journal={Current Opinion in Food Science}, publisher={Elsevier BV}, author={Monte, Daniel F and Lincopan, Nilton and Fedorka-Cray, Paula J and Landgraf, Mariza}, year={2019}, month={Apr}, pages={35–46} }
 @misc{monte_lincopan_cerdeira_fedorka-cray_landgraf_2019, title={Early Dissemination of qnrE1 in Salmonella enterica Serovar Typhimurium from Livestock in South America}, volume={63}, ISSN={["1098-6596"]}, DOI={10.1128/AAC.00571-19}, number={9}, journal={ANTIMICROBIAL AGENTS AND CHEMOTHERAPY}, author={Monte, Daniel F. and Lincopan, Nilton and Cerdeira, Louise and Fedorka-Cray, Paula J. and Landgraf, Mariza}, year={2019}, month={Sep} }
 @article{monte_nelson_cerdeira_keelara_greene_griffin_rath_hall_page_fedorka-cray_et al._2019, title={Multidrug- and colistin-resistant Salmonella enterica 4,[5],12:i:- sequence type 34 carrying the mcr-3.1 gene on the IncHI2 plasmid recovered from a human}, volume={68}, ISSN={0022-2615 1473-5644}, url={http://dx.doi.org/10.1099/jmm.0.001012}, DOI={10.1099/jmm.0.001012}, abstractNote={A colistin-resistant Salmonella enterica 4, [5],12:i:- sequence type (ST) 34 harbouring mcr-3.1 was recovered from a patient who travelled to China 2 weeks prior to diarrhoea onset. Genomic analysis revealed the presence of the mcr-3.1 gene located in the globally disseminated IncHI2 plasmid, highlighting the intercontinental dissemination of the colistin-resistant S. enterica 4, [5],12:i:- ST34 pandemic clone.}, number={7}, journal={Journal of Medical Microbiology}, publisher={Microbiology Society}, author={Monte, Daniel F. and Nelson, Valerie and Cerdeira, Louise and Keelara, Shivaramu and Greene, Shermalyn and Griffin, Denise and Rath, Shadia and Hall, Robbie and Page, Nichole and Fedorka-Cray, Paula J. and et al.}, year={2019}, month={Jul}, pages={986–990} }
 @article{monte_nelson_cerdeira_keelara_greene_griffin_rath_hall_page_lawson_et al._2019, title={Multidrug- and colistin-resistant Salmonella enterica 4,[5],12:i:- sequence type 34 carrying the mcr-3.1 gene on the IncHI2 plasmid recovered from a human (vol 68, pg 986, 2019)}, volume={68}, ISSN={["1473-5644"]}, DOI={10.1099/jmm.0.001057}, abstractNote={Microbiology Society journals contain high-quality research papers and topical review articles. We are a not-for-profit publisher and we support and invest in the microbiology community, to the benefit of everyone. This supports our principal goal to develop, expand and strengthen the networks available to our members so that they can generate new knowledge about microbes and ensure that it is shared with other communities.}, number={11}, journal={JOURNAL OF MEDICAL MICROBIOLOGY}, author={Monte, Daniel F. and Nelson, Valerie and Cerdeira, Louise and Keelara, Shivaramu and Greene, Shermalyn and Griffin, Denise and Rath, Shadia and Hall, Robbie and Page, Nichole and Lawson, Thomas and et al.}, year={2019}, month={Nov}, pages={1694–1694} }
 @article{yuan_krull_wang_erdman_fedorka-cray_logue_o'connor_2018, title={Changes in the prevalence of Salmonella serovars associated swine production and correlations of avian, bovine and swine-associated serovars with human-associated serovars in the United States (1997-2015)}, volume={65}, ISSN={1863-1959}, url={http://dx.doi.org/10.1111/zph.12473}, DOI={10.1111/zph.12473}, abstractNote={Summary As Salmonella enterica is an important pathogen of food animals, surveillance programmes for S. enterica serovars have existed for many years in the United States. Surveillance programmes serve many purposes, one of which is to evaluate alterations in the prevalence of serovars that may signal changes in the ecology of the target organism. The primary aim of this study was to evaluate changes in the proportion of S. enterica serovars isolated from swine over a near 20‐year observation period (1997–2015) using four longitudinal data sets from different food animal species. The secondary aim was to evaluate correlations between changes in S. enterica serovars frequently recovered from food animals and changes in S. enterica serovars associated with disease in humans. We found decreasing proportions of S. enterica serovar Typhimurium, serovar Derby and serovar Heidelberg and increasing proportions of S. enterica serovar 4,[5],12:i:‐, serovar Infantis and serovar Johannesburg in swine over time. We also found positive correlations for the yearly changes in S. enterica serovar 4,[5],12:i:‐, serovar Anatum and serovar Johannesburg between swine and human data; in S. enterica Worthington between avian and human data; and in S. enterica serovar 4,[5],12:i:‐ between bovine and human data. We found negative correlations for the yearly changes in S. enterica serovar 4,[5],12:i:‐ and serovar Johannesburg between avian and human data.}, number={6}, journal={Zoonoses and Public Health}, publisher={Wiley}, author={Yuan, C. and Krull, A. and Wang, C. and Erdman, M. and Fedorka-Cray, P. J. and Logue, C. M. and O'Connor, A. M.}, year={2018}, month={Apr}, pages={648–661} }
 @article{iwamoto_reynolds_karp_tate_fedorka-cray_plumblee_hoekstra_whichard_mahon_2017, title={Ceftriaxone-Resistant Nontyphoidal Salmonella from Humans, Retail Meats, and Food Animals in the United States, 1996–2013}, volume={14}, ISSN={1535-3141 1556-7125}, url={http://dx.doi.org/10.1089/fpd.2016.2180}, DOI={10.1089/fpd.2016.2180}, abstractNote={Ceftriaxone resistance in Salmonella is a serious public health threat. Ceftriaxone is commonly used to treat severe Salmonella infections, especially in children. Identifying the sources and drivers of ceftriaxone resistance among nontyphoidal Salmonella is crucial.The National Antimicrobial Resistance Monitoring System (NARMS) tracks antimicrobial resistance in foodborne and other enteric bacteria from humans, retail meats, and food animals. We examined NARMS data reported during 1996-2013 to characterize ceftriaxone-resistant Salmonella infections in humans. We used Spearman rank correlation to examine the relationships between the annual percentage of ceftriaxone resistance among Salmonella isolates from humans with isolates from retail meats and food animals.A total of 978 (2.9%) of 34,100 nontyphoidal Salmonella isolates from humans were resistant to ceftriaxone. Many (40%) ceftriaxone-resistant isolates were from children younger than 18 years. Most ceftriaxone-resistant isolates were one of three serotypes: Newport (40%), Typhimurium (26%), or Heidelberg (12%). All were resistant to other antimicrobials, and resistance varied by serotype. We found statistically significant correlations in ceftriaxone resistance between human and ground beef Newport isolates (r = 0.83), between human and cattle Typhimurium isolates (r = 0.57), between human and chicken Heidelberg isolates (r = 0.65), and between human and turkey Heidelberg isolates (r = 0.67).Ceftriaxone resistance among Salmonella Newport, Typhimurium, and Heidelberg isolates from humans strongly correlates with ceftriaxone resistance in isolates from ground beef, cattle, and poultry, respectively. These findings support other lines of evidence that food animals are important reservoirs of ceftriaxone-resistant Salmonella that cause human illness in the United States.}, number={2}, journal={Foodborne Pathogens and Disease}, publisher={Mary Ann Liebert Inc}, author={Iwamoto, Martha and Reynolds, Jared and Karp, Beth E. and Tate, Heather and Fedorka-Cray, Paula J. and Plumblee, Jodie R. and Hoekstra, Robert M. and Whichard, Jean M. and Mahon, Barbara E.}, year={2017}, month={Feb}, pages={74–83} }
 @article{ladely_meinersmann_ball_fedorka-cray_2016, title={Antimicrobial Susceptibility and Plasmid Replicon Typing of Salmonella enterica Serovar Kentucky Isolates Recovered from Broilers}, volume={13}, ISSN={["1556-7125"]}, DOI={10.1089/fpd.2015.2102}, abstractNote={Salmonella Kentucky has become the predominant serovar recovered from broilers slaughtered in the United States, and the prevalence of antimicrobial resistance (AMR) has increased dramatically in this serovar. Relationships between AMR, genotype, and plasmid replicon types were characterized for 600 Salmonella Kentucky isolates recovered from chicken carcasses from 2004 to 2013. Pulsed-field gel electrophoresis cluster analysis revealed 112 unique types sharing 79% similarity. Over half of the isolates studies were assigned to two large clusters (unique restriction patterns) consisting of 190 (A) and 151 (B) isolates. The remaining (n = 259) more diverse isolates (110 unique patterns) shall be designated cluster C for discussion. Clusters A had significantly more (p < 0.05) isolates resistant to streptomycin (68.4%) and tetracycline (91.6%) compared to cluster C (50.6% and 40.9% to streptomycin and tetracycline, respectively) or cluster B, which had the least (p < 0.05) resistance (11.9% and 13.2% to streptomycin and tetracycline, respectively). In addition, there was segregation of plasmid replicon types among clusters. Cluster A had significantly more (p < 0.05) replicon type FIB (90.5%) compared to cluster C (37.1%), which had significantly more compared to cluster B (10.6%). Cluster B had significantly more (p < 0.05) replicon type I1 (87.4%) compared to cluster C (68.7%), which had significantly more (p < 0.05) compared to cluster A (32.6%). Cluster C harbored significantly more (p < 0.05) HI2 replicon type (18.1%) compared to clonal clusters A (1.6%) or B (1.3%). The prevalence of plasmid replicon type A/C did not differ among clusters (A, 0.5%; B, 2.0%; C, 0.4%). Both streptomycin and tetracycline resistance were significantly linked (p < 0.05) to plasmid replicon type FIB. In addition, replicon type HI2 was also significantly linked (p < 0.05) to streptomycin resistance. We conclude that the dramatic increase in streptomycin and tetracycline resistance among Salmonella Kentucky isolated from poultry is due to the expansion of strains harboring plasmid replicon types FIB and HI2.}, number={6}, journal={FOODBORNE PATHOGENS AND DISEASE}, author={Ladely, Scott R. and Meinersmann, Richard J. and Ball, Takiyah A. and Fedorka-Cray, Paula J.}, year={2016}, month={Jun}, pages={309–315} }
 @article{thitaram_frank_siragusa_bailey_dargatz_lombard_haley_lyon_fedorka-cray_2016, title={Antimicrobial susceptibility of Clostridium difficile isolated from food animals on farms}, volume={227}, ISSN={["1879-3460"]}, DOI={10.1016/j.ijfoodmicro.2016.03.017}, abstractNote={Clostridium difficile is commonly associated with a spectrum of disease in humans referred to as C. difficile-associated disease (CDAD) and use of antimicrobials is considered a risk factor for development of disease in humans. C. difficile can also inhabit healthy food animals and transmission to humans is possible. As a result of the complexity and cost of testing, C. difficile is rarely tested for antimicrobial susceptibility. A total of 376 C. difficile strains (94 each from swine and dairy feces, and 188 from beef cattle feces) were isolated from healthy food animals on farms during studies conducted by the National Animal Health Monitoring System. Using the Etest (AB Biodisk, Solna, Sweden), samples were tested for susceptibility to nine antimicrobials implicated as risk factors for CDAD (linezolid, amoxicillin-clavulanic acid, ampicillin, clindamycin, erythromycin, levofloxacin, metronidazole, rifampicin, and vancomycin). Vancomycin was active against all isolates of C. difficile (MIC90=3.0μg/ml) while almost all isolates (n=369; 98.1%) were resistant to levofloxacin. With the exception of vancomycin, resistance varied by animal species as follows: linezolid (8.5% resistance among swine versus 2.1 and 1.1% resistance among dairy and beef, respectively), clindamycin (56.4% resistance among swine versus 80% and 90.9% resistance among dairy and beef, respectively), and rifampicin (2.1% and 0% resistance among swine and dairy cattle isolates, respectively versus 14.3% resistance among beef isolates). Regardless of species, multiple drug resistance was observed most often to combinations of clindamycin and levofloxacin (n=195; 51.9%) and ampicillin, clindamycin and levofloxacin (n=41; 10.9%). The reason for the variability of resistance between animal species is unknown and requires further research.}, journal={INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY}, author={Thitaram, S. N. and Frank, J. F. and Siragusa, G. R. and Bailey, J. S. and Dargatz, D. A. and Lombard, J. E. and Haley, C. A. and Lyon, S. A. and Fedorka-Cray, P. J.}, year={2016}, month={Jun}, pages={1–5} }
 @article{vieira_grass_fedorka cray_plumblee_tate_cole_2016, title={Attribution of Salmonella enterica serotype Hadar infections using antimicrobial resistance data from two points in the food supply system}, volume={144}, ISSN={0950-2688 1469-4409}, url={http://dx.doi.org/10.1017/s0950268816000066}, DOI={10.1017/s0950268816000066}, abstractNote={SUMMARY A challenge to the development of foodborne illness prevention measures is determining the sources of enteric illness. Microbial subtyping source-attribution models attribute illnesses to various sources, requiring data characterizing bacterial isolate subtypes collected from human and food sources. We evaluated the use of antimicrobial resistance data on isolates of Salmonella enterica serotype Hadar, collected from ill humans, food animals, and from retail meats, in two microbial subtyping attribution models. We also compared model results when either antimicrobial resistance or pulsed-field gel electrophoresis (PFGE) patterns were used to subtype isolates. Depending on the subtyping model used, 68–96% of the human infections were attributed to meat and poultry food products. All models yielded similar outcomes, with 86% [95% confidence interval (CI) 80–91] to 91% (95% CI 88–96) of the attributable infections attributed to turkey, and 6% (95% CI 2–10) to 14% (95% CI 8–20) to chicken. Few illnesses (<3%) were attributed to cattle or swine. Results were similar whether the isolates were obtained from food animals during processing or from retail meat products. Our results support the view that microbial subtyping models are a flexible and robust approach for attributing Salmonella Hadar.}, number={9}, journal={Epidemiology and Infection}, publisher={Cambridge University Press (CUP)}, author={Vieira, A. R. and Grass, J. and Fedorka Cray, P. J. and Plumblee, J. R. and Tate, H. and Cole, D. J.}, year={2016}, month={Feb}, pages={1983–1990} }
 @article{jones_guard_gast_buhr_fedorka-cray_abdo_plumblee_bourassa_cox_rigsby_et al._2016, title={Influence of commercial laying hen housing systems on the incidence and identification of Salmonella and Campylobacter}, volume={95}, ISSN={["1525-3171"]}, DOI={10.3382/ps/pew036}, abstractNote={The housing of laying hens is important for social, industrial, and regulatory aspects. Many studies have compared hen housing systems on the research farm, but few have fully examined commercial housing systems and management strategies. The current study compared hens housed in commercial cage-free aviary, conventional cage, and enriched colony cage systems. Environmental and eggshell pool samples were collected from selected cages/segments of the housing systems throughout the production cycle and monitored for Salmonella and Campylobacter prevalence. At 77 wk of age, 120 hens per housing system were examined for Salmonella and Campylobacter colonization in the: adrenal glands, spleen, ceca, follicles, and upper reproductive tract. All isolates detected from environmental swabs, eggshell pools, and tissues were identified for serotype. Two predominant Salmonella were detected in all samples:S.Braenderup andS.Kentucky.Campylobacter coli and C. jejuni were the only Campylobacter detected in the flocks. Across all housing systems, approximately 7% of hens were colonized with Salmonella, whereas >90% were colonized with Campylobacter Salmonella Braenderup was the isolate most frequently detected in environmental swabs (P<0.0001) and housing system impacted Salmonella spp. shedding (P<0.0001).Campylobacter jejuni was the isolate most frequently found in environmental swabs (P<0.01), while housing system impacted the prevalence of C. coli and jejuniin ceca (P<0.0001). The results of this study provide a greater understanding of the impact of hen housing systems on hen health and product safety. Additionally, producers and academia can utilize the findings to make informed decisions on hen housing and management strategies to enhance hen health and food safety.}, number={5}, journal={POULTRY SCIENCE}, author={Jones, D. R. and Guard, J. and Gast, R. K. and Buhr, R. J. and Fedorka-Cray, P. J. and Abdo, Z. and Plumblee, J. R. and Bourassa, D. V. and Cox, N. A. and Rigsby, L. L. and et al.}, year={2016}, month={May}, pages={1116–1124} }
 @article{ladely_meinersmann_plumblee_fedorka-cray_2016, title={Isolation Method (Direct Plating or Enrichment) does Not Affect Antimicrobial Susceptibility of Campylobacter from Chicken Carcasses}, volume={37}, ISSN={0149-6085}, url={http://dx.doi.org/10.1111/jfs.12279}, DOI={10.1111/jfs.12279}, abstractNote={Abstract To determine if Campylobacter isolation method influenced antimicrobial susceptibility results, the minimum inhibitory concentrations (MIC) of nine antimicrobials were compared for 291 pairs of Campylobacter isolates recovered from chicken carcass rinse samples using direct plating and an enrichment method. Among the isolates 64.1% were C. jejuni , 35.7% were C. coli , and 0.2% were C. lari . Direct plating yielded significantly less ( P < 0.05) C. coli (21.3%) compared to sample enrichment (50.2%). Antimicrobial resistance was most common for tetracycline (41.4%), nalidixic acid (26.3%), and ciprofloxacin (25.9%). Significantly more ( P < 0.05) C. coli were resistant to nalidixic acid, ciprofloxacin, gentamicin, azithromycin, and erythromycin as compared to C. jejuni isolates. Nonparametric bootstrap analysis of antimicrobial MICs showed no significant differences between direct plating and the enrichment method for any of the antimicrobials tested. These data indicate that bacterial isolation method can bias Campylobacter species recovery. However, isolation method did not significantly affect antimicrobial susceptibility results of C. jejuni or C. coli recovered from broiler carcasses. Practical Applications To monitor trends in food safety and public health, antimicrobial susceptibility testing of Campylobacter derived from poultry products and infected patients has become common practice in both regulatory food safety and public health programs. Various methods have been employed for Campylobacter recovery including direct plating for enumeration of contamination levels and enrichment protocols for detection of low numbers or injured cells. This study was conducted to determine if the method of Campylobacter isolation from chicken carcass rinsate, direct plating or enrichment, influences antimicrobial susceptibility testing results.}, number={1}, journal={Journal of Food Safety}, publisher={Wiley}, author={Ladely, Scott R. and Meinersmann, Richard J. and Plumblee, Jodie R. and Fedorka-Cray, Paula J.}, year={2016}, month={Mar}, pages={e12279} }
 @article{dargatz_kopral_erdman_fedorka-cray_2016, title={Prevalence and Antimicrobial Resistance of Salmonella Isolated from Cattle Feces in United States Feedlots in 2011}, volume={13}, ISSN={1535-3141 1556-7125}, url={http://dx.doi.org/10.1089/fpd.2016.2128}, DOI={10.1089/fpd.2016.2128}, abstractNote={The objective of this study was to determine the prevalence and characteristics of Salmonella spp. isolated from feces of cattle in feedlots in the United States. Fecal samples were collected from up to three pens of cattle in each of 68 feedlots in 12 states. Samples included up to 25 individual fecal pats from the pen floors and up to five composite samples from the floors of the same pens. The prevalence of Salmonella-positive samples was 9.1% (460/5050) and 11.3% (114/1009) for individual and composite samples, respectively. The prevalences of Salmonella at the pen level were 35.6% (72/202) and 22.8% (46/202) for individual and composite samples, respectively. Dietary factors, including inclusion of cottonseed hulls, coccidiostats, and antimicrobial drugs, were associated with differences in prevalence of Salmonella isolation. Overall, 32 serotypes of Salmonella were identified, but six serotypes accounted for 69.1% (495/716) of the isolates. Nearly two-thirds (64.7%, 44/68) of feedlots had at least one positive sample. All isolates were evaluated for susceptibility to a panel of 15 antimicrobial drugs. Most isolates (74.4%, 533/716) were susceptible to all antimicrobial drugs in the panel. When resistance was detected, it was most commonly to tetracycline (21.7%, 155/716 of isolates) or sulfisoxazole (12.4%, 89/716 of isolates). Less than 10% of the isolates were resistant to any other antimicrobials in the panel. The results of this study indicate that the prevalence of Salmonella in individual fecal samples was less than 10%, but that Salmonella is widely distributed among feedlot cattle. Furthermore, when Salmonella is present in feedlot cattle, there is a low occurrence of antimicrobial resistance with the exception of tetracycline and sulfisoxazole. More research is indicated to understand the ecology of Salmonella and antimicrobial resistance, when present, in cattle-feeding operations.}, number={9}, journal={Foodborne Pathogens and Disease}, publisher={Mary Ann Liebert Inc}, author={Dargatz, David A. and Kopral, Christine A. and Erdman, Matthew M. and Fedorka-Cray, Paula J.}, year={2016}, month={Sep}, pages={483–489} }
 @article{collignon_conly_andremont_mcewen_aidara-kane_agerso_ninh_donado-godoy_fedorka-cray_fernandez_et al._2016, title={World Health Organization Ranking of Antimicrobials According to Their Importance in Human Medicine: A Critical Step for Developing Risk Management Strategies to Control Antimicrobial Resistance From Food Animal Production}, volume={63}, ISSN={1058-4838 1537-6591}, url={http://dx.doi.org/10.1093/cid/ciw475}, DOI={10.1093/cid/ciw475}, abstractNote={Antimicrobial use in food animals selects for antimicrobial resistance in bacteria, which can spread to people. Reducing use of antimicrobials—particularly those deemed to be critically important for human medicine—in food production animals continues to be an important step for preserving the benefits of these antimicrobials for people. The World Health Organization ranking of antimicrobials according to their relative importance in human medicine was recently updated. Antimicrobials considered the highest priority among the critically important antimicrobials were quinolones, third- and fourth-generation cephalosporins, macrolides and ketolides, and glycopeptides. The updated ranking allows stakeholders in the agriculture sector and regulatory agencies to focus risk management efforts on drugs used in food animals that are the most important to human medicine. In particular, the current large-scale use of fluoroquinolones, macrolides, and third-generation cephalosporins and any potential use of glycopeptides and carbapenems need to be addressed urgently.}, number={8}, journal={Clinical Infectious Diseases}, publisher={Oxford University Press (OUP)}, author={Collignon, P.C. and Conly, J.M. and Andremont, A. and McEwen, S.A. and Aidara-Kane, A. and Agerso, Y. and Ninh, T.D. and Donado-Godoy, P. and Fedorka-Cray, P. and Fernandez, H. and et al.}, editor={Griffin, Patricia M.Editor}, year={2016}, month={Jul}, pages={1087–1093} }
 @article{folster_campbell_grass_brown_bicknese_tolar_joseph_plumblee_walker_fedorka-cray_et al._2015, title={Identification and Characterization of Multidrug-Resistant Salmonella enterica Serotype Albert Isolates in the United States}, volume={59}, ISSN={["1098-6596"]}, DOI={10.1128/aac.05183-14}, abstractNote={ABSTRACT Salmonella enterica is one of the most common causes of bacterial foodborne illness in the United States. Although most Salmonella infections are self-limiting, antimicrobial treatment of invasive salmonellosis is critical. The primary antimicrobial treatment options include fluoroquinolones or extended-spectrum cephalosporins, and resistance to these antimicrobial drugs may complicate treatment. At present, S. enterica is composed of more than 2,600 unique serotypes, which vary greatly in geographic prevalence, ecological niche, and the ability to cause human disease, and it is important to understand and mitigate the source of human infection, particularly when antimicrobial resistance is found. In this study, we identified and characterized 19 S. enterica serotype Albert isolates collected from food animals, retail meat, and humans in the United States during 2005 to 2013. All five isolates from nonhuman sources were obtained from turkeys or ground turkey, and epidemiologic data suggest poultry consumption or live-poultry exposure as the probable source of infection. S. enterica serotype Albert also appears to be geographically localized to the midwestern United States. All 19 isolates displayed multidrug resistance, including decreased susceptibility to fluoroquinolones and resistance to extended-spectrum cephalosporins. Turkeys are a likely source of multidrug-resistant S. enterica serotype Albert, and circulation of resistance plasmids, as opposed to the expansion of a single resistant strain, is playing a role. More work is needed to understand why these resistance plasmids spread and how their presence and the serotype they reside in contribute to human disease.}, number={5}, journal={ANTIMICROBIAL AGENTS AND CHEMOTHERAPY}, author={Folster, Jason P. and Campbell, Davina and Grass, Julian and Brown, Allison C. and Bicknese, Amelia and Tolar, Beth and Joseph, Lavin A. and Plumblee, Jodie R. and Walker, Carrie and Fedorka-Cray, Paula J. and et al.}, year={2015}, month={May}, pages={2774–2779} }
 @article{dargatz_marshall_fedorka-cray_erdman_kopral_2015, title={Salmonella Prevalence and Antimicrobial Susceptibility from the National Animal Health Monitoring System Sheep 2011 Study}, volume={12}, ISSN={1535-3141 1556-7125}, url={http://dx.doi.org/10.1089/fpd.2015.2016}, DOI={10.1089/fpd.2015.2016}, abstractNote={Salmonella is a major cause of foodborne illness and can cause clinical disease in animals. Understanding the on-farm ecology of Salmonella will be helpful in decreasing the risk of foodborne transmission. An objective of this study was to determine the prevalence of Salmonella among fecal samples collected on sheep operations in the United States. Another objective was to compare the use of composite fecal samples with fecal samples collected from individual sheep as a tool for screening sheep flocks for Salmonella. Sheep fecal samples (individual and composite) were collected on operations in 22 states. Salmonella isolates were characterized with regard to species, serotype, and antimicrobial susceptibility profile. Most operations (72.1%) had at least one positive sample and overall 26.9% of samples were positive. The percentage of positive samples varied by animal age class. Composite and individual samples gave similar results. The majority of the isolates (94%) were Salmonella enterica subspecies diarizonae serotype 61:-:1,5,7. Nearly all of the isolates (91.2%) tested for antimicrobial susceptibility were susceptible to all antimicrobials in the panel. The findings suggest that salmonellae typically associated with foodborne disease transmission are infrequently found on sheep operations in the United States.}, number={12}, journal={Foodborne Pathogens and Disease}, publisher={Mary Ann Liebert Inc}, author={Dargatz, David A. and Marshall, Katherine L. and Fedorka-Cray, Paula J. and Erdman, Matthew M. and Kopral, Christine A.}, year={2015}, month={Dec}, pages={953–957} }
 @article{cosby_cox_harrison_wilson_buhr_fedorka-cray_2015, place={Cosby, D.E., Cox, N.A., Harrison, M.A., Wilson}, title={Salmonella and antimicrobial resistance in broilers: A review}, volume={24}, ISSN={1056-6171 1537-0437}, url={http://dx.doi.org/10.3382/japr/pfv038}, DOI={10.3382/japr/pfv038}, abstractNote={Salmonella enterica is a zoonotic pathogen which can readily pass from animal to man through the consumption of contaminated food. The prevalence of Salmonella enterica associated with poultry and poultry meat products has been well-documented and this prevalence has both public health and economic implications. The estimated total cost for nontyphoidal Salmonella is in excess of 14 billion dollars/year in the United States alone. Almost 41,930 cases of nontyphoidal foodborne salmonellosis are confirmed annually with an estimated total number of 1 million cases of foodborne salmonellosis not reported. The emergence of antimicrobial resistant Salmonella recovered from meat products has heightened concerns regarding antimicrobial use in food animal production. This review will cover the history and taxonmy of Salmonella enterica, Salmonella in poultry and poultry products, colonization factors, transmission, detection and characterization, antibiotics, antimicrobial resistance, mechanisms of resistance in Salmonella by class, transmission of antimicrobial resistance, and the global implications of antimicrobial resistance.}, number={3}, journal={The Journal of Applied Poultry Research}, publisher={Oxford University Press (OUP)}, author={Cosby, Douglas E. and Cox, Nelson A. and Harrison, Mark A. and Wilson, Jeanna L. and Buhr, R. Jeff and Fedorka-Cray, Paula J.}, year={2015}, month={Jul}, pages={408–426} }
 @article{davis_jackson_fedorka-cray_barrett_brousse_gustafson_kucher_2014, title={Carriage of methicillin-resistant staphylococci by healthy companion animals in the US}, volume={59}, ISSN={0266-8254}, url={http://dx.doi.org/10.1111/lam.12254}, DOI={10.1111/lam.12254}, abstractNote={Abstract Antimicrobial-resistant staphylococci have been associated with wounded or ill companion animals, but little is known about the prevalence of resistant staphylococci among healthy animals. In this study, 276 healthy dogs and cats from veterinary clinics were tested for the presence of antimicrobial-resistant Staphylococcus spp. Isolates were tested for antimicrobial susceptibility and the presence of select resistance genes, and typed using Pulsed-Field Gel Electrophoresis (PFGE). Staphylococcus aureus and Staphylococcus pseudintermedius were also characterized using multilocus sequence typing (MLST), spa typing and SCCmec typing. Approximately 5% (14/276) of the animals were positive by enrichment for five species of staphylococci [Staph. aureus (n = 11), Staph. pseudintermedius (n = 4), Staphylococcus sciuri (n = 6), Staphylococcus simulans (n = 1) and Staphylococcus warneri (n = 1)]. Seventy-eight per cent (18/23) of staphylococci were resistant to oxacillin and also multidrug resistant (resistance to ≥ 2 antimicrobials). All Staph. aureus isolates were mecA+ and blaZ+, SCCmec type II, spa type t002, ST5 and clonal using PFGE. Staphylococcus pseudintermedius were SCCmec type IV or V, spa type t06 and ST170; two of the isolates were pvl+. These results suggest that healthy companion animals may be a reservoir of multidrug-resistant staphylococci, which may be transferred to owners and others who handle companion animals. Significance and Impact of the Study In this study, antimicrobial-resistant coagulase-negative and coagulase-positive staphylococci were isolated from various body sites on healthy dogs and cats. Resistance to 14 antimicrobials was observed including resistance to oxacillin; the majority of staphylococci were also multidrug resistant. Results from this study suggest that healthy dogs and cats may act as reservoirs of antimicrobial-resistant bacteria that may be transferred to people by simple interaction with the animals. Such carriage poses an underlying risk of infection, which should be considered during handling of healthy dogs and cats by pet owners and veterinary personnel.}, number={1}, journal={Letters in Applied Microbiology}, publisher={Wiley}, author={Davis, J.A. and Jackson, C.R. and Fedorka-Cray, P.J. and Barrett, J.B. and Brousse, J.H. and Gustafson, J. and Kucher, M.}, year={2014}, month={Apr}, pages={1–8} }
 @article{folster_tolar_pecic_sheehan_rickert_hise_zhao_fedorka-cray_mcdermott_whichard_2014, title={Characterization of blaCMY Plasmids and Their Possible Role in Source Attribution of Salmonella enterica Serotype Typhimurium Infections}, volume={11}, ISSN={1535-3141 1556-7125}, url={http://dx.doi.org/10.1089/fpd.2013.1670}, DOI={10.1089/fpd.2013.1670}, abstractNote={Salmonella is an important cause of foodborne illness; however, identifying the source of these infections can be difficult. This is especially true for Salmonella serotype Typhimurium, which is found in diverse agricultural niches. Extended-spectrum cephalosporins (ESC) are one of the primary treatment choices for complicated Salmonella infections. In Salmonella, ESC resistance in the United States is mainly mediated by blaCMY genes carried on various plasmids. In this study, we examined whether the characterization of blaCMY plasmids, along with additional information, can help us identify potential sources of infection by Salmonella, and used serotype Typhimurium as a model. In the United States, monitoring of retail meat, food animals, and ill persons for antimicrobial-resistant Salmonella is conducted by the National Antimicrobial Resistance Monitoring System. In 2008, 70 isolates (70/581; 12.0%) (34 isolates from retail meat, 23 food animal, and 13 human) were resistant to ceftriaxone and amoxicillin/clavulanic acid. All were polymerase chain reaction (PCR)–positive for blaCMY and 59/70 (84.3%) of these genes were plasmid encoded. PCR-based replicon typing identified 42/59 (71.2%) IncI1-blaCMY plasmids and 17/59 (28.8%) IncA/C-blaCMY plasmids. Isolates from chickens or chicken products with blaCMY plasmids primarily had IncI1-blaCMY plasmids (37/40; 92.5%), while all isolates from cattle had IncA/C-blaCMY plasmids. Isolates from humans had either IncA/C- blaCMY (n=8/12; [66.7%]) or IncI1- blaCMY (n=4/12 [33.3%]) plasmids. All of the IncI1-blaCMY plasmids were ST12 or were closely related to ST12. Antimicrobial susceptibility patterns (AST) and pulsed-field gel electrophoresis (PFGE) patterns of the isolates were also compared and differences were identified between isolate sources. When the source of a Typhimurium outbreak or sporadic illness is unknown, characterizing the outbreak isolate's blaCMY plasmids, AST, and PFGE patterns may help identify it.}, number={4}, journal={Foodborne Pathogens and Disease}, publisher={Mary Ann Liebert Inc}, author={Folster, Jason P. and Tolar, Beth and Pecic, Gary and Sheehan, Deborah and Rickert, Regan and Hise, Kelley and Zhao, Shaohua and Fedorka-Cray, Paula J. and McDermott, Patrick and Whichard, Jean M.}, year={2014}, month={Apr}, pages={301–306} }
 @article{lindsey_fedorka-cray_abley_turpin_meinersmann_2014, title={Evaluating the Occurrence of Escherichia albertii in Chicken Carcass Rinses by PCR, Vitek Analysis, and Sequencing of the rpoB Gene}, volume={81}, ISSN={0099-2240 1098-5336}, url={http://dx.doi.org/10.1128/aem.03681-14}, DOI={10.1128/aem.03681-14}, abstractNote={Escherichia albertii is a recently described species that has been associated with gastroenteritis in humans and with healthy and ill birds. Most recently, it has been identified as the causative agent in a food-borne outbreak in Japan. The distribution and clinical importance of E. albertii are not well studied because its importance is unclear. Culture methods for clinical isolation frequently miss E. albertii or incorrectly identify it as Shigella spp., Escherichia coli, or Hafnia alvei. This study was designed to determine if E. albertii could be recovered from chicken carcass rinses collected at slaughter during a 1-year period from November 2009 until October 2010. Colonies were isolated from chicken carcass rinses and tested by PCR for the presence or absence of clpX, lysP, mdh, intimin (eae), Shiga toxins 1 and 2 (stx1, stx2, and stx2f), heat-stable enterotoxin A (staA), and cytolethal distending toxins 1 and 2 (cdtB) genes. Sixty-five isolates were analyzed by sequencing a section of the rpoB gene. Analysis of the rpoB gene sequences revealed 14 fixed differences between E. albertii and other, closely related organisms. The fixed differences found in the rpoB gene could aid in future discrimination of E. albertii from closely related bacteria.}, number={5}, journal={Applied and Environmental Microbiology}, publisher={American Society for Microbiology}, author={Lindsey, Rebecca L. and Fedorka-Cray, Paula J. and Abley, Melanie and Turpin, Jennifer B. and Meinersmann, Richard J.}, editor={Griffiths, M. W.Editor}, year={2014}, month={Dec}, pages={1727–1734} }
 @inbook{fedorka-cray_2014, title={MICROORGANISMS AND RESISTANCE TO ANTIBIOTICS, THE UBIQUITY OF | Antibiotic Resistance by Microorganisms}, ISBN={9780123847348}, url={http://dx.doi.org/10.1016/b978-0-12-384731-7.00205-1}, DOI={10.1016/b978-0-12-384731-7.00205-1}, abstractNote={Antimicrobial agents are necessary for use in veterinary medicine, including the production of food-producing animals. Antibiotic use is indicated for the treatment of target bacterial organisms and/or diseases for which the antibiotic was developed. However, an unintended consequence of antibiotic use is the development of antimicrobial resistance in nontarget bacteria, such as commensal bacteria and zoonotic pathogens, such as Salmonella and Campylobacter. This article provides an overview of antimicrobial resistance in bacteria associated with food animals and, by association, meat.}, booktitle={Encyclopedia of Meat Sciences}, publisher={Elsevier}, author={Fedorka-Cray, P.J.}, year={2014}, pages={412–416} }
 @article{jones_cox_guard_fedorka-cray_buhr_gast_abdo_rigsby_plumblee_karcher_et al._2014, title={Microbiological impact of three commercial laying hen housing systems}, volume={94}, ISSN={0032-5791 1525-3171}, url={http://dx.doi.org/10.3382/ps/peu010}, DOI={10.3382/ps/peu010}, abstractNote={Hen housing for commercial egg production continues to be a societal and regulatory concern. Controlled studies have examined various aspects of egg safety, but a comprehensive assessment of commercial hen housing systems in the US has not been conducted. The current study is part of a holistic, multidisciplinary comparison of the diverse aspects of commercial conventional cage, enriched colony cage, and cage-free aviary housing systems and focuses on environmental and egg microbiology. Environmental swabs and eggshell pools were collected from all housing systems during 4 production periods. Total aerobes and coliforms were enumerated, and the prevalence of Salmonella and Campylobacter spp. was determined. Environmental aerobic and coliform counts were highest for aviary drag swabs (7.5 and 4.0 log cfu/mL, respectively) and enriched colony cage scratch pad swabs (6.8 and 3.8 log cfu/mL, respectively). Aviary floor and system wire shell pools had the greatest levels of aerobic contamination for all eggshell pools (4.9 and 4.1 log cfu/mL, respectively). Hens from all housing systems were shedding Salmonella spp. (89-100% of manure belt scraper blade swabs). The dry belt litter removal processes for all housing systems appear to affect Campylobacter spp. detection (0-41% of manure belt scraper blade swabs) considering detection of Campylobacter spp. was much higher for other environmental samples. Aviary forage area drag swabs were 100% contaminated with Campylobacter spp., whereas enriched colony cage scratch pads had a 93% positive rate. There were no differences in pathogen detection in the shell pools from the 3 housing systems. Results indicate egg safety is enhanced when hens in alternative housing systems use nest boxes. Additionally, current outcomes indicate the use of scratch pads in hen housing systems needs to be more thoroughly investigated for effects on hen health and egg safety.}, number={3}, journal={Poultry Science}, publisher={Oxford University Press (OUP)}, author={Jones, D. R. and Cox, N. A. and Guard, J. and Fedorka-Cray, P. J. and Buhr, R. J. and Gast, R. K. and Abdo, Z. and Rigsby, L. L. and Plumblee, J. R. and Karcher, D. M. and et al.}, year={2014}, month={Dec}, pages={544–551} }
 @article{cox_buhr_smith_cason_rigsby_bourassa_fedorka-cray_cosby_2014, title={Sampling Naturally Contaminated Broiler Carcasses for <I>Salmonella</I> by Three Different Methods}, volume={77}, ISSN={0362-028X}, url={http://dx.doi.org/10.4315/0362-028x.jfp-13-320}, DOI={10.4315/0362-028x.jfp-13-320}, abstractNote={Postchill neck skin maceration (NSM) and whole-carcass rinsing (WCR) are frequently used methods to detect salmonellae from processed broilers. These are practical, nondestructive methods, but they are insensitive and may result in false negatives (20 to 40%). Neck skin samples comprise only 4% of the skin from the broiler carcass by weight, while WCR will not detect firmly attached Salmonella organisms and only 7.5% of the rinsate is utilized. Whole-carcass enrichment (WCE) involves incubation of the whole carcass overnight in a preenrichment broth and can recover as few as 8 inoculated Salmonella cells per carcass. The objective of this study was to use NSM, WCR, and WCE sampling to detect naturally occurring Salmonella from the same commercially processed broiler either prechill or postchill. Ten carcasses were obtained prechill and another 10 postchill on each of two replicate days from each of two commercial processing plants. From each carcass, 8.3 g of neck skin was sampled, and then the carcass was rinsed with 400 ml of 1% buffered peptone water. Thirty milliliters was removed and incubated (WCR), and the remaining 370 ml of broth and the carcass were incubated at 37°C for 24 h (WCE). Overall, Salmonella organisms were detected on 21, 24, and 32 of 40 prechill carcasses by NSM, WCR, and WCE, respectively, while 2, 2, and 19 of 40 postchill carcasses were positive by the respective methods. Prechill carcasses were 64% (77 of 120) positive for Salmonella, while postchill carcasses were 19% (23 of 120) positive. Commercial processing reduced the positive-sample prevalence by 45%. Salmonella organisms were detected on 20% (24 of 120) of the samples from plant 1 and 63% (76 of 120) of the carcasses from plant 2. This study demonstrates significant differences in the results for Salmonella prevalence among sampling methods both before and after immersion chilling, as well as between processing plants on days that samples were taken.}, number={3}, journal={Journal of Food Protection}, publisher={International Association for Food Protection}, author={Cox, N. A. and Buhr, R. J. and Smith, D. P. and Cason, J. A. and Rigsby, L. L. and Bourassa, D. V. and Fedorka-Cray, P. J. and Cosby, D.}, year={2014}, month={Mar}, pages={493–495} }
 @article{cox_richardson_berrang_rigsby_buhr_plumblee_fedorka-cray_2014, title={Survival of Naturally Occurring Campylobacter in Refrigerated and Frozen Rinsate From a Broiler Carcass - a Research Note}, volume={34}, ISSN={0149-6085}, url={http://dx.doi.org/10.1111/jfs.12098}, DOI={10.1111/jfs.12098}, abstractNote={Each of the 10 carcasses were rinsed and tested for Campylobacter. Each rinse was subdivided into twelve 25-mL aliquots, without cryoprotectant. Six were stored at 4C and six at −23C. At 4-month intervals, one aliquot from each was streaked onto Campy-Cefex plates and then 5 mL added to 45 mL of Bolton's (B) or 45 mL of Tecra (T) broth; after 48 h at 42C, both enrichments were streaked onto Campy-Cefex plates. At 4 months (4C), 0 of 10, seven of 10 and three of 10 were positive by direct streak, B and T, respectively, while 0 of 10, one of 10 and four of 10 were positive by direct streak, B and T, respectively, at −23C. At 4 months, all 4C samples were negative, while two of 10 frozen samples were positive in both B and T after 8 months and one of 10 in B at 12, 16 and 20 months. Foods contaminated with Campylobacter may still pose a health hazard after long-term freezing. Practical Applications In this study, naturally occurring Campylobacter were able to survive in the rinsate of commercially processed broiler carcasses without the use of a cryoprotectant. The Campylobacter isolate was identified as a nalidixic acid and ciprofloxacin resistant strain of Campylobacter jejuni. Survival and periodic recovery were demonstrated after 20 months of frozen storage in broiler carcass rinsate alone. Therefore, naturally contaminated uncooked frozen poultry may pose a potential health hazard.}, number={1}, journal={Journal of Food Safety}, publisher={Wiley}, author={Cox, N.A. and Richardson, L.J. and Berrang, M.E. and Rigsby, L.L. and Buhr, R.J. and Plumblee, J.R. and Fedorka-Cray, P.J.}, year={2014}, month={Jan}, pages={76–78} }
 @article{sandt_fedorka-cray_tewari_ostroff_joyce_m’ikanatha_2013, title={A Comparison of Non-Typhoidal Salmonella from Humans and Food Animals Using Pulsed-Field Gel Electrophoresis and Antimicrobial Susceptibility Patterns}, volume={8}, ISSN={1932-6203}, url={http://dx.doi.org/10.1371/journal.pone.0077836}, DOI={10.1371/journal.pone.0077836}, abstractNote={Salmonellosis is one of the most important foodborne diseases affecting humans. To characterize the relationship between Salmonella causing human infections and their food animal reservoirs, we compared pulsed-field gel electrophoresis (PFGE) and antimicrobial susceptibility patterns of non-typhoidal Salmonella isolated from ill humans in Pennsylvania and from food animals before retail. Human clinical isolates were received from 2005 through 2011 during routine public health operations in Pennsylvania. Isolates from cattle, chickens, swine and turkeys were recovered during the same period from federally inspected slaughter and processing facilities in the northeastern United States. We found that subtyping Salmonella isolates by PFGE revealed differences in antimicrobial susceptibility patterns and, for human Salmonella, differences in sources and invasiveness that were not evident from serotyping alone. Sixteen of the 20 most common human Salmonella PFGE patterns were identified in Salmonella recovered from food animals. The most common human Salmonella PFGE pattern, Enteritidis pattern JEGX01.0004 (JEGX01.0003ARS), was associated with more cases of invasive salmonellosis than all other patterns. In food animals, this pattern was almost exclusively (99%) found in Salmonella recovered from chickens and was present in poultry meat in every year of the study. Enteritidis pattern JEGX01.0004 (JEGX01.0003ARS) was associated with susceptibility to all antimicrobial agents tested in 94.7% of human and 97.2% of food animal Salmonella isolates. In contrast, multidrug resistance (resistance to three or more classes of antimicrobial agents) was observed in five PFGE patterns. Typhimurium patterns JPXX01.0003 (JPXX01.0003 ARS) and JPXX01.0018 (JPXX01.0002 ARS), considered together, were associated with resistance to five or more classes of antimicrobial agents: ampicillin, chloramphenicol, streptomycin, sulfonamides and tetracycline (ACSSuT), in 92% of human and 80% of food animal Salmonella isolates. The information from our study can assist in source attribution, outbreak investigations, and tailoring of interventions to maximize their impact on prevention.}, number={10}, journal={PLoS ONE}, publisher={Public Library of Science (PLoS)}, author={Sandt, Carol H. and Fedorka-Cray, Paula J. and Tewari, Deepanker and Ostroff, Stephen and Joyce, Kevin and M’ikanatha, Nkuchia M.}, editor={Tse, HermanEditor}, year={2013}, month={Oct}, pages={e77836} }
 @article{glenn_lindsey_folster_pecic_boerlin_gilmour_harbottle_zhao_mcdermott_fedorka-cray_et al._2013, title={Antimicrobial Resistance Genes in Multidrug-Resistant Salmonella enterica Isolated from Animals, Retail Meats, and Humans in the United States and Canada}, volume={19}, ISSN={1076-6294 1931-8448}, url={http://dx.doi.org/10.1089/mdr.2012.0177}, DOI={10.1089/mdr.2012.0177}, abstractNote={Salmonella enterica is a prevalent foodborne pathogen that can carry multidrug resistance (MDR) and pose a threat to human health. Identifying the genetics associated with MDR in Salmonella isolated from animals, foods, and humans can help determine sources of MDR in food animals and their impact on humans. S. enterica serovars most frequently carrying MDR from healthy animals, retail meats, and human infections in the United States and Canada were identified and isolates resistant to the largest number of antimicrobials were chosen. Isolates were from U.S. slaughter (n=12), retail (9), and humans (9), and Canadian slaughter (9), retail (9), and humans (8; total n=56). These isolates were assayed by microarray for antimicrobial resistance and MDR plasmid genes. Genes detected encoded resistance to aminoglycosides (alleles of aac, aad, aph, strA/B); beta-lactams (bla(TEM), bla(CMY), bla(PSE-1)); chloramphenicol (cat, flo, cmlA); sulfamethoxazole (sulI); tetracycline (tet(A, B, C, D) and tetR); and trimethoprim (dfrA). Hybridization with IncA/C plasmid gene probes indicated that 27/56 isolates carried one of these plasmids; however, they differed in several variable regions. Cluster analysis based on genes detected separated most of the isolates into two groups, one with IncA/C plasmids and one without IncA/C plasmids. Other plasmid replicons were detected in all but one isolate, and included I1 (25/56), N (23/56), and FIB (10/56). The presence of different mobile elements along with similar resistance genes suggest that these genetic elements may acquire similar resistance cassettes, and serve as multiple sources for MDR in Salmonella from food animals, retail meats, and human infections.}, number={3}, journal={Microbial Drug Resistance}, publisher={Mary Ann Liebert Inc}, author={Glenn, LaShanda M. and Lindsey, Rebecca L. and Folster, Jason P. and Pecic, Gary and Boerlin, Patrick and Gilmour, Mathew W. and Harbottle, Heather and Zhao, Shaohua and McDermott, Patrick F. and Fedorka-Cray, Paula J. and et al.}, year={2013}, month={Jun}, pages={175–184} }
 @article{sjölund-karlsson_howie_blickenstaff_boerlin_ball_chalmers_duval_haro_rickert_zhao_et al._2013, title={Occurrence of β-Lactamase Genes Among Non-Typhi Salmonella enterica Isolated from Humans, Food Animals, and Retail Meats in the United States and Canada}, volume={19}, ISSN={1076-6294 1931-8448}, url={http://dx.doi.org/10.1089/mdr.2012.0178}, DOI={10.1089/mdr.2012.0178}, abstractNote={Non-Typhi Salmonella cause over 1.7 million cases of gastroenteritis in North America each year, and food-animal products are commonly implicated in human infections. For invasive infections, antimicrobial therapy is indicated. In North America, the antimicrobial susceptibility of Salmonella is monitored by the U.S. National Antimicrobial Resistance Monitoring System (NARMS) and The Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS). In this study, we determined the susceptibility to cephalosporins by broth microdilution among 5,041 non-Typhi Salmonella enterica isolated from food animals, retail meats, and humans. In the United States, 109 (4.6%) of isolates collected from humans, 77 (15.7%) from retail meat, and 140 (10.6%) from food animals displayed decreased susceptibility to cephalosporins (DSC). Among the Canadian retail meat and food animal isolates, 52 (13.0%) and 42 (9.4%) displayed DSC. All isolates displaying DSC were screened for β-lactamase genes (blaTEM, blaSHV, blaCMY, blaCTX-M, and blaOXA-1) by polymerase chain reaction. At least one β-lactamase gene was detected in 74/109 (67.9%) isolates collected from humans, and the blaCMY genes were most prevalent (69/109; 63.3%). Similarly, the blaCMY genes predominated among the β-lactamase-producing isolates collected from retail meats and food animals. Three isolates from humans harbored a blaCTX-M-15 gene. No animal or retail meat isolates harbored a blaCTX-M or blaOXA-1 gene. A blaTEM gene was found in 5 human, 9 retail meat, and 17 animal isolates. Although serotype distributions varied among human, retail meat, and animal sources, overlap in blaCMY-positive serotypes across sample sources supports meat and food-animal sources as reservoirs for human infection.}, number={3}, journal={Microbial Drug Resistance}, publisher={Mary Ann Liebert Inc}, author={Sjölund-Karlsson, Maria and Howie, Rebecca L. and Blickenstaff, Karen and Boerlin, Patrick and Ball, Takiyah and Chalmers, Gabhan and Duval, Brea and Haro, Jovita and Rickert, Regan and Zhao, Shaohua and et al.}, year={2013}, month={Jun}, pages={191–197} }
 @article{cox_cason_buhr_richardson_richardson_rigsby_fedorka-cray_2013, title={Variations in preenrichment pH of poultry feed and feed ingredients after incubation periods up to 48 hours}, volume={22}, ISSN={1056-6171 1537-0437}, url={http://dx.doi.org/10.3382/japr.2012-00552}, DOI={10.3382/japr.2012-00552}, abstractNote={Human salmonellosis outbreaks have been linked to contamination of animal feeds. Thus, it is crucial to employ sensitive Salmonella detection methods for animal feeds. Based on a review of the literature, Salmonella sustains acid injury at about pH 4.0 to 5.0. Low pH can also alter the metabolism of Salmonella, hampering the identification process. Because most Salmonella bacteria present in feed and feed ingredients are already stressed by desiccation and heat during conditioning, pelleting, or both, exposure to low pH may kill or severely injure these cells and result in contamination going undetected. Five grams of 7 different feed ingredients and 5 types of feed were added to 45 mL of buffered peptone water (BPW), lactose broth (LB), minimal salts medium (M-9), or universal preenrichment (UP). Media were incubated at 37°C for 18, 24, and 48 h, and the pH of the media was determined. In the case of cereal grains, in general, the initial pH of the preenrichment media ranged from 6.1 to 7.2. Distillers dried grains with solubles in lactose broth was the exception to this trend (pH 4.5). After 18 h of incubation, the pH of the media had decreased to a pH range of 4.0 to 6.1. The preenrichment media behaved in a similar fashion when testing oilseed meals, canola, and soy (i.e., initial pH range was 6.2 to 7.2 and decreased to pH 4.2 to 5.4 for soy and pH 4.4 to 6.0 for canola). With these ingredients, the buffering capacity of BPW, LB, and M-9 was similar. There was more variation in the pH of the preenrichment media among the different poultry feed types. The media from broiler and layer feeds had an initial pH of 6.2 to 7.0, whereas turkey feed was 6.4 to 7.1. After 18 to 48 h incubation in broiler and in layer feed, the pH was 3.9 to 5.6, compared with pH values of 4.5 to 6.8 for turkey feed. For feed, the buffering capacities of BPW, LB, and M-9 were similar. After incubation in commonly used preenrichment media, mixed feeds and feed ingredients can reach a pH that may kill or injure Salmonella. In light of these data, detection methods for Salmonella in feed and feed ingredients may need to be re-evaluated.}, number={2}, journal={The Journal of Applied Poultry Research}, publisher={Oxford University Press (OUP)}, author={Cox, N. A. and Cason, J. A. and Buhr, R. J. and Richardson, K. E. and Richardson, L. J. and Rigsby, L. L. and Fedorka-Cray, P. J.}, year={2013}, month={Jun}, pages={190–195} }
 @article{pittenger_frye_mcnerney_reeves_haro_fedorka-cray_harrison_englen_2012, title={Analysis of Campylobacter jejuni Whole-Genome DNA Microarrays: Significance of Prophage and Hypervariable Regions for Discriminating Isolates}, volume={9}, ISSN={1535-3141 1556-7125}, url={http://dx.doi.org/10.1089/fpd.2011.1048}, DOI={10.1089/fpd.2011.1048}, abstractNote={Campylobacter is a leading cause of foodborne illness in humans, and improving our understanding of the epidemiology of this organism is essential. The objective of this study was to identify the genes that discriminate isolates of C. jejuni by analysis with whole-genome DNA microarrays. Statistical analyses of whole-genome data from 95 geographically diverse cattle, chicken, and human C. jejuni isolates identified 142 most significant variable genes. Of this total, 125 (88%) belonged to genomic prophage and hypervariable regions. The significance of genomic prophage and hypervariable regions in determining C. jejuni isolate genomic diversity is emphasized by these results. These genes will be useful as biomarkers and components of genotyping systems for C. jejuni to improve our understanding of the epidemiology and population genetics of this major foodborne pathogen.}, number={5}, journal={Foodborne Pathogens and Disease}, publisher={Mary Ann Liebert Inc}, author={Pittenger, Lauren G. and Frye, Jonathan G. and McNerney, Victoria and Reeves, Jaxk and Haro, Jovita and Fedorka-Cray, Paula J. and Harrison, Mark A. and Englen, Mark D.}, year={2012}, month={May}, pages={473–479} }
 @article{folster_pecic_singh_duval_rickert_ayers_abbott_mcglinchey_bauer-turpin_haro_et al._2012, title={Characterization of Extended-Spectrum Cephalosporin–Resistant Salmonella enterica Serovar Heidelberg Isolated from Food Animals, Retail Meat, and Humans in the United States 2009}, volume={9}, ISSN={1535-3141 1556-7125}, url={http://dx.doi.org/10.1089/fpd.2012.1130}, DOI={10.1089/fpd.2012.1130}, abstractNote={Salmonella enterica is one of the most common causes of foodborne illness in the United States. Although salmonellosis is usually self-limiting, severe infections typically require antimicrobial treatment, and ceftriaxone, an extended-spectrum cephalosporin (ESC), is commonly used in both adults and children. Surveillance conducted by the National Antimicrobial Resistance Monitoring System (NARMS) has shown a recent increase in ESC resistance among Salmonella Heidelberg isolated from food animals at slaughter, retail meat, and humans. ESC resistance among Salmonella in the United States is usually mediated by a plasmid-encoded blaCMY β-lactamase. In 2009, we identified 47 ESC-resistant blaCMY-positive Heidelberg isolates from humans (n=18), food animals at slaughter (n=16), and retail meats (n=13) associated with a spike in the prevalence of this serovar. Almost 90% (26/29) of the animal and meat isolates were isolated from chicken carcasses or retail chicken meat. We screened NARMS isolates for the presence of blaCMY, determined whether the gene was plasmid-encoded, examined pulsed-field gel electrophoresis patterns to assess the genetic diversities of the isolates, and categorized the blaCMY plasmids by plasmid incompatibility groups and plasmid multi-locus sequence typing (pMLST). All 47 blaCMY genes were found to be plasmid encoded. Incompatibility/replicon typing demonstrated that 41 were IncI1 plasmids, 40 of which only conferred blaCMY-associated resistance. Six were IncA/C plasmids that carried additional resistance genes. pMLST of the IncI1-blaCMY plasmids showed that 27 (65.8%) were sequence type (ST) 12, the most common ST among blaCMY-IncI1 plasmids from Heidelberg isolated from humans. Ten plasmids had a new ST profile, ST66, a type very similar to ST12. This work showed that the 2009 increase in ESC resistance among Salmonella Heidelberg was caused mainly by the dissemination of blaCMY on IncI1 and IncA/C plasmids in a variety of genetic backgrounds, and is likely not the result of clonal expansion.}, number={7}, journal={Foodborne Pathogens and Disease}, publisher={Mary Ann Liebert Inc}, author={Folster, J.P. and Pecic, G. and Singh, A. and Duval, B. and Rickert, R. and Ayers, S. and Abbott, J. and McGlinchey, B. and Bauer-Turpin, J. and Haro, J. and et al.}, year={2012}, month={Jul}, pages={638–645} }
 @article{folster_pecic_rickert_taylor_zhao_fedorka-cray_whichard_mcdermott_2012, title={Characterization of Multidrug-Resistant Salmonella enterica Serovar Heidelberg from a Ground Turkey-Associated Outbreak in the United States in 2011}, volume={56}, ISSN={0066-4804 1098-6596}, url={http://dx.doi.org/10.1128/aac.00201-12}, DOI={10.1128/aac.00201-12}, abstractNote={Salmonella enterica serotype Heidelberg is the fifth-most-common serotype that causes human disease in the United States, and it appears to be more invasive than other nontyphoidal serotypes ([3][1], [6][2]). In March 2011, a multistate outbreak of Salmonella enterica serotype Heidelberg infections}, number={6}, journal={Antimicrobial Agents and Chemotherapy}, publisher={American Society for Microbiology}, author={Folster, Jason P. and Pecic, G. and Rickert, R. and Taylor, J. and Zhao, S. and Fedorka-Cray, P. J. and Whichard, J. and McDermott, P.}, year={2012}, month={Mar}, pages={3465–3466} }
 @article{lombard_beam_nifong_fossler_kopral_dargatz_wagner_erdman_fedorka cray_2012, title={Comparison of Individual, Pooled, and Composite Fecal Sampling Methods for Detection of Salmonella on U.S. Dairy Operations}, volume={75}, ISSN={0362-028X}, url={http://dx.doi.org/10.4315/0362-028x.jfp-12-012}, DOI={10.4315/0362-028x.jfp-12-012}, abstractNote={The objectives of this study were to estimate the prevalence of Salmonella for individual, pooled, and composite fecal samples and to compare culture results from each sample type for determining herd Salmonella infection status and identifying Salmonella serovar(s). During the U.S. Department of Agriculture National Animal Health Monitoring System Dairy 2007 study, data and samples were collected from dairy operations in 17 major dairy states. As part of the study, composite fecal samples (six per operation) were collected from cow areas, such as holding pens, alleyways, and lagoons, where manure accumulates. Fecal samples also were collected from individual cows (35 per operation), and fecal sample pools were created by combining samples from 5 cows (7 per operation). A total of 1,541 composite fecal samples were collected from 260 operations in 17 states, and 406 (26.3%) of these samples were culture positive for Salmonella. Among the 116 operations for which all three sample types were obtained, 41.4% (48 operations) were Salmonella culture positive based on individual samples, 39.7% (46 operations) were positive based on pooled samples, and 49.1% (57 operations) were positive based on composite fecal samples. Relative to individual samples, the sensitivity of composite fecal samples for determining herd infection status was 85.4% and the sensitivity of pooled fecal samples was 91.7%. On 33.6% of operations (39 of 116), Salmonella was cultured from all three fecal sample types (individual, pooled, and composite), and 20 (51.3%) of these operations had exactly the same serovar in all three sample types. Use of composite fecal samples is less costly and time-consuming than use of individual or pooled samples and provides similar results for detecting the presence and identifying serovars of Salmonella in dairy herds. Therefore, composite sampling may be an appropriate alternative to culture of individual samples when assessing Salmonella status in dairy herds.}, number={9}, journal={Journal of Food Protection}, publisher={International Association for Food Protection}, author={Lombard, J. E. and Beam, A. L. and Nifong, E. M. and Fossler, C. P. and Kopral, C. A. and Dargatz, D. A. and Wagner, B. A. and Erdman, M. M. and Fedorka Cray, P. J.}, year={2012}, month={Sep}, pages={1562–1571} }
 @article{guard_sanchez-ingunza_morales_stewart_liljebjelke_van kessel_ingram_jones_jackson_fedorka-cray_et al._2012, title={Comparison of dkgB-linked intergenic sequence ribotyping to DNA microarray hybridization for assigning serotype to Salmonella enterica}, volume={337}, ISSN={0378-1097}, url={http://dx.doi.org/10.1111/1574-6968.12010}, DOI={10.1111/1574-6968.12010}, abstractNote={Two DNA-based methods were compared for the ability to assign serotype to 139 isolates of Salmonella enterica ssp. I. Intergenic sequence ribotyping (ISR) evaluated single nucleotide polymorphisms occurring in a 5S ribosomal gene region and flanking sequences bordering the gene dkgB. A DNA microarray hybridization method that assessed the presence and the absence of sets of genes was the second method. Serotype was assigned for 128 (92.1%) of submissions by the two DNA methods. ISR detected mixtures of serotypes within single colonies and it cost substantially less than Kauffmann–White serotyping and DNA microarray hybridization. Decreasing the cost of serotyping S. enterica while maintaining reliability may encourage routine testing and research.}, number={1}, journal={FEMS Microbiology Letters}, publisher={Oxford University Press (OUP)}, author={Guard, Jean and Sanchez-Ingunza, Roxana and Morales, Cesar and Stewart, Tod and Liljebjelke, Karen and Van Kessel, JoAnn and Ingram, Kim and Jones, Deana and Jackson, Charlene and Fedorka-Cray, Paula and et al.}, year={2012}, month={Oct}, pages={61–72} }
 @article{molla_byrne_abley_mathews_jackson_fedorka-cray_sreevatsan_wang_gebreyes_2012, title={Epidemiology and Genotypic Characteristics of Methicillin-Resistant Staphylococcus aureus Strains of Porcine Origin}, volume={50}, ISSN={0095-1137}, url={http://dx.doi.org/10.1128/jcm.01971-12}, DOI={10.1128/jcm.01971-12}, abstractNote={ABSTRACT The main goal of this study was to determine the prevalence of methicillin-resistant Staphylococcus aureus (MRSA), particularly livestock-associated MRSA (LA-MRSA) in pigs and pork. The genotypic relatedness of isolates on the farm, at slaughter, and at the retail level was assessed. Paired nasal and perianal swab samples were collected from 10 cohorts of market-age pigs (24 pigs per cohort) and carcasses at slaughterhouse, and pork samples were collected at retail. Staphylococci were isolated using selective enrichment method. Isolates were tested for antimicrobial resistance by broth microdilution. Duplex PCR was used to confirm MRSA using species-specific ( nuc ) and methicillin resistance ( mecA ) genes. The clonal relatedness of isolates was determined using pulsed-field gel electrophoresis (PFGE), Staphylococcus protein A ( spa ) typing, multilocus sequence typing (MLST), and staphylococcal cassette chromosome mec element (SCC mec ) typing. MRSA was detected in 5 of the 10 cohorts (50%), with the prevalence ranging from 0% to 12.5% per cohort. Of all the pigs sampled on the farm before they went to market, 3% (7/240) were MRSA positive. A higher prevalence of MRSA was detected at holding pens at the slaughterhouse (11% [27/240]). MRSA was also detected in 2% (4/235) of the carcasses and 4% (5/135) of the retail pork. While the isolates appear predominantly to be highly clonal, PFGE had a relatively higher discriminatory power (discriminatory index [DI] = 0.624). Four genotypic clusters were identified by PFGE; of the four clusters, clonal type B was predominant across the farm-to-retail continuum. MLST findings revealed that sequence type 5 (ST5) was the most predominant subtype (32/50). The livestock-associated MRSA (clonal complex 398 [CC398] or sequence type 398 [ST398]) was the second common type (12/50) and was detected at all stages from farm to retail. Nine of the 50 (18%) MRSA isolates belonged to spa type 539/t034 that were of ST398 based on MLST. The results of this study confirm that MRSA, including LA-MRSA, is common in herds of swine in Ohio and hereby shown to persist in the farm to processing and retail continuum.}, number={11}, journal={Journal of Clinical Microbiology}, publisher={American Society for Microbiology}, author={Molla, B. and Byrne, M. and Abley, M. and Mathews, J. and Jackson, C. R. and Fedorka-Cray, P. and Sreevatsan, S. and Wang, P. and Gebreyes, W. A.}, year={2012}, month={Sep}, pages={3687–3693} }
 @article{cox_richardson_maurer_berrang_fedorka cray_buhr_byrd_lee_hofacre_o'kane_et al._2012, title={Evidence for Horizontal and Vertical Transmission in Campylobacter Passage from Hen to Her Progeny}, volume={75}, ISSN={0362-028X}, url={http://dx.doi.org/10.4315/0362-028.jfp-11-322}, DOI={10.4315/0362-028.jfp-11-322}, abstractNote={Campylobacter is an important human pathogen, and consumption of undercooked poultry has been linked to significant human illnesses. To reduce human illness, intervention strategies targeting Campylobacter reduction in poultry are in development. For more than a decade, there has been an ongoing national and international controversy about whether Campylobacter can pass from one generation of poultry to the next via the fertile egg. We recognize that there are numerous sources of Campylobacter entry into flocks of commercial poultry (including egg transmission), yet the environment is often cited as the only source. There has been an abundance of published research globally that refutes this contention, and this article lists and discusses many of them, along with other studies that support environment as the sole or primary source. One must remember that egg passage can mean more than vertical, transovarian transmission. Fecal bacteria, including Campylobacter, can contaminate the shell, shell membranes, and albumen of freshly laid fertile eggs. This contamination is drawn through the shell by temperature differential, aided by the presence of moisture (the "sweating" of the egg); then, when the chick emerges from the egg, it can ingest bacteria such as Campylobacter, become colonized, and spread this contamination to flock mates in the grow house. Improvements in cultural laboratory methods continue to advance our knowledge of the ecology of Campylobacter, and in the not-so-distant future, egg passage will not be a subject continuously debated but will be embraced, thus allowing the development and implementation of more effective intervention strategies.}, number={10}, journal={Journal of Food Protection}, publisher={International Association for Food Protection}, author={Cox, N. A. and Richardson, L. J. and Maurer, J. J. and Berrang, M. E. and Fedorka Cray, P. J. and Buhr, R. J. and Byrd, J. A. and Lee, M. D. and Hofacre, C. L. and O'kane, P. M. and et al.}, year={2012}, month={Oct}, pages={1896–1902} }
 @article{haley_dargatz_bush_erdman_fedorka cray_2012, title={Salmonella Prevalence and Antimicrobial Susceptibility from the National Animal Health Monitoring System Swine 2000 and 2006 Studies}, volume={75}, ISSN={0362-028X}, url={http://dx.doi.org/10.4315/0362-028x.jfp-11-363}, DOI={10.4315/0362-028x.jfp-11-363}, abstractNote={Concern about Salmonella contamination of food is compounded by fear that antimicrobials traditionally used to combat the infection will become useless due to rising antibiotic resistance. Livestock, in particular swine, often are blamed for illnesses caused by Salmonella and for increasing antibiotic resistance due to use of antibiotics in pigs. As part of the National Animal Health Monitoring System Swine 2000 and 2006 studies, swine fecal samples were cultured for Salmonella. These samples were collected from 123 operations in 17 states in 2000 and from 135 operations in 17 states in 2006. At each operation, 50 and 60 fecal samples were collected from late finisher pig pens in 2000 and 2006, respectively. Salmonella isolates were characterized to determine serogroup and serotype and were tested for susceptibility to a panel of 17 and 15 antimicrobial drugs in 2000 and 2006, respectively. A total of 5,470 and 7,788 samples were cultured for Salmonella in 2000 and 2006, respectively. Overall, 6.2% of the samples and 34.2% of the farms were positive for Salmonella in 2000. In 2006, 7.2% of the samples and 52.6% of the farms were positive. Salmonella Derby, Salmonella Typhimurium var. 5- (formerly Salmonella Typhimurium var. Copenhagen), and Salmonella Agona were the three serotypes most often recovered in both study years. The most common antimicrobial resistance pattern for Salmonella Derby in the two study years was resistance to streptomycin, sulfisoxazole, and tetracycline. Most isolates were resistant to tetracycline, sulfisoxazole, and streptomycin in both study years. The proportion of Salmonella isolates that were susceptible to all antimicrobials (pansusceptible) was 38.1% in 2000 and 20.4% in 2006. The proportion of Salmonella isolates that were resistant to three or more antimicrobials (multidrug resistant) was similar in 2000 and in 2006 (52.8 and 57.7%, respectively).}, number={3}, journal={Journal of Food Protection}, publisher={International Association for Food Protection}, author={Haley, C. A. and Dargatz, D. A. and Bush, E. J. and Erdman, M. M. and Fedorka Cray, P. J.}, year={2012}, month={Mar}, pages={428–436} }
 @article{glenn_lindsey_frank_meinersmann_englen_fedorka-cray_frye_2011, title={Analysis of Antimicrobial Resistance Genes Detected in Multidrug-ResistantSalmonella entericaSerovar Typhimurium Isolated from Food Animals}, volume={17}, ISSN={1076-6294 1931-8448}, url={http://dx.doi.org/10.1089/mdr.2010.0189}, DOI={10.1089/mdr.2010.0189}, abstractNote={Multidrug-resistant (MDR) Salmonella enterica serovar Typhimurium is the most prevalent penta-resistant serovar isolated from animals by the U.S. National Antimicrobial Resistance Monitoring System. Penta-resistant isolates are often resistant to ampicillin, chloramphenicol, streptomycin, sulfamethoxazole, and tetracycline. To investigate MDR in Salmonella Typhimurium (including variant 5-), one isolate each from cattle, poultry, and swine with at least the ampicillin, chloramphenicol, streptomycin, sulfamethoxazole, and tetracycline phenotype were selected for each year from 1997 to 2007 (n = 33) for microarray analysis of antimicrobial resistance, incompatibility IncA/C, and HI1 plasmid genes. Cluster analysis based on these data separated 31 of the isolates into two groups A and B (15 and 16 isolates, respectively). Isolates in group A were phage type DT104 or U302 and were mostly swine isolates (7/15). Genes detected included intI1, blaPSE-1, floR, aadA, sulI, tet(G), and tetR, which are often found in Salmonella Genomic Island I. Isolates in group B had numerous IncA/C plasmid genes detected and were mostly cattle isolates (9/16). Genes detected included blaCMY-2, floR, aac(3), aadA, aphA1, strA, strB, sulI, sulII, dfrA, dhf, tet(A)(B)(C)(D), and tetR, which are often found on MDR-AmpC IncA/C plasmids. The IncA/C replicon was also detected in all group B isolates. The two remaining isolates did not cluster with any others and both had many HI1 plasmid genes detected. Linkage disequilibrium analysis detected significant associations between plasmid replicon type, phage type, and animal source. These data suggest that MDR in Salmonella Typhimurium is associated with DT104/Salmonella Genomic Island I or IncA/C MDR-AmpC encoding plasmids and these genetic elements have persisted throughout the study period.}, number={3}, journal={Microbial Drug Resistance}, publisher={Mary Ann Liebert Inc}, author={Glenn, LaShanda M. and Lindsey, Rebecca L. and Frank, Joseph F. and Meinersmann, Richard J. and Englen, Mark D. and Fedorka-Cray, Paula J. and Frye, Jonathan G.}, year={2011}, month={Aug}, pages={407–418} }
 @article{davis_jackson_fedorka-cray_barrett_brousse_gustafson_kucher_2011, title={Anatomical distribution and genetic relatedness of antimicrobial-resistant Escherichia coli from healthy companion animals}, volume={110}, ISSN={1364-5072}, url={http://dx.doi.org/10.1111/j.1365-2672.2010.04920.x}, DOI={10.1111/j.1365-2672.2010.04920.x}, abstractNote={Journal Article Anatomical distribution and genetic relatedness of antimicrobial‐resistant Escherichia coli from healthy companion animals Get access J.A. Davis, J.A. Davis Bacterial Epidemiology and Antimicrobial Resistance Research Unit, US Department of Agriculture, Agricultural Research Service, Richard B. Russell Research Center, Athens, GA USA Search for other works by this author on: Oxford Academic Google Scholar C.R. Jackson, C.R. Jackson Bacterial Epidemiology and Antimicrobial Resistance Research Unit, US Department of Agriculture, Agricultural Research Service, Richard B. Russell Research Center, Athens, GA USA Charlene R. Jackson, Bacterial Epidemiology and Antimicrobial Resistance Research Unit, US Department of Agriculture Agricultural Research Service, Richard B. Russell Research Center, 950 College Station Rd, RRC, Athens, GA 30605, USA. E‐mail: charlene.jackson@ars.usda.gov Search for other works by this author on: Oxford Academic Google Scholar P.J. Fedorka‐Cray, P.J. Fedorka‐Cray Bacterial Epidemiology and Antimicrobial Resistance Research Unit, US Department of Agriculture, Agricultural Research Service, Richard B. Russell Research Center, Athens, GA USA Search for other works by this author on: Oxford Academic Google Scholar J.B. Barrett, J.B. Barrett Bacterial Epidemiology and Antimicrobial Resistance Research Unit, US Department of Agriculture, Agricultural Research Service, Richard B. Russell Research Center, Athens, GA USA Search for other works by this author on: Oxford Academic Google Scholar J.H. Brousse, J.H. Brousse Classic City Cat and Dog Clinic, Athens, GA, USA Search for other works by this author on: Oxford Academic Google Scholar J. Gustafson, J. Gustafson Hope Animal Medical Center, Athens, GA, USA Search for other works by this author on: Oxford Academic Google Scholar M. Kucher M. Kucher Good Hands Veterinary Hospital, Athens, GA, USA Search for other works by this author on: Oxford Academic Google Scholar Journal of Applied Microbiology, Volume 110, Issue 2, 1 February 2011, Pages 597–604, https://doi.org/10.1111/j.1365-2672.2010.04920.x Published: 01 February 2011 Article history Received: 30 August 2010 Revision received: 03 December 2010 Accepted: 09 December 2010 Published: 01 February 2011}, number={2}, journal={Journal of Applied Microbiology}, publisher={Wiley}, author={Davis, J.A. and Jackson, C.R. and Fedorka-Cray, P.J. and Barrett, J.B. and Brousse, J.H. and Gustafson, J. and Kucher, M.}, year={2011}, month={Jan}, pages={597–604} }
 @article{sjölund-karlsson_joyce_blickenstaff_ball_haro_medalla_fedorka-cray_zhao_crump_whichard_2011, title={Antimicrobial Susceptibility to Azithromycin among Salmonella enterica Isolates from the United States}, volume={55}, ISSN={0066-4804 1098-6596}, url={http://dx.doi.org/10.1128/aac.00590-11}, DOI={10.1128/aac.00590-11}, abstractNote={Due to emerging resistance to traditional antimicrobial agents, such as ampicillin, trimethoprim-sulfamethoxazole, and chloramphenicol, azithromycin is increasingly used for the treatment of invasive Salmonella infections. In the present study, 696 isolates of non-Typhi Salmonella collected from humans, food animals, and retail meats in the United States were investigated for antimicrobial susceptibility to azithromycin. Seventy-two Salmonella enterica serotype Typhi isolates from humans were also tested. For each isolate, MICs of azithromycin and 15 other antimicrobial agents were determined by broth microdilution. Among the non-Typhi Salmonella isolates, azithromycin MICs among human isolates ranged from 1 to 32 μg/ml, whereas the MICs among the animal and retail meat isolates ranged from 2 to 16 μg/ml and 4 to 16 μg/ml, respectively. Among Salmonella serotype Typhi isolates, the azithromycin MICs ranged from 4 to 16 μg/ml. The highest MIC observed in the present study was 32 μg/ml, and it was detected in three human isolates belonging to serotypes Kentucky, Montevideo, and Paratyphi A. Based on our findings, we propose an epidemiological cutoff value (ECOFF) for wild-type Salmonella of ≤16 μg/ml of azithromycin. The susceptibility data provided could be used in combination with clinical outcome data to determine tentative clinical breakpoints for azithromycin and Salmonella enterica.}, number={9}, journal={Antimicrobial Agents and Chemotherapy}, publisher={American Society for Microbiology}, author={Sjölund-Karlsson, Maria and Joyce, Kevin and Blickenstaff, Karen and Ball, Takiyah and Haro, Jovita and Medalla, Felicita M. and Fedorka-Cray, Paula and Zhao, Shaohua and Crump, John A. and Whichard, Jean M.}, year={2011}, month={Jun}, pages={3985–3989} }
 @article{berrang_meinersmann_cox_fedorka-cray_2011, title={Application of chlorine dioxide to lessen bacterial contamination during broiler defeathering}, volume={20}, ISSN={1056-6171 1537-0437}, url={http://dx.doi.org/10.3382/japr.2010-00178}, DOI={10.3382/japr.2010-00178}, abstractNote={Because of the escape of contaminated gut contents, the number of Campylobacter spp. recovered from broiler carcasses increases during defeathering. Chlorine dioxide is approved for use as an antimicrobial treatment during poultry processing. A study was designed to test if application of 50 ppm of ClO2 during defeathering could prevent the expected increase in Campylobacter numbers on carcasses. Three replications were conducted, each using carcasses from different Campylobacter-positive flocks. Carcasses were collected from the shackle line immediately before and after defeathering with and without ClO2 spray; all carcasses were subjected to a whole-carcass rinse. Rinsate was cultured for Campylobacter, Escherichia coli, and Salmonella. Carcasses sprayed with ClO2 during defeathering had significantly lower numbers of Campylobacter and E. coli than carcasses treated with the water spray control defeathering. The ClO2 defeathering treatment also resulted in a lower prevalence of Salmonella than did control defeathering. Antimicrobial resistance profiles of Campylobacter and Salmonella isolates collected from ClO2-treated carcasses were not different from those collected from control carcasses. Application of ClO2 during feather removal may have potential as a means to mitigate the increase in bacterial contamination associated with broiler defeathering.}, number={1}, journal={The Journal of Applied Poultry Research}, publisher={Oxford University Press (OUP)}, author={Berrang, M. E. and Meinersmann, R. J. and Cox, N. A. and Fedorka-Cray, P. J.}, year={2011}, month={Mar}, pages={33–39} }
 @article{lindsey_frye_thitaram_meinersmann_fedorka-cray_englen_2011, title={Characterization of Multidrug-Resistant Escherichia coli by Antimicrobial Resistance Profiles, Plasmid Replicon Typing, and Pulsed-Field Gel Electrophoresis}, volume={17}, ISSN={1076-6294 1931-8448}, url={http://dx.doi.org/10.1089/mdr.2010.0148}, DOI={10.1089/mdr.2010.0148}, abstractNote={The objective of this study was to examine the distribution of multidrug resistance in Escherichia coli in relation to plasmid replicon types, animal sources, and genotypes. E. coli isolates (n = 35) from seven different animal sources were selected and tested for susceptibility to 15 antimicrobials; pulsed-field gel electrophoresis was used to determine genetic relationships among the E. coli isolates. Plasmid types based on their incompatibility (Inc) replicon types were determined, and linkage disequilibrium analysis was performed for antimicrobial resistance profiles, replicon types, and animal source. A high degree of genotypic diversity was observed: 34 different pulsed-field gel electrophoresis types among the 35 isolates examined. Twelve different plasmid Inc types were detected, and all isolates carried at least one replicon type. IncF (n = 25; 71.4%) and IncFIB (n = 19; 54.3%) were the most common replicon types identified. Chloramphenicol resistance was significantly linked with four Inc types (A/C, FIIA, F, and Y), and amoxicillin/clavulanic acid was linked with three Inc types (B/O, P and Y). Resistance to any other antimicrobial was linked to two or fewer replicon types. The isolate source was linked with resistance to seven antimicrobials and IncI1. We conclude that commensal E. coli from animal sources are highly variable genotypically and are reservoirs of a diverse array of plasmids carrying antimicrobial resistance.}, number={2}, journal={Microbial Drug Resistance}, publisher={Mary Ann Liebert Inc}, author={Lindsey, Rebecca L. and Frye, Jonathan G. and Thitaram, Sutawee N. and Meinersmann, Richard J. and Fedorka-Cray, Paula J. and Englen, Mark D.}, year={2011}, month={Jun}, pages={157–163} }
 @article{thitaram_frank_lyon_siragusa_bailey_lombard_haley_wagner_dargatz_fedorka cray_2011, title={Clostridium difficile from Healthy Food Animals: Optimized Isolation and Prevalence}, volume={74}, ISSN={0362-028X}, url={http://dx.doi.org/10.4315/0362-028x.jfp-10-229}, DOI={10.4315/0362-028x.jfp-10-229}, abstractNote={Two isolation methods were compared for isolation of Clostridium difficile from food animal feces. The single alcohol shock method (SS) used selective enrichment in cycloserine-cefoxitin fructose broth supplemented with 0.1% sodium taurocholate, followed by alcohol shock and isolation on tryptic soy agar supplemented with 5% sheep blood, and cycloserine-cefoxitin fructose agar. The double alcohol shock method (DS) used alcohol shock prior to and after selective enrichment in cycloserine-cefoxitin fructose broth supplemented with 0.1% sodium taurocholate, followed by isolation on tryptic soy agar supplemented with 5% sheep blood and cycloserine-cefoxitin fructose agar. A total of 55 (15.9%, n = 345) swine fecal samples, 32 (2.4%, n = 1,325) dairy cattle fecal samples, and 188 (6.3%, n = 2,965) beef cattle fecal samples were positive for C. difficile by either method. However, the DS was significantly better than the SS for the recovery of C. difficile from swine feces, while the SS was significantly better than the DS for the recovery of C. difficile from beef cattle feces. There was no significant difference between methods for the recovery of C. difficile from dairy cattle feces. This study suggests that food animals might harbor C. difficile and it provides critical information that isolation methods might not have universal application across animal species.}, number={1}, journal={Journal of Food Protection}, publisher={International Association for Food Protection}, author={Thitaram, S. N. and Frank, J. F. and Lyon, S. A. and Siragusa, G. R. and Bailey, J. S. and Lombard, J. E. and Haley, C. A. and Wagner, B. A. and Dargatz, D. A. and Fedorka Cray, P. J.}, year={2011}, month={Jan}, pages={130–133} }
 @article{lindsey_frye_fedorka-cray_meinersmann_2011, title={Microarray-Based Analysis of IncA/C Plasmid-Associated Genes from Multidrug-Resistant Salmonella enterica}, volume={77}, ISSN={0099-2240 1098-5336}, url={http://dx.doi.org/10.1128/aem.00567-11}, DOI={10.1128/aem.00567-11}, abstractNote={ABSTRACT In the family Enterobacteriaceae , plasmids have been classified according to 27 incompatibility (Inc) or replicon types that are based on the inability of different plasmids with the same replication mechanism to coexist in the same cell. Certain replicon types such as IncA/C are associated with multidrug resistance (MDR). We developed a microarray that contains 286 unique 70-mer oligonucleotide probes based on sequences from five IncA/C plasmids: pYR1 ( Yersinia ruckeri ), pPIP1202 ( Yersinia pestis ), pP99-018 ( Photobacterium damselae ), pSN254 ( Salmonella enterica serovar Newport), and pP91278 ( Photobacterium damselae ). DNA from 59 Salmonella enterica isolates was hybridized to the microarray and analyzed for the presence or absence of genes. These isolates represented 17 serovars from 14 different animal hosts and from different geographical regions in the United States. Qualitative cluster analysis was performed using CLUSTER 3.0 to group microarray hybridization results. We found that IncA/C plasmids occurred in two lineages distinguished by a major insertion-deletion (indel) region that contains genes encoding mostly hypothetical proteins. The most variable genes were represented by transposon-associated genes as well as four antimicrobial resistance genes ( aphA , merP , merA , and aadA ). Sixteen mercury resistance genes were identified and highly conserved, suggesting that mercury ion-related exposure is a stronger pressure than anticipated. We used these data to construct a core IncA/C genome and an accessory genome. The results of our studies suggest that the transfer of antimicrobial resistance determinants by transfer of IncA/C plasmids is somewhat less common than exchange within the plasmids orchestrated by transposable elements, such as transposons, integrating and conjugative elements (ICEs), and insertion sequence common regions (IS CR s), and thus pose less opportunity for exchange of antimicrobial resistance.}, number={19}, journal={Applied and Environmental Microbiology}, publisher={American Society for Microbiology}, author={Lindsey, Rebecca L. and Frye, Jonathan G. and Fedorka-Cray, Paula J. and Meinersmann, Richard J.}, year={2011}, month={Aug}, pages={6991–6999} }
 @article{kich_coldebella_morés_nogueira_cardoso_fratamico_call_fedorka-cray_luchansky_2011, title={Prevalence, distribution, and molecular characterization of Salmonella recovered from swine finishing herds and a slaughter facility in Santa Catarina, Brazil}, volume={151}, ISSN={0168-1605}, url={http://dx.doi.org/10.1016/j.ijfoodmicro.2011.09.024}, DOI={10.1016/j.ijfoodmicro.2011.09.024}, abstractNote={Swine can carry Salmonella strains that may be transmitted to humans by pork products. This investigation determined the distribution and types of Salmonella in 12 swine finishing herds and a slaughter facility in Santa Catarina, Brazil. A total of 1258 samples, consisting of environmental, feed, carcass, lymph node, and fecal material were collected and submitted to bacteriological isolation of Salmonella. From 487 positive samples, 1255 isolates were recovered and confirmed to be Salmonella. The distribution of positive samples was as follows: finishing pen floors 26% (16/61); feed 29% (42/143); feces 44% (52/119); pooled feces 59% (35/59); slaughter holding pens 90% (36/40); lymph nodes 46% (220/478); pre-chilled carcass surfaces 24% (24/98); and post-chilled carcass surfaces 24% (62/260). The most prevalent serovars were Typhimurium, Panama, Senftenberg, Derby, and Mbandaka. By pulsed-field gel electrophoresis, 1071 isolates were subtyped using XbaI, and duplicate isolates were removed. From the remaining 747 isolates, 163 macrorestriction profiles (pulsotypes) were identified. Six pulsotypes were considered very frequent, occurring in 33 isolates or more. The multiple correspondence analyses showed correlations between pulsotypes from shedding pigs (feces), herd environment (pen floors), and subiliac and prescapular lymph nodes and between lairage and carcass surface samples before and after chilling. All sources of Salmonella investigated contributed to the carrier state; however, pre-slaughter contamination at lairage was the variable most strongly associated with carcass contamination. A total of 59 different antimicrobial resistance profiles were observed in 572 Salmonella isolates. From these isolates, 17% (97/572) were susceptible to all 15 antibiotics tested, 83% (475/572) were resistant to at least one, and 43% (246/572) were resistant to four or more antibiotics (multi-resistant). The AmpGenKanTet profile was the most prevalent in carcass isolates and was associated with farm origin.}, number={3}, journal={International Journal of Food Microbiology}, publisher={Elsevier BV}, author={Kich, Jalusa D. and Coldebella, Arlei and Morés, Nelson and Nogueira, Mariana Gomes and Cardoso, Marisa and Fratamico, Pina M. and Call, Jeffrey E. and Fedorka-Cray, Paula and Luchansky, John B.}, year={2011}, month={Dec}, pages={307–313} }
 @article{frye_lindsey_meinersmann_berrang_jackson_englen_turpin_fedorka-cray_2011, title={Related Antimicrobial Resistance Genes Detected in Different Bacterial Species Co-isolated from Swine Fecal Samples}, volume={8}, ISSN={1535-3141 1556-7125}, url={http://dx.doi.org/10.1089/fpd.2010.0695}, DOI={10.1089/fpd.2010.0695}, abstractNote={A potential factor leading to the spread of antimicrobial resistance (AR) in bacteria is the horizontal transfer of resistance genes between bacteria in animals or their environment. To investigate this, swine fecal samples were collected on-farm and cultured for Escherichia coli, Salmonella enterica, Campylobacter spp., and Enterococcus spp. which are all commonly found in swine. Forty-nine of the samples from which all four bacteria were recovered were selected yielding a total of 196 isolates for analysis. Isolates were tested for antimicrobial susceptibility followed by hybridization to a DNA microarray designed to detect 775 AR-related genes. E. coli and Salmonella isolated from the same fecal sample had the most AR genes in common among the four bacteria. Genes detected encoded resistance to aminoglycosides (aac(3), aadA1, aadB, and strAB), β-lactams (ampC, ampR, and bla(TEM)), chloramphenicols (cat and floR), sulfanillic acid (sul1/sulI), tetracyclines (tet(A), tet(D), tet(C), tet(G), and tet(R)), and trimethoprim (dfrA1 and dfh). Campylobacter coli and Enterococcus isolated from the same sample frequently had tet(O) and aphA-3 genes detected in common. Almost half (47%) of E. coli and Salmonella isolated from the same fecal sample shared resistance genes at a significant level (χ², p < 0.0000001). These data suggest that there may have been horizontal exchange of AR genes between these bacteria or there may be a common source of AR genes in the swine environment for E. coli and Salmonella.}, number={6}, journal={Foodborne Pathogens and Disease}, publisher={Mary Ann Liebert Inc}, author={Frye, Jonathan G. and Lindsey, Rebecca L. and Meinersmann, Richard J. and Berrang, Mark E. and Jackson, Charlene R. and Englen, Mark D. and Turpin, Jennifer B. and Fedorka-Cray, Paula J.}, year={2011}, month={Jun}, pages={663–679} }
 @article{guard_morales_fedorka-cray_gast_2011, title={Single nucleotide polymorphisms that differentiate two subpopulations of Salmonella enteritidis within phage type}, volume={4}, ISSN={1756-0500}, url={http://dx.doi.org/10.1186/1756-0500-4-369}, DOI={10.1186/1756-0500-4-369}, abstractNote={Salmonella Enteritidis is currently the world's leading cause of salmonellosis, in part because of its ability to contaminate the internal contents of eggs. Previous analyses have shown that it is an exceptionally clonal serotype, which nonetheless generates considerable phenotypic heterogeneity. Due to its clonality, whole genome analysis is required to find genetic determinants that contribute to strain heterogeneity of Salmonella Enteritidis. Comparative whole genome mutational mapping of two PT13a strains that varied in the ability to contaminate eggs and to form biofilm was achieved using a high-density tiling platform with primers designed from a PT4 reference genome. Confirmatory Sanger sequencing was used on each putative SNP identified by mutational mapping to confirm its presence and location as compared to the reference sequence. High coverage pyrosequencing was used as a supporting technology to review results.A total of 250 confirmed SNPs were detected that differentiated the PT13a strains. From these 250 SNPS, 247 were in the chromosome and 3 were in the large virulence plasmid. SNPs ranged from single base pair substitutions to a deletion of 215 bp. A total of 15 SNPs (3 in egg-contaminating PT13a 21046 and 12 in biofilm forming PT13a 21027) altered coding sequences of 16 genes. Pyrosequencing of the two PT13a subpopulations detected 8.9% fewer SNPs than were detected by high-density tiling. Deletions and ribosomal gene differences were classes of SNPs not efficiently detected by pyrosequencing.These results increase knowledge of evolutionary trends within Salmonella enterica that impact the safety of the food supply. Results may also facilitate designing 2nd generation vaccines, because gene targets were identified that differentiate subpopulations with variant phenotypes. High-throughput genome sequencing platforms should be assessed for the ability to detect classes of SNPs equivalently, because each platform has different advantages and limits of detection.}, number={1}, journal={BMC Research Notes}, publisher={Springer Nature}, author={Guard, Jean and Morales, Cesar A and Fedorka-Cray, Paula and Gast, Richard K}, year={2011}, month={Sep} }
 @article{lindsey_frye_fedorka-cray_welch_meinersmann_2010, title={An oligonucleotide microarray to characterize multidrug resistant plasmids}, volume={81}, ISSN={0167-7012}, url={http://dx.doi.org/10.1016/j.mimet.2010.01.024}, DOI={10.1016/j.mimet.2010.01.024}, abstractNote={Many of the Enterobacteriaceae carry multiple drug resistance (MDR) genes on large plasmids of replicon type Inc A/C and Inc H1. It is important to understand the transmission of these MDR plasmids because the genes they carry can affect the outcome of antimicrobial therapy. The aim of this study was to design a microarray with oligonucleotide probes for every gene in the six Inc A/C and one Inc H1 plasmids of interest while representing all redundant sequences only once. The microarray is printed in triplicate with 493 unique oligonucleotide probes 70 nucleotides in length. Salmonella enterica and Escherichia coli control strains and test plasmids (in the parent strain and transformed into a known E. coli background strain) were hybridized to the plasmid microarray. This hybridization arrays presents a rapid and cost effective method for high-density screening of isolates to evaluate the gene content of Inc A/C and H1 plasmids and will show how plasmids can change content with transmission.}, number={2}, journal={Journal of Microbiological Methods}, publisher={Elsevier BV}, author={Lindsey, Rebecca L. and Frye, Jonathan G. and Fedorka-Cray, Paula J. and Welch, Timothy J. and Meinersmann, Richard J.}, year={2010}, month={May}, pages={96–100} }
 @article{green_dargatz_wagner_fedorka-cray_ladely_kopral_2010, title={Analysis of Risk Factors Associated with Salmonella spp. Isolated from U.S. Feedlot Cattle}, volume={7}, ISSN={1535-3141 1556-7125}, url={http://dx.doi.org/10.1089/fpd.2007.0068}, DOI={10.1089/fpd.2007.0068}, abstractNote={Contamination can occur at a number of stages during farm-to-fork processing. Preharvest intervention is an ongoing area of interest in reduction of risk of foodborne illness. This study examined risk factors associated with detection of Salmonella from cattle in U.S. feedlots. During two visits to 73 feedlots, 25 fresh fecal samples were collected from each of three pen floors. Associations between management and demographic factors and culture status were evaluated using logistic regression. Factors positively associated with culture-positive status included brewers' grains (odds ratio [OR] = 26.35; confidence interval [CI], 10.33–67.20), corn gluten (OR = 10.35; CI, 5.98–17.91), or cottonseed hulls (OR = 8.34; CI, 3.58–19.42) in the ration, and sourcing animals in a pen from multiple herds of origin (OR = 5.17; CI, 2.32–11.51). Factors negatively associated with positive culture status included urea (OR = 0.27; CI, 0.16–0.44), alfalfa, clover, or sorghum silage (OR = 0.31; CI, 0.12–0.79), and antimicrobials of the tetracycline class in the ration (within 2 weeks before sampling, OR = 0.04 and CI, 0.02–0.09; more than 2 weeks before sampling, OR = 0.23 and CI, 0.06–0.80). Since 18.3% of positive samples were on a single operation, a second model was constructed after excluding data from this operation. Three additional variables were retained in the second model, including grain-processing method (OR for dry roll, cracked, or unprocessed grain = 2.99; CI, 1.55–5.75), soybean meal (OR = 2.74; CI, 1.58–4.75), and use of a coccidiostat in the ration (OR for no coccidiostat = 4.50; CI, 2.03–10.01). Considering the increasing use of by-products of the biofuel industry as feeds, further investigation of the association between feeding brewers' grains and corn gluten and Salmonella recovery is warranted.}, number={7}, journal={Foodborne Pathogens and Disease}, publisher={Mary Ann Liebert Inc}, author={Green, Alice L. and Dargatz, David A. and Wagner, Bruce A. and Fedorka-Cray, Paula J. and Ladely, Scott R. and Kopral, Chris A.}, year={2010}, month={Jul}, pages={825–833} }
 @article{cox_richardson_cason_buhr_vizzier thaxton_smith_fedorka cray_romanenghi_pereira_doyle_2010, title={Comparison of Neck Skin Excision and Whole Carcass Rinse Sampling Methods for Microbiological Evaluation of Broiler Carcasses before and after Immersion Chilling}, volume={73}, ISSN={0362-028X}, url={http://dx.doi.org/10.4315/0362-028x-73.5.976}, DOI={10.4315/0362-028x-73.5.976}, abstractNote={Sampling protocols for detecting Salmonella on poultry differ among various countries. In the United States, the U.S. Department of Agriculture Food Safety and Inspection Service dictates that whole broiler carcasses should be rinsed with 400 ml of 1% buffered peptone water, whereas in the European Union 25-g samples composed of neck skin from three carcasses are evaluated. The purpose of this study was to evaluate a whole carcass rinse (WCR) and a neck skin excision (NS) procedure for Salmonella and Escherichia coli isolation from the same broiler carcass. Carcasses were obtained from three broiler processing plants. The skin around the neck area was aseptically removed and bagged separately from the carcass, and microbiological analysis was performed. The corresponding carcass was bagged and a WCR sample was evaluated. No significant difference (alpha </= 0.05) in Salmonella prevalence was found between the samples processed by the two methods, but both procedures produced many false-negative Salmonella results. Prechill, 37% (66 carcasses), 28% (50 carcasses), and 51% (91 carcasses) of the 180 carcasses examined were positive for Salmonella by WCR, NS, and both procedures combined, respectively. Postchill, 3% (5 carcasses), 7% (12 carcasses), and 10% (17 carcasses) of the 177 carcasses examined were positive for Salmonella by the WCR, NS, and combination of both procedures, respectively. Prechill, E. coli plus coliform counts were 3.0 and 2.6 log CFU/ml by the WCR and NS methods, respectively. Postchill, E. coli plus coliform counts were 1.7 and 1.4 log CFU/ml by the WCR and NS methods, respectively.}, number={5}, journal={Journal of Food Protection}, publisher={International Association for Food Protection}, author={Cox, N. A. and Richardson, L. J. and Cason, J. A. and Buhr, R. J. and Vizzier Thaxton, Y. and Smith, D. P. and Fedorka Cray, P. J. and Romanenghi, C. P. and Pereira, L. V. B. and Doyle, M. P.}, year={2010}, month={May}, pages={976–980} }
 @article{frye_lindsey_rondeau_porwollik_long_mcclelland_jackson_englen_meinersmann_berrang_et al._2010, title={Development of a DNA Microarray to Detect Antimicrobial Resistance Genes Identified in the National Center for Biotechnology Information Database}, volume={16}, ISSN={1076-6294 1931-8448}, url={http://dx.doi.org/10.1089/mdr.2009.0082}, DOI={10.1089/mdr.2009.0082}, abstractNote={To understand the mechanisms and epidemiology of antimicrobial resistance (AR), the genetic elements responsible must be identified. Due to the myriad of possible genes, a high-density genotyping technique is needed for initial screening. To achieve this, AR genes in the National Center for Biotechnology Information GenBank database were identified by their annotations and compiled into a nonredundant list of 775 genes. A DNA microarray was constructed of 70mer oligonucelotide probes designed to detect these genes encoding resistances to aminoglycosides, β-lactams, chloramphenicols, glycopeptides, heavy metals, lincosamides, macrolides, metronidazoles, polyketides, quaternary ammonium compounds, streptogramins, sulfonamides, tetracyclines, and trimethoprims as well as resistance transfer genes. The microarray was validated with two fully sequenced control strains of Salmonella enterica: Typhimurium LT2 (sensitive) and Typhi CT18 (multidrug resistance [MDR]). All resistance genes encoded on the MDR plasmid, pHCM1, harbored by CT18 were detected in that strain, whereas no resistance genes were detected in LT2. The microarray was also tested with a variety of bacteria, including MDR Salmonella enterica serovars, Escherichia coli, Campylobacter spp., Enterococcus spp., methicillin-resistant Staphylococcus aureus, Listeria spp., and Clostridium difficile. The results presented here demonstrate that a microarray can be designed to detect virtually all AR genes found in the National Center for Biotechnology Information database, thus reducing the subsequent assays necessary to identify specific resistance gene alleles.}, number={1}, journal={Microbial Drug Resistance}, publisher={Mary Ann Liebert Inc}, author={Frye, Jonathan G. and Lindsey, Rebecca L. and Rondeau, Gaelle and Porwollik, Steffen and Long, Fred and McClelland, Michael and Jackson, Charlene R. and Englen, Mark D. and Meinersmann, Richard J. and Berrang, Mark E. and et al.}, year={2010}, month={Mar}, pages={9–19} }
 @article{englen_berrang_meinersmann_fedorka-cray_2010, title={Evaluation of two commercial real-time PCR assays for detecting Campylobacter in broiler carcass rinses}, volume={30}, ISSN={0149-6085 1745-4565}, url={http://dx.doi.org/10.1111/j.1745-4565.2010.00237.x}, DOI={10.1111/j.1745-4565.2010.00237.x}, abstractNote={ABSTRACT
Traditional plating methods are reliable means for Campylobacter identification from poultry samples but automated gene-based detection systems now available can reduce assay time, data collection and analysis. Bio-Rad and DuPont Qualicon recently introduced Campylobacter assays for their real-time polymerase chain reaction (PCR) instruments. We evaluated the utility of these assays compared with standard plating and enumeration methods routinely used in our laboratory. Two replicates of 40 broiler carcass rinses collected before and after defeathering at a commercial processing plant were tested. All samples were positive for Campylobacter by direct plating of rinses: log10 cfu values ranged from 0.24 to 4.61. In contrast, the Bio-Rad iQ-Check assay returned 60–72.5% positives on direct rinses; the Qualicon BAX Q7 test produced 60–85% positives with direct rinse samples. Using aliquots of 24 h enrichment broth from rinses in the real-time assays significantly improved detection: the Bio-Rad test had 95–100% positive while the Qualicon assay found 90–95% positive.

PRACTICAL APPLICATIONS
Traditional detection methods for Campylobacter are time-consuming, requiring as much as 5 days to complete. The recent introduction of commercial real-time PCR instruments for the identification of Campylobacter offer more rapid, simplified alternatives to standard culture-based techniques.}, number={3}, journal={Journal of Food Safety}, publisher={Wiley}, author={Englen, Mark D. and Berrang, Mark E. and Meinersmann, Richard J. and Fedorka-Cray, Paula J.}, year={2010}, month={May}, pages={732–739} }
 @article{sjölund-karlsson_howie_rickert_krueger_tran_zhao_ball_haro_pecic_joyce_et al._2010, title={Plasmid-mediated Quinolone Resistance among Non-Typhi Salmonella enterica Isolates, USA}, volume={16}, ISSN={1080-6040 1080-6059}, url={http://dx.doi.org/10.3201/eid1611.100464}, DOI={10.3201/eid1611.100464}, abstractNote={Abstract We determined the prevalence of plasmid-mediated quinolone resistance mechanisms among non-Typhi Salmonella spp. isolated from humans, food animals, and retail meat in the United States in 2007. Six isolates collected from humans harbored aac(6′)Ib-cr or a qnr gene. Most prevalent was qnrS1. No animal or retail meat isolates harbored a plasmid-mediated mechanism.}, number={11}, journal={Emerging Infectious Diseases}, publisher={Centers for Disease Control and Prevention (CDC)}, author={Sjölund-Karlsson, Maria and Howie, Rebecca and Rickert, Regan and Krueger, Amy and Tran, Thu-Thuy and Zhao, Shaohua and Ball, Takiyah and Haro, Jovita and Pecic, Gary and Joyce, Kevin and et al.}, year={2010}, month={Nov}, pages={1789–1791} }
 @article{jackson_lombard_dargatz_fedorka-cray_2010, title={Prevalence, species distribution and antimicrobial resistance of enterococci isolated from US dairy cattle}, volume={52}, ISSN={0266-8254}, url={http://dx.doi.org/10.1111/j.1472-765x.2010.02964.x}, DOI={10.1111/j.1472-765x.2010.02964.x}, abstractNote={To estimate prevalence and antimicrobial susceptibility of enterococci in faeces collected in 2007 from U.S. dairy cattle.A total of 718 faecal samples from 122 dairy cattle operations from 17 US States were collected and cultured for the presence of enterococci. One hundred and eighteen of the 122 operations (96·7%) had at least one dairy cow positive for enterococci and 88·7% (637 of 718) of the faecal samples were positive. At least ten different enterococcal species were found on the dairy operations and 90·7% (107 of 118) of the operations were positive for Enterococcus hirae followed by E. faecalis (40·7%; 48 of 118) and E. faecium (39%; 46 of 118). The highest percentage of resistant isolates were to lincomycin (92·3%; 587 of 636), flavomycin (71·9%; 457 of 636) and tetracycline (24·5%; 156 of 636). Multi-drug resistance (MDR) (resistance ≥ 2 antimicrobials) was observed to as many as seven antimicrobials regardless of class.In contrast to previous studies, faecal shedding of enterococci in dairy cattle occurred in almost 90% of cows sampled and represented a variety of enterococcal species.Although this study demonstrated a high prevalence of antimicrobial-resistant enterococci from dairy cattle faeces in the United States, the contribution of dairy cattle as a source of antimicrobial-resistant enterococci that can be transmitted to humans remains unclear.}, number={1}, journal={Letters in Applied Microbiology}, publisher={Wiley}, author={Jackson, C. R. and Lombard, J. E. and Dargatz, D. A. and Fedorka-Cray, P. J.}, year={2010}, month={Nov}, pages={41–48} }
 @article{ladely_meinersmann_englen_fedorka-cray_harrison_2009, title={23S rRNA Gene Mutations Contributing to Macrolide Resistance in Campylobacter jejuni and Campylobacter coli}, volume={6}, ISSN={1535-3141 1556-7125}, url={http://dx.doi.org/10.1089/fpd.2008.0098}, DOI={10.1089/fpd.2008.0098}, abstractNote={The genetic basis of macrolide resistance in Campylobacter coli (n = 17) and C. jejuni (n = 35) isolates previously subjected to in vivo selective pressure was investigated to determine if the number of copies of 23S rRNA genes with macrolide-associated mutations affects the minimum inhibitory concentration (MIC) of macrolides. Sequence data for domain V of the 23S rRNA gene revealed that two macrolide-resistant C. coli isolates had adenine→guanine transitions at position 2059 (A2059G, Escherichia coli numbering). One of the two isolates had the A2059G transition in only two of the three gene copies. Among the macrolide-resistant C. jejuni isolates (n = 9), two different point mutations within domain V were observed. Three macrolide-resistant C. jejuni isolates had A2059G transitions. One of these three C. jejuni isolates had the A2059G transition in only two of the three gene copies. Six macrolide-resistant C. jejuni isolates had an adenine→cytosine transversion at position 2058 (A2058C, E. coli numbering) in all three copies of the 23S rRNA gene. Campylobacter jejuni isolates with the A2058C transversion had higher erythromycin MICs (>256 μg/mL) compared to C. jejuni isolates with A2059G transitions (64–128 μg/mL). In addition, the C. jejuni and C. coli isolates with only two copies of the 23S rRNA gene having A2059G substitutions had lower macrolide MICs compared to isolates with all three copies of the gene mutated. No isolates were observed having only one copy of the 23S rRNA gene with a mutation. Sequence analysis of ribosomal proteins L4 (rplD) and L22 (rplV) indicated that ribosomal protein modifications did not contribute to macrolide resistance among the collection of Campylobacter examined.}, number={1}, journal={Foodborne Pathogens and Disease}, publisher={Mary Ann Liebert Inc}, author={Ladely, Scott R. and Meinersmann, Richard J. and Englen, Mark D. and Fedorka-Cray, Paula J. and Harrison, Mark A.}, year={2009}, month={Feb}, pages={91–98} }
 @article{fricke_mcdermott_mammel_zhao_johnson_rasko_fedorka-cray_pedroso_whichard_leclerc_et al._2009, title={Antimicrobial Resistance-Conferring Plasmids with Similarity to Virulence Plasmids from Avian Pathogenic Escherichia coli Strains in Salmonella enterica Serovar Kentucky Isolates from Poultry}, volume={75}, ISSN={0099-2240}, url={http://dx.doi.org/10.1128/aem.00786-09}, DOI={10.1128/aem.00786-09}, abstractNote={ABSTRACT Salmonella enterica , a leading cause of food-borne gastroenteritis worldwide, may be found in any raw food of animal, vegetable, or fruit origin. Salmonella serovars differ in distribution, virulence, and host specificity. S almonella enterica serovar Kentucky, though often found in the food supply, is less commonly isolated from ill humans. The multidrug-resistant isolate S . Kentucky CVM29188, isolated from a chicken breast sample in 2003, contains three plasmids (146,811 bp, 101,461 bp, and 46,121 bp), two of which carry resistance determinants (pCVM29188_146 [ strAB and tetRA ] and pCVM29188_101 [ bla CMY-2 and sugE ]). Both resistance plasmids were transferable by conjugation, alone or in combination, to S. Kentucky, S almonella enterica serovar Newport, and E scherichia coli recipients. pCVM29188_146 shares a highly conserved plasmid backbone of 106 kb (>90% nucleotide identity) with two virulence plasmids from a vian p athogenic E scherichia c oli strains (pAPEC-O1-ColBM and pAPEC-O2-ColV). Shared avian pathogenic E. coli (APEC) virulence factors include iutA iucABCD , sitABCD , etsABC , iss , and iroBCDEN. PCR analyses of recent (1997 to 2005) S. Kentucky isolates from food animal, retail meat, and human sources revealed that 172 (60%) contained similar APEC-like plasmid backbones. Notably, though rare in human- and cattle-derived isolates, this plasmid backbone was found at a high frequency (50 to 100%) among S. Kentucky isolates from chickens within the same time span. Ninety-four percent of the APEC-positive isolates showed resistance to tetracycline and streptomycin. Together, our findings of a resistance-conferring APEC virulence plasmid in a poultry-derived S. Kentucky isolate and of similar resistance/virulence plasmids in most recent S. Kentucky isolates from chickens and, to lesser degree, from humans and cattle highlight the need for additional research in order to examine the prevalence and spread of combined virulence and resistance plasmids in bacteria in agricultural, environmental, and clinical settings.}, number={18}, journal={Applied and Environmental Microbiology}, publisher={American Society for Microbiology}, author={Fricke, W. F. and McDermott, P. F. and Mammel, M. K. and Zhao, S. and Johnson, T. J. and Rasko, D. A. and Fedorka-Cray, P. J. and Pedroso, A. and Whichard, J. M. and LeClerc, J. E. and et al.}, year={2009}, month={Jul}, pages={5963–5971} }
 @article{cox_richardson_berrang_fedorka cray_buhr_2009, title={Campylobacter coli Naturally Resistant to Elevated Levels of Gentamicin as a Marker Strain in Poultry Research}, volume={72}, ISSN={0362-028X}, url={http://dx.doi.org/10.4315/0362-028x-72.6.1288}, DOI={10.4315/0362-028x-72.6.1288}, abstractNote={Campylobacter inoculation studies are limited without a suitable marker strain. The lurpose of this study was to screen Campylobacter strains (n=2073) obtained from poultry carcass rinses through the Centers for Disease Control and Prevention's National Antimicrobial Resistant Monitoring System for resistance to gentamicin and evaluate one strain's efficacy as a marker. A C. coli strain was found resistant to gentamicin at >32 microg/ml. Gentamicin was incorporated into media (Campy-Cefex agar, Brucella agar, and blood agar) from 0 to 1000 microg/ml, and the upper level of gentamicin resistance was determined. C. coli strain's upper level of growth on Campy-Cefex plates, blood agar plates, and Brucella agar plates was 400, 300, and 200 pg/ml, respectively. Ceca and postpick carcass rinses were obtained and streaked onto Campy-Cefex agar at the above gentamicin levels to evaluate background microflora exclusion. Campy-Cefex agar containing gentamicin at 100 ag/ml prevented from the ceca, and reduced from the rinse, background microflora. The C. coli strain was orally or intracloacally inoculated into chicks. At 1, 3, and 6 weeks of age, inoculated broilers were removed and several tissue types sampled for the presence of the marker strain. At 6 weeks of age, 10 additional noninoculated penmates were sampled. The C. coli strain colonized chicks, disseminated to body tissues, colonized penmates, and persisted throughout the 6-week grow-out. The C. coli strain's unique characteristic, being resistant to high levels of gentamicin, allows for a marker that can be used in a wide range of Campylobacter research projects.}, number={6}, journal={Journal of Food Protection}, publisher={International Association for Food Protection}, author={Cox, N. A. and Richardson, L. J. and Berrang, M. E. and Fedorka Cray, P. J. and Buhr, R. J.}, year={2009}, month={Jun}, pages={1288–1292} }
 @article{cox_richardson_buhr_fedorka-cray_2009, title={Campylobacter species occurrence within internal organs and tissues of commercial caged Leghorn laying hens}, volume={88}, ISSN={0032-5791 1525-3171}, url={http://dx.doi.org/10.3382/ps.2009-00195}, DOI={10.3382/ps.2009-00195}, abstractNote={Campylobacter spp. are frequently present in the intestinal tract and internal tissues of broiler breeder and broiler chickens. Campylobacter spp. ecology in commercial Leghorn laying hens has not been extensively studied. The objectives of the current study were to determine 1) Campylobacter spp. presence in the reproductive tract, lymphoid organs, liver-gallbladder, and ceca of commercial Leghorn laying hens; 2) species of Campylobacter present; and 3) antimicrobial resistance pattern of Campylobacter isolates. In study 1, three flocks ranging from 94 to 105 wk of age were sampled from a commercial laying complex. In study 2, two flocks, 82 and 84 wk of age, were sampled from a separate complex. Hens were killed, defeathered, aseptically necropsied, and the spleen, liver-gallbladder, ovarian follicles, and upper (infundibulum, magnum, and isthmus) and lower (shell gland and vagina) reproductive tracts were aseptically removed before the ceca. Samples were packed on ice and transported to the laboratory for evaluation. For speciation, a standard BAX real-time PCR method was used while susceptibility testing was performed using US National Antimicrobial Resistance Monitoring System (NARMS) standards and recommended quality control organisms. Isolates were examined for susceptibility using a semi-automated testing system (Sensititer) to the following 9 antimicrobials: azithromycin, clindamycin, ciprofloxacin, erythromycin, florfenicol, gentamicin, nalidixic acid, telithromycin, and tetracycline. In study 1, the isolation rate was 13, 67, 53, 3, 13, and 57% from the ovarian follicles, lower reproductive tract, upper reproductive tract, spleen, liver-gallbladder, and ceca, respectively. In study 2, the isolation rate was 17, 43, 33, 20, 17, and 73% from the ovarian follicles, lower reproductive tract, upper reproductive tract, spleen, liver-gallbladder, and ceca, respectively. Overall, 50% of isolates were Campylobacter jejuni, 49% Campylobacter coli, and 1% Campylobacter lari. In study 1, all of the isolates were pan-susceptible. In study 2, thirty-seven percent of the isolates were resistant to tetracycline. Commercial table egg laying hens housed in colony cages on wire floors had diverse Campylobacter spp. recovered from different tissues and these isolates were not resistant to a broad range of antimicrobials.}, number={11}, journal={Poultry Science}, publisher={Oxford University Press (OUP)}, author={Cox, N. A. and Richardson, L. J. and Buhr, R. J. and Fedorka-Cray, P. J.}, year={2009}, month={Nov}, pages={2449–2456} }
 @article{pradhan_van kessel_karns_wolfgang_hovingh_nelen_smith_whitlock_fyock_ladely_et al._2009, title={Dynamics of endemic infectious diseases of animal and human importance on three dairy herds in the northeastern United States}, volume={92}, ISSN={0022-0302}, url={http://dx.doi.org/10.3168/jds.2008-1486}, DOI={10.3168/jds.2008-1486}, abstractNote={Endemic infectious diseases in dairy cattle are of significant concern to the industry as well as for public health because of their potential impact on animal and human health, milk and meat production, food safety, and economics. We sought to provide insight into the dynamics of important endemic infectious diseases in 3 northeastern US dairy herds. Fecal samples from individual cows and various environmental samples from these farms were tested for the presence of major zoonotic pathogens (i.e., Salmonella, Campylobacter, and Listeria) as well as commensal bacteria Escherichia coli and enterococci. Additionally, the presence of Mycobacterium avium ssp. paratuberculosis was tested in fecal and serum samples from individual cows. Test results and health and reproductive records were maintained in a database, and fecal, plasma, DNA, and tissue samples were kept in a biobank. All bacteria of interest were detected on these farms and their presence was variable both within and between farms. The prevalence of Listeria spp. and L. monocytogenes in individual fecal samples within farm A ranged from 0 to 68.2% and 0 to 25.5%, respectively, over a period of 3 yr. Within farm B, continuous fecal shedding of Salmonella spp. was observed with a prevalence ranging from 8 to 88%; Salmonella Cerro was the predominant serotype. Farm C appeared less contaminated with Salmonella and Listeria, although in the summer of 2005, 50 and 19.2% of fecal samples were positive for Listeria and L. monocytogenes, respectively. The high prevalence of E. coli (89 to 100%), Enterococcus (75 to 100%), and Campylobacter (0 to 81%) in feces suggested they were ubiquitous throughout the farm environment. Fecal culture and ELISA results indicated a low prevalence of Mycobacterium avium ssp. paratuberculosis infection in these farms (0 to 13.6% and 0 to 4.9% for culture-positive and ELISA-positive, respectively), although the occasional presence of high shedders was observed. Results have major implications for food safety and epidemiology by providing a better understanding of infectious disease dynamics on dairy farms. Comprehensive understanding of these infections may lead to better farm management practices and pathogen reduction programs to control and reduce the on-farm contamination of these pathogens and to prevent their further entry into the food-chain.}, number={4}, journal={Journal of Dairy Science}, publisher={American Dairy Science Association}, author={Pradhan, A.K. and Van Kessel, J.S. and Karns, J.S. and Wolfgang, D.R. and Hovingh, E. and Nelen, K.A. and Smith, J.M. and Whitlock, R.H. and Fyock, T. and Ladely, S. and et al.}, year={2009}, month={Apr}, pages={1811–1825} }
 @article{richardson_cox_bailey_berrang_cox_buhr_fedorka cray_harrison_2009, title={Evaluation of TECRA Broth, Bolton Broth, and Direct Plating for Recovery of Campylobacter spp. from Broiler Carcass Rinsates from Commercial Processing Plants}, volume={72}, ISSN={0362-028X}, url={http://dx.doi.org/10.4315/0362-028x-72.5.972}, DOI={10.4315/0362-028x-72.5.972}, abstractNote={The purpose of this study was to compare a conventional culture broth method (Bolton enrichment), a newly developed proprietary broth method (TECRA Campylobacter enrichment), and direct plating for recovery of Campylobacter spp. from chicken carcass rinsates. Whole carcass rinses were taken from 140 carcasses at rehang (immediately after defeathering but before evisceration) and from 140 carcasses at postchill from eight different processing plants in the United States. The rinsate samples were packed in ice and shipped overnight to the laboratory. Aliquots of the rinsate were transferred into Bolton and TECRA enrichment broths and were direct plated. Standard laboratory procedures with Campy-cefex plates were followed for recovery of Campylobacter spp. For rehang carcasses, 94% were positive for Campylobacter spp. with the TECRA enrichment broth and 74% were positive with the Bolton enrichment broth. For postchill carcasses, 74% were positive for Campylobacter spp. with the TECRA enrichment broth and 71% were positive with the Bolton enrichment broth. Compared with the Bolton enrichment broth, TECRA enrichment broth significantly suppressed non-Campylobacter microflora (P < 0.05). Overall, TECRA enrichment broth yielded an 11% higher total number of Campylobacter-positive samples compared with the Bolton enrichment broth. Campylobacter spp. detection in postchill samples was significantly greater (P < 0.05) by enrichment (84%) than by direct plating (19%). The high number of Campylobacter-positive samples obtained with all procedures indicated that 99% of the carcass rinsates obtained at rehang and 84% obtained at postchill contained Campylobacter spp.}, number={5}, journal={Journal of Food Protection}, publisher={International Association for Food Protection}, author={Richardson, L. J. and Cox, N. A. and Bailey, J. S. and Berrang, M. E. and Cox, J. M. and Buhr, R. J. and Fedorka Cray, P. J. and Harrison, M. A.}, year={2009}, month={May}, pages={972–977} }
 @article{o'regan_quinn_frye_pages_porwollik_fedorka-cray_mcclelland_fanning_2009, title={Fitness Costs and Stability of a High-Level Ciprofloxacin Resistance Phenotype in Salmonella enterica Serotype Enteritidis: Reduced Infectivity Associated with Decreased Expression of Salmonella Pathogenicity Island 1 Genes}, volume={54}, ISSN={0066-4804 1098-6596}, url={http://dx.doi.org/10.1128/aac.00801-09}, DOI={10.1128/aac.00801-09}, abstractNote={ABSTRACT The fitness costs associated with high-level fluoroquinolone resistance were examined for phenotypically and genotypically characterized ciprofloxacin-resistant Salmonella enterica serotype Enteritidis mutants (104-cip and 5408-cip; MIC, >32 μg/ml). The stability of the fluoroquinolone resistance phenotype in both mutants was investigated to assess whether clones with better fitness could emerge in the absence of antibiotic selective pressure. Mutants 104-cip and 5408-cip displayed altered morphology on agar and by electron microscopy, reduced growth rates, motility and invasiveness in Caco-2 cells, and increased sensitivity to environmental stresses. Microarray data revealed decreased expression of virulence and motility genes in both mutants. Two clones, 104-revert and 1A-revertC2, with ciprofloxacin MICs of 3 and 2 μg/ml, respectively, were recovered from separate lineages of 104-cip after 20 and 70 passages, respectively, on antibiotic-free agar. All fitness costs, except motility, were reversed in 104-revert. Potential mechanisms associated with reversal of the resistance phenotype were examined. Compared to 104-cip, both 104-revert and 1A-revertC2 showed decreased expression of acrB and soxS but still overexpressed marA . Both acquired additional mutations in SoxR and ParC, and 1A-revertC2 acquired two mutations in MarA. The altered porin and lipopolysaccharide (LPS) profiles observed in 104-cip were reversed. In contrast, 5408-cip showed no reversal in fitness costs and maintained its high-level ciprofloxacin resistance for 200 passages on antibiotic-free agar. In conclusion, high-level ciprofloxacin resistance in S . Enteritidis is associated with fitness costs. In the absence of antibiotic selection pressure, isolates may acquire mutations enabling reversion to an intermediate-level ciprofloxacin resistance phenotype associated with less significant fitness costs.}, number={1}, journal={Antimicrobial Agents and Chemotherapy}, publisher={American Society for Microbiology}, author={O'Regan, E. and Quinn, T. and Frye, J. G. and Pages, J.-M. and Porwollik, S. and Fedorka-Cray, P. J. and McClelland, M. and Fanning, S.}, year={2009}, month={Nov}, pages={367–374} }
 @article{sohn_himmelsbach_barton_fedorka-cray_2009, title={Fluorescence Spectroscopy for Rapid Detection and Classification of Bacterial Pathogens}, volume={63}, ISSN={0003-7028 1943-3530}, url={http://dx.doi.org/10.1366/000370209789806993}, DOI={10.1366/000370209789806993}, abstractNote={This study deals with the rapid detection and differentiation of Escherichia coli, Salmonella, and Campylobacter, which are the most commonly identified commensal and pathogenic bacteria in foods, using fluorescence spectroscopy and multivariate analysis. Each bacterial sample cultured under controlled conditions was diluted in physiologic saline for analysis. Fluorescence spectra were collected over a range of 200-700 nm with 0.5 nm intervals on the PerkinElmer Fluorescence Spectrometer. The synchronous scan technique was employed to find the optimum excitation (lambda(ex)) and emission (lambda(em)) wavelengths for individual bacteria with the wavelength interval (Deltalambda) being varied from 10 to 200 nm. The synchronous spectra and two-dimensional plots showed two maximum lambda(ex) values at 225 nm and 280 nm and one maximum lambda(em) at 335-345 nm (lambda(em) = lambda(ex) + Deltalambda), which correspond to the lambda(ex) = 225 nm, Deltalambda = 110-120 nm, and lambda(ex) = 280 nm, Deltalambda = 60-65 nm. For all three bacterial genera, the same synchronous scan results were obtained. The emission spectra from the three bacteria groups were very similar, creating difficulty in classification. However, the application of principal component analysis (PCA) to the fluorescence spectra resulted in successful classification of the bacteria by their genus as well as determining their concentration. The detection limit was approximately 10(3)-10(4) cells/mL for each bacterial sample. These results demonstrated that fluorescence spectroscopy, when coupled with PCA processing, has the potential to detect and to classify bacterial pathogens in liquids. The methodology is rapid (>10 min), inexpensive, and requires minimal sample preparation compared to standard analytical methods for bacterial detection.}, number={11}, journal={Applied Spectroscopy}, publisher={SAGE Publications}, author={Sohn, Miryeong and Himmelsbach, David S. and Barton, Franklin E., II and Fedorka-Cray, Paula J.}, year={2009}, month={Nov}, pages={1251–1255} }
 @article{pittenger_englen_parker_frye_quiñones_horn_son_fedorka-cray_harrison_2009, title={Genotyping Campylobacter jejuni by Comparative Genome Indexing: An Evaluation with Pulsed-Field Gel Electrophoresis and flaA SVR Sequencing}, volume={6}, ISSN={1535-3141 1556-7125}, url={http://dx.doi.org/10.1089/fpd.2008.0185}, DOI={10.1089/fpd.2008.0185}, abstractNote={Comparative genome indexing (CGI) using whole-genome DNA microarrays was evaluated as a means of genotyping Campylobacter jejuni relative to two standard methods, pulsed-field gel electrophoresis (PFGE) and flaA short variable region sequencing (flaA SVR typing). Thirty-six geographically diverse C. jejuni isolates were selected from a collection of cattle and chicken isolates. The BioNumerics software program was used for cluster analysis of the data from all 36 isolates for each of the three typing methods. Comparative genome indexing assigned a unique type to each isolate while PFGE and flaA SVR distinguished 29 and 35 different types, respectively. The four common types identified by PFGE were also closely related by CGI, and the overall similarity of the CGI results to those for PFGE indicates the value of CGI as a more informative alternative to PFGE. While flaA SVR was very discriminative, the isolates were all highly similar (>78%) resulting in finer distinctions between isolates and fewer genotypic relations to CGI or PFGE. Campylobacter jejuni is one of the most common causative agents of bacterial gastroenteritis in the world. The development of CGI as a molecular typing tool for C. jejuni offers a highly effective and informative means of further understanding the epidemiology of this ubiquitous pathogen.}, number={3}, journal={Foodborne Pathogens and Disease}, publisher={Mary Ann Liebert Inc}, author={Pittenger, Lauren G. and Englen, Mark D. and Parker, Craig T. and Frye, Jonathan G. and Quiñones, Beatriz and Horn, Sharon T. and Son, Insook and Fedorka-Cray, Paula J. and Harrison, Mark A.}, year={2009}, month={Apr}, pages={337–349} }
 @article{leader_frye_hu_fedorka-cray_boyle_2009, title={High-Throughput Molecular Determination of Salmonella enterica Serovars by Use of Multiplex PCR and Capillary Electrophoresis Analysis}, volume={47}, ISSN={0095-1137}, url={http://dx.doi.org/10.1128/jcm.02095-08}, DOI={10.1128/jcm.02095-08}, abstractNote={ABSTRACT Salmonella enterica is a leading cause of food-borne illness worldwide and is also a major cause of morbidity and mortality in domestic and wild animals. In the current study, a high-throughput molecular assay was developed to determine the most common clinical and nonhuman serovars of S. enterica in the United States. Sixteen genomic targets were identified based on their differential distribution among common serovars. Primers were designed to amplify regions of each of these targets in a single multiplex PCR while incorporating a 6-carboxyfluorescein-labeled universal primer to fluorescently label all amplicons. The fluorescently labeled PCR products were separated using capillary electrophoresis, and a Salmonella multiplex assay for rapid typing (SMART) code was generated for each isolate, based upon the presence or absence of PCR products generated from each target gene. Seven hundred fifty-one blind clinical isolates of Salmonella from Washington State, collected in 2007 and previously serotyped via antisera, were screened with the assay. A total of 89.6% of the isolates were correctly identified based on comparison to a panel of representative SMART codes previously determined for the top 50 most common serovars in the United States. Of the remaining isolates, 6.2% represented isolates that produced a new SMART code for a previously determined serotype, while the final 8.8% were from serotypes not screened in the original panel used to score isolates in the blinded study. This high-throughput multiplex PCR assay allowed simple and accurate typing of the most prevalent clinical serovars of Salmonella enterica at a level comparable to that of conventional serotyping, but at a fraction of both the cost and time required per test.}, number={5}, journal={Journal of Clinical Microbiology}, publisher={American Society for Microbiology}, author={Leader, B. T. and Frye, J. G. and Hu, J. and Fedorka-Cray, P. J. and Boyle, D. S.}, year={2009}, month={Mar}, pages={1290–1299} }
 @article{lindsey_fedorka-cray_frye_meinersmann_2009, title={Inc A/C Plasmids Are Prevalent in Multidrug-Resistant Salmonella enterica Isolates}, volume={75}, ISSN={0099-2240}, url={http://dx.doi.org/10.1128/aem.02228-08}, DOI={10.1128/aem.02228-08}, abstractNote={Bacterial plasmids are fragments of extrachromosomal double-stranded DNA that can contain a variety of genes that are beneficial to the host organism, like those responsible for antimicrobial resistance. The objective of this study was to characterize a collection of 437 Salmonella enterica isolates from different animal sources for their antimicrobial resistance phenotypes and plasmid replicon types and, in some cases, by pulsed-field gel electrophoresis (PFGE) in an effort to learn more about the distribution of multidrug resistance in relation to replicon types. A PCR-based replicon typing assay consisting of three multiplex PCRs was used to detect 18 of the 26 known plasmid types in the Enterobacteriaceae based on their incompatibility (Inc) replicon types. Linkage analysis was completed with antibiograms, replicon types, serovars, and Inc A/C. Inc A/C plasmids were prevalent in multidrug-resistant isolates with the notable exception of Salmonella enterica serovar Typhimurium. Cluster analysis based on PFGE of a subset of 216 isolates showed 155 unique types, suggesting a variable population, but distinct clusters of isolates with Inc A/C plasmids were apparent. Significant linkage of serovar was also seen with Inc replicon types B/O, I1, Frep, and HI1. The present study showed that the combination of Salmonella, the Inc A/C plasmids, and multiple-drug-resistant genes is very old. Our results suggest that some strains, notably serovar Typhimurium and closely related types, may have once carried the plasmid but that the resistance genes were transferred to the chromosome with the subsequent loss of the plasmid.}, number={7}, journal={Applied and Environmental Microbiology}, publisher={American Society for Microbiology}, author={Lindsey, R. L. and Fedorka-Cray, P. J. and Frye, J. G. and Meinersmann, R. J.}, year={2009}, month={Jan}, pages={1908–1915} }
 @article{jackson_fedorka-cray_davis_barrett_brousse_gustafson_kucher_2009, title={Mechanisms of antimicrobial resistance and genetic relatedness among enterococci isolated from dogs and cats in the United States}, volume={108}, ISSN={1364-5072 1365-2672}, url={http://dx.doi.org/10.1111/j.1365-2672.2009.04619.x}, DOI={10.1111/j.1365-2672.2009.04619.x}, abstractNote={Aims: In this study, mechanisms of antimicrobial resistance and genetic relatedness among resistant enterococci from dogs and cats in the United States were determined. Methods and Results: Enterococci resistant to chloramphenicol, ciprofloxacin, erythromycin, gentamicin, kanamycin, streptomycin, lincomycin, quinupristin/dalfopristin and tetracycline were screened for the presence of 15 antimicrobial resistance genes. Five tetracycline resistance genes [tet(M), tet(O), tet(L), tet(S) and tet(U)] were detected with tet(M) accounting for approx. 60% (130/216) of tetracycline resistance; erm(B) was also widely distributed among 96% (43/45) of the erythromycin-resistant enterococci. Five aminoglycoside resistance genes were also detected among the kanamycin-resistant isolates with the majority of isolates (25/36; 69%) containing aph(3′)-IIIa. The bifunctional aminoglycoside resistance gene, aac(6′)-Ie-aph(2″)-Ia, was detected in gentamicin-resistant isolates and ant(6)-Ia in streptomycin-resistant isolates. The most common gene combination among enterococci from dogs (n = 11) was erm(B), aac(6′)-Ie-aph(2″)-Ia, aph(3′)-IIIa, tet(M), while tet(O), tet(L) were most common among cats (n = 18). Using pulsed-field gel electrophoresis (PFGE), isolates clustered according to enterococcal species, source and antimicrobial gene content and indistinguishable patterns were observed for some isolates from dogs and cats. Conclusion: Enterococci from dogs and cats may be a source of antimicrobial resistance genes. Significance and Impact of the Study: Dogs and cats may act as reservoirs of antimicrobial resistance genes that can be transferred from pets to people. Although host-specific ecovars of enterococcal species have been described, identical PFGE patterns suggest that enterococcal strains may be exchanged between these two animal species.}, number={6}, journal={Journal of Applied Microbiology}, publisher={Wiley}, author={Jackson, C.R. and Fedorka-Cray, P.J. and Davis, J.A. and Barrett, J.B. and Brousse, J.H. and Gustafson, J. and Kucher, M.}, year={2009}, month={Nov}, pages={2171–2179} }
 @article{wise_siragusa_plumblee_healy_cray_seal_2009, title={Predicting Salmonella enterica serotypes by repetitive sequence-based PCR}, volume={76}, ISSN={0167-7012}, url={http://dx.doi.org/10.1016/j.mimet.2008.09.006}, DOI={10.1016/j.mimet.2008.09.006}, abstractNote={Repetitive extragenic palindromic sequence-based PCR (rep-PCR) utilizing a semi-automated system, was evaluated as a method to determine Salmonella serotypes. A group of 216 Salmonella isolates belonging to 13 frequently isolated serotypes and one rarer serotype from poultry were used to create a DNA fingerprint library with the DiversiLab™ System software. Subsequently, a blinded set of 44 poultry isolates were fingerprinted and queried against the library in an attempt to putatively assign a serotype designation to each Salmonella isolate. The query isolates were previously typed employing standard serological techniques. Utilizing pair-wise similarity percentages as calculated by the Pearson correlation coefficient, the predicted serotype of 28 isolates matched the serological typing result. For eight isolates, rep-PCR results were interpreted as one of two very closely-related serotypes, Hadar and the rarer Istanbul. Traditional serological assays have difficulty distinguishing between these groups, and sequencing interspacer regions of the rrfH gene was unable to differentiate among isolates of these two serovars. Six of the remaining isolates resulted in no match to the database (similarity values < 95%) and these indeed proved to be serotypes not included in the original library. The two remaining samples proved discrepant at the 95% similarity threshold, however examination of electropherograms clearly indicated fingerprint variability between query and library samples, suggesting an expanded rep-PCR library will be necessary for increased utility. Since serological assays can take several days to weeks to provide information, the DiversiLab System holds promise for more rapid serotype classification for members of this group.}, number={1}, journal={Journal of Microbiological Methods}, publisher={Elsevier BV}, author={Wise, Mark G. and Siragusa, Gregory R. and Plumblee, Jodie and Healy, Mimi and Cray, Paula J. and Seal, Bruce S.}, year={2009}, month={Jan}, pages={18–24} }
 @article{berrang_bailey_altekruse_shaw_patel_meinersmann_fedorka cray_2009, title={Prevalence, Serotype, and Antimicrobial Resistance of Salmonella on Broiler Carcasses Postpick and Postchill in 20 U.S. Processing Plants}, volume={72}, ISSN={0362-028X}, url={http://dx.doi.org/10.4315/0362-028x-72.8.1610}, DOI={10.4315/0362-028x-72.8.1610}, abstractNote={The objective of this study was to measure the effect of broiler processing on the prevalence, serotype, and antimicrobial resistance profiles of salmonellae. Twenty U.S. commercial processing plants representing eight integrators in 13 states were included in the survey. In each of four replications, 10 carcasses from one flock were collected at rehang and 10 more carcasses were collected at postchill; each carcass was sampled by whole-carcass rinse. Salmonella organisms were isolated from carcass rinses by standard cultural techniques, serotypes were determined, and the resistance to 15 antimicrobials was measured. Overall, Salmonella was detected on 72% of carcasses at rehang (ranging from 35 to 97%) and on 20% of carcasses postchill (ranging from 2.5 to 60%). In every instance, a significant (P < 0.05) decrease in Salmonella prevalence was noted between rehang and postchill. The four most common serotypes, accounting for 64% of all Salmonella isolates, were Kentucky, Heidelberg, Typhimurium, and Typhimurium var. 5-; most isolates of Kentucky (52%), Heidelberg (79%), and Typhimurium (54%) serotypes were susceptible to all antimicrobial drugs tested. However, only 15% of the Typhimurium var. 5- isolates were pansusceptible; more than one-half of the isolates of this serotype were resistant to three or more drugs. No isolate of any serotype exhibited resistance to amikacin, ceftriaxone, ciprofloxacin, or trimethoprim-sulfamethoxazole. These data demonstrate that although processing lessens carcass contamination with Salmonella, antimicrobial-resistant isolates may still be present.}, number={8}, journal={Journal of Food Protection}, publisher={International Association for Food Protection}, author={Berrang, M. E. and Bailey, J. S. and Altekruse, S. F. and Shaw, W. K. and Patel, B. L. and Meinersmann, R. J. and Fedorka Cray, P. J.}, year={2009}, month={Aug}, pages={1610–1615} }
 @article{jackson_fedorka-cray_davis_barrett_frye_2009, title={Prevalence, species distribution and antimicrobial resistance of enterococci isolated from dogs and cats in the United States}, volume={107}, ISSN={1364-5072}, url={http://dx.doi.org/10.1111/j.1365-2672.2009.04310.x}, DOI={10.1111/j.1365-2672.2009.04310.x}, abstractNote={The contribution of dogs and cats as reservoirs of antimicrobial resistant enterococci remains largely undefined. This is increasingly important considering the possibility of transfer of bacteria from companion animals to the human host. In this study, dogs and cats from veterinary clinics were screened for the presence of enterococci.A total of 420 enterococci were isolated from nasal, teeth, rectal, belly and hindquarters sites of 155 dogs and 121 cats from three clinics in Athens, GA. Eighty per cent (124 out of 155) of the dogs and 60% (72 out of 121) of the cats were positive for enterococci. From the total number of dog samples (n = 275), 32% (n = 87) were from hindquarter, 31% (n = 86) were rectal, and 29% (n = 79) were from the belly area. The majority of isolates originated from rectal samples (53 out of 145; 37%) from cats. The predominant species identified was Enterococcus faecalis (105 out of 155; 68%) from dogs and E. hirae (63 out of 121; 52%) from cats. Significantly more E. faecalis were isolated from rectal samples than any other enterococcal species (P < 0.05) for both dogs and cats suggesting site specific colonization of enterococcal species. The highest levels of resistance were to ciprofloxacin in E. faecium (9 out of 10; 90%), chloramphenicol resistance in E. faecalis (17 out of 20; 85%) and gentamicin resistance in E. faecalis (19 out of 24; 79%) from dog samples and nitrofurantoin resistance in E. faecium (15 out of 19; 79%) from cats. Multi-drug resistance (MDR) (resistance > or =2 antimicrobials) was observed to as few as two and as many as eight antimicrobials regardless of class.This study demonstrated that dogs and cats are commonly colonized with antimicrobial resistant enterococci.Dogs and cats may act as reservoirs of antimicrobial resistance genes that can be transferred from pets to people.}, number={4}, journal={Journal of Applied Microbiology}, publisher={Wiley}, author={Jackson, C.R. and Fedorka-Cray, P.J. and Davis, J.A. and Barrett, J.B. and Frye, J.G.}, year={2009}, month={Apr}, pages={1269–1278} }
 @inbook{fedorka-cray_gray_wray_2009, title={Salmonella infections in pigs.}, ISBN={9780851992617}, url={http://dx.doi.org/10.1079/9780851992617.0191}, DOI={10.1079/9780851992617.0191}, booktitle={Salmonella in domestic animals.}, publisher={CABI}, author={Fedorka-Cray, P. J. and Gray, J. T. and Wray, C.}, year={2009}, month={Nov}, pages={191–207} }
 @article{frye_fedorka-cray_jackson_rose_2008, title={Analysis of Salmonella enterica with Reduced Susceptibility to the Third-Generation Cephalosporin Ceftriaxone Isolated from U.S. Cattle During 2000–2004}, volume={14}, ISSN={1076-6294 1931-8448}, url={http://dx.doi.org/10.1089/mdr.2008.0844}, DOI={10.1089/mdr.2008.0844}, abstractNote={Over the past decade enteric bacteria in Europe, Africa, and Asia have become increasingly resistant to cephalosporin antimicrobial agents. This is largely due to the spread of genes encoding extended-spectrum β-lactamase (ESBL) enzymes that can inactivate many cephalosporins. Recently, these resistance mechanisms have been identified in Salmonella isolated from humans in the United States. Due to the potential for transmission of resistant bacteria to humans via food animals, Salmonella animal isolates were monitored for ESBL production. During 2000–2004, Salmonella cattle slaughter isolates (n = 3,984) were tested, and 97 (2.4%) of these were found to have decreased susceptibility (minimum inhibitory concentration [MIC] >32 μg/ml) to the third-generation cephalosporin ceftriaxone. The majority of these were serotypes Newport (58) and Agona (14), some of which were genetically indistinguishable by pulsed field gel electrophoresis (PFGE) analysis. None of the isolates had an ESBL phenotype; all were susceptible to the fourth-generation cephalosporins cefepime and cefquinome. PCR and sequence analysis for resistance genes detected the blaCMY-2 gene in 93 isolates and the blaTEM-1 gene in 12 isolates; however, neither gene encodes an ESBL. These data indicate that bovine Salmonella isolates from the United States with decreased susceptibility or resistance to ceftriaxone do not exhibit an ESBL phenotype and most contain the blaCMY-2 gene.}, number={4}, journal={Microbial Drug Resistance}, publisher={Mary Ann Liebert Inc}, author={Frye, Jonathan G. and Fedorka-Cray, Paula J. and Jackson, Charlene R. and Rose, Markus}, year={2008}, month={Dec}, pages={251–258} }
 @article{mcgowan-spicer_fedorka cray_frye_meinersmann_barrett_jackson_2008, title={Antimicrobial Resistance and Virulence of Enterococcus faecalis Isolated from Retail Food}, volume={71}, ISSN={0362-028X}, url={http://dx.doi.org/10.4315/0362-028x-71.4.760}, DOI={10.4315/0362-028x-71.4.760}, abstractNote={Although enterococci are considered opportunistic nosocomial pathogens, their contribution to foodborne illnesses via dissemination through retail food remains undefined. In this study, prevalence and association of antimicrobial resistance and virulence factors of 80 Enterococcus faecalis isolates from retail food items were investigated. The highest rates of resistance were observed for lincomycin (73 of 80 isolates, 91%) and bacitracin (57 of 80 isolates, 71%), and lower rates of resistance (< or =40%) were found for chloramphenicol, ciprofloxacin, erythromycin, flavomycin, gentamicin, kanamycin, nitrofurantoin, penicillin, and tylosin. Overall resistance to antimicrobials was low for most isolates tested. Of the virulence factors tested, the majority of isolates were positive for ccf (78 of 80 isolates, 98%), efaAfs (77 of 80, 96%), and cpd (74 of 80, 93%). Isolates also commonly contained cob (72 of 80 isolates, 90%) and gelE (68 of 80, 85%). Very few isolates contained cylMBA (12 of 80 isolates [15%] for cylM and 9 of 80 isolates [11%] for both cylB and cylA) and efaAfm (2 of 80 isolates, 3%). Positive statistical associations (significance level of 0.05) were found between agg and tetracycline resistance, cylM and erythromycin resistance, and gelE and efaAfs and lincomycin resistance. The presence of the cylB and cylA alleles also was positively correlated with bacitracin and tetracycline resistance. Negative correlations were observed between many of the virulence attributes and resistance to ciprofloxacin, erythromycin, flavomycin, gentamicin, kanamycin, and tylosin. These data suggest that both positive and negative associations exist between antimicrobial resistance genes and virulence factors in E. faecalis isolates from foods commonly purchased from grocery stores.}, number={4}, journal={Journal of Food Protection}, publisher={International Association for Food Protection}, author={McGowan-Spicer, Lori L. and Fedorka Cray, Paula J. and Frye, Jonathan G. and Meinersmann, Richard J. and Barrett, John B. and Jackson, Charlene R.}, year={2008}, month={Apr}, pages={760–769} }
 @article{lyon_berrang_fedorka-cray_fletcher_meinersmann_2008, title={Antimicrobial Resistance of Listeria monocytogenes Isolated from a Poultry Further Processing Plant}, volume={5}, ISSN={1535-3141 1556-7125}, url={http://dx.doi.org/10.1089/fpd.2007.0070}, DOI={10.1089/fpd.2007.0070}, abstractNote={The aim of this study was to compare antimicrobial resistance profiles of distinct types of Listeria monocytogenes isolated from a commercial poultry cooking plant. One hundred fifty-seven L. monocytogenes isolates representing 14 different actA types were tested for susceptibility to 19 antimicrobial drugs using the broth microdilution method. All isolates were susceptible to antimicrobials except for ceftriaxone (153 isolates [97%] intermediate or resistant), oxacillin with 2% NaCl (142 isolates [90%] resistant), ciprofloxacin (59 isolates [37%] intermediate or resistant), tetracycline (5 isolates [3%] resistant), clindamycin (43 isolates [27%] intermediate), linezolid (3 isolates [2%] intermediate), and trimethoprim/sulfamethoxazole (1 isolate [<1%] intermediate). Prevalence of antimicrobial resistance was low among all actA types. There was a low amount of diversity of resistotypes, which were defined in this study as subdivisions of actA types according to antimicrobial resistance profiles of the isolates. The five tetracycline-resistant isolates represented all the members of one actA type in lineage II. This study showed that antimicrobial resistance is not highly prevalent in L. monocytogenes from a poultry further processing environment. Types of L. monocytogenes as distinguished by actA sequencing do not predict antimicrobial resistance except possibly for tetracycline resistance. L. monocytogenes types that persist in a poultry cook plant are not related to antimicrobial resistance, and excluding tetracycline resistance, antimicrobial resistance does not seem to differ according to actA type or lineage.}, number={3}, journal={Foodborne Pathogens and Disease}, publisher={Mary Ann Liebert Inc}, author={Lyon, Steven A. and Berrang, Mark E. and Fedorka-Cray, Paula J. and Fletcher, Daniel L. and Meinersmann, Richard J.}, year={2008}, month={Jun}, pages={253–259} }
 @article{douris_fedorka-cray_jackson_2008, title={Characterization of Salmonella enterica Serovar Agona Slaughter Isolates from the Animal Arm of the National Antimicrobial Resistance Monitoring System—Enteric Bacteria (NARMS): 1997 through 2003}, volume={14}, ISSN={1076-6294 1931-8448}, url={http://dx.doi.org/10.1089/mdr.2008.0787}, DOI={10.1089/mdr.2008.0787}, abstractNote={A total of 499 Salmonella enterica serovar Agona isolates from cattle, swine, chicken, and turkey samples were assayed for antimicrobial susceptibility and subtyped using pulsed-field gel electrophoresis (PFGE). Salmonella Agona isolates exhibited increased resistance to amoxicillin/clavulanic acid, ampicillin, cefoxitin, ceftiofur, cephalothin, and chloramphenicol, and a single isolate was resistant to ceftriaxone. Multiple drug resistance (MDR; resistance ≥ 2 antimicrobials) was exhibited in 57% (n = 282/499) of the Salmonella Agona isolates and 22% (n = 111/499) of these Salmonella Agona isolates were resistant to five or more antimicrobials. PFGE patterns of 482 Salmonella Agona slaughter samples resulted in 165 unique patterns. Cluster analysis indicated that isolates indistinguishable by PFGE appeared to group according to antimicrobial resistance profiles. These data suggest that Salmonella Agona is increasing in prevalence in U.S. cattle presented for slaughter and should be further monitored.}, number={1}, journal={Microbial Drug Resistance}, publisher={Mary Ann Liebert Inc}, author={Douris, Aphrodite and Fedorka-Cray, Paula J. and Jackson, Charlene R.}, year={2008}, month={Mar}, pages={55–63} }
 @article{fratamico_bhagwat_injaian_fedorka-cray_2008, title={Characterization of Shiga Toxin–Producing Escherichia coli Strains Isolated from Swine Feces}, volume={5}, ISSN={1535-3141 1556-7125}, url={http://dx.doi.org/10.1089/fpd.2008.0147}, DOI={10.1089/fpd.2008.0147}, abstractNote={The virulence gene and antibiotic resistance profiles of Shiga toxin–producing Escherichia coli (STEC) strains belonging to 58 different O:H serotypes (219 strains) isolated from swine feces were determined. Of the 219 isolates, 29 (13%) carried the stx1 gene, 14 (6%) stx2, 176 (80%) stx2e, 46 (21%) estIa, 14 (6.4%) estIb, 10 (4.6%) fedA, 94 (42.9%) astA, 25 (11.4%) hly933, and one (0.46%) cdt-III. None of the strains possessed the elt, bfp, faeG, fanA, fasA, fimF41a, cnf-1, cnf-2, eae, cdt-I, or cdt-IV genes. The strains were also tested for antibiotic susceptibility using 16 antibiotics. The STEC isolates displayed resistance most often to tetracycline (95.4%), sulfamethoxazole (53.4%), kanamycin (38.4%), streptomycin (34.7%), and chloramphenicol (22.4%). An E. coli serotype O20:H42 strain, which was positive for stx2e and astA, was resistant to all of the antibiotics tested except for amikacin. In addition, 52 of the swine isolates, representing 16 serogroups and 30 different serotypes, were examined for their ability to withstand acid challenge by three types of acid resistance (AR) pathways, AR1 (rpoS dependent), AR2 (glutamate dependent), and AR3 (arginine dependent). None of the strains was defective in the AR1 resistance pathway, while one strain was defective in the AR2 pathway under aerobic growth conditions but fully functional under anaerobic growth conditions. Among the three AR pathways, the AR3 pathway offered the least protection, and 8 out of 52 strains were defective in this pathway. The strain that was defective in AR2 was fully functional in the AR3 pathway. Since AR plays a vital role in the survival and virulence of these strains, differences among the isolates to induce AR pathways may play a significant role in determining their infective dose. This study demonstrates that swine STEC comprise a heterogeneous group of organisms, and the possession of different combinations of E. coli virulence genes indicate that some swine STEC can potentially cause human illness.}, number={6}, journal={Foodborne Pathogens and Disease}, publisher={Mary Ann Liebert Inc}, author={Fratamico, Pina M. and Bhagwat, Arvind A. and Injaian, Lisa and Fedorka-Cray, Paula J.}, year={2008}, month={Dec}, pages={827–838} }
 @article{bailey_fedorka cray_richardson_cox_cox_2008, title={Detection of Campylobacter from Broiler Carcass Rinse Samples Utilizing the Tecra Visual Immunoassay (via)}, volume={16}, ISSN={1060-3999 1745-4581}, url={http://dx.doi.org/10.1111/j.1745-4581.2008.00142.x}, DOI={10.1111/j.1745-4581.2008.00142.x}, abstractNote={ABSTRACT
Poultry meat is considered to be a major vector of transmission of Campylobacter, either directly, through consumption of poorly prepared product or cross-contamination, or indirectly, through introduction of the bacterium into the food production environment. Efficient detection of Campylobacter is intrinsic to the management of the pathogen during poultry production. The TECRA Campylobacter Visual Immunoassay (CAMVIA) protocol, enrichment in a proprietary TECRA Campylobacter enrichment broth followed by an ELISA, was compared with a conventional cultural method, with enrichment in Bolton medium (containing lysed horse blood), followed by plating onto Campy-cefex agar. Of the 398 broiler carcass rinses tested from 19 commercial processing plants, a total of 350 carcasses (88%) were found to be positive for Campylobacter by at least one method. The TECRA CAMVIA yielded 317 Campylobacter-positive results, four of which were false positive and 22 of which were false negative, while conventional enrichment and plating detected the bacterium in only 280 samples with 48 false negatives. These data demonstrate that the TECRA CAMVIA has a statistically higher sensitivity and specificity than a conventional culture procedure using Bolton broth as the enrichment.

PRACTICAL APPLICATIONS
Standard Campylobacter methodology procedures currently take 4–5 days for detection of Campylobacter spp. in a sample when using an enrichment step. The TECRA Campylobacter Visual Immunoassay (VIA) reduces the amount of time it takes to determine whether Campylobacter spp. are present on poultry carcasses that have been rinsed. The procedure can effectively determine the presence of Campylobacter spp. in 2 days and has a statistically higher sensitivity and specificity than a conventional culture procedure using Bolton broth as the enrichment.}, number={4}, journal={Journal of Rapid Methods & Automation in Microbiology}, publisher={Wiley}, author={Bailey, J.S. and Fedorka Cray, P. and Richardson, L.J. and Cox, N.A. and Cox, J.M.}, year={2008}, month={Dec}, pages={374–380} }
 @article{wagner_straw_fedorka-cray_dargatz_2008, title={Effect of Antimicrobial Dosage Regimen on Salmonella and Escherichia coli Isolates from Feeder Swine}, volume={74}, ISSN={0099-2240}, url={http://dx.doi.org/10.1128/aem.01132-07}, DOI={10.1128/aem.01132-07}, abstractNote={A body of evidence exists that suggests that antimicrobial use in food animals leads to resistance in both pathogenic and commensal bacteria. This study focused on the impact of three different antimicrobial regimes (low-level continuous, pulse, and no antimicrobial) for two antimicrobials (chlortetracycline and tylosin) on the presence of Salmonella spp. and on the prevalence of antimicrobial resistance of both Salmonella spp. and nonspecific Escherichia coli in fecal samples from feeder swine. The prevalence of fecal samples positive for Salmonella spp. significantly decreased between the samples taken at feeder placement compared to samples taken when the animals were close to market weight. Differences in resistance of Salmonella spp. did not appear to be influenced by dosing treatment including the control. Analysis of antimicrobial resistance examining both susceptibility and resistance, as well as MIC outcomes, demonstrated that only resistance to cephalothin increased in E. coli under the pulse chlortetracycline treatment. These results suggest that the dosing regimes examined in this study did not lead to an increase in either the prevalence of Salmonella spp. or the prevalence of antimicrobial resistance in isolates of Salmonella spp. or E. coli.}, number={6}, journal={Applied and Environmental Microbiology}, publisher={American Society for Microbiology}, author={Wagner, B. A. and Straw, B. E. and Fedorka-Cray, P. J. and Dargatz, D. A.}, year={2008}, month={Jan}, pages={1731–1739} }
 @article{riley_loneragan_phillips_gray_fedorka cray_2008, title={Fecal Shedding of Foodborne Pathogens by Florida-Born Heifers and Steers in U.S. Beef Production Segments}, volume={71}, ISSN={0362-028X}, url={http://dx.doi.org/10.4315/0362-028x-71.4.807}, DOI={10.4315/0362-028x-71.4.807}, abstractNote={The objective in this study was to assess breed effects in fecal prevalence of Escherichia coli O157:H7 in heifers on a development program in Florida and in their steer half siblings in stocker and feedlot phases in Oklahoma. A secondary objective was to characterize fecal shedding of Campylobacter and Salmonella in subsets of the same samples. After weaning, heifers (n = 501; purebreds and F1 crosses of Angus, Brahman, and Romosinuano) were preconditioned and placed in a local development program. Steers (n = 481) were transported to Oklahoma, where they grazed wheat for 6 months and then were placed in feedlot pens. Fecal samples were obtained at least every 28 days for 12 months on most animals. None of the 10,982 samples tested positive for E. coli O157:H7. Overall fecal prevalences of Campylobacter and Salmonella in heifers were 1.7 and 0.04%, respectively. Corresponding overall prevalences in steer samples were 27.2 and 0.6%. Campylobacter isolates were mostly C. jejuni and were tetracycline resistant. Eight Salmonella isolates were Salmonella Typhimurium that were either quad or penta resistant, most often to ampicillin, chloramphenicol, sulfamexathole, and tetracycline. Feedlot steers had greater odds of positive detection of Campylobacter (odds ratio, 8.5; confidence interval, 3.7, 19.5) than when grazing winter wheat. No breed effect was detected for fecal prevalence of these pathogens.}, number={4}, journal={Journal of Food Protection}, publisher={International Association for Food Protection}, author={Riley, D. G. and Loneragan, G. H. and Phillips, W. A. and Gray, J. T. and Fedorka Cray, P. J.}, year={2008}, month={Apr}, pages={807–810} }
 @article{jackson_fedorka-cray_barrett_hiott_woodley_2008, title={First report of vatB and vgaB from Enterococcus gallinarum in the USA}, volume={31}, ISSN={0924-8579}, url={http://dx.doi.org/10.1016/j.ijantimicag.2007.08.020}, DOI={10.1016/j.ijantimicag.2007.08.020}, number={2}, journal={International Journal of Antimicrobial Agents}, publisher={Elsevier BV}, author={Jackson, Charlene R. and Fedorka-Cray, Paula J. and Barrett, John B. and Hiott, Lari M. and Woodley, Tiffanie A.}, year={2008}, month={Feb}, pages={175–176} }
 @article{son_englen_berrang_fedorka-cray_harrison_2007, title={Antimicrobial resistance of Arcobacter and Campylobacter from broiler carcasses}, volume={29}, ISSN={0924-8579}, url={http://dx.doi.org/10.1016/j.ijantimicag.2006.10.016}, DOI={10.1016/j.ijantimicag.2006.10.016}, abstractNote={The antimicrobial resistance of Arcobacter (n = 174) and Campylobacter (n = 215) isolated from broiler carcasses in a US poultry processing plant was examined. For Arcobacter, 93.7% (n = 163) were resistant to one or more antimicrobials and 71.8% (n = 125) were resistant to two or more antimicrobials. For Campylobacter, 99.5% (n = 214) were resistant to one or more antimicrobials and 28.4% (n = 61) were resistant to two or more antimicrobials. Arcobacter butzleri isolates were particularly resistant to clindamycin (90%; n = 126), azithromycin (81.4%; n = 114) and nalidixic acid (23.6%; n = 33). Resistance to tetracycline was very high in Campylobacter jejuni (99.5%) and Campylobacter coli (96.3%). Our results demonstrate substantial resistance in Arcobacter and Campylobacter to common antimicrobial agents.}, number={4}, journal={International Journal of Antimicrobial Agents}, publisher={Elsevier BV}, author={Son, Insook and Englen, Mark D. and Berrang, Mark E. and Fedorka-Cray, Paula J. and Harrison, Mark A.}, year={2007}, month={Apr}, pages={451–455} }
 @article{douris_fedorka-cray_jackson_2007, title={Detection of Plasmids and Class 1 Integrons in Salmonella enterica Serovar Agona Isolated from NARMS Slaughter Samples Collected in the Years 1997–2003}, volume={13}, ISSN={1076-6294 1931-8448}, url={http://dx.doi.org/10.1089/mdr.2007.752}, DOI={10.1089/mdr.2007.752}, abstractNote={A total of 60 Salmonella enterica serovar Agona isolates (25 pan-susceptible isolates and 35 isolates resistant to five or more antimicrobials) submitted to the National Antimicrobial Resistance Monitoring System–Enteric Bacteria (NARMS) from 1997 through 2003 were examined for plasmids and class 1 integrons. Samples originated from cattle, turkey, chicken, and swine presented at federally inspected slaughter and processing plants. Large plasmids (33–291 kb) were present in 83% of the isolates resistant to five or more antimicrobials; however, 16% of the pan-susceptible isolates also had large plasmids. The presence of large plasmids did not correspond to the isolate source or the year the isolate was recovered but did appear to correspond to XbaI pulsed-field gel electrophoresis (PFGE) patterns. Two sizes of large plasmids appeared most often: 145.4 kb and 97 kb. Class 1 integrons were not detected on plasmids but were detected on the chromosome of 8% (2/25) of the pan-susceptible isolates and 49% (17/35) of the isolates with multiple drug resistance. Expression of multiple drug resistance among S. Agona isolates occurred regardless of the presence of class 1 integrons, suggesting that plasmids play an equally important role in the development of resistant S. Agona. More research is needed to understand better the mechanisms by which S. Agona acquires, harbors, and transfers resistance determinants.}, number={3}, journal={Microbial Drug Resistance}, publisher={Mary Ann Liebert Inc}, author={Douris, Aphrodite and Fedorka-Cray, Paula J. and Jackson, Charlene R.}, year={2007}, month={Sep}, pages={212–219} }
 @article{ladely_harrison_fedorka cray_berrang_englen_meinersmann_2007, title={Development of Macrolide-Resistant Campylobacter in Broilers Administered Subtherapeutic or Therapeutic Concentrations of Tylosin}, volume={70}, ISSN={0362-028X}, url={http://dx.doi.org/10.4315/0362-028x-70.8.1945}, DOI={10.4315/0362-028x-70.8.1945}, abstractNote={The use of antimicrobials in food animal production, particularly those commonly used to treat infections in humans, has become a source of debate in recent years. However, limited data are available regarding the development of resistance following the subtherapeutic or therapeutic administration of antimicrobials in animal production. The objective of this study was to evaluate the effect of the administration of therapeutic and subtherapeutic concentrations of tylosin on the erythromycin susceptibility of Campylobacter jejuni and Campylobacter coli isolated from the ceca of treated broilers. In three replicated studies, day-of-hatch chicks were exposed to macrolide-susceptible C. jejuni or C. coli. At 2 weeks of age, tylosin was administered at subtherapeutic (22 ppm, continuously in the diet) or therapeutic concentrations (529 ppm, in the drinking water for 5 days). Broilers were sacrificed weekly. Total and erythromycin-resistant Campylobacter spp. were enumerated from individual ceca plus cecal contents. Overall erythromycin resistance was observed at a higher frequency (P < 0.01) among C. coli isolates (70.8%) than among C. jejuni isolates (36.8%) following tylosin administration. Across Campylobacter species, erythromycin resistance was observed at a higher frequency (P < 0.001) when tylosin was administered at subtherapeutic (62.7%) than at therapeutic (11.4%) concentrations. Subtherapeutic administration resulted in the recovery of 83.3 and 56.1% erythromycin-resistant isolates compared with only 33.3 and 7.9% of the isolates expressing erythromycin resistance following the administration of therapeutic concentrations for C. coli and C. jejuni, respectively. Further studies are needed to determine the factors involved in the apparent difference in the acquisition of macrolide resistance in C. coli compared with C. jejuni.}, number={8}, journal={Journal of Food Protection}, publisher={International Association for Food Protection}, author={Ladely, Scott R. and Harrison, Mark A. and Fedorka Cray, Paula J. and Berrang, Mark E. and Englen, Mark D. and Meinersmann, Richard J.}, year={2007}, month={Aug}, pages={1945–1951} }
 @article{jackson_fedorka-cray_wineland_tankson_barrett_douris_gresham_jackson-hall_mcglinchey_price_2007, title={Introduction to United States Department of Agriculture VetNet: Status of Salmonella and Campylobacter Databases from 2004 Through 2005}, volume={4}, ISSN={1535-3141 1556-7125}, url={http://dx.doi.org/10.1089/fpd.2006.0067}, DOI={10.1089/fpd.2006.0067}, abstractNote={In 2003 the United States Department of Agriculture established USDA VetNet. It was modeled after PulseNet USA, the national molecular subtyping network for foodborne disease surveillance. The objectives of USDA VetNet are: to use pulsed-field gel electrophoresis (PFGE) to subtype zoonotic pathogens submitted to the animal arm of the National Antimicrobial Resistance Monitoring System (NARMS); examine VetNet and PulseNet PFGE patterns; and use the data for surveillance and investigation of suspected foodborne illness outbreaks. Whereas PulseNet subtypes 7 foodborne disease-causing bacteria— Escherichia coli O157:H7, Salmonella, Shigella, Listeria monocytogenes, Campylobacter, Yersinia pestis, and Vibrio cholerae—VetNet at present subtypes nontyphoidal Salmonella serotypes and Campylobacter from animals, including diagnostic specimens, healthy farm animals, and carcasses of food-producing animals at slaughter. By the end of 2005, VetNet had two functioning databases: the NARMS Salmonella and the NARMS Campylobacter databases. The Salmonella database contained 6763 Salmonella isolates and 2514 unique XbaI patterns, while the Campylobacter database contained 58 Campylobacter isolates and 53 unique SmaI patterns. Both databases contain the PFGE tagged image file format (TIFF) images, demographic information, and the antimicrobial resistance profiles assigned by NARMS. In the future, veterinary diagnostic laboratories will be invited to participate in VetNet. The establishment of USDA VetNet enhances the mission of the agriculture and public health communities in the surveillance and investigation of foodborne illness outbreaks.}, number={2}, journal={Foodborne Pathogens and Disease}, publisher={Mary Ann Liebert Inc}, author={Jackson, Charlene R. and Fedorka-Cray, Paula J. and Wineland, Nora and Tankson, Jeanetta D. and Barrett, John B. and Douris, Aphrodite and Gresham, Cheryl P. and Jackson-Hall, Carolina and McGlinchey, Beth M. and Price, Maria Victoria}, year={2007}, month={Jun}, pages={241–248} }
 @article{hiett_stern_fedorka-cray_cox_seal_2007, title={Molecular Phylogeny of the flaA Short Variable Region Among Campylobacter jejuni Isolates Collected During an Annual Evaluation of Poultry Flocks in the Southeastern United States}, volume={4}, ISSN={1535-3141 1556-7125}, url={http://dx.doi.org/10.1089/fpd.2007.0008}, DOI={10.1089/fpd.2007.0008}, abstractNote={Production and processing samples were collected from eight commercial poultry flocks in the southeastern United States and examined for the presence of Campylobacter spp. In an effort to determine relatedness, recovered isolates were typed using flaA short variable region (SVR) DNA sequence analysis. Six of the eight production flocks tested were Campylobacter positive. In general, multiple Campylobacter flaA SVR types were present within a flock. Additionally, types found within a flock were also recovered from the final processed carcass. However, in two cases, the population of Campylobacter flaA SVR types on the processed carcass differed from those recovered from the production samples. Comparison of subtypes among flocks reared on different farms and during different seasons revealed that subtypes of Campylobacter spp. persisted throughout the year and in different locations. Environmental samples from seven of the eight farms tested were also Campylobacter positive. In one flock, a drag swab of the rearing facility was Campylobacter spp. positive while the flock and the final product were both negative. For the remaining sampling periods, environmental samples were positive for Campylobacter spp. concomitant with recovery of Campylobacter spp. from the chickens. In the remaining six flocks, the majority of environmental isolates recovered possessed flaA SVR types identical to isolates recovered from the birds, while in only one case, a recovered environmental isolate possessed a flaA SVR type that was not related to isolates obtained from the flock. Interpretation of these data suggest that the external environment and the poultry production environment share common subtypes of Campylobacter spp. and that these subtypes can contribute to contamination of the final commercial product.}, number={3}, journal={Foodborne Pathogens and Disease}, publisher={Mary Ann Liebert Inc}, author={Hiett, Kelli L. and Stern, Norman J. and Fedorka-Cray, Paula and Cox, Nelson A. and Seal, Bruce S.}, year={2007}, month={Sep}, pages={339–347} }
 @article{berrang_bailey_altekruse_patel_shaw_meinersmann_fedorka cray_2007, title={Prevalence and Numbers of Campylobacter on Broiler Carcasses Collected at Rehang and Postchill in 20 U.S. Processing Plants}, volume={70}, ISSN={0362-028X}, url={http://dx.doi.org/10.4315/0362-028x-70.7.1556}, DOI={10.4315/0362-028x-70.7.1556}, abstractNote={Campylobacter is a human pathogen associated with chicken and chicken meat products. This study was designed to examine the prevalence and number of Campylobacter on broiler chicken carcasses in commercial processing plants in the United States. Carcass samples were collected from each of 20 U.S. plants four times, roughly approximating the four seasons of 2005. At each plant on each sample day, 10 carcasses were collected at rehang (prior to evisceration), and 10 carcasses from the same flock were collected postchill. A total of 800 carcasses were collected at rehang and another 800 were collected postchill. All carcasses were subjected to a whole-carcass rinse, and the rinse diluent was cultured for Campylobacter. The overall mean number of Campylobacter detected on carcasses at rehang was 2.66 log CFU per ml of carcass rinse. In each plant, the Campylobacter numbers were significantly reduced by broiler processing; the mean concentration after chill was 0.43 log CFU/ml. Overall prevalence was also reduced by processing from a mean of > or =30 of 40 carcasses at rehang to > or =14 of 40 carcasses at postchill. Seven different on-line reprocessing techniques were applied in the test plants, and all techniques resulted in <1 log CFU/ml after chilling. Use of a chlorinated carcass wash before evisceration did not affect the postchill Campylobacter numbers. However, use of chlorine in the chill tank was related to lower numbers on postchill carcasses. Overall, U.S. commercial poultry slaughter operations are successful in significantly lowering the prevalence and number of Campylobacter on broiler carcasses during processing.}, number={7}, journal={Journal of Food Protection}, publisher={International Association for Food Protection}, author={Berrang, M. E. and Bailey, J. S. and Altekruse, S. F. and Patel, B. and Shaw, W. K. and Meinersmann, R. J. and Fedorka Cray, P. J.}, year={2007}, month={Jul}, pages={1556–1560} }
 @article{englen_hill_dargatz_ladely_fedorka-cray_2007, title={Prevalence and antimicrobial resistance of Campylobacter in US dairy cattle}, volume={102}, ISSN={1364-5072 1365-2672}, url={http://dx.doi.org/10.1111/j.1365-2672.2006.03189.x}, DOI={10.1111/j.1365-2672.2006.03189.x}, abstractNote={Aims: To obtain an overview of the prevalence and antimicrobial resistance of Campylobacter in faeces of US dairy cows in 2002. Methods and Results: Faeces from 1435 cows, representing 96 dairy operations in 21 US states, were collected for the culture of Campylobacter. A total of 735 Campylobacter strains were isolated (51·2% positive samples) with 94 operations positive (97·9%) for Campylobacter. From this collection, 532 isolates (473 Campylobacter jejuni and 59 Campylobacter coli) were randomly selected for susceptibility testing to eight antimicrobials: azithromycin, chloramphenicol, ciprofloxacin, clindamycin, erythromycin, gentamicin, nalidixic acid and tetracycline. The C. jejuni isolates exhibited resistance to tetracycline (47·4%), nalidixic acid (4·0%) and ciprofloxacin (2·5%), while the C. coli strains exhibited some resistance to all antimicrobials except chloramphenicol and ciprofloxacin. Only 3·6% of the C. jejuni isolates were resistant to two or more antimicrobials but 20·3% of the C. coli strains were multiresistant. Conclusions: On most operations, at least one cow was positive for Campylobacter and more than half of the cows sampled were shedding Campylobacter. The C. coli isolates had significantly higher levels of resistance to macrolides and to tetracycline compared with the C. jejuni strains, but were susceptible to ciprofloxacin. Significance and Impact of the Study: This study demonstrated a high prevalence of Campylobacter on US dairy operations; however, US dairy cattle have not been recognized as a major source of human infection compared with poultry. Campylobacter coli appears to develop antimicrobial resistance more readily than C. jejuni from the same environment.}, number={6}, journal={Journal of Applied Microbiology}, publisher={Wiley}, author={Englen, M.D. and Hill, A.E. and Dargatz, D.A. and Ladely, S.R. and Fedorka-Cray, P.J.}, year={2007}, month={Jun}, pages={1570–1577} }
 @article{son_englen_berrang_fedorka-cray_harrison_2007, title={Prevalence of Arcobacter and Campylobacter on broiler carcasses during processing}, volume={113}, ISSN={0168-1605}, url={http://dx.doi.org/10.1016/j.ijfoodmicro.2006.06.033}, DOI={10.1016/j.ijfoodmicro.2006.06.033}, abstractNote={Broiler carcasses (n = 325) were sampled in a U.S. commercial poultry processing plant for the prevalence of Arcobacter and Campylobacter at three sites along the processing line: pre-scald, pre-chill and post-chill. Samples (75–125 broilers per site) were collected during five plant visits from August to October of 2004. Arcobacter was recovered from pre-scald carcasses more frequently (96.8%) than from pre-chill (61.3%) and post-chill carcasses (9.6%). Campylobacter was isolated from 92% of pre-scald carcasses, 100% of pre-chill carcasses, and 52% of post-chill carcasses. In total, Arcobacter was isolated from 55.1% (179 of 325), while Campylobacter was isolated from 78.5% (255 of 325) of the carcasses from the three collection sites. For Arcobacter identification, a species-specific multiplex PCR showed that A. butzleri was the most prevalent species (79.1%) followed by A. cryaerophilus 1B (18.6%). A. cryaerophilus 1A was found at low levels (2.3%). PCR identified the most common Campylobacter species as C. jejuni (87.6%) followed by C. coli (12.4%). Overall, significant contamination of broiler carcasses by Arcobacter was observed, although less than that found for Campylobacter. From pre-scald to post-chill, a far greater reduction in Arcobacter numbers was observed than for Campylobacter. Our results for Arcobacter, obtained from the same environment as the closely related pathogen Campylobacter, will aid in the development of control measures for this emerging pathogen.}, number={1}, journal={International Journal of Food Microbiology}, publisher={Elsevier BV}, author={Son, Insook and Englen, Mark D. and Berrang, Mark E. and Fedorka-Cray, Paula J. and Harrison, Mark A.}, year={2007}, month={Jan}, pages={16–22} }
 @article{jackson_fedorka-cray_barrett_hiott_woodley_2007, title={Prevalence of streptogramin resistance in enterococci from animals: identification of vatD from animal sources in the USA}, volume={30}, ISSN={0924-8579}, url={http://dx.doi.org/10.1016/j.ijantimicag.2007.03.010}, DOI={10.1016/j.ijantimicag.2007.03.010}, abstractNote={There is considerable debate over the contribution of virginiamycin use in animals to quinupristin/dalfopristin (Q/D) resistance in humans. In this study, the prevalence and mechanisms of streptogramin resistance in enterococci from animals and the environment were investigated. From 2000–2004, enterococci from samples were tested for antimicrobial susceptibility. Q/D-resistant isolates (minimum inhibitory concentration ≥4 μg/mL) were subjected to polymerase chain reaction (PCR) using primers for streptogramin resistance genes (ermB, msrC, vatD and vatE). From the analysis, 1029/6227 (17%) Q/D-resistant non-Enterococcus faecalis enterococci were identified. The majority of Q/D-resistant isolates were Enterococcus hirae (n = 349; 34%), Enterococcus casseliflavus (n = 271; 26%) and Enterococcus faecium (n = 259; 25%). Using PCR, 55.5% (n = 571) were positive for ermB, 3% (n = 34) for msrC, 2% (n = 20) for vatE and 0.3% (n = 3) for vatD; 39% (n = 401) were negative for all four genes. The vatD-positive samples comprised two E. faecium from chicken and one E. hirae from swine. The nucleotide sequence of vatD from the three isolates was 100% homologous to published vatD sequences. These data indicate that Q/D resistance among enterococci from animals remains low despite the long history of virginiamycin use. To date, this is the first report of vatD from enterococci in animals in the USA.}, number={1}, journal={International Journal of Antimicrobial Agents}, publisher={Elsevier BV}, author={Jackson, Charlene R. and Fedorka-Cray, Paula J. and Barrett, John B. and Hiott, Lari M. and Woodley, Tiffanie A.}, year={2007}, month={Jul}, pages={60–66} }
 @article{frye_fedorka-cray_2007, title={Prevalence, distribution and characterisation of ceftiofur resistance in Salmonella enterica isolated from animals in the USA from 1999 to 2003}, volume={30}, ISSN={0924-8579}, url={http://dx.doi.org/10.1016/j.ijantimicag.2007.03.013}, DOI={10.1016/j.ijantimicag.2007.03.013}, abstractNote={Third-generation cephalosporin (3GC) antimicrobials are the drugs of choice for treatment of salmonellosis in children. Salmonella isolated in the USA are assayed by the National Antimicrobial Resistance Monitoring System (NARMS) for resistance to antimicrobials including first-, second- and third-generation cephalosporins. From 1999 to 2003, 34,411 Salmonella were isolated from animals in the USA, of which 10.9% were found to be resistant to ceftiofur, a 3GC used in animals, whilst only 0.3% were resistant to ceftriaxone, a 3GC used in human medicine. Ceftiofur resistance rose from 4.0% in 1999 to 18.8% in 2003. Isolates from diagnostic laboratories had higher levels of resistance (18.5%), whereas levels in isolates from on-farm (3.4%) and slaughter (7.1%) sources were lower. Animals with a higher than average proportion of resistant Salmonella included cattle (17.6%), horses (19.2%) and dogs (20.8%). Levels in turkeys (6.8%), chickens (7.1%), eggs (3.6%) and swine (4.6%) were lower. Resistance varied between Salmonella serotypes. A few serotypes had significantly high levels, e.g. S. Newport was 70.4% ceftiofur resistant. Resistance was predominantly associated with bla(CMY-2)-encoding plasmids. These data suggest that the acquisition of resistance plasmids and the spread of specific serotypes harbouring these plasmids are driving the observed resistance to ceftiofur in Salmonella animal isolates.}, number={2}, journal={International Journal of Antimicrobial Agents}, publisher={Elsevier BV}, author={Frye, Jonathan G. and Fedorka-Cray, Paula J.}, year={2007}, month={Aug}, pages={134–142} }
 @article{cox_richardson_buhr_northcutt_bailey_cray_hiett_2007, title={Recovery of Campylobacter and Salmonella Serovars From the Spleen, Liver and Gallbladder, and Ceca of Six-and Eight-Week-Old Commercial Broilers}, volume={16}, ISSN={1056-6171 1537-0437}, url={http://dx.doi.org/10.3382/japr.2006-00123}, DOI={10.3382/japr.2006-00123}, abstractNote={Previous studies have demonstrated that when Campylobacter or Salmonella were either orally or intracloacally inoculated into day-old broiler chicks, within 1 h, these bacteria moved rapidly to the lymphoid organs. These bacteria were still present 1 wk after inoculation. Two different market-age (6 and 8 wk old) broilers were obtained from 2 commercial poultry operations and brought to the laboratory for analysis. Necropsy was limited to the removal of the spleen, liver and gallbladder (L-GB), and ceca using aseptic techniques. To reduce the possibility of cross-contamination between samples, the spleen and L-GB were aseptically removed before the ceca. Samples were individually bagged, and standard laboratory procedures for Campylobacter and Salmonella were carried out for all samples. Fifty-two 6-wk-old broilers were analyzed, and Campylobacter were found in 19 of 52 L-GB, 19 of 52 spleens, and 26 of 52 ceca. Salmonella were found in 5 of 52 L-GB, 8 of 52 spleen, and 4 of 52 ceca. Eighty 8-wk-old broilers were analyzed, and Campylobacter were found in 3 of 80 L-GB, 5 of 80 spleens, and 19 of 80 ceca. Salmonella were found in 41 of 80 L-GB, 38 of 80 spleens, and 52 of 80 ceca. The internal organs of the younger birds were more heavily contaminated with Campylobacter, whereas Salmonella was the predominant organism isolated in the older birds. All Campylobacter isolates were found to be Campylobacter jejuni. The predominant Salmonella serotype was Salmonella Typhimurium; however, 7 other serotypes were found. Overall, C. jejuni was found in 22 of 132 L-GB, 24 of 132 spleen, and 45 of 132 ceca, whereas Salmonella serovars were isolated from 46 of 132 L-GB, 46 of 132 spleen, and 56 of 132 ceca. There is no doubt that these bacteria are naturally present in these organs. The significance of these reservoirs in the internal organs of commercial broilers is yet to be determined but could play a role in the microbiology of the intestinal tract and hence the final food product.}, number={4}, journal={The Journal of Applied Poultry Research}, publisher={Oxford University Press (OUP)}, author={Cox, N. A. and Richardson, L. J. and Buhr, R. J. and Northcutt, J. K. and Bailey, J. S. and Cray, P. F. and Hiett, K. L.}, year={2007}, month={Jan}, pages={477–480} }
 @article{white_naugle_jackson_fedorka cray_rose_pritchard_levine_saini_schroeder_dreyfuss_et al._2007, title={Salmonella Enteritidis in Meat, Poultry, and Pasteurized Egg Products Regulated by the U.S. Food Safety and Inspection Service, 1998 through 2003}, volume={70}, ISSN={0362-028X}, url={http://dx.doi.org/10.4315/0362-028x-70.3.582}, DOI={10.4315/0362-028x-70.3.582}, abstractNote={The U.S. Food Safety and Inspection Service (FSIS) tests for Salmonella in meat, poultry, and egg products through three regulatory testing programs: the Pathogen Reduction-Hazard Analysis and Critical Control Point (PR-HACCP) program, the ready-to-eat program for meat and poultry products, and the pasteurized egg products program. From 1998 through 2003, 293,938 samples collected for these testing programs were analyzed for the presence of Salmonella enterica serotypes. Of these samples, 12,699 (4.3%) were positive for Salmonella, and 167 (1.3%) of the positive samples (0.06% of all samples) contained Salmonella Enteritidis. The highest incidence of Salmonella Enteritidis was observed in ground chicken PR-HACCP samples (8 of 1,722 samples, 0.46%), and the lowest was found in steer-heifer PR-HACCP samples (0 of 12,835 samples). Salmonella Enteritidis isolates were characterized by phage type, pulsed-field gel electrophoretic pattern, and antimicrobial susceptibility. Phage typing of 94 Salmonella Enteritidis isolates identified PT13 (39 isolates) and PT8 (36 isolates) as the most common types. One isolate from a ready-to-eat ham product was characterized as PT4. Electrophoretic analysis of 148 Salmonella Enteritidis isolates indicated genetic diversity among the isolates, with 28 unique XbaI electrophoretic patterns identified. Of these 148 isolates, 136 (92%) were susceptible to each of 16 antimicrobials tested. Two isolates were resistant to ampicillin alone, and 10 isolates were resistant to two or more antimicrobials. Isolation of Salmonella Enteritidis from FSIS-regulated products emphasizes the need for continued consumer education on proper food handling and cooking practices and continued work to decrease the prevalence of Salmonella in meat, poultry, and pasteurized egg products.}, number={3}, journal={Journal of Food Protection}, publisher={International Association for Food Protection}, author={White, Patricia L. and Naugle, Alecia L. and Jackson, Charlene R. and Fedorka Cray, Paula J. and Rose, Bonnie E. and Pritchard, Katrine M. and Levine, Priscilla and Saini, Parmesh K. and Schroeder, Carl M. and Dreyfuss, Moshe S. and et al.}, year={2007}, month={Mar}, pages={582–591} }
 @article{meinersmann_berrang_jackson_fedorka-cray_ladely_little_frye_mattsson_2007, title={Salmonella, Campylobacter and Enterococcus spp.: Their Antimicrobial Resistance Profiles and their Spatial Relationships in a Synoptic Study of the Upper Oconee River Basin}, volume={55}, ISSN={0095-3628 1432-184X}, url={http://dx.doi.org/10.1007/s00248-007-9290-6}, DOI={10.1007/s00248-007-9290-6}, number={3}, journal={Microbial Ecology}, publisher={Springer Science and Business Media LLC}, author={Meinersmann, R. J. and Berrang, M. E. and Jackson, C. R. and Fedorka-Cray, P. and Ladely, S. and Little, E. and Frye, J. G. and Mattsson, B.}, year={2007}, month={Aug}, pages={444–452} }
 @article{berrang_ladely_meinersmann_fedorka-cray_2007, title={Subtherapeutic Tylosin Phosphate in Broiler Feed Affects Campylobacter on Carcasses During Processing}, volume={86}, ISSN={0032-5791 1525-3171}, url={http://dx.doi.org/10.1093/ps/86.6.1229}, DOI={10.1093/ps/86.6.1229}, abstractNote={Tylosin phosphate is an antimicrobial drug approved for use in broiler feed at subtherapeutic levels for growth promotion. Erythromycin is often the drug of choice for treating humans with campylobacteriosis. Both tylosin and erythromycin are classified as macrolide drugs and cross-resistance between these antimicrobials occurs. Commercial broiler chicks were placed in isolation grow-out chambers and colonized with Campylobacter jejuni. From 14 d of age through grow-out, broilers were fed ad libitim a diet that included 22 ppm of tylosin phosphate (20 g/ton). Control broilers received the same diet without tylosin phosphate. At 42 d of age, broilers were processed in a pilot plant with equipment that closely modeled commercial conditions. Carcass rinses were collected after feather removal, after inside and outside washing, and after immersion chilling. Campylobacter numbers recovered from carcasses after feather removal did not differ according to feed type (3.53 log cfu/mL of rinse for control carcasses, and 3.60 log cfu/mL of rinse for those fed medicated feed). Likewise, medicated feed did not affect Campylobacter numbers on carcasses after inside-outside washing (3.11 and 3.07 log cfu/mL of rinse). However, carcasses of broilers fed tylosin phosphate had lower numbers of Campylobacter after chilling (1.45 log cfu/mL of rinse) than control carcasses (2.31 log cfu/mL of rinse). No Campylobacter isolated from control carcasses were resistant to erythromycin; all Campylobacter recovered from carcasses fed tylosin phosphate were resistant to erythromycin. Application of tylosin phosphate in feed results in lower numbers of Campylobacter on chilled carcasses; however, the Campylobacter that do remain are resistant to erythromycin.}, number={6}, journal={Poultry Science}, publisher={Oxford University Press (OUP)}, author={Berrang, M. E. and Ladely, S. R. and Meinersmann, R. J. and Fedorka-Cray, P. J.}, year={2007}, month={Jun}, pages={1229–1233} }
 @article{feder_gray_pearce_fratamico_bush_porto fett_wallace_fedorka cray_luchansky_2007, title={Testing of Swine Feces Obtained through the National Animal Health Monitoring System's Swine 2000 Study for the Presence of Escherichia coli O157:H7}, volume={70}, ISSN={0362-028X}, url={http://dx.doi.org/10.4315/0362-028x-70.6.1489}, DOI={10.4315/0362-028x-70.6.1489}, abstractNote={Fecal samples collected from healthy pigs from 13 of the top 17 swine-producing states were tested for Escherichia coli O157:H7 as part of the National Animal Health Monitoring System Swine 2000 study. Serogroup O157 strains were isolated from 106 of 2,526 fecal samples. None of the isolates were positive by PCR for the fliCh7 (H7 flagellin) gene or for the hly933 (hemolysin) gene; however, one isolate was positive for the stxl gene (Shiga toxin 1), an additional four isolates were positive for the stx2 gene (Shiga toxin 2), and three isolates possessed the eae gene (intimin).}, number={6}, journal={Journal of Food Protection}, publisher={International Association for Food Protection}, author={Feder, Ingrid and Gray, Jeffrey T. and Pearce, Rachel A. and Fratamico, Pina M. and Bush, Eric and Porto Fett, Anna and Wallace, F. Morgan and Fedorka Cray, Paula J. and Luchansky, John B.}, year={2007}, month={Jun}, pages={1489–1492} }
 @article{berrang_ladely_simmons_fletcher_fedorka-cray_2006, title={Antimicrobial Resistance Patterns of Salmonella from Retail Chicken}, volume={5}, ISSN={1682-8356}, url={http://dx.doi.org/10.3923/ijps.2006.351.354}, DOI={10.3923/ijps.2006.351.354}, abstractNote={2 Abstract: Salmonella is frequently reported as a cause of food-borne illness. The emergence of antimicrobial resistant Salmonella associated with meat products has heightened concerns regarding antimicrobial use in food animal production. Eighty Salmonella isolates recovered from fresh whole chicken carcasses purchased at retail outlets were examined for susceptibility to 18 antimicrobials. Fifteen serotypes were identified; the top five included; S. Heidelberg (25%), S. Typhimurium 5- (formerly var. Copenhagen) (18.75%), S. Kentucky (17.5%), S. Berta (11.25%), and S. Hadar (8.75%). Overall, resistance was most commonly observed to tetracycline (25%), ampicillin (22.5%), streptomycin (21.25%) and cephalosporin derivatives (cephalothin 18.75%, ceftiofur 16.25%, and cefoxitin 15%). Of all isolates, 43.75% were resistant to one or more antimicrobial and 36 % were identified as multi-drug resistant (MDR, resistant to 2 or more antimicrobials). Fourteen resistance patterns were observed and among isolates showing resistance, 22.5% were resistant to 1-3 antimicrobials, 16.25% were resistant to 4-6 antimicrobials, and 5.0% were resistant to = 7 antimicrobials. The prevalence of antimicrobial resistance varied by serotype. All 7 S. Hadar isolates were resistant to 1-2 antimicrobials, 4 of 20 S. Heidelberg isolates were resistant to 1- 3 antimicrobials, 10 of 15 S. Typhimurium 5- isolates were resistant to 4-5 antimicrobials, 7 of 14 S. Kentucky isolates were resistant to 1-7 antimicrobials, and 3 of 9 S. Berta isolates expressed resistance to 9-1 1 antimicrobials. These data indicate that Salmonella recovered from retail poultry carcasses may be resistant to multiple antimicrobials, and that resistance among these isolates varies by serotype.}, number={4}, journal={International Journal of Poultry Science}, publisher={Science Alert}, author={Berrang, M.E. and Ladely, S.R. and Simmons, M. and Fletcher, D.L. and Fedorka-Cray, P.J.}, year={2006}, month={Apr}, pages={351–354} }
 @article{musgrove_jones_northcutt_cox_harrison_fedorka-cray_ladely_2006, title={Antimicrobial Resistance in Salmonella and Escherichia coli Isolated from Commercial Shell Eggs}, volume={85}, ISSN={0032-5791 1525-3171}, url={http://dx.doi.org/10.1093/ps/85.9.1665}, DOI={10.1093/ps/85.9.1665}, abstractNote={The development of antimicrobial resistance in bacteria has become a global problem. Isolates of Salmonella and Escherichia coli recovered from shell egg samples, collected at 3 commercial plants, were analyzed for resistance to 16 antimicrobial agents (n = 990). Eggs were sampled by rinsing in a saline solution. Pooled samples were preenriched in buffered peptone water and then selectively isolated using standard broths and agars. Salmonella-positive isolates were serogrouped immunologically before being serotyped. Enterobacteriaceae were enumerated from individual samples using violet red bile glucose agar plates. Escherichia coli were identified biochemically from presumptive Enterobacteriaceae isolates. Salmonella and generic E. coli antimicrobial-susceptibility testing was conducted using a semiautomated broth microdilution system. More resistance was observed in the Salmonella isolates (n = 41) than in the E. coli isolates (n = 194). Salmonella Typhimurium was the most prevalent (69.0%) serotype and demonstrated the greatest multiple resistance. Salmonella Kentucky, the least prevalent (5.0%) serotype recovered, was the most susceptible. Although 34.1% of the Salmonella serotypes were susceptible to all antimicrobial agents, 60.1% were resistant to 11 or more compounds. Many Salmonella isolates exhibited resistance to tetracycline (63.4%), nalidixic acid (63.4%), and streptomycin (61.0%). Most E. coli isolates (73.2%) were susceptible to all antimicrobial drugs. Many E. coli isolates exhibited resistance to tetracycline (29.9%), streptomycin (6.2%), and gentamicin (3.1%). Only 1% of the E. coli isolates were resistant to 4 antimicrobial agents. These data indicate that shell eggs can harbor resistant foodborne and commensal bacteria; among Salmonella isolates, resistance was serotype-dependent.}, number={9}, journal={Poultry Science}, publisher={Oxford University Press (OUP)}, author={Musgrove, M. T. and Jones, D. R. and Northcutt, J. K. and Cox, N. A. and Harrison, M. A. and Fedorka-Cray, P. J. and Ladely, S. R.}, year={2006}, month={Sep}, pages={1665–1669} }
 @article{foley_white_mcdermott_walker_rhodes_fedorka-cray_simjee_zhao_2006, title={Comparison of Subtyping Methods for Differentiating Salmonella enterica Serovar Typhimurium Isolates Obtained from Food Animal Sources}, volume={44}, ISSN={0095-1137}, url={http://dx.doi.org/10.1128/jcm.00745-06}, DOI={10.1128/jcm.00745-06}, abstractNote={ABSTRACT Molecular characterization (e.g., DNA-based typing methods) of Salmonella isolates is frequently employed to compare and distinguish clinical isolates recovered from animals and from patients with food-borne disease and nosocomial infections. In this study, we compared the abilities of different phenotyping and genotyping methods to distinguish isolates of Salmonella enterica serovar Typhimurium from different food animal sources. One hundred twenty-eight S. enterica serovar Typhimurium strains isolated from cattle, pigs, chickens, and turkeys or derived food products were characterized using pulsed-field gel electrophoresis (PFGE), repetitive element PCR (Rep-PCR), multilocus sequence typing (MLST), plasmid profiling, and antimicrobial susceptibility testing. Among the 128 Salmonella isolates tested, we observed 84 Rep-PCR profiles, 86 PFGE patterns, 89 MLST patterns, 36 plasmid profiles, and 38 susceptibility profiles. The molecular typing methods, i.e., PFGE, MLST, and Rep-PCR, demonstrated the best discriminatory power among Salmonella isolates. However, no apparent correlation was evident between the results of one molecular typing method and those of the others, suggesting that a combination of multiple methods is needed to differentiate S. enterica serovar Typhimurium isolates that genetically cluster according to one particular typing method.}, number={10}, journal={Journal of Clinical Microbiology}, publisher={American Society for Microbiology}, author={Foley, S. L. and White, D. G. and McDermott, P. F. and Walker, R. D. and Rhodes, B. and Fedorka-Cray, P. J. and Simjee, S. and Zhao, S.}, year={2006}, month={Oct}, pages={3569–3577} }
 @article{frye_jesse_long_rondeau_porwollik_mcclelland_jackson_englen_fedorka-cray_2006, title={DNA microarray detection of antimicrobial resistance genes in diverse bacteria}, volume={27}, ISSN={0924-8579}, url={http://dx.doi.org/10.1016/j.ijantimicag.2005.09.021}, DOI={10.1016/j.ijantimicag.2005.09.021}, abstractNote={High throughput genotyping is essential for studying the spread of multiple antimicrobial resistance. A test oligonucleotide microarray designed to detect 94 antimicrobial resistance genes was constructed and successfully used to identify antimicrobial resistance genes in control strains. The microarray was then used to assay 51 distantly related bacteria, including Gram-negative and Gram-positive isolates, resulting in the identification of 61 different antimicrobial resistance genes in these bacteria. These results were consistent with their known gene content and resistance phenotypes. Microarray results were confirmed by polymerase chain reaction and Southern blot analysis. These results demonstrate that this approach could be used to construct a microarray to detect all sequenced antimicrobial resistance genes in nearly all bacteria.}, number={2}, journal={International Journal of Antimicrobial Agents}, publisher={Elsevier BV}, author={Frye, Jonathan G. and Jesse, Troy and Long, Fred and Rondeau, Gaelle and Porwollik, Steffen and McClelland, Michael and Jackson, Charlene R. and Englen, Mark and Fedorka-Cray, Paula J.}, year={2006}, month={Feb}, pages={138–151} }
 @article{morley_strohmeyer_tankson_hyatt_dargatz_fedorka-cray_2006, title={Evaluation of the association between feeding raw meat and Salmonella enterica infections at a Greyhound breeding facility}, volume={228}, ISSN={0003-1488}, url={http://dx.doi.org/10.2460/javma.228.10.1524}, DOI={10.2460/javma.228.10.1524}, abstractNote={Abstract Objective —To investigate Salmonella enterica infections at a Greyhound breeding facility. Design —Cross-sectional study. Animal and Sample Populations —138 adult and juvenile dogs and S enterica isolates recovered from the dogs and their environment. Procedures —The investigation was conducted at the request of a Greyhound breeder. Observations regarding the environment and population of dogs were recorded. Fecal, food, and environmental specimens were collected and submitted for Salmonellaculture . Isolates were serotyped and tested for susceptibility to 16 antimicrobials. Isolates underwent genetic analyses by use of pulsed-field gel electrophoresis and ribotyping. Results —S enterica was recovered from 88 of 133 (66%) samples of all types and from 57 of 61 (93%) fecal samples. Eighty-three (94.3%) of the isolates were serotype Newport, 77 (87.5%) of which had identical resistance phenotypes. Genetic evaluations suggested that several strains of S enterica existed at the facility, but there was a high degree of relatedness among many of the Newport isolates. Multiple strains of Salmonella enterica serotype Newport were recovered from raw meat fed on 1 day. Conclusions and Clinical Relevance — S enterica infections and environmental contamination were common at this facility. A portion of the Salmonellastrains detected on the premises was likely introduced via raw meat that was the primary dietary constituent. Some strains appeared to be widely disseminated in the population. Feeding meat that had not been cooked properly, particularly meat classified as unfit for human consumption, likely contributed to the infections in these dogs.}, number={10}, journal={Journal of the American Veterinary Medical Association}, publisher={American Veterinary Medical Association (AVMA)}, author={Morley, Paul S. and Strohmeyer, Rachel A. and Tankson, Jeanetta D. and Hyatt, Doreene R. and Dargatz, David A. and Fedorka-Cray, Paula J.}, year={2006}, month={May}, pages={1524–1532} }
 @article{son_englen_berrang_fedorka cray_harrison_2006, title={Genetic Diversity of Arcobacter and Campylobacter on Broiler Carcasses during Processing}, volume={69}, ISSN={0362-028X}, url={http://dx.doi.org/10.4315/0362-028x-69.5.1028}, DOI={10.4315/0362-028x-69.5.1028}, abstractNote={Broiler carcasses (n=325) were sampled at three sites along the processing line (prescalding, prechilling, and postchilling) in a commercial poultry processing plant during five plant visits from August to October 2004. Pulsed-field gel electrophoresis (PFGE) was used to determine the genomic fingerprints of Camospylobacter coli (n=27), Campylobacter jejuni (n=188), Arcobacter butzleri (n=138), Arcobacter cryaerophilus 1A (n=4), and A. cryaerophilus 1B (n=31) with the restriction enzymes SmaI and KpnI for Campylobacter and Arcobacter, respectively. Campylobacter species were subtyped by the Centers for Disease Control and Prevention PulseNet 24-h standardized protocol for C. jejuni. A modification of this protocol with a different restriction endonuclease (KpnI) and different electrophoresis running conditions produced the best separation of restriction fragment patterns for Arcobacter species. Both unique and common PFGE types of Arcobacter and Campylobacter strains were identified. A total of 32.8% (57 of 174) of the Arcobacter isolates had unique PFGE profiles, whereas only 2.3% (5 of 215) of the Campylobacter isolates belonged to this category. The remaining Arcobacter strains were distributed among 25 common PFGE types; only eight common Campylobacter PFGE types were observed. Cluster analysis showed no associations among the common PFGE types for either genus. Each of the eight common Campylobacter types consisted entirely of isolates from one sampling day, whereas more than half of the common Arcobacter types contained isolates from different sampling days. Our results demonstrate far greater genetic diversity for Arcobacter than for Campylobacter and suggest that the Campylobacter types are specific to individual flocks of birds processed on each sampling day.}, number={5}, journal={Journal of Food Protection}, publisher={International Association for Food Protection}, author={Son, Insook and Englen, Mark D. and Berrang, Mark E. and Fedorka Cray, Paula J. and Harrison, Mark A.}, year={2006}, month={May}, pages={1028–1033} }
 @article{bahnson_fedorka-cray_ladely_mateus-pinilla_2006, title={Herd-level risk factors for Salmonella enterica subsp. enterica in U.S. market pigs}, volume={76}, ISSN={0167-5877}, url={http://dx.doi.org/10.1016/j.prevetmed.2006.05.009}, DOI={10.1016/j.prevetmed.2006.05.009}, abstractNote={Midwest U.S. herds (n=63) were studied to identify risk factors for harboring Salmonella enterica among slaughter-weight pigs. Samples collected on farms (feces) and at slaughter (distal colonic content, cecal content and ileocolic lymph nodes) were cultured using conventional means. Approximately 15 pigs were studied per herd, for a total of 3754 samples. The proportion of pigs positive in one or more samples was calculated for each herd. Herd characteristics were described by a combination of interview and written survey. Logistic regression was used to detect relationships between the detection of Salmonella and potential herd-level risk factors. The mean individual pig prevalence was 5% for feces, 4% for distal colonic content, 15% for ileocolic lymph nodes, and 17% for cecal contents. One or more Salmonella isolates were detected in at least one sample type in every herd. The five most common serovars were S. Agona, S. Derby, S. Schwarzengrund, S. Typhimurium and S. Senftenberg, with 25 additional serovars detected. Salmonella prevalence estimates were positively correlated among all samples except distal colonic content and ileocolic lymph nodes. Pigs with culture positive fecal samples were at increased odds of being detected positive for each of the slaughter-collected samples examined, namely distal colonic content (OR=30.5), ileocolic lymph nodes (OR=12.9) and cecal content (OR=23.2). Herds with positive fecal sample(s) had increased odds of having positive cecal content (OR>1.5), distal colonic content (OR=15.3) and ileocolic lymph nodes (OR=12.7). Pigs from herds with at least some bowl drinkers had eight-fold higher odds of testing Salmonella positive than did pigs from herds with only nipple drinkers. Pigs from herds with only dry feeders had five-fold higher odds of testing Salmonella positive when compared with pigs from herds with combinations of wet/dry style feeders. Interventions at these two points should be considered when designing growing pig facilities to reduce Salmonella shedding.}, number={3-4}, journal={Preventive Veterinary Medicine}, publisher={Elsevier BV}, author={Bahnson, P.B. and Fedorka-Cray, P.J. and Ladely, S.R. and Mateus-Pinilla, N.E.}, year={2006}, month={Oct}, pages={249–262} }
 @article{miller_englen_kathariou_wesley_wang_pittenger-alley_siletz_muraoka_fedorka-cray_mandrell_2006, title={Identification of host-associated alleles by multilocus sequence typing of Campylobacter coli strains from food animals}, volume={152}, ISSN={1350-0872 1465-2080}, url={http://dx.doi.org/10.1099/mic.0.28348-0}, DOI={10.1099/mic.0.28348-0}, abstractNote={Campylobacter coli is a food-borne pathogen associated increasingly with human gastroenteritis. C. coli has a high prevalence in swine, but is isolated also from cattle and poultry. Multilocus sequence typing (MLST) systems have been developed to differentiate C. coli strains. Although substantial allelic diversity was identified across all seven C. coli MLST loci, no correlations were made in two previous studies between allele or sequence type (ST) and the source of the organism. However, this may be due to either the relatively small number or the low diversity of C. coli strains used to validate both MLST studies. This study describes the typing of 488 C. coli strains from 4 different food animal sources (cattle, chickens, swine and turkeys), collected at different times over a 6 year period from different USA geographical locations. A total of 149 STs were identified. The 185 swine strains were the most diverse, possessing 82 STs. The cattle strains were the most clonal; 52/63 (83 %) strains possessed a single ST (ST-1068). A subpopulation of C. coli strains, collected primarily from turkeys, was identified, containing both C. coli- and Campylobacter jejuni-associated MLST alleles, specifically the C. jejuni allele aspA103. The majority of STs and alleles were host associated, i.e. found primarily in strains from a single food-animal source. Only 12/149 (8 %) STs were found in multiple sources. Additionally, the majority (34/46, 74 %) of major (n>5) alleles were more prevalent in certain hosts (swine, poultry). The presence of host-associated C. coli MLST alleles could lead potentially to more efficient source tracking in this species, especially in the trace-back of both sporadic and outbreak human clinical C. coli strains to animal sources.}, number={1}, journal={Microbiology}, publisher={Microbiology Society}, author={Miller, M.A. and Englen, M.D. and Kathariou, S. and Wesley, I. and Wang, Guilin and Pittenger-Alley, Lauren and Siletz, Robin M. and Muraoka, Wayne and Fedorka-Cray, P.J. and Mandrell, R.E.}, year={2006}, month={Jan}, pages={245–255} }
 @article{traub-dargatz_ladely_dargatz_fedorka-cray_2006, title={Impact of Heat Stress on the Fecal Shedding Patterns of Salmonella enterica Typhimurium DT104 and Salmonella enterica Infantis by 5-Week-Old Male Broilers}, volume={3}, ISSN={1535-3141 1556-7125}, url={http://dx.doi.org/10.1089/fpd.2006.3.178}, DOI={10.1089/fpd.2006.3.178}, abstractNote={The objective of this study was to determine if there is an impact of heat stress of broiler chickens on number and survival of two types of Salmonella shed in the chicken's feces after an oral challenge. The data from this study indicate that heat stress did not result in higher levels or longer survival of Salmonella spp. shed in feces. It is possible that the duration or intensity of the heat stress employed was not sufficient or that heat stress does not alter the number or survivability for these particular strains of Salmonella spp. Feces stored at room temperature after collection, resulted in the numbers of both strains of Salmonella increasing by one to three logs in the first week. This finding indicates that there could be an increase in environmental contamination under certain conditions.}, number={2}, journal={Foodborne Pathogens and Disease}, publisher={Mary Ann Liebert Inc}, author={Traub-Dargatz, Josie L. and Ladely, Scott R. and Dargatz, David A. and Fedorka-Cray, Paula J.}, year={2006}, month={Jun}, pages={178–183} }
 @article{kim_frye_hu_fedorka-cray_gautom_boyle_2006, title={Multiplex PCR-Based Method for Identification of Common Clinical Serotypes of Salmonella enterica subsp. enterica}, volume={44}, ISSN={0095-1137}, url={http://dx.doi.org/10.1128/jcm.00701-06}, DOI={10.1128/jcm.00701-06}, abstractNote={ABSTRACT A multiplex PCR method has been developed to differentiate between the most common clinical serotypes of Salmonella enterica subsp. enterica encountered in Washington State and the United States in general. Six genetic loci from S. enterica serovar Typhimurium and four from S. enterica serovar Typhi were used to create an assay consisting of two five-plex PCRs. The assays gave reproducible results with 30 different serotypes that represent the most common clinical isolates of S. enterica subsp. enterica . Of these, 22 serotypes gave unique amplification patterns compared with each other and the other 8 serotypes were grouped into four pairs. These were further resolved by two additional PCRs. We compared the data from PCR serotyping with conventional serotyping and found that PCR serotyping was nearly as discriminatory as conventional serotyping was. The results from a blind test screening 111 clinical isolates revealed that 97% were correctly identified using the multiplex PCR assay. The assay can be easily performed on multiple samples with final results in less than 5 h and, in conjunction with pulsed-field gel electrophoresis, forms a very robust test method for the molecular subtyping of Salmonella enterica subsp. enterica .}, number={10}, journal={Journal of Clinical Microbiology}, publisher={American Society for Microbiology}, author={Kim, S. and Frye, J. G. and Hu, J. and Fedorka-Cray, P. J. and Gautom, R. and Boyle, D. S.}, year={2006}, month={Aug}, pages={3608–3615} }
 @article{cox_richardson_buhr_northcutt_fedorka-cray_bailey_fairchild_mauldin_2006, title={Natural Occurrence of Campylobacter Species, Salmonella Serovars, and Other Bacteria in Unabsorbed Yolks of Market-Age Commercial Broilers}, volume={15}, ISSN={1056-6171 1537-0437}, url={http://dx.doi.org/10.1093/japr/15.4.551}, DOI={10.1093/japr/15.4.551}, abstractNote={In the developing avian embryo, the main energy source is the yolk. Toward the end of the incubation period, the remaining yolk sac is internalized into the abdominal cavity. At hatch, the remaining yolk comprises 20% of the chick's BW and provides the nutrients needed for maintenance. Posthatch, chicks rapidly initiate the transition from yolk dependence to the utilization of exogenous feed. However, at present, it is not known what types of bacteria are found to be associated with unabsorbed yolk sacs from market-age broilers. For Experiment 1, one hundred 6-wk-old defeathered broiler carcasses were obtained from a commercial processing facility during each of 3 visits. In the second experiment, one hundred 8-wk-old defeathered broiler carcasses were obtained from a different commercial processing plant on 4 separate occasions. For both experiments, each carcass was aseptically opened and inspected for the presence of an unabsorbed yolk sac. Three to 5 carcasses containing a free-floating yolk sac (within the abdominal cavity) and the yolk stalk (without a yolk sac) and 3 to 5 carcasses containing an attached yolk and yolk stalk from each repetition were randomly selected and analyzed for levels and types of total aerobic bacteria (APC), Enterobacteriaceae (ENT), and for the presence of Campylobacter spp. and Salmonella serovars. The APC ranged from log 3.3 to >log 6.0, and the ENT ranged from log 2.8 to >log 6.0. Staphylococcus spp. and Streptococcus spp. were the predominant organisms in APC, whereas Escherichia coli and Hafnia alvei were found to comprise the ENT. Campylobacter spp. was found in 29% of the yolk stalks, 32% of the attached yolk sacs, and 13% of the free-floating yolk sacs. All Campylobacter isolates were determined to be Campylobacter jejuni, except for 1 attached yolk and yolk stalk, which was Campylobacter coli. Salmonella serovars were found in 26% of the yolk stalks, 48% of the attached yolk sacs, and 23% of the free-floating yolk sacs, and the majority of Salmonella isolates were Salmonella Typhimurium. The significance of these bacterial reservoirs and carcass contamination during processing is yet to be determined.}, number={4}, journal={The Journal of Applied Poultry Research}, publisher={Oxford University Press (OUP)}, author={Cox, N. A. and Richardson, L. J. and Buhr, R. J. and Northcutt, J. K. and Fedorka-Cray, P. J. and Bailey, J. S. and Fairchild, B. D. and Mauldin, J. M.}, year={2006}, month={Dec}, pages={551–557} }
 @article{cox_richardson_buhr_fedorka-cray_bailey_wilson_hiett_2006, title={Natural Presence of Campylobacter spp. in Various Internal Organs of Commercial Broiler Breeder Hens}, volume={50}, ISSN={0005-2086 1938-4351}, url={http://dx.doi.org/10.1637/7481-120205r.1}, DOI={10.1637/7481-120205r.1}, abstractNote={Campylobacter are known to cause acute bacterial gastroenteritis in humans. Poultry products have been implicated as a significant source of these infections. Six experiments were performed to determine whether Campylobacter could be isolated naturally from the primary and secondary lymphoid organs, liver/gallbladder, and ceca of commercial broiler breeder hens. Broiler breeder hens were acquired from different commercial sources during the early, middle, and late lay cycles. The birds were euthanatized, defeathered, and aseptically opened. To reduce the possibility of cross-contamination between samples, the thymus, spleen, and liver/gallbladder were aseptically removed prior to removal of the ceca. Individual samples were placed in sterile bags, packed on ice, and transported to the laboratory for evaluation. In this study Campylobacter were found in 11 of 43 thymii, eight of 43 spleens, four of 43 liver/gallbladders, and 30 of 43 ceca. Overall, 28 of 53 isolates from the above samples were Campylobacter coli and 25 of 53 isolates were found to be Campylobacter jejuni.}, number={3}, journal={Avian Diseases}, publisher={American Association of Avian Pathologists (AAAP)}, author={Cox, N. A. and Richardson, L. J. and Buhr, R. J. and Fedorka-Cray, P. J. and Bailey, J. S. and Wilson, J. L. and Hiett, K. L.}, year={2006}, month={Sep}, pages={450–453} }
 @article{zaidi_mcdermott_fedorka-cray_leon_canche_hubert_abbott_león_zhao_headrick_et al._2006, title={Nontyphoidal Salmonella from Human Clinical Cases, Asymptomatic Children, and Raw Retail Meats in Yucatan, Mexico}, volume={42}, ISSN={1537-6591 1058-4838}, url={http://dx.doi.org/10.1086/498508}, DOI={10.1086/498508}, abstractNote={Background. We report the results of a 3-year Salmonella surveillance study of persons with diarrhea; asymptomatic children; and retail pork, poultry, and beef in Yucatan, Mexico. Methods. Isolates were characterized according to serotype, antimicrobial susceptibility, and genetic relatedness with pulsed-field gel electrophoresis. Results. Salmonella Typhimurium was the most common serotype found in ill humans (21.8% of isolates), followed by Salmonella Agona (21% of isolates). Salmonella Enteritidis was a minor serotype (4.2% of isolates). Asymptomatic children carried S. Agona (12.1% of isolates), Salmonella Meleagridis (11.6% of isolates), Salmonella Anatum (8% of isolates) and S. Enteritidis (5.8% of isolates). A high percentage of retail meat samples contained Salmonella; it was most commonly found in pork (58.1% of samples), followed by beef (54% of samples) and poultry (39.7% of samples). Resistance to oral drugs used for the treatment of salmonellosis was observed for ampicillin (14.6% of isolates were resistant), chloramphenicol (14.0% of isolates), and trimethoprim-sulfamethoxazole (19.7% of isolates). Resistance to ceftriaxone emerged in 2002 and was limited to the serotype S. Typhimurium. Twenty-seven percent of the isolates were resistant to nalidixic acid, and none were resistant to ciprofloxacin. Multidrug resistance was most common among isolates of serotypes S. Typhimurium and S. Anatum. Pulsed-field gel electrophoresis showed that strains found in retail meats were genetically identical to strains found in both asymptomatic children and ill patients. Conclusions. Our study found a high prevalence of Salmonella in retail meats and persons with enteric infection; many of these isolates were resistant to clinically important antimicrobials. A random selection of isolates from people and retail meat showed genetic relatedness, which suggests that, in Yucatan, considerable transfer of Salmonella occurs through the food chain.}, number={1}, journal={Clinical Infectious Diseases}, publisher={Oxford University Press (OUP)}, author={Zaidi, Mussaret B. and McDermott, Patrick F. and Fedorka-Cray, Paula and Leon, Verónica and Canche, Claudia and Hubert, Susannah K. and Abbott, Jason and León, Magda and Zhao, Shaohua and Headrick, Marcia and et al.}, year={2006}, month={Jan}, pages={21–28} }
 @article{mcgowan_jackson_barrett_hiott_fedorka cray_2006, title={Prevalence and Antimicrobial Resistance of Enterococci Isolated from Retail Fruits, Vegetables, and Meats}, volume={69}, ISSN={0362-028X}, url={http://dx.doi.org/10.4315/0362-028x-69.12.2976}, DOI={10.4315/0362-028x-69.12.2976}, abstractNote={Although enterococci are considered opportunistic pathogens, they can be reservoirs of antimicrobial resistance. Antimicrobial resistance is increasingly important because of foodborne illnesses from meat and infections from produce. From 2000 through 2001, food items (vegetables, fruits, and meats) were obtained from grocery store chains in northern Georgia and cultured for the presence of enterococci; 47.7% (189 of 396) of these samples were positive for enterococci. For the fruits and vegetables, enterococci were cultured most often from tomatoes (9 of 27 samples, 33%) and radishes (10 of 11 samples, 91%), respectively. Among the meat items tested, enterococci were isolated from 95% (21 of 22) of the chicken samples, 73% (16 of 22) of the beef samples, 95% (20 of 21) of the turkey samples, and 68% (15 of 22) of the pork samples. The predominant species identified was Enterococcus faecalis (n = 80) from meat and Enterococcus casseliflavus (n = 66) from fruits and vegetables. Although high numbers of isolates were resistant to lincomycin (176 of 185 isolates, 95.1%) and bacitracin (150 of 185 isolates, 81.1%), very few isolates were resistant to salinomycin (2 isolates, 1.1%), penicillin (3 isolates, 1.6%), or nitrofurantoin (9 isolates, 4.9%). None of the isolates were resistant to linezolid or vancomycin. These data suggest that foods commonly purchased from grocery stores are a source of enterococci; however, overall resistance to antimicrobials is relatively low.}, number={12}, journal={Journal of Food Protection}, publisher={International Association for Food Protection}, author={McGowan, Lori L. and Jackson, Charlene R. and Barrett, John B. and Hiott, Lari M. and Fedorka Cray, Paula J.}, year={2006}, month={Dec}, pages={2976–2982} }
 @article{bauer-garland_frye_gray_berrang_harrison_fedorka-cray_2006, title={Transmission of Salmonella enterica serotype Typhimurium in poultry with and without antimicrobial selective pressure}, volume={101}, ISSN={1364-5072 1365-2672}, url={http://dx.doi.org/10.1111/j.1365-2672.2006.03036.x}, DOI={10.1111/j.1365-2672.2006.03036.x}, abstractNote={To determine the effect of antimicrobial selective pressure on the transmission of antimicrobial resistant and sensitive strains of Salmonella in poultry.Eight pens housed 12 broiler chicks each. Two chicks in four of the pens were inoculated with a Salm. Typhimurium strain resistant to 12 antimicrobials (including tetracycline), and two chicks in each of the four other pens were inoculated with a strain sensitive to all antimicrobials tested. Two pens inoculated with each strain were treated with chlortetracycline and two were not. Chicks were killed on day 7 and caeca were cultured for Salmonella. Experiments were performed independently twice. Chicks exposed to pen mates inoculated with the resistant strain and treated with tetracycline were 90% positive for Salmonella; whereas 60% of chicks given no antimicrobials were positive. Chicks exposed to the sensitive strain were 95% positive with tetracycline treatment and 90% positive without treatment.A multidrug-resistant Salm. Typhimurium strain had significantly increased transmission when chicks were treated with tetracycline. Transmission of a sensitive strain was not inhibited by antimicrobial selective pressure at recommended therapeutic dose.This study demonstrates that antimicrobial usage may influence the transmission of antimicrobial-resistant pathogens in poultry.}, number={6}, journal={Journal of Applied Microbiology}, publisher={Wiley}, author={Bauer-Garland, J. and Frye, J.G. and Gray, J.T. and Berrang, M.E. and Harrison, M.A. and Fedorka-Cray, P.J.}, year={2006}, month={Dec}, pages={1301–1308} }
 @article{jesse_englen_pittenger-alley_fedorka-cray_2006, title={Two distinct mutations in gyrA lead to ciprofloxacin and nalidixic acid resistance in Campylobacter coli and Campylobacter jejuni isolated from chickens and beef cattle*}, volume={100}, ISSN={1364-5072 1365-2672}, url={http://dx.doi.org/10.1111/j.1365-2672.2005.02796.x}, DOI={10.1111/j.1365-2672.2005.02796.x}, abstractNote={The aim of this study was to identify point mutations in the gyrA quinolone resistance determining region (QRDR) of Campylobacter coli (n = 27) and Campylobacter jejuni (n = 26) that confer nalidixic acid (NAL) resistance without conferring resistance to ciprofloxacin (CIP).Point mutations in the QRDR of gyrA from C. coli and C. jejuni isolates were identified by direct sequencing. All isolates (n = 14) with minimum inhibitory concentrations (MICs) >or=4 microg ml(-1) for CIP and >or=32 microg ml(-1) for NAL possessed a missense mutation leading to substitution of Ile for Thr at codon 86. Three isolates with a missense mutation leading to a Thr86Ala substitution had MICs <4 mug ml(-1) for CIP and >or=32 microg ml(-1) for NAL.These data confirm previous findings that Thr86Ile mutations confer resistance to both CIP and NAL. However, resistance to NAL alone was conferred by a single Thr86Ala mutation.Resistance to NAL alone arises independently from CIP resistance. In addition, the role of other previously described point mutations in quinolone resistance is discussed.}, number={4}, journal={Journal of Applied Microbiology}, publisher={Wiley}, author={Jesse, T.W. and Englen, M.D. and Pittenger-Alley, L.G. and Fedorka-Cray, P.J.}, year={2006}, month={Apr}, pages={682–688} }
 @article{morley_apley_besser_burney_fedorka-cray_papich_traub-dargatz_weese_2005, title={Antimicrobial Drug Use in Veterinary Medicine}, volume={19}, ISSN={0891-6640 1939-1676}, url={http://dx.doi.org/10.1111/j.1939-1676.2005.tb02739.x}, DOI={10.1111/j.1939-1676.2005.tb02739.x}, abstractNote={Recognizing the importance of antimicrobial resistance and the need for veterinarians to aid in efforts for maintaining the usefulness of antimicrobial drugs in animals and humans, the Board of Regents of the American College of Veterinary Internal Medicine charged a special committee with responsibility for drafting this position statement regarding antimicrobial drug use in veterinary medicine. The Committee believes that veterinarians are obligated to balance the well‐being of animals under their care with the protection of other animals and public health. Therefore, if an animal's medical condition can be reasonably expected to improve as a result of treatment with antimicrobial drugs, and the animal is under a veterinarian's care with an appropriate veterinarian‐client‐patient relationship, veterinarians have an obligation to offer antimicrobial treatment as a therapeutic option. Veterinarians also have an obligation to actively promote disease prevention efforts, to treat as conservatively as possible, and to explain the potential consequences associated with antimicrobial treatment to animal owners and managers, including the possibility of promoting selection of resistant bacteria. However, the consequences of losing usefulness of an antimicrobial drug that is used as a last resort in humans or animals with resistant bacterial infections might be unacceptable from a public or population health perspective. Veterinarians could therefore face the difficult choice of treating animals with a drug that is less likely to be successful, possibly resulting in prolonged or exacerbated morbidity, to protect the good of society. The Committee recommends that voluntary actions be taken by the veterinary profession to promote conservative use of antimicrobial drugs to minimize the potential adverse effects on animal or human health. The veterinary profession must work to educate all veterinarians about issues related to conservative antimicrobial drug use and antimicrobial resistance so that each individual is better able to balance ethical obligations regarding the perceived benefit to their patients versus the perceived risk to public health. Specific means by which the veterinary profession can promote stewardship of this valuable resource are presented and discussed in this document.}, number={4}, journal={Journal of Veterinary Internal Medicine}, publisher={Wiley}, author={Morley, Paul S. and Apley, Michael D. and Besser, Thomas E. and Burney, Derek P. and Fedorka-Cray, Paula J. and Papich, Mark G. and Traub-Dargatz, Josie L. and Weese, J. Scott}, year={2005}, month={Jul}, pages={617–629} }
 @article{englen_fedorka-cray_ladely_dargatz_2005, title={Antimicrobial resistance patterns of Campylobacter from feedlot cattle*}, volume={99}, ISSN={1364-5072 1365-2672}, url={http://dx.doi.org/10.1111/j.1365-2672.2005.02609.x}, DOI={10.1111/j.1365-2672.2005.02609.x}, abstractNote={This study examined 448 Campylobacter strains isolated in 1999 and 2000 from US feedlot cattle for resistance to 12 antimicrobials.Isolates were tested for antimicrobial susceptibility using the E-test method. Approximately 60% (n = 267) were resistant to one or more antimicrobials, and 19.6% (n = 88) were resistant to two or more antimicrobials. Of the Campylobacter jejuni isolates, 49.1% (n = 187) were resistant to tetracycline, 10.2% (n = 39) were resistant to nalidixic acid, 8.4% were resistant to trimethoprim/sulfamethoxazole, and 1.8% (n = 7) were resistant to ciprofloxacin. Resistance to any of the other eight antimicrobials was 1.3% or less, but 14.4% (n = 55) were resistant to two or more antimicrobials. In the Campylobacter coli group, 65.7% (n = 44) were resistant to tetracycline, 52.2% (n = 35) were resistant to trimethoprim/sulfamethoxazole, 22.4% (n = 15) were resistant to nalidixic acid, and 9.0% (n = 6) were resistant to ciprofloxacin. Resistance to any of the remaining eight antimicrobials was 3.0% or less, although 49.3% (n = 33) were resistant to two or more antimicrobials.Although antimicrobials are widely used in US feedlot cattle production, our results demonstrate generally low levels of resistance to a broad range of commonly used antimicrobials relative to other recent studies.Resistance data on Campylobacter isolated from this major US livestock commodity is lacking. This overview enhances current knowledge and provides a basis for further studies.}, number={2}, journal={Journal of Applied Microbiology}, publisher={Wiley}, author={Englen, M.D. and Fedorka-Cray, P.J. and Ladely, S.R. and Dargatz, D.A.}, year={2005}, month={Aug}, pages={285–291} }
 @article{zhao_fedorka-cray_friedman_mcdermott_walker_qaiyumi_foley_hubert_ayers_english_et al._2005, title={Characterization of Salmonella Typhimurium of Animal Origin Obtained from the National Antimicrobial Resistance Monitoring System}, volume={2}, ISSN={1535-3141 1556-7125}, url={http://dx.doi.org/10.1089/fpd.2005.2.169}, DOI={10.1089/fpd.2005.2.169}, abstractNote={Salmonella Typhimurium remains one of the most common causes of salmonellosis in animals and humans in the United States. The emergence of multi-drug resistant Salmonella reduces the therapeutic options in cases of invasive infections, and has been shown to be associated with an increased burden of illness. In this study, 588 S. Typhimurium (including var. Copenhagen) isolates obtained from either animal diagnostic specimens (n = 199) or food animals after slaughter/processing (n = 389) were examined for antimicrobial susceptibility, presence of class-1 integrons, and characterized using pulsed-field gel electrophoresis and phage typing. Seventy-six percent (448/588) of isolates were resistant to at least one antimicrobial. Salmonella isolates displayed resistance most often to streptomycin (63%), tetracycline (61%), ampicillin (61%), and to a lesser extent, chloramphenicol (36%), ceftiofur (15%), gentamicin (9%), and nalidixic acid (4%), with more resistance observed among diagnostic isolates. Salmonella recovered from turkeys (n = 38) exhibited the highest rates of resistance, with 92% of isolates resistant to least one antimicrobial, and 58% resistant to ≥10 antimicrobials. Class 1 integrons were present in 51% of all isolates. Five integron associated resistance genes (aadA, aadB, pse-1, oxa-2 and dhfr) were identified. A total of 311 PFGE patterns were generated using XbaI, indicating a genetically diverse population. The largest PFGE cluster contained 146 isolates, including DT104 isolates obtained from all seven animal species. Results demonstrated a varied spectrum of antimicrobial resistance, including several multidrug resistant clonal groups, among S. Typhimurium and S. Typhimurium var. Copenhagen isolates recovered from both diagnostic and slaughter/processing samples.}, number={2}, journal={Foodborne Pathogens and Disease}, publisher={Mary Ann Liebert Inc}, author={Zhao, S. and Fedorka-Cray, P.J. and Friedman, S. and McDermott, P.F. and Walker, R.D. and Qaiyumi, S. and Foley, S.L. and Hubert, S.K. and Ayers, S. and English, L. and et al.}, year={2005}, month={Jun}, pages={169–181} }
 @article{meinersmann_phillips_hiett_fedorka-cray_2005, title={Differentiation of Campylobacter Populations as Demonstrated by Flagellin Short Variable Region Sequences}, volume={71}, ISSN={0099-2240}, url={http://dx.doi.org/10.1128/aem.71.10.6368-6374.2005}, DOI={10.1128/aem.71.10.6368-6374.2005}, abstractNote={ABSTRACT The DNA sequence of the flaA short variable region (SVR) was used to analyze a random population of Campylobacter isolates to investigate the weakly clonal population structure of members of the genus. The SVR sequence from 197 strains of C. jejuni and C. coli isolated from humans, bovine, swine, and chickens identified a group of 43 strains containing disparate short variable region sequences compared to the rest of the population. This group contains both C. jejuni and C. coli strains but disproportionately consisted of bovine isolates. Relative synonymous codon usage analysis of the sequences identified two groups: one group typified C. jejuni , and the second group was characteristic for C. coli and the disparate alleles were not clustered. The data show that there is significant differentiation of Campylobacter populations according to the source of the isolate even without considering the disparate isolates. Even though there is significant differentiation of chicken and bovine isolates, the bovine isolates did not show any difference in ability to colonize chickens. It is possible that disparate sequences were obtained through the lateral transfer of DNA from Campylobacter species other than C. jejuni and C. coli . It is evident that recombination within the flaA SVR occurs rapidly. However, the rate of migration between populations appears to limit the distribution of sequences and results in a weakly clonal population structure.}, number={10}, journal={Applied and Environmental Microbiology}, publisher={American Society for Microbiology}, author={Meinersmann, R. J. and Phillips, R. W. and Hiett, K. L. and Fedorka-Cray, P.}, year={2005}, month={Oct}, pages={6368–6374} }
 @article{kim_gray_bailey_jones_fedorka-cray_2005, title={Effect of Porcine-Derived Mucosal Competitive Exclusion Culture on Antimicrobial Resistance in Escherichia coli from Growing Piglets}, volume={2}, ISSN={1535-3141 1556-7125}, url={http://dx.doi.org/10.1089/fpd.2005.2.317}, DOI={10.1089/fpd.2005.2.317}, abstractNote={While use of antimicrobial drugs in livestock production has made a significant impact on animal health, welfare, and productivity, interest in suitable alternatives such as pre/probiotics, organic acids, and cultures of normal flora or "competitive exclusion" cultures from young animals has increased significantly in the wake of the antimicrobial resistance issue. The present study was undertaken to determine the effect of porcine-derived mucosal competitive exclusion (PCE) culture on both the antimicrobial susceptibility of commensal E. coli and on growth performance in piglets. Two replicate trials were conducted using growing piglets fed standard antimicrobial- free production diets. Piglets in the treatment group were orally dosed with PCE (1010 cfu/mL) twice within 24 h of birth, at weaning, and 18–24 h post-weaning; control group piglets were dosed with sterile broth as a placebo. Fecal samples from all piglets were cultured for commensal E. coli at dosing times and when feed type was changed. A significantly higher proportion of E. coli from PCE-treated piglets demonstrated resistance to tetracycline (p < 0.0001), and streptomycin (p < 0.0001) when compared to controls. Resistance to streptomycin resistance in E. coli from piglets treated with PCE culture was variable, returning to baseline levels by day 21 (weaning). Piglets treated with the PCE culture demonstrated improved feed efficiencies when compared to control piglets (p < 0.005) during feeding of the starter and first growth diets. The PCE culture used in the present study had previously been shown to effectively exclude Salmonella in pigs. To the best of the authors' knowledge, this is the first report characterizing the effect of a competitive exclusion culture on antimicrobial resistance of commensal E. coli.}, number={4}, journal={Foodborne Pathogens and Disease}, publisher={Mary Ann Liebert Inc}, author={Kim, L.M. and Gray, Jeffery T. and Bailey, J. Stan and Jones, Richard D. and Fedorka-Cray, Paula J.}, year={2005}, month={Dec}, pages={317–329} }
 @article{jackson_fedorka-cray_jackson-hall_hiott_2005, title={Effect of media, temperature and culture conditions on the species population and antibiotic resistance of enterococci from broiler chickens*}, volume={41}, ISSN={0266-8254 1365-2673}, url={http://dx.doi.org/10.1111/j.1472-765x.2005.01749.x}, DOI={10.1111/j.1472-765x.2005.01749.x}, abstractNote={The effect of media type, incubation temperature and enrichment period on the species population and antibiotic susceptibility of enterococci from poultry carcass rinsates was determined.Aliquots of rinsates, incubated in BBL Enterococcosel broth at 37 degrees C, 42 degrees C, or 45 degrees C for 24 and 48 h, were inoculated onto BBL Enterococcosel and M-enterococcus agar. Presumptive positive colonies were identified to species and tested for antibiotic resistance. Significant differences (P < or = 0.05) were observed for media and temperature. More Enterococcus faecalis were isolated from M-enterococcus media and at 37 degrees C while more E. faecium were isolated from Enterococcosel agar and at 45 degrees C. The number of antibiotic-resistant E. faecalis and E. faecium were also affected by media and temperature.Culture conditions for enterococci affect the observed species and antibiotic resistance patterns and therefore should be carefully considered.This study indicates that media and temperature can influence the recovery and selection of enterococcal species and antibiotic susceptibility.}, number={3}, journal={Letters in Applied Microbiology}, publisher={Wiley}, author={Jackson, C.R. and Fedorka-Cray, P.J. and Jackson-Hall, M.C. and Hiott, L.M.}, year={2005}, month={Sep}, pages={262–268} }
 @article{tankson_fedorka-cray_jackson_headrick_2005, title={Genetic relatedness of a rarely isolated Salmonella: Salmonella enterica serotype Niakhar from NARMS animal isolates}, volume={57}, ISSN={1460-2091 0305-7453}, url={http://dx.doi.org/10.1093/jac/dki439}, DOI={10.1093/jac/dki439}, abstractNote={In the United States, Salmonella enterica serotype Niakhar is infrequently isolated. Between 1997 and 2000, the animal arm of the National Antimicrobial Resistance Monitoring System-Enteric Bacteria (NARMS) assayed a total of 22,383 Salmonella isolates from various animal sources (swine, cattle, chickens, turkeys, cats, horses, exotics and dogs) for antimicrobial susceptibility. Isolates originated from diagnostic and non-diagnostic submissions.To study the phenotypic and genotypic characteristics of Salmonella Niakhar.Only five (0.02%) of the 22,383 isolates were identified as Salmonella Niakhar. Antimicrobial resistance testing indicated that three isolates were pan-susceptible, one isolate was resistant to ampicillin and one isolate was resistant to ampicillin, chloramphenicol, ciprofloxacin, kanamycin, nalidixic acid, streptomycin, sulfamethoxazole, tetracycline and trimethoprim/sulfamethoxazole. RAPD-PCR analysis, PFGE and ribotyping indicated that two pan-susceptible isolates were genetically similar, whereas the three remaining isolates were genetically different. The one Salmonella Niakhar isolate that was multiresistant harboured a class I integron, intI1 and two large plasmids.This study represents the first report of a ciprofloxacin-resistant Salmonella isolate from the animal arm of NARMS.}, number={2}, journal={Journal of Antimicrobial Chemotherapy}, publisher={Oxford University Press (OUP)}, author={Tankson, J. D. and Fedorka-Cray, P. J. and Jackson, C. R. and Headrick, M.}, year={2005}, month={Dec}, pages={190–198} }
 @article{cox_hofacre_bailey_buhr_wilson_hiett_richardson_musgrove_cosby_tankson_et al._2005, title={Presence of Campylobacter jejuni in Various Organs One Hour, One Day, and One Week Following Oral or Intracloacal Inoculations of Broiler Chicks}, volume={49}, ISSN={0005-2086 1938-4351}, url={http://dx.doi.org/10.1637/7234-070704r}, DOI={10.1637/7234-070704r}, abstractNote={Day-old broiler chicks (n=30) were obtained from a commercial hatchery and inoculated, either orally or intracloacally, with a characterized strain of Campylobacter jejuni. At 1 hr, 1 day, and 1 wk after inoculation, broilers (n = 5) from the orally and intracloacally inoculated groups along with control birds (n=4) were humanely killed by cervical dislocation. The broilers from the control and treatment groups were aseptically opened, and the thymus, spleen, liver/gallbladder, bursa of Fabricius, and ceca were aseptically removed and individually analyzed for C. jejuni. Overall, C. jejuni was isolated after oral inoculation from 13% (10/ 75), 17% (13/75), and 28% (14/50) of the 1-hr, 1-day, and 1-wk samples, respectively. Campylobacter jejuni was isolated from 10% (4/ 40), 8% (3/40), 10% (4/40), 25% (10/40), and 40% (16/40) of the thymus, spleen, liver/gallbladder, bursa of Fabricius, and ceca samples, respectively. Following the intracloacal route of inoculation, C. jejuni was recovered from 32% (24/75), 8% (6/75), and 16% (8/50) of the 1-hr, 1-day, and 1-wk samples, respectively. Campylobacter jejuni was isolated from 5% (2/40), 5% (2/40), 5% (2/40), 45% (18/40), and 40% (16/40) of the thymus, spleen, liver/gallbladder, bursa of Fabricius, and ceca samples, respectively, for all sampling periods. Campylobacter spp. were not recovered from sample sites examined from the control broilers from trial one, trial two, or trial three samples examined after 1 hr and 1 day. However, one control sample was positive from the 1-wk sampling from repetition three; therefore, those data were omitted. The rapid movement of Campylobacter to internal organs following both oral and intracloacal inoculation may be significant, particularly if it persists in these organs as reservoirs throughout the 65-wk life cycle of breeding birds.}, number={1}, journal={Avian Diseases}, publisher={American Association of Avian Pathologists (AAAP)}, author={Cox, N. A. and Hofacre, C. L. and Bailey, J. S. and Buhr, R. J. and Wilson, J. L. and Hiett, K. L. and Richardson, L. J. and Musgrove, M. T. and Cosby, D. E. and Tankson, J. D. and et al.}, year={2005}, month={Mar}, pages={155–158} }
 @article{blau_mccluskey_ladely_dargatz_fedorka-cray_ferris_headrick_2005, title={Salmonella in Dairy Operations in the United States: Prevalence and Antimicrobial Drug Susceptibility}, volume={68}, ISSN={0362-028X}, url={http://dx.doi.org/10.4315/0362-028x-68.4.696}, DOI={10.4315/0362-028x-68.4.696}, abstractNote={Salmonella serotypes are important foodborne pathogens of humans that can be acquired through consumption of contaminated meat and dairy products. Salmonella infection also can be a significant animal health issue. As part of a national study of U.S. dairy operations conducted between March and September 2002, fecal samples were collected from representative cows in 97 dairy herds in 21 states and were cultured to determine the prevalence of Salmonella shedding. Salmonella was recovered from the feces of at least one cow in 30.9% of the herds. Overall, 7.3% of fecal samples were culture positive for Salmonella. The three most frequently recovered serotypes were Salmonella Meleagridis (24.1%), Salmonella Montevideo (11.9%), and Salmonella Typhimurium (9.9%). The susceptibilities of Salmonella isolates recovered were determined using a panel of 16 antimicrobial drugs. Salmonella isolates recovered from dairy cows had relatively little resistance to these antimicrobial agents; 83.0% of the isolates were susceptible to all antimicrobials tested. This study provides updated information on the prevalence and susceptibility patterns of Salmonella in dairy herds and on cow and herd characteristics. These data contribute to our understanding of the ecology of Salmonella in the dairy farm environment.}, number={4}, journal={Journal of Food Protection}, publisher={International Association for Food Protection}, author={Blau, D. M. and McCluskey, B. J. and Ladely, S. R. and Dargatz, D. A. and Fedorka-Cray, P. J. and Ferris, K. E. and Headrick, M. L.}, year={2005}, month={Apr}, pages={696–702} }
 @article{kim_gray_harmon_jones_fedorka-cray_2005, title={Susceptibility of Escherichia coli from Growing Piglets Receiving Antimicrobial Feed Additives}, volume={2}, ISSN={1535-3141 1556-7125}, url={http://dx.doi.org/10.1089/fpd.2005.2.304}, DOI={10.1089/fpd.2005.2.304}, abstractNote={Concerns regarding an apparent association between the use of antimicrobial feed additives (AFAs) in food animal production and a concomitant increase in antimicrobial drug resistance among zoonotic enteropathogens have provided the impetus to propose cessation of their use. While AFAs have been used in food animal production for nearly 50 years, the future use of AFAs will require an understanding of the effects of different classes of antimicrobials on the antimicrobial resistance of commensal flora. The present study examines the effect of three AFAs (apramycin, carbadox, and chlortetracycline) on the antimicrobial susceptibility of Escherichia coli in growing piglets and on animal performance. Three replicate trials were conducted using growing piglets fed standard diets with and without antimicrobial feed additives (AFAs). Fecal samples were cultured selectively for E. coli at regular intervals from all piglets from birth to market and antimicrobial susceptibility testing of E. coli isolates was performed using a replica-plate screening method and a broth microdilution method. While resistance to tetracycline in E. coli varied widely by sample, group, and trial, a significant increase in the percentage of resistant isolates was observed in piglets receiving AFAs when compared to controls (p < 0.0001). Resistance to apramycin increased in E. coli from piglets fed apramycin when compared to controls (p < 0.0001). However, upon removal of apramycin, resistance in E. coli declined to baseline levels by day 75. Piglets receiving AFAs demonstrated improved feed efficiency during phase 4 (p < 0.001), and higher average daily gains in phases 3 and 4 (p < 0.0001). This study suggests that antimicrobial resistance to AFAs in E. coli is drug-dependent and that some antimicrobials may be suitable for continued use in feeds during specified growth periods without concern for persistence of resistant E. coli populations.}, number={4}, journal={Foodborne Pathogens and Disease}, publisher={Mary Ann Liebert Inc}, author={Kim, L.M. and Gray, Jeffery T. and Harmon, Barry G. and Jones, Richard D. and Fedorka-Cray, Paula J.}, year={2005}, month={Dec}, pages={304–316} }
 @article{mcdermott_bodeis_aarestrup_brown_traczewski_fedorka-cray_wallace_critchley_thornsberry_graff_et al._2004, title={Development of a Standardized Susceptibility Test for Campylobacter with Quality-Control Ranges for Ciprofloxacin, Doxycycline, Erythromycin, Gentamicin, and Meropenem}, volume={10}, ISSN={1076-6294 1931-8448}, url={http://dx.doi.org/10.1089/1076629041310064}, DOI={10.1089/1076629041310064}, abstractNote={A standardized agar dilution susceptibility testing method was developed for Campylobacter that consisted of testing on Mueller–Hinton medium supplemented with 5% defibrinated sheep blood in an atmosphere of 10% CO2, 5% O2, and 85% N2. Campylobacter jejuni ATCC 33560 was identified as a quality-control (QC) strain. Minimal inhibitory concentration (MIC) QC ranges were determined for two incubation time/temperature combinations: 36°C for 48 hr and 42°C for 24 hr. Quality-control ranges were determined for ciprofloxacin, doxycycline, erythromycin, gentamicin, and meropenem. For all antimicrobial agents tested at both temperatures, 95–100% of the QC MIC results fell within recommended QC ranges. Twenty-one Campylobacter clinical isolates, encompassing five species of Campylobacter (C. jejuni, C. coli, C. jejuni, subsp. doylei, C. fetus, and C. lari) were tested in conjunction with the C. jejuni QC strain. While C. jejuni and C. coli could be reliably tested under both test conditions, growth of C. jejuni subsp. doylei, C. fetus, and C. lari isolates was inconsistent when incubated at 42°C. Therefore, it is recommended that these species only be tested at 36°C.}, number={2}, journal={Microbial Drug Resistance}, publisher={Mary Ann Liebert Inc}, author={McDermott, P.F. and Bodeis, S.M. and Aarestrup, F.M. and Brown, S. and Traczewski, M. and Fedorka-Cray, P. and Wallace, M. and Critchley, I.A. and Thornsberry, C. and Graff, S. and et al.}, year={2004}, month={Jun}, pages={124–131} }
 @article{stabel_fedorka-cray_2004, title={Effect of 2-deoxy-d-glucose induced stress on Salmonella choleraesuis shedding and persistence in swine}, volume={76}, ISSN={0034-5288}, url={http://dx.doi.org/10.1016/j.rvsc.2003.11.005}, DOI={10.1016/j.rvsc.2003.11.005}, abstractNote={A glucose analog, 2-deoxy-d-glucose (2DG), previously shown in swine to induce many of the hallmark parameters of stress, was administered to Salmonella choleraesuis carrier-swine and the effects on Salmonella fecal shedding and tissue colonization were evaluated. Initially, pigs were divided into two groups, one that received 1×106 S. choleraesuis and one group that received saline. At 3 or 6 weeks post inoculation (PI), half of each group received an injection of 2DG and the other half received saline. Throughout the study, individual fecal samples were collected and quantitatively cultured for Salmonella, tonsil and nasal swabs were qualitatively cultured, clinical signs were monitored, temperatures were measured and whole blood collected. Pigs were necropsied 8–18 days after 2DG treatment. The experimental stress induced by 2DG was not sufficient to cause recrudescence of Salmonella fecal shedding even when tissues were culture positive for Salmonella. In addition, persistent shedding was not affected by 2DG administration. Although the complex set of parameters that constitute the stress phenomenon is still relatively unknown, it is now apparent that the stressful event(s) sufficient to trigger Salmonella recrudescence involves more than just increased blood glucose, increased cortisol, and inhibition of lymphocyte proliferation.}, number={3}, journal={Research in Veterinary Science}, publisher={Elsevier BV}, author={Stabel, T.J. and Fedorka-Cray, P.J.}, year={2004}, month={Jun}, pages={187–194} }
 @article{jackson_fedorka-cray_barrett_ladely_2004, title={Effects of Tylosin Use on Erythromycin Resistance in Enterococci Isolated from Swine}, volume={70}, ISSN={0099-2240}, url={http://dx.doi.org/10.1128/aem.70.7.4205-4210.2004}, DOI={10.1128/aem.70.7.4205-4210.2004}, abstractNote={The effect of tylosin on erythromycin-resistant enterococci was examined on three farms; farm A used tylosin for growth promotion, farm B used tylosin for treatment of disease, and farm C did not use tylosin for either growth promotion or disease treatment. A total of 1,187 enterococci were isolated from gestation, farrowing, suckling, nursery, and finishing swine from the farms. From a subset of those isolates (n = 662), 59% (124 out of 208), 28% (80 out of 281), and 2% (4 out of 170) were resistant to erythromycin (MIC >/= 8 microg/ml) from farms A, B, and C, respectively. PCR analysis and Southern blotting revealed that 95% (65 out of 68) of isolates chosen from all three farms for further study were positive for ermB, but all were negative for ermA and ermC. By using Southern blotting, ermB was localized to the chromosome in 56 of the isolates while 9 isolates from farms A and B contained ermB on two similar-sized plasmid bands (12 to 16 kb). Pulsed-field gel electrophoresis revealed that the isolates were genetically diverse and represented a heterogeneous population of enterococci. This study suggests that although there was resistance to a greater number of enterococcal isolates on a farm where tylosin was used as a growth promotant, resistant enterococci also existed on a farm where no antimicrobial agents were used.}, number={7}, journal={Applied and Environmental Microbiology}, publisher={American Society for Microbiology}, author={Jackson, C. R. and Fedorka-Cray, P. J. and Barrett, J. B. and Ladely, S. R.}, year={2004}, month={Jul}, pages={4205–4210} }
 @article{gray_hungerford_fedorka-cray_headrick_2004, title={Extended-Spectrum-Cephalosporin Resistance in Salmonella enterica Isolates of Animal Origin}, volume={48}, ISSN={0066-4804 1098-6596}, url={http://dx.doi.org/10.1128/aac.48.8.3179-3181.2004}, DOI={10.1128/aac.48.8.3179-3181.2004}, abstractNote={ABSTRACT A total of 112 out of 5,709 Salmonella enterica isolates from domestic animal species exhibited decreased susceptibilities to ceftiofur and ceftriaxone, and each possessed the bla CMY gene. Ten Salmonella serotypes were significantly more likely to include resistant isolates. Isolates from turkeys, horses, cats, and dogs were significantly more likely to include resistant isolates.}, number={8}, journal={Antimicrobial Agents and Chemotherapy}, publisher={American Society for Microbiology}, author={Gray, J. T. and Hungerford, L. L. and Fedorka-Cray, P. J. and Headrick, M. L.}, year={2004}, month={Jul}, pages={3179–3181} }
 @article{jackson_fedorka-cray_barrett_ladely_2004, title={Genetic Relatedness of High-Level Aminoglycoside-Resistant Enterococci Isolated from Poultry Carcasses}, volume={48}, ISSN={0005-2086 1938-4351}, url={http://dx.doi.org/10.1637/7071}, DOI={10.1637/7071}, abstractNote={Approximately 46% (75/162) or poultry enterococci collected between 1999 and 2000 exhibited high-level resistance to gentamicin (minimum inhibitory concentration [MIC] > or = 500 microg/ml), kanamycin (MIC > or = 500 microg/ml), or streptomycin (MIC > or = 1000 microg/ml). Forty-one percent of the isolates were resistant to kanamycin (n = 67), whereas 23% and 19% were resistant to genramicin (n = 37) and streptomycin (n = 31), respectively. The predominant species identified was Enterococcus faecium (n = 105), followed by Enterococcus faecalis (n = 40) and Enterococcus durans (n = 8). Using polymerase chain reaction, the isolates were examined for the presence of 10 aminoglycoside resistance genes [ant(6)-Ia, ant(9)-Ia, ant(4')-Ia, aph(3')-IIIa, aph(2")-Ib, aph(2")-Ic, aph(2")-Id, aac(6')-Ie-aph(2")-Ia, and aac(6')-Ii]. Five aminoglycoside resistance genes were detected, most frequently aac(6')-Ii and ant(6)-Ia from E. faecium. Seven E. faecalis isolates resistant to gentamicin, kanamycin, or streptomycin were negative for all genes tested, indicating that additional resistance genes may exist. Phylogenetic analysis revealed that the isolates were genetically different with little clonality. These data indicate that enterococci from poultry are diverse and contain potentially unidentified aminoglycoside resistance genes.}, number={1}, journal={Avian Diseases}, publisher={American Association of Avian Pathologists (AAAP)}, author={Jackson, Charlene R. and Fedorka-Cray, Paula J. and Barrett, John B. and Ladely, Scott R.}, year={2004}, month={Jan}, pages={100–107} }
 @article{jackson_fedorka cray_barrett_ladely_2004, title={High-level aminoglycoside resistant enterococci isolated from swine}, volume={133}, ISSN={0950-2688 1469-4409}, url={http://dx.doi.org/10.1017/s0950268804003395}, DOI={10.1017/s0950268804003395}, abstractNote={Approximately 42% (187/444) of swine enterococci collected between the years 1999 and 2000 exhibited high-level resistance to gentamicin (MIC > or =500 microg/ml), kanamycin (MIC > or =500 microg/ml), or streptomycin (MIC > or =1000 microg/ml). Eight aminoglycoside resistance genes were detected using PCR, most frequently ant(6)-Ia and aac(6')-Ii from Enterococcus faecium. Twenty-four per cent (45/187) of total high-level aminoglycoside-resistant isolates and 26% (4/15) of isolates resistant to high levels of all three antimicrobials were negative for all genes tested. These data suggest that enterococci isolated from swine contain diverse and possibly unidentified aminoglycoside resistance genes.}, number={2}, journal={Epidemiology and Infection}, publisher={Cambridge University Press (CUP)}, author={Jackson, C. R. and Fedorka Cray, P. J. and Barrett, J. B. and Ladely, S. R.}, year={2004}, month={Dec}, pages={367–371} }
 @article{davies_hurd_funk_fedorka-cray_jones_2004, title={The Role of Contaminated Feed in the Epidemiology and Control of Salmonella enterica in Pork Production}, volume={1}, ISSN={1535-3141 1556-7125}, url={http://dx.doi.org/10.1089/fpd.2004.1.202}, DOI={10.1089/fpd.2004.1.202}, abstractNote={Food animal producers have ethical obligations to reduce the risk of foodborne hazards in animals under their care. Contaminated feed is a recognized source of Salmonella infection of food animals and regulations to control Salmonella contamination of animal feed have existed in some countries for decades. The impact of reducing Salmonella contamination of animal feeds on the risk of human foodborne salmonellosis is difficult to assess, and is likely to vary among food animal industries. In the context of U.S. pork production, factors that may attenuate or negate the impact (on public health) of regulatory interventions to control Salmonella in commercial feed include widespread use of on-farm mixing of swine feed; incomplete decontamination of feed during processing; post-processing contamination of feed at feed mills or in transportation or on-farm storage; the multitude of nonfeed sources of Salmonella infection; an apparently high risk of post-farm infection in lairage; and post-harvest sources of contamination. A structured survey of the extent of Salmonella contamination of animal feed in the United States is necessary to enable more informed debate on the feasibility and likely efficacy of enforcing a Salmonella-negative standard for animal feeds to reduce the incidence of human salmonellosis.}, number={4}, journal={Foodborne Pathogens and Disease}, publisher={Mary Ann Liebert Inc}, author={Davies, Peter R. and Hurd, H. Scott and Funk, Julie A. and Fedorka-Cray, Paula J. and Jones, Frank T.}, year={2004}, month={Dec}, pages={202–215} }
 @article{jackson_fedorka-cray_barrett_2004, title={Use of a Genus- and Species-Specific Multiplex PCR for Identification of Enterococci}, volume={42}, ISSN={0095-1137}, url={http://dx.doi.org/10.1128/jcm.42.8.3558-3565.2004}, DOI={10.1128/jcm.42.8.3558-3565.2004}, abstractNote={ABSTRACT The 16S rRNA gene has previously been used to develop genus-specific PCR primers for identification of enterococci. In addition, the superoxide dismutase gene ( sodA ) has been identified as a potential target for species differentiation of enterococci. In this study, Enterococcus genus-specific primers developed by Deasy et al. (E1/E2) were incorporated with species-specific primers based upon the superoxide dismutase ( sodA ) gene for development of a multiplex PCR. This assay provides simultaneous genus and species identification of 23 species of enterococci using seven different reaction mixtures. Accuracy of identification of the multiplex PCR was determined by comparisons to standard biochemical testing, the BBL Crystal kit, VITEK, and API Rapid ID 32 Strep. Isolates from swine feces, poultry carcasses, environmental sources, and retail food were evaluated and, overall, results for 90% of the isolates tested by PCR agreed with results obtained using standard biochemical testing and VITEK. Eighty-five percent and 82% of PCR results agreed with results from the API Rapid ID 32 Strep and BBL Crystal tests, respectively. With the exception of concurrence between identification using standard biochemical testing and VITEK (85%) and between BBL Crystal and VITEK (83%), the percent agreement for PCR was higher than or equal to any other pairwise comparison. Multiplex PCR for genus and species determination of enterococci provides an improved, rapid method for identification of this group of bacteria.}, number={8}, journal={Journal of Clinical Microbiology}, publisher={American Society for Microbiology}, author={Jackson, C. R. and Fedorka-Cray, P. J. and Barrett, J. B.}, year={2004}, month={Aug}, pages={3558–3565} }
 @article{hudson_fedorka-cray_jackson-hall_hiott_2003, title={Anomalies in species identification of enterococci from veterinary sources using a commercial biochemical identification system}, volume={36}, ISSN={0266-8254}, url={http://dx.doi.org/10.1046/j.1472-765x.2003.01302.x}, DOI={10.1046/j.1472-765x.2003.01302.x}, abstractNote={A commercial biochemical panel ID kit was used to identify presumptive enterococci isolates of veterinary or agricultural origin obtained during different steps of culture.Fifty isolates identified as enterococci using a genus PCR assay were tested for genus and species identification using the BBL Crystal Identification Gram-Positive ID kit (Becton Dickinson, Sparks, MD, USA). Following sub-culture of the isolates three times, 59% agreement with the original panel ID was obtained. After four and six sub-cultures, percentage agreement increased to 61 and 64%, respectively. Nineteen of the 50 cultures were identified as both Enterococcus faecalis and E. faecium.As a result of the variability between speciation of isolates following re-culture, additional methods for speciation are warranted.This study suggests that the identification of the genus and species of non-human enterococcal isolates can vary greatly during successive passages when using this kit.}, number={4}, journal={Letters in Applied Microbiology}, publisher={Wiley}, author={Hudson, C.R. and Fedorka-Cray, P.J. and Jackson-Hall, M.C. and Hiott, L.M.}, year={2003}, month={Mar}, pages={245–250} }
 @article{byrne_erol_call_kaspar_buege_hiemke_fedorka-cray_benson_wallace_luchansky_2003, title={Characterization of Escherichia coli O157:H7 from Downer and Healthy Dairy Cattle in the Upper Midwest Region of the United States}, volume={69}, ISSN={0099-2240}, url={http://dx.doi.org/10.1128/aem.69.8.4683-4688.2003}, DOI={10.1128/aem.69.8.4683-4688.2003}, abstractNote={ABSTRACT While cattle in general have been identified as a reservoir of Escherichia coli O157:H7, there are limited data regarding the prevalence and clonality of this pathogen in downer dairy cattle and the potential impact to human health that may occur following consumption of meat derived from downer dairy cattle. In the present study, conducted at two slaughter facilities in Wisconsin between May and October of 2001, we established a higher prevalence of E. coli O157:H7 in fecal and/or tissue samples obtained aseptically from intact colons of downer dairy cattle (10 of 203, 4.9%) than in those from healthy dairy cattle (3 of 201, 1.5%). Analyses of 57 isolates, representing these 13 positive samples (one to five isolates per sample), by pulsed-field gel electrophoresis, revealed 13 distinct Xba I restriction endonuclease digestion profiles (REDP). Typically, isolates from different animals displayed distinct REDP and isolates from the same fecal or colon sample displayed indistinguishable REDP. However, in one sample, two different, but highly related, REDP were displayed by the isolates recovered. Antimicrobial susceptibility testing indicated that 10 of the 57 isolates, recovered from 2 (1 downer and 1 healthy animal) of the 13 positive samples, were resistant to at least 1 of 18 antimicrobials tested. However, there was no appreciable difference in the frequency of resistance of isolates recovered from downer and healthy dairy cattle, and not all isolates with the same REDP displayed the same antimicrobial susceptibility profile. Lastly, it was not possible to distinguish between isolates recovered from downer and healthy cattle based on their Xba I REDP or antimicrobial susceptibility. These results indicate that downer cattle had a 3.3-fold-higher prevalence of E. coli O157:H7 than healthy cattle within the time frame and geographic scope of this study.}, number={8}, journal={Applied and Environmental Microbiology}, publisher={American Society for Microbiology}, author={Byrne, C. M. and Erol, I. and Call, J. E. and Kaspar, C. W. and Buege, D. R. and Hiemke, C. J. and Fedorka-Cray, P. J. and Benson, A. K. and Wallace, F. M. and Luchansky, J. B.}, year={2003}, month={Aug}, pages={4683–4688} }
 @article{genovese_anderson_harvey_callaway_poole_edrington_fedorka cray_nisbet_2003, title={Competitive Exclusion of Salmonella from the Gut of Neonatal and Weaned Pigs}, volume={66}, ISSN={0362-028X}, url={http://dx.doi.org/10.4315/0362-028x-66.8.1353}, DOI={10.4315/0362-028x-66.8.1353}, abstractNote={Our laboratory has developed a bacterial competitive-exclusion (CE) culture against enteropathogens (which are considered human foodborne pathogens) for use in swine. In this article, we document the effects of this CE culture, PCF1, on cecal colonization by and fecal shedding of Salmonella Choleraesuis in neonatal and weaned pigs and its effects on the horizontal transmission of this pathogen between weaned penmates. Piglets treated with the PCF1 culture twice within their first day of life and challenged with Salmonella 48 h after birth shed Salmonella at a significantly (P < 0.05) lower rate than did control pigs in experiment 1. Significant reductions of the pathogen were also observed in the cecum, the cecal contents, the ileocolic junction, and the colon contents (P < 0.05). In experiment 2, culture of the cecal contents and lymph nodes revealed a significant reduction in Salmonella isolated from PCF1-treated pigs (P < 0.05). Pigs in experiment 3 were treated as pigs in experiments 1 and 2 were: however, they were followed through day 10 postweaning. Significant reductions in shedding were noted for treated groups both pre- and postweaning (P < 0.05). Experiments 4 and 5 assessed the effects of PCF1 treatment on the horizontal transmission of Salmonella between littermates that were followed through day 14 postweaning. In these experiments, litters were divided into untreated contacts (UC), untreated seeders (US), treated contacts (TC), and treated seeders (TS). Overall, TC in experiment 4 shed Salmonella at a significantly lower rate than UC and US did (P < 0.05). In experiment 5, the transmission of Salmonella was significantly reduced for litters in which TS or TC were present, as evidenced by reduced shedding of Salmonella by both treated and untreated animals within these litters (P < 0.05). TS shed less often than US did, resulting in reduced levels of Salmonella shedding by both treated and untreated contacts (P < 0.05). Litters containing both TC and UC or both TC and US also shed Salmonella at lower rates than did litters in which only UC and US were present (P < 0.05).}, number={8}, journal={Journal of Food Protection}, publisher={International Association for Food Protection}, author={Genovese, K. J. and Anderson, R. C. and Harvey, R. B. and Callaway, T. R. and Poole, T. L. and Edrington, T. S. and Fedorka Cray, P. J. and Nisbet, D. J.}, year={2003}, month={Aug}, pages={1353–1359} }
 @inbook{englen_ladely_fedorka-cray_2003, title={Isolation of Campylobacter and Identification by PCR}, ISBN={1592593445}, url={http://dx.doi.org/10.1385/1-59259-344-5:109}, DOI={10.1385/1-59259-344-5:109}, abstractNote={Campylobacter is now recognized worldwide as a leading cause of bacterial gastroenteritis in humans (). Campylobacter species are common commensals in the intestinal tracts of poultry and livestock, and food products of animal origin are frequently associated with reported cases of illness (). This chapter provides methods for the identification of C. jejuni and C. coli, which are the two species accounting for the majority of human infections. The protocols are routinely used in our laboratory and are intended to provide workers unfamiliar with Campylobacter culture and identification a useful set of methods to serve as a practical starting point.}, booktitle={PCR Detection of Microbial Pathogens}, publisher={Humana Press}, author={Englen, Mark D. and Ladely, Scott R. and Fedorka-Cray, Paula J.}, year={2003}, month={Nov}, pages={109–122} }
 @article{feder_wallace_gray_fratamico_fedorka-cray_pearce_call_perrine_luchansky_2003, title={Isolation of Escherichia coli O157:H7 from Intact Colon Fecal Samples of Swine}, volume={9}, ISSN={1080-6040 1080-6059}, url={http://dx.doi.org/10.3201/eid0903.020350}, DOI={10.3201/eid0903.020350}, abstractNote={Escherichia coli O157:H7 was recovered from colon fecal samples of pigs. Polymerase chain reaction confirmed two genotypes: isolates harboring the eaeA, stx(1), and stx(2) genes and isolates harboring the eaeA, stx(1), and hly(933) genes. We demonstrate that swine in the United States can harbor potentially pathogenic E. coli O157:H7.}, number={3}, journal={Emerging Infectious Diseases}, publisher={Centers for Disease Control and Prevention (CDC)}, author={Feder, Ingrid and Wallace, F. Morgan and Gray, Jeffrey T. and Fratamico, Pina and Fedorka-Cray, Paula J. and Pearce, Rachel A. and Call, Jeffrey E. and Perrine, Richard and Luchansky, John B.}, year={2003}, month={Mar}, pages={380–383} }
 @article{dargatz_fedorka-cray_ladely_kopral_ferris_headrick_2003, title={Prevalence and antimicrobial susceptibility of Salmonella spp. isolates from US cattle in feedlots in 1999 and 2000}, volume={95}, ISSN={1364-5072 1365-2672}, url={http://dx.doi.org/10.1046/j.1365-2672.2003.02034.x}, DOI={10.1046/j.1365-2672.2003.02034.x}, abstractNote={Faecal samples from cattle in US feedlots were evaluated for the presence of Salmonella. When Salmonella isolates were recovered the antimicrobial resistance patterns were determined.Faecal samples were collected from pen floors in 73 feedlots in 12 states during the period from October 1999 to September 2000. Pens of cattle selected for sampling were those that had been in the feedlot for the shortest period of time, the longest period of time and a randomly selected pen from the remaining pens. Faecal samples were cultured for Salmonella spp. and all Salmonella isolates were categorized by serotype. The susceptibilities of all isolates were determined using a panel of 17 antimicrobials. Overall, 6.3% (654/10,417) of the samples cultured positive for Salmonella spp. and 22.2% (94/422) of pens and 50.7% (37/73) of feedlots had one or more positive samples. There was little difference in the proportion of positive samples from short-fed (6.1%, 212/3482), random (6.4%, 217/3400) and long-fed (6.4%, 224/3485) pens of cattle. One of two pens of cattle that could not be attributed to a pen type had a single positive sample (2.0%, 1/50). Samples collected during the period of April to June (6.8%, 209/3054) and July to September (11.4%, 286/2500) were more likely to be positive than those collected during October to December (4.0%, 73/1838) and January to March (2.8%, 86/3025). The most common serotypes of Salmonella were dissimilar from those that are typically seen in human illness and cattle illness. The majority of isolates (62.8%, 441/702) were sensitive to all of the antimicrobials tested. Resistance was most frequently observed to tetracycline (35.9%, 252/702) followed by streptomycin (11.1%, 78/702), ampicillin (10.4%, 73/702) and chloramphenicol (10.4%, 73/702). Multiple resistance (resistance to > or =2 antimicrobials) was observed for 11.7% (82/702) of the isolates.Salmonella was isolated at low frequency from faeces of feedlot cattle and the serotypes were not those commonly associated with human illness. In addition most of the Salmonella isolates were sensitive to all the antimicrobials tested.This study contributes to understanding the ecology of Salmonella in cattle feedlots and the prevalence of resistance among potential food-borne pathogens.}, number={4}, journal={Journal of Applied Microbiology}, publisher={Wiley}, author={Dargatz, D.A. and Fedorka-Cray, P.J. and Ladely, S.R. and Kopral, C.A. and Ferris, K.E. and Headrick, M.L.}, year={2003}, month={Oct}, pages={753–761} }
 @article{zaidi_zamora_diaz_tollefson_fedorka-cray_headrick_2003, title={Risk Factors for Fecal Quinolone-Resistant Escherichia coli in Mexican Children}, volume={47}, ISSN={0066-4804 1098-6596}, url={http://dx.doi.org/10.1128/aac.47.6.1999-2001.2003}, DOI={10.1128/aac.47.6.1999-2001.2003}, abstractNote={ABSTRACT We determined the prevalence of, and risk factors for, fecal quinolone-resistant Escherichia coli (QREC) in 324 children from Yucatan, Mexico. QREC was higher in children with recent Salmonella infection (100%) than in children with diarrhea (61%) or healthy children (54%) ( P = 0.007). Multivariate analysis identified recent hospitalization of a family member ( P = 0.011, odds ratio [OR] = 5.1) and carriage of Salmonella ( P = 0.004, OR = 3.7) as independent risk factors for QREC.}, number={6}, journal={Antimicrobial Agents and Chemotherapy}, publisher={American Society for Microbiology}, author={Zaidi, M. B. and Zamora, E. and Diaz, P. and Tollefson, L. and Fedorka-Cray, P. J. and Headrick, M. L.}, year={2003}, month={Jun}, pages={1999–2001} }
 @article{garber_smeltzer_fedorka-cray_ladely_ferris_2003, title={Salmonella enterica serotype Enteritidis in table egg layer house environments and in mice in U.S. layer houses and associated risk factors}, volume={47}, number={1}, journal={Avian Diseases}, author={Garber, L. and Smeltzer, M. and Fedorka-Cray, P. and Ladely, S. and Ferris, K.}, year={2003}, pages={134–142} }
 @article{althouse_patterson_fedorka-cray_isaacson_2003, title={Type 1 Fimbriae of Salmonella enterica Serovar Typhimurium Bind to Enterocytes and Contribute to Colonization of Swine In Vivo}, volume={71}, ISSN={0019-9567}, url={http://dx.doi.org/10.1128/iai.71.11.6446-6452.2003}, DOI={10.1128/iai.71.11.6446-6452.2003}, abstractNote={ABSTRACT Salmonella enterica serovar Typhimurium strain 798 is a clinical isolate from a pig and is known to be able to cause persistent, asymptomatic infections. This strain also is known to exist in two phenotypes (adhesive and nonadhesive to enterocytes) and can switch between the two phenotypes at a rate consistent with phase variation. Cells in the adhesive phenotype are more readily phagocytosed by leukocytes than nonadhesive cells. Once in a leukocyte, adhesive-phase cells survive while nonadhesive-phase cells die. In the present study, nonadhesive mutants were obtained with the transposon Tn phoA . A nonadhesive mutant was selected for study and was shown by electron microscopy not to produce fimbriae. The gene encoding the adhesin was cloned and sequenced. Based on its sequence, the adhesin was shown to be FimA, the major subunit of type 1 fimbriae. The nonadhesive mutant was attenuated in its ability to colonize both mouse and pig intestines, but remained capable of systemic spread in mice. The nonadhesive mutant was phagocytosed to the same extent as parental cells in the adhesive phase and then survived intracellularly. These results demonstrated that type 1 fimbriae were important for attachment to enterocytes and promoted intestinal colonization. However, they were not important in promoting phagocytosis or intracellular survival.}, number={11}, journal={Infection and Immunity}, publisher={American Society for Microbiology}, author={Althouse, C. and Patterson, S. and Fedorka-Cray, P. and Isaacson, R. E.}, year={2003}, month={Oct}, pages={6446–6452} }
 @article{mcewen_fedorka‐cray_2002, title={Antimicrobial Use and Resistance in Animals}, volume={34}, ISSN={1058-4838 1537-6591}, url={http://dx.doi.org/10.1086/340246}, DOI={10.1086/340246}, abstractNote={Food animals in the United States are often exposed to antimicrobials to treat and prevent infectious disease or to promote growth. Many of these antimicrobials are identical to or closely resemble drugs used in humans. Precise figures for the quantity of antimicrobials used in animals are not publicly available in the United States, and estimates vary widely. Antimicrobial resistance has emerged in zoonotic enteropathogens (e.g., Salmonella spp., Campylobacter spp.), commensal bacteria (e.g., Escherichia coli, enterococci), and bacterial pathogens of animals (e.g., Pasteurella, Actinobacillus spp.), but the prevalence of resistance varies. Antimicrobial resistance emerges from the use of antimicrobials in animals and the subsequent transfer of resistance genes and bacteria among animals and animal products and the environment. To slow the development of resistance, some countries have restricted antimicrobial use in feed, and some groups advocate similar measures in the United States. Alternatives to growth-promoting and prophylactic uses of antimicrobials in agriculture include improved management practices, wider use of vaccines, and introduction of probiotics. Monitoring programs, prudent use guidelines, and educational campaigns provide approaches to minimize the further development of antimicrobial resistance.}, number={s3}, journal={Clinical Infectious Diseases}, publisher={Oxford University Press (OUP)}, author={McEwen, Scott A. and Fedorka‐Cray, Paula J.}, year={2002}, month={Jun}, pages={S93–S106} }
 @article{dargatz_fedorka-cray_ladely_ferris_green_headrick_2002, title={Antimicrobial susceptibility patterns of Salmonella isolates from cattle in feedlots}, volume={221}, ISSN={0003-1488}, url={http://dx.doi.org/10.2460/javma.2002.221.268}, DOI={10.2460/javma.2002.221.268}, abstractNote={Abstract Objective —To evaluate the antimicrobial susceptibility patterns of Salmonella isolates from feedlot cattle. Design —Cross-sectional study. Sample Population —263 Salmonella isolates. Procedures —Fecal samples were collected from the floor of 2 pens in each of 100 feedlots. Two hundred eighty Salmonella isolates were recovered after bacteriologic culture from 38 pens. Of these, 263 isolates were available for antimicrobial susceptibility testing to 16 antimicrobials, using microbroth dilution breakpoint plates. Results —Less than 5% of isolates were resistant to any of the antimicrobials tested, with the exception of sulfamethoxazole (15; 5.7%) and tetracycline (61; 23.2%). Most isolates (197; 74.9%) were susceptible to all antimicrobials tested, whereas 18 (6.8%) were resistant to 2 or more antimicrobials. The percentage of isolates with resistance to any antimicrobial varied by serotype. The percentage of isolates resistant to various antimicrobials was not related to concurrent use of antimicrobials in the feed. Conclusions and Clinical Relevance —With the exception of tetracycline and sulfamethoxazole, resistance of Salmonella isolates to any of the antimicrobials was uncommon. Most isolates were susceptible to all antimicrobials tested. Antimicrobial resistance was not related to the presence of antimicrobials in the ration being fed at the time of sample collection. ( J Am Vet Med Assoc 2002;221:268–272)}, number={2}, journal={Journal of the American Veterinary Medical Association}, publisher={American Veterinary Medical Association (AVMA)}, author={Dargatz, David A. and Fedorka-Cray, Paula J. and Ladely, Scott R. and Ferris, Kathleen E. and Green, Alice L. and Headrick, Marcia L.}, year={2002}, month={Jul}, pages={268–272} }
 @article{englen_fedorka-cray_2002, title={Evaluation of a commercial diagnostic PCR for the identification of Campylobacter jejuni and Campylobacter coli}, volume={35}, ISSN={0266-8254 1365-2673}, url={http://dx.doi.org/10.1046/j.1472-765x.2002.01193.x}, DOI={10.1046/j.1472-765x.2002.01193.x}, abstractNote={Journal Article Evaluation of a commercial diagnostic PCR for the identification of Campylobacter jejuni and Campylobacter coli Get access M.D. Englen, M.D. Englen Antimicrobial Resistance Research Unit, USDA, Agricultural Research Service, Richard B. Russell Agricultural Research Center, Athens, GA, USA Correspondence to: M.D. Englen, Antimicrobial Resistance Research Unit, US Department of Agriculture, Agricultural Research Service, Richard B. Russell Agricultural Research Center, Box 5677, 950 College Station Road, Athens, GA 30604–5677, USA (e‐mail: menglen@saa.ars.usda.gov). Search for other works by this author on: Oxford Academic Google Scholar P.J. Fedorka‐Cray P.J. Fedorka‐Cray Antimicrobial Resistance Research Unit, USDA, Agricultural Research Service, Richard B. Russell Agricultural Research Center, Athens, GA, USA Search for other works by this author on: Oxford Academic Google Scholar Letters in Applied Microbiology, Volume 35, Issue 4, 1 October 2002, Pages 353–356, https://doi.org/10.1046/j.1472-765X.2002.01193.x Published: 01 October 2002 Article history Received: 23 April 2002 Revision received: 05 June 2002 Accepted: 26 June 2002 Published: 01 October 2002}, number={4}, journal={Letters in Applied Microbiology}, publisher={Wiley}, author={Englen, M.D. and Fedorka-Cray, P.J.}, year={2002}, month={Oct}, pages={353–356} }
 @article{losinger_traub-dargatz_garber_fedorka-cray_ladely_ferris_morgan_2002, title={Factors associated with fecal-shedding of Salmonella spp by horses on US operations}, volume={54}, ISSN={0102-0935}, url={http://dx.doi.org/10.1590/s0102-09352002000200001}, DOI={10.1590/s0102-09352002000200001}, abstractNote={In a cross-sectional national study that included 972 operations with > 3 horses on 1/1/98 in 28 states in the USA, 8,417 fecal specimens were collected from horses and cultured to test for the presence of Salmonella spp. Operations were characterized as Salmonella spp-positive if at least one fecal specimen tested positive for Salmonella spp. Percentages of Salmonella spp-positive operations were computed by management and other factors (collected from operation-level questionnaires) that were hypothesized to be related to fecal shedding of Salmonella spp. A logistic-regression model was constructed to identify factors associated with horses’ shedding Salmonella spp in feces on an operation. The odds of an operation being Salmonella spp positive increased as the number of resident horses increased. In addition, the following factors were found to be associated with increased odds of an operation being Salmonella spp positive: horses were used primarily for breeding; operation cleanliness was characterized as poor by the data collector; and new resident equids had been added to the operation without routine quarantine.}, number={2}, journal={Arquivo Brasileiro de Medicina Veterinária e Zootecnia}, publisher={FapUNIFESP (SciELO)}, author={Losinger, W.C. and Traub-Dargatz, J.L. and Garber, L.P. and Fedorka-Cray, P.J. and Ladely, S. and Ferris, K.E. and Morgan, K.}, year={2002}, month={Apr}, pages={109–116} }
 @article{hiett_stern_fedorka-cray_cox_musgrove_ladely_2002, title={Molecular Subtype Analyses of Campylobacter spp. from Arkansas and California Poultry Operations}, volume={68}, ISSN={0099-2240}, url={http://dx.doi.org/10.1128/aem.68.12.6220-6236.2002}, DOI={10.1128/aem.68.12.6220-6236.2002}, abstractNote={ABSTRACT Campylobacter isolates from diverse samples within broiler production and processing environments were typed by using flaA short variable region DNA sequence analysis. Sixteen flocks from four different farms representing two broiler producers in Arkansas and California were analyzed. Fourteen of the flocks (87.5%) were Campylobacter -positive; two remained negative throughout the 6-week rearing period. In general, multiple clones were present within a flock. Additionally, clones found within a flock were also present on the final product, although the diversity of Campylobacter spp. on the final product appeared to be reduced relative to that observed within the flock. Comparison of clones between flocks on the same farm revealed that some clones of Campylobacter persisted in multiple flocks. Furthermore, some clones were identified across the two farms that were under the same management. In two sampling periods, environmental isolates were positive for Campylobacter prior to flock shedding. Environmental samples associated with five additional flocks were positive for Campylobacter concomitantly with recovery of Campylobacter from the birds. Analysis of the environmental isolates that were positive prior to flock shedding demonstrated that in some instances the environmental isolates possessed genotypes identical to those of isolates originating from the flock, while in other cases the environmental isolates possessed genotypes that were distantly related to isolates obtained from the flock. Analyses of environmental isolates that tested positive concurrently with the positive isolates from the flocks demonstrated varied results; in some instances the environmental isolates possessed genotypes identical to those of isolates originating from the flock, while in other cases the environmental isolates possessed genotypes that were distantly related to isolates obtained from the flock. These data suggest that the external environment may contribute to Campylobacter contamination during poultry production and processing. However, environmental contamination with Campylobacter does not appear to be the sole contributing factor.}, number={12}, journal={Applied and Environmental Microbiology}, publisher={American Society for Microbiology}, author={Hiett, K. L and Stern, N. J. and Fedorka-Cray, P. and Cox, N. A. and Musgrove, M. T. and Ladely, S.}, year={2002}, month={Dec}, pages={6220–6236} }
 @article{stabel_fedorka-cray_gray_2002, title={Neutrophil phagocytosis following inoculation of Salmonella choleraesuis into swine}, volume={26}, ISSN={0165-7380}, url={http://dx.doi.org/10.1023/a:1014091517217}, DOI={10.1023/a:1014091517217}, number={2}, journal={Veterinary Research Communications}, publisher={Springer Nature}, author={Stabel, T.J. and Fedorka-Cray, P.J. and Gray, J.T.}, year={2002}, pages={103–109} }
 @article{zhao_doyle_fedorka cray_zhao_ladely_2002, title={Occurrence of Salmonella enterica Serotype Typhimurium DT104A in Retail Ground Beef}, volume={65}, ISSN={0362-028X}, url={http://dx.doi.org/10.4315/0362-028x-65.2.403}, DOI={10.4315/0362-028x-65.2.403}, abstractNote={Surveillance data of cattle and human isolates of Salmonella enterica serovar Typhimurium DT104 indicate that this pathogen emerged worldwide in the 1980s, particularly in cattle. Studies were conducted to determine the prevalence of Salmonella Typhimurium DT104 in ground beef. Samples were also tested for the presence of generic Escherichia coli. A total of 404 fresh ground beef samples obtained at retail stores from New York, San Francisco, Philadelphia, Denver, Atlanta, Houston, and Chicago were shipped overnight to Georgia for processing. Salmonella spp. were isolated from 14 (3.5%) samples. Eight different serotypes were identified among the isolates, including Salmonella Typhimurium (5), Salmonella Lille (3), Salmonella Montevideo (1), Salmonella Hadar (1), Salmonella Meleagridis (1), Salmonella Cerro (1), Salmonella Kentucky (1), and Salmonella Muenster (1). Antibiotic resistance profiles indicated that all five Salmonella Typhimurium isolates were resistant to ampicillin, streptomycin, sulfamethoxazole, ticarcillin, and tetracycline but that they were sensitive to chloramphenicol. Phage typing revealed that all five Salmonella Typhimurium isolates were DT104A, a subtype of DT104. All five Salmonella Typhimurium DT104A isolates were obtained from ground beef sampled from retail outlets in San Francisco. Pulsed-field gel electrophoresis (PFGE) genomic DNA profiles of the five Salmonella Typhimurium DT104A isolates from ground beef were indistinguishable from those of four control Salmonella Typhimurium DT104 penta-resistant isolates from cattle that were used for comparison. A total of 102 generic E. coli isolates were obtained, only three of which were multiresistant to antibiotics. In addition, three E. coli isolates were recovered from samples that were positive for Salmonella Typhimurium DT104A. No correlation of antibiotic resistance profiles was observed between Salmonella Typhimurium DT104A and generic E. coli, as two of the three E. coli isolates were susceptible to all of the antibiotics tested, and the third isolate was resistant only to cephalothin. These data indicate that Salmonella Typhimurium DT104A can be isolated from retail ground beef, and because there was little overlap in antibiotic resistance patterns between Salmonella Typhimurium DT104A and E. coli isolates from the same ground beef samples, these limited data suggest that the transfer of antibiotic resistance genes among enteric bacteria in ground beef may not be common. This latter observation is further supported by the limited isolation of multiantibiotic-resistant E. coli from retail ground beef.}, number={2}, journal={Journal of Food Protection}, publisher={International Association for Food Protection}, author={Zhao, Tong and Doyle, Michael P. and Fedorka Cray, Paula J. and Zhao, Ping and Ladely, Scott}, year={2002}, month={Feb}, pages={403–407} }
 @article{cox_stern_musgrove_bailey_craven_cray_buhr_hiett_2002, title={Prevalence and Level of Campylobacter in Commercial Broiler Breeders (Parents) and Broilers}, volume={11}, ISSN={1056-6171 1537-0437}, url={http://dx.doi.org/10.1093/japr/11.2.187}, DOI={10.1093/japr/11.2.187}, abstractNote={Campylobacter is the leading cause of bacteria-induced diarrheal disease, and the major vehicle for transmitting this microorganism to humans is poultry. Recent research has shown that Campylobacter can pass from the breeder hen to her progeny through the fertile egg, which is now considered to be a significant source of entry into the broiler flocks. Because of the importance of the organism in parent flocks, this work was carried out to determine the prevalence and level of Campylobacter in the parents (breeders) and offspring (broilers) of commercially reared birds.}, number={2}, journal={The Journal of Applied Poultry Research}, publisher={Oxford University Press (OUP)}, author={Cox, N. A. and Stern, N. J. and Musgrove, M. T. and Bailey, J. S. and Craven, S. E. and Cray, P. F. and Buhr, R. J. and Hiett, K. L.}, year={2002}, month={Jun}, pages={187–190} }
 @article{fedorka-cray_englen_gray_hudson_headrick_2002, title={Programs for Monitoring Antimicrobial Resistance}, volume={13}, ISSN={1049-5398 1532-2378}, url={http://dx.doi.org/10.1081/abio-120005769}, DOI={10.1081/abio-120005769}, abstractNote={Use of antimicrobials has increased in both human and veterinary medicine and the emergence of resistance to antimicrobials has become a global problem. This is due, in part, to the widespread availability of antimicrobials and the efficacy they impart in control of certain infectious diseases. Antimicrobial resistance (AR) can diminish the effectiveness or render an antimicrobic ineffective as a therapeutic. Although use may result in bacteria (both food borne and commensal) that are resistant, the exact fate of these populations in terms of persistence and transmission has been difficult to determine. Use patterns in veterinary medicine (therapeutic vs. subtherapeutic use) and agriculture further complicates the picture. Additionally, while transmission of resistant bacteria from animals to humans occurs, it has been difficult to assess the extent to which this occurs and the impact transmission has on actually disseminating resistant populations among humans.}, number={1}, journal={Animal Biotechnology}, publisher={Informa UK Limited}, author={Fedorka-Cray, Paula J. and Englen, Mark D. and Gray, Jeffrey T. and Hudson, Charlene and Headrick, Marcia L.}, year={2002}, month={Jul}, pages={43–54} }
 @article{bailey_fedorka-cray_stern_craven_cox_cosby_2002, title={Serotyping and Ribotyping of Salmonella Using Restriction Enzyme PvuII}, volume={65}, ISSN={0362-028X}, url={http://dx.doi.org/10.4315/0362-028x-65.6.1005}, DOI={10.4315/0362-028x-65.6.1005}, abstractNote={The subtyping and identification of bacterial pathogens throughout food processing and production chains is useful to the new hazard analysis critical control point-based food safety plans. Traditional manual serotyping remains the primary means of subtyping Salmonella isolates. Molecular biology techniques, however, offer the promise of more rapid and sensitive subtyping of Salmonella. This study evaluates the potential of restriction enzyme PvuII, followed by probing with the rRNA operon from Escherichia coli, to generate serotype-specific DNA fingerprints. A total of 32 identified serotypes were found with an overall agreement in 208 of the 259 (80%) isolates tested between U.S. Department of Agriculture serotype identification and riboprint serotype identification. Many of the isolates that did not correlate were serotype identified as Salmonella Montevideo, which indicates that for this serotype, there are multiple ribotypes. When Salmonella Montevideo isolates were not included, the ribotype identification agreed with serotyping in 207 of the 231 (90%) isolates. The primary outcome of any ribotyping procedure is to give distinct ribotype patterns. This extensive poultry epidemiological study demonstrates that, in addition to ribotype patterns, the identification of isolates to known serotypes provides the investigator with additional information that can be more useful than traditional epidemiology and isolate identification studies.}, number={6}, journal={Journal of Food Protection}, publisher={International Association for Food Protection}, author={Bailey, J. S. and Fedorka-Cray, P. J. and Stern, N. J. and Craven, S. E. and Cox, N. A. and Cosby, D. E.}, year={2002}, month={Jun}, pages={1005–1007} }
 @article{fedorka cray_ladely_bailey_stern_2001, title={Colonization of Broiler Chicks by Salmonella Typhimurium Definitive Phage Type 104}, volume={64}, ISSN={0362-028X}, url={http://dx.doi.org/10.4315/0362-028x-64.11.1698}, DOI={10.4315/0362-028x-64.11.1698}, abstractNote={The prevalence of an antibiotic-resistant strain of Salmonella Typhimurium definitive phage type 104 (DT104) has increased dramatically in recent years resulting in increased morbidity and mortality in both animals and humans. Colonization and shedding of Salmonella Typhimurium DT104 was studied in broiler chickens in two trials. In trial 1, 180 day-of-hatch chicks (n = 60 per group, n = 30 per replicate) were challenged with 10(6) CFU DT104 (wild-type isolate from poultry) or were commingled with a seeder chick challenged with 10(6) CFU DT104. In trial 2, 360 day-of-hatch chicks (n = 120 per treatment, n = 30 per rep) were divided into three groups. Chicks in the susceptible group were commingled with two seeder chicks that were orally challenged with 10(7) CFU/bird of a pan-sensitive strain of Salmonella Typhimurium DT104. Chicks in the resistant group were commingled with two seeder chicks that were orally challenged with 10(7) CFU/bird DT104 used in trial 1. For both trials, a control group was not exposed to DT104, composite fecal samples were evaluated twice weekly for levels of Salmonella shedding and 20 chicks per group were necropsied weekly and their cecal contents were cultured. At hatch all groups were colonized with naturally occurring Salmonella Senftenberg and Salmonella Mbandaka (trial 1) or Salmonella Senftenberg and Salmonella Ohio (trial 2) prior to exposure to DT104. Throughout the study, the level of Salmonella spp. shedding in feces (trial 1 means 3.1, 2.9, and 3.0 log10 CFU per g feces for challenged, seeder, and control groups, respectively) or ceca (trial 2 means 2.9. 2.9. and 2.5 log10 CFU per g ceca for resistant, susceptible, and control groups, respectively) did not differ among groups. In trial 1, colonization of DT104 remained constant at higher levels in the challenged group (mean 87%, P < 0.01), increased over time in the seeder group (10 to 50%, P < 0.02) and was not recovered from the control chicks. Salmonella Mbandaka colonization remained steady within each group with challenge and seeder groups maintaining higher levels of colonization than the control group. Salmonella Senftenberg colonization levels tended to decline (P = .058) over time in the challenged group (20 to 0%) and significantly decreased (P < 0.01) over time for both the seeder (80 to 0%) and control chicks (85 to 10%). In trial 2, the percentage of chicks colonized with susceptible DT104 declined (r = 0.90, P < 0.05) over the course of the trial from 45 to 0%, while recovery of the resistant DT104 persisted at a mean percentage of 27%. DT104 was not recovered from the control chicks. Salmonella Ohio colonization levels tended to decline (r = 0.79, P > 0.05) over time in the control group (75 to 20%) and significantly decreased (P < 0.05) over time in both susceptible and resistant groups (40 to 10%, r = 0.82 and 55 to 5%, r = 0.85, respectively). Salmonella Senftenberg was recovered from the control group at low frequency throughout the trial and was not recovered from the other groups. For either trial, no apparent affect on morbidity or mortality was observed. Introduction of DT104 by commingling may induce colonization resulting in persistent high levels of shedding in flocks simultaneously with other Salmonella species.}, number={11}, journal={Journal of Food Protection}, publisher={International Association for Food Protection}, author={Fedorka Cray, Paula J. and Ladely, Scott R. and Bailey, J. Stan and Stern, Norman J.}, year={2001}, month={Nov}, pages={1698–1704} }
 @article{stern_fedorka cray_bailey_cox_craven_hiett_musgrove_ladely_cosby_mead_2001, title={Distribution of Campylobacter spp. in Selected U.S. Poultry Production and Processing Operations}, volume={64}, ISSN={0362-028X}, url={http://dx.doi.org/10.4315/0362-028x-64.11.1705}, DOI={10.4315/0362-028x-64.11.1705}, abstractNote={A study was conducted of 32 broiler flocks on eight different farms, belonging to four major U.S. producers. The farms were studied over I complete calendar year. Overall, 28 (87.5%) of the flocks became Campylobacter positive, and only four (12.5%) remained negative throughout the 6- to 8-week rearing period. In the majority of flocks, sampled every 2 weeks throughout production, Campylobacter-positive fecal and cecal samples were not detected until 4 to 8 weeks of age. In only six of the flocks were environmental samples found to be positive before shedding of Campylobacter was detected in the birds. Even in some of the Campylobacter-negative flocks, contamination of the rearing environment was positive for Campylobacter but did not result in the birds subsequently excreting the organism. These findings are discussed in relation to U.S. husbandry practices and present uncertainty about sources of Campylobacter infection for poultry flocks. Birds were often transported to the processing plant in coops that were already contaminated with Campylobacter, and the organisms were sometimes found in samples of scald water and chill water. After chilling, the proportions of Campylobacter-positive carcasses from different producers ranged from 21.0 to 40.9%, which is lower than in other studies, and possible reasons are considered.}, number={11}, journal={Journal of Food Protection}, publisher={International Association for Food Protection}, author={Stern, N. J. and Fedorka Cray, P. and Bailey, J. S. and Cox, N. A. and Craven, S. E. and Hiett, K. L. and Musgrove, M. T. and Ladely, S. and Cosby, D. and Mead, G. C.}, year={2001}, month={Nov}, pages={1705–1710} }
 @article{wells_fedorka cray_dargatz_ferris_green_2001, title={Fecal Shedding of Salmonella spp. by Dairy Cows on Farm and at Cull Cow Markets}, volume={64}, ISSN={0362-028X}, url={http://dx.doi.org/10.4315/0362-028x-64.1.3}, DOI={10.4315/0362-028x-64.1.3}, abstractNote={As part of a national study of the U.S. dairy cow population, fecal samples were collected from representative cows on 91 dairies and 97 cull dairy cow markets in 19 states. Salmonella spp. were recovered from 5.4% of milk cows, 18.1% of milk cows expected to be culled within 7 days, and 14.9% of culled dairy cows at markets. On a premise basis, Salmonella shedding in milk cows was detected on 21.1% of dairies and 66% of cull dairy cow markets. The percentage of herds with at least one cow with detectable Salmonella fecal shedding was higher during the sampling period from May through July, in herds with at least 100 milk cows, and in herds in the South region. The most common Salmonella serogroups isolated were E (30.8% of isolates) and C1 (28.6%); the most common serotypes isolated were Salmonella Montevideo (21.5% of isolates), Salmonella Cerro (13.3%), and Salmonella Kentucky (8.5%). Fecal shedding of Salmonella Typhimurium or Salmonella Typhimurium var. copenhagen was infrequent (2.8% of isolates). Most isolates (88.9%) were susceptible to all 17 antimicrobials evaluated; multiple resistance was an infrequent occurrence. This study provides information describing the distribution of Salmonella fecal shedding from dairy cows on farm and at markets and will serve as a baseline for future studies.}, number={1}, journal={Journal of Food Protection}, publisher={International Association for Food Protection}, author={Wells, S. J. and Fedorka Cray, P. J. and Dargatz, D. A. and Ferris, K. and Green, A.}, year={2001}, month={Jan}, pages={3–11} }
 @article{allen_fedorka-cray_vazquez-torres_suyemoto_altier_ryder_fang_libby_2001, title={In Vitro and In Vivo Assessment of Salmonella enterica Serovar Typhimurium DT104 Virulence}, volume={69}, ISSN={0019-9567}, url={http://dx.doi.org/10.1128/iai.69.7.4673-4677.2001}, DOI={10.1128/iai.69.7.4673-4677.2001}, abstractNote={Multidrug-resistant Salmonella enterica serovar Typhimurium phage type DT104 has become a widespread cause of human and other animal infection worldwide. The severity of clinical illness in S. enterica serovar Typhimurium DT104 outbreaks has led to the suggestion that this strain possesses enhanced virulence. In the present study, in vitro and in vivo virulence-associated phenotypes of several clinical isolates of S. enterica serovar Typhimurium DT104 were examined and compared to S. enterica serovar Typhimurium ATCC 14028s. The ability of these DT104 isolates to survive within murine peritoneal macrophages, invade cultured epithelial cells, resist antimicrobial actions of reactive oxygen and nitrogen compounds, and cause lethal infection in mice were assessed. Our results failed to demonstrate that S. enterica serovar Typhimurium DT104 isolates are more virulent than S. enterica serovar Typhimurium ATCC 14028s.}, number={7}, journal={Infection and Immunity}, publisher={American Society for Microbiology}, author={Allen, C. A. and Fedorka-Cray, P. J. and Vazquez-Torres, A. and Suyemoto, M. and Altier, C. and Ryder, L. R. and Fang, F. C. and Libby, S. J.}, year={2001}, month={Jul}, pages={4673–4677} }
 @article{gray_fedorka-cray_2001, title={Long term survival and infectivity of Salmonella choleraesuis}, volume={114}, number={9-10}, journal={Berliner und MunchenerTierarztlche Wochenschrift}, author={Gray, J.T. and Fedorka-Cray, P.J.}, year={2001}, pages={370–374} }
 @article{bailey_stern_fedorka cray_craven_cox_cosby_ladely_musgrove_2001, title={Sources and Movement of Salmonella through Integrated Poultry Operations: A Multistate Epidemiological Investigation}, volume={64}, ISSN={0362-028X}, url={http://dx.doi.org/10.4315/0362-028x-64.11.1690}, DOI={10.4315/0362-028x-64.11.1690}, abstractNote={The prevalence of Salmonella from numerous sources in 32 integrated broiler operations of high- and low-performing broiler houses was characterized from four states across four seasons. Previous studies of Salmonella in broilers have been limited in scope, offering only a snapshot of pathogen prevalence as seen on a small number of individual farms. Twenty-six different sample types were collected from the hatchery to the end of processing, and Salmonella was found in all sample types. A total of 10,740 samples were analyzed for Salmonella, and 973 (9.1%) of these samples, including 49 of 798 (6.1%) carcass rinse samples, were Salmonella positive. Hatchery transport pads (389 of 765, 50.8%), flies (28 of 150, 18.7%), drag swabs (57 of 402, 14.2%), and boot swabs (20 of 167, 12%) were samples from which Salmonella was most frequently isolated. Thirty-six different serotypes were identified, and the most frequently encountered serotypes were Salmonella Senftenberg, Salmonella Thompson, and Salmonella Montevideo. Determining critical contaminating sources and following the movement of Salmonella through integrated poultry operations will help researchers and the industry develop practical intervention strategies.}, number={11}, journal={Journal of Food Protection}, publisher={International Association for Food Protection}, author={Bailey, J. S. and Stern, N. J. and Fedorka Cray, P. and Craven, S. E. and Cox, N. A. and Cosby, D. E. and Ladely, S. and Musgrove, M. T.}, year={2001}, month={Nov}, pages={1690–1697} }
 @article{garcia-sierra_rozeboom_straw_thacker_granger_fedorka-cray_gray_2001, title={Studies on survival of pseudorabies virus, Actinobacillus pleuropneumoniae, and Salmonella serovar Choleraesuis in composted swine carcasses}, volume={9}, number={5}, journal={Journal of Swine Health and Production}, author={Garcia-Sierra, J. and Rozeboom, D.W. and Straw, B.E. and Thacker, B.J. and Granger, L.M. and Fedorka-Cray, P.J. and Gray, J.T.}, year={2001}, pages={225–231} }
 @inbook{fedorka‐cray_2001, place={London, UK}, title={Surveillance resistance in animals and man: current programmes and possibilities}, booktitle={Antimicrobial Resistance}, publisher={Royal Society of Medicine Press Limited}, author={Fedorka‐Cray, P.J.}, editor={Wilbur, R. and Soulsby, E. J. L.Editors}, year={2001}, pages={177–181} }
 @article{gray_fedorka cray_2001, title={Survival and Infectivity of Salmonella Choleraesuis in Swine Feces}, volume={64}, ISSN={0362-028X}, url={http://dx.doi.org/10.4315/0362-028x-64.7.945}, DOI={10.4315/0362-028x-64.7.945}, abstractNote={Many serotypes of Salmonella survive well in the environment. Conversely, it is believed that Salmonella Choleraesuis, the host-adapted serotype of swine, does not survive well outside the host. We examined the survival capability of Salmonella Choleraesuis in swine feces. Six pigs were infected with Salmonella Choleraesuis and feces were collected and pooled on days 2, 4, 7, and 10 postinoculation (PI). Feces were stored in a wet and a dry form, and survival was measured over 13 months. Salmonella Choleraesuis was recovered from wet feces through 3 months of storage. In a desiccated (dry) form, Salmonella Choleraesuis was recovered from at least 13 months. Salmonella Choleraesuis shed from swine prior to 4 days PI did not survive as well as that shed 4 days PI or later. We also examined the infectivity of Salmonella Choleraesuis resident in dry feces. Six- or 13-week-old pigs were inoculated with dry feces that had been stored either 2 months or 4 months, respectively. Pigs were inoculated either intranasally or by mixing dry feces with the swine ration. Although clinical signs were mild, Salmonella Choleraesuis was widely disseminated among the tissues of all the pigs inoculated. This study demonstrates that Salmonella Choleraesuis remains viable and infective in the environment. Therefore, contaminated fecal matter can serve as a reservoir for Salmonella Choleraesuis as well as other Salmonella spp. Control measures must consider this environmental reservoir as a source of new infections.}, number={7}, journal={Journal of Food Protection}, publisher={International Association for Food Protection}, author={Gray, Jeffrey T. and Fedorka Cray, Paula J.}, year={2001}, month={Jul}, pages={945–949} }
 @article{davies_turkson_funk_nichols_ladely_fedorka-cray_2000, title={Comparison of methods for isolating Salmonella bacteria from faeces of naturally infected pigs}, volume={89}, ISSN={1364-5072 1365-2672}, url={http://dx.doi.org/10.1046/j.1365-2672.2000.01101.x}, DOI={10.1046/j.1365-2672.2000.01101.x}, abstractNote={A series of experiments was conducted using faecal samples collected from commercial swine farms to evaluate the effects of variation in methods used for the detection of Salmonella bacteria. The primary objective of the studies was to compare the protocols routinely used in two laboratories in the USA. The studies included five experiments comparing the enrichment protocols used routinely in the respective laboratories (Method 1: 10 g faeces--buffered peptone water (BPW) pre-enrichment--selective enrichment in Rappaport/Vassiliadis (RV) broth; Method 2: approximately 1g faeces--primary enrichments in tetrathionate and Hajna GN broths--secondary enrichment in RV broth). The effects of enrichment temperatures (37 vs 42 degrees C) using RV broth (two experiments) and delayed secondary enrichment (four experiments) were also evaluated. Direct comparison of Method 1 and Method 2 indicated comparable results. However, when compared using faecal samples of equal weight, the Method 2 enrichment protocol was more sensitive for detecting Salmonella bacteria than the Method 1 protocol. Enrichment in RV at 42 degrees C was superior to 37 degrees C, particularly for samples that were pre-enriched in BPW. Delayed secondary enrichment increased detection of Salmonella bacteria in swine faeces. These results highlight the imperfect sensitivity of culture methods, and the need for researchers to consider the sensitivity of bacteriological methods in the design and interpretation of the results of epidemiologic studies based on faecal culture.}, number={1}, journal={Journal of Applied Microbiology}, publisher={Wiley}, author={Davies, P.R. and Turkson, P.K. and Funk, J.A. and Nichols, M.A. and Ladely, S.R. and Fedorka-Cray, P.J.}, year={2000}, month={Jul}, pages={169–177} }
 @article{craven_stern_line_bailey_cox_fedorka-cray_2000, title={Determination of the Incidence of Salmonella spp., Campylobacter jejuni, and Clostridium perfringens in Wild Birds near Broiler Chicken Houses by Sampling Intestinal Droppings}, volume={44}, ISSN={0005-2086}, url={http://dx.doi.org/10.2307/1593118}, DOI={10.2307/1593118}, abstractNote={Several methods were evaluated for collecting fecal and intestinal samples from wild birds found near broiler chicken houses. A few intestinal samples and cloacal swabs were obtained from European starlings and house sparrows. Most of the samples collected consisted of wild bird droppings found on or near the houses. Samples were collected from each of four farms of a broiler integrator during a grow-out cycle: a cycle in the summer for farm A, fall for farm B, and spring, summer, fall, and winter for farms C and D. Of the 25 wild bird intestinal and fecal samples collected from a broiler house on farm A during a grow-out cycle in July-August 1997, 24% were positive for Salmonella spp., 4% for Campylobacter jejuni, and 28% for Clostridium perfringens. Of the nine fecal samples collected from broiler house B in a grow-out cycle in September-November 1997, 33% were positive for Salmonella spp., 11% for C. jejuni, and 22% for C. perfringens. For farms C and D, of the 23 samples collected in March-April 1998, 0 were positive for Salmonella spp., 11% for C. jejuni, and 52% for C. perfringens; of 27 samples collected in June-July 1998, 4% were positive for Salmonella spp., 0 for C. jejuni, and 13% for C. perfringens; of 24 samples collected in August-October 1998, 14% were positive for Salmonella spp., 5% for C. jejuni, and 4% for C. perfringens; of 14 samples collected December 1998-January 1999, 0 were positive for Salmonella, 50% for C. jejuni, and 14% for C. perfringens. The incidence of these bacterial enteropathogens in wild birds near the broiler chicken houses suggests that wild birds that gain entry to poultry grow-out houses have the potential to transmit these pathogens to poultry.}, number={3}, journal={Avian Diseases}, publisher={JSTOR}, author={Craven, S. E. and Stern, N. J. and Line, E. and Bailey, J. S. and Cox, N. A. and Fedorka-Cray, P.}, year={2000}, month={Jul}, pages={715} }
 @article{traub-dargatz_garber_fedorka-cray_ladely_ferris_2000, title={Fecal shedding of Salmonella spp by horses in the United States during 1998 and 1999 and detection of Salmonella spp in grain and concentrate sources on equine operations}, volume={217}, ISSN={0003-1488}, url={http://dx.doi.org/10.2460/javma.2000.217.226}, DOI={10.2460/javma.2000.217.226}, abstractNote={To estimate prevalence of fecal shedding of Salmonella spp among horses in the US horse population and prevalence of Salmonella spp in grain or other concentrate used as horse feed on equine operations in the United States.Cross-sectional survey.Horses on 972 operations in 28 states.Fecal samples were collected from horses resident at each operation. Only a single sample was collected from any individual horse; number of horses from which samples were collected on each operation was determined on the basis of number of horses on the operation. A single sample of grain or concentrate was also collected from each operation. All samples were tested for Salmonella spp by means of bacterial culture.Overall, 0.8% (SE, 0.5) of resident horses shed Salmonella spp in their feces. The overall prevalence of operations positive for fecal shedding of Salmonella spp (i.e., operations with > or = 1 horse shedding Salmonella spp in its feces) was 1.8% (SE, 0.7). Prevalence of grain or other concentrate samples positive for Salmonella spp was 0.4%. Serotypes of Salmonella spp that were identified in grain or other concentrate were not those typically associated with clinical disease in horses.Results suggest that the national prevalence of fecal shedding of Salmonella spp by horses in the United States was 0.8%, and that prevalence of Salmonella spp in grain or other concentrate used for horse feed was 0.4%.}, number={2}, journal={Journal of the American Veterinary Medical Association}, publisher={American Veterinary Medical Association (AVMA)}, author={Traub-Dargatz, Josie L. and Garber, Lindsey P. and Fedorka-Cray, Paula J. and Ladely, Scott and Ferris, Kathy E.}, year={2000}, month={Jul}, pages={226–230} }
 @article{kabagambe_wells_garber_salman_wagner_fedorka-cray_2000, title={Risk factors for fecal shedding of Salmonella in 91 US dairy herds in 1996}, volume={43}, ISSN={0167-5877}, url={http://dx.doi.org/10.1016/s0167-5877(99)00094-x}, DOI={10.1016/s0167-5877(99)00094-x}, abstractNote={In 1996, data on management practices used on US dairy operations were collected and analyzed for association with fecal shedding of Salmonella by dairy cows. A total of 4299 fecal samples from 91 herds was cultured for Salmonella isolation. Herd-size (adjusted odds ratios (OR) = 5.8, 95% CI 1.1, 31.3), region (OR = 5.7, CI 1.4, 23.5), use of flush water systems (OR = 3.5, CI 0.9, 14.7), and feeding brewers' products to lactating cows (OR = 3.4, CI 0.9, 12.9) were identified as the most important predictive risk factors. The population attributable risks (PARs) for herd-size, region, flush water system, and feeding brewers' products to lactating cows were 0.76, 0.46, 0.37, and 0.42, respectively. The estimated PAR for all four risk factors combined was 0.95. The effects of these factors need to be more-closely evaluated in more-controlled studies, in order to develop intervention programs that reduce Salmonella shedding.}, number={3}, journal={Preventive Veterinary Medicine}, publisher={Elsevier BV}, author={Kabagambe, E.K. and Wells, S.J. and Garber, L.P. and Salman, M.D. and Wagner, B. and Fedorka-Cray, P.J.}, year={2000}, month={Feb}, pages={177–194} }
 @article{dargatz_fedorka cray_ladely_ferris_2000, title={Survey of Salmonella Serotypes Shed in Feces of Beef Cows and Their Antimicrobial Susceptibility Patterns}, volume={63}, ISSN={0362-028X}, url={http://dx.doi.org/10.4315/0362-028x-63.12.1648}, DOI={10.4315/0362-028x-63.12.1648}, abstractNote={Salmonella prevalence on cow-calf operations was studied as a part of a national study of health and management of the U.S. beef cow-calf industry and was conducted as part of the National Animal Health Monitoring System. Within this study, the prevalence of Salmonella spp. shed in feces was determined. A total of 5,049 fecal samples were collected from 187 beef cow-calf operations each visited on a single occasion. The number of fecal samples collected per operation was predetermined based on herd size. Salmonellae were recovered from 1 or more fecal samples collected on 11.2% (21 of 187) of the operations. Overall 78 salmonellae representing 22 serotypes were recovered from 1.4% (70 of 5,049) of samples. Multiple serotypes were recovered from eight samples from a single operation. The five most common serotypes were Salmonella Oranienburg (21.8% of isolates), and Salmonella Cerro (21.8%), followed by Salmonella Anatum (10.3%), Salmonella Bredeney (9.0%), and Salmonella Mbandaka (5.1%). The most common serogroups identified were C1 (33.3%), K (21.8%), B (16.7%), and E (15.4%). Even though the recovery rate of salmonellae from fecal samples was very low, 43.6% (34 of 78) and 38.5% (30 of 78) of the isolates were among the 10 most common serotypes from cattle with clinical signs of disease or isolated from humans, respectively. The majority of the isolates (50 of 78; 64.1%) were recovered from fecal samples from two operations. All isolates were screened for resistance to a panel of 17 antimicrobics, and 87.2% (68 of 78) were susceptible to all of the antimicrobics. The resistant isolates were most commonly resistant to streptomycin (n = 9) and/or sulfamethoxazole (n = 9). Nine isolates showed multiple (> or =2 antimicrobics) resistance most commonly to streptomycin and sulfamethoxazole (n = 6).}, number={12}, journal={Journal of Food Protection}, publisher={International Association for Food Protection}, author={Dargatz, D. A. and Fedorka Cray, P. J. and Ladely, S. R. and Ferris, K. E.}, year={2000}, month={Dec}, pages={1648–1653} }
 @article{wills_gray_fedorka-cray_yoon_ladely_zimmerman_2000, title={Synergism between porcine reproductive and respiratory syndrome virus (PRRSV) and Salmonella choleraesuis in swine}, volume={71}, ISSN={0378-1135}, url={http://dx.doi.org/10.1016/s0378-1135(99)00175-3}, DOI={10.1016/s0378-1135(99)00175-3}, abstractNote={Porcine reproductive and respiratory syndrome virus (PRRSV) and Salmonella choleraesuis are two leading causes of economic loss in the swine industry. While respiratory disease is common in both S. choleraesuis and PRRSV infections, the factors that contribute to its development remain largely undefined. We investigated the interaction of PRRSV, S. choleraesuis, and stress in 5-week-old swine. All combinations of three factors (inoculation with S. choleraesuis on Day 0, PRRSV on Day 3, and treatment with dexamethasone on Days 3–7) were used to produce eight treatment groups in two independent trials. Fecal samples, tonsil and nasal swabs, serum samples and postmortem tissues were collected for bacteriologic and virologic examinations. No clinical signs were observed in pigs inoculated with only PRRSV or only S. choleraesuis. In contrast, pigs which were dually infected with S. choleraesuis and PRRSV exhibited unthriftiness, rough hair coats, dyspnea, and diarrhea. The pigs which received all three treatment factors were the most severely affected and 43% (three of seven) of the animals in this group died. Individuals in this group shed significantly higher quantities of S. choleraesuis in feces and had significantly higher serum PRRSV titers compared to other treatments (p ≤ 0.05). In addition, S. choleraesuis and PRRSV were shed longer and by more pigs in this group than other groups and S. choleraesuis was recovered from more tissues in this group on Day 21 post inoculation. These results suggested that PRRSV, S. choleraesuis, and dexamethasone acted synergistically to produce a syndrome similar to that observed in the field.}, number={3-4}, journal={Veterinary Microbiology}, publisher={Elsevier BV}, author={Wills, Robert W. and Gray, Jeffery T. and Fedorka-Cray, Paula J. and Yoon, K.-J. and Ladely, Scott and Zimmerman, J.J.}, year={2000}, month={Feb}, pages={177–192} }
 @article{bolton_kelley_lee_fedorka-cray_maurer_1999, place={Bolton, L.F., Kelley, L.C., Lee, M.D}, title={Detection of multidrug-resistant Salmonella enterica serotype Typhimurium DT104 based on a gene which confers cross-resistance to florfenicol and chloramphenicol}, volume={37}, number={5}, journal={Journal of Clinical Microbiology}, author={Bolton, LF and Kelley, LC and Lee, MD and Fedorka-Cray, P.J. and Maurer, J.J.}, year={1999}, pages={1348–1351} }
 @article{carlson_bolton_briggs_hurd_sharma_fedorka-cray_jones_1999, title={Detection of multiresistant Salmonella typhimurium DT104 using multiplex and fluorogenic PCR}, volume={13}, ISSN={0890-8508}, url={http://dx.doi.org/10.1006/mcpr.1999.0240}, DOI={10.1006/mcpr.1999.0240}, abstractNote={Salmonellainfections continue to cause gastrointestinal and systemic disease throughout the world.Salmonella typhimuriumDT104 further poses a major health concern due to its acquisition of resistance to multiple antibiotics. The rapid detection of multiresistantS. typhimuriumDT104 would facilitate strategies aimed at controlling this pathogen. We developed a specific and sensitive polymerase chain reaction (PCR) assay that amplifies a segment of DNA that is conserved in multiresistantS. typhimuriumDT104. To provide further specificity for this PCR-based diagnostic test, we amplified two other gene fragments that are present inS. typhimuriumDT104. A multiplex PCR containing primers for targeted sequences resulted in the amplification of predicted size fragments fromS. typhimuriumDT104 exhibiting the ACSSuT (ampicillin, chloramphenicol, streptomycin, sulphamethoxazole and tetracycline) or ASSuT resistance phenotypes. A minor modification of the multiplex PCR enabled the detection of other related multiresistantSalmonellasuch asS. typhimuriumU302. To augment the detection process, we also designed a fluorogenic PCR assay that can detect the DNA of multiresistantS. typhimuriumDT104 in the presence of excess contaminating bacterial DNA. These results provide a method by which multiresistantS. typhimuriumDT104, or potentially the next emerging multiresistantSalmonella, can be accurately detected in only 3–4 h.}, number={3}, journal={Molecular and Cellular Probes}, publisher={Elsevier BV}, author={Carlson, S.A. and Bolton, L.F. and Briggs, C.E. and Hurd, H.S. and Sharma, V.K. and Fedorka-Cray, P.J. and Jones, B.D.}, year={1999}, month={Jun}, pages={213–222} }
 @article{akkina_hogue_angulo_johnson_petersen_saini_fedorka-cray_schlosser_1999, title={Epidemiologic aspects, control, and importance of multiple-drug resistant Salmonella Typhimurium DT104 in the United States}, volume={214}, number={6}, journal={Journal of the American Veterinary Medical Association}, author={Akkina, J.E. and Hogue, A.T. and Angulo, F.J. and Johnson, R. and Petersen, K.E. and Saini, P.K. and Fedorka-Cray, P.J. and Schlosser, W.D.}, year={1999}, pages={790–798} }
 @article{fedorka cray_bailey_stern_cox_ladely_musgrove_1999, title={Mucosal Competitive Exclusion to Reduce Salmonella in Swine}, volume={62}, ISSN={0362-028X}, url={http://dx.doi.org/10.4315/0362-028x-62.12.1376}, DOI={10.4315/0362-028x-62.12.1376}, abstractNote={A mucosal competitive exclusion culture has been shown to reduce or eliminate Salmonella spp. in poultry. Using similar techniques, a mucosal competitive exclusion culture from swine (MCES) was produced from the cecum of a 6-week-old pig. Suckling pigs were inoculated with 5 ml of MCES by oral gavage within 6 h postfarrowing (PF) and again at 24 h PE All pigs were challenged with 10(3) CFU of Salmonella Choleraesuis at 48 h PF by intranasal instillation, including pigs from two sows that had not been given MCES. Clinical signs and rectal swabs were monitored daily, and pigs were allowed to suckle throughout the experiment. All pigs underwent necropsy on day 7 PF, and presence of Salmonella was determined in both qualitative (10 tissues) and quantitative (two tissues) samples. Clinical signs were inapparent in all pigs throughout the experiment. Recovery of Salmonella from rectal swabs was variable. However, 28% of the gut tissues were positive from the MCES-treated pigs versus 79% from the control pigs. A 2- to 5-log10 reduction of Salmonella in the cecal contents or ileocolic junction was observed in the MCES-treated pigs when compared with the controls. These data indicate that use of MCES may be a useful approach for control of Salmonella.}, number={12}, journal={Journal of Food Protection}, publisher={International Association for Food Protection}, author={Fedorka Cray, Paula J. and Bailey, J. Stan and Stern, Norman J. and Cox, Nelson A. and Ladely, Scott R. and Musgrove, Michael}, year={1999}, month={Dec}, pages={1376–1380} }
 @article{tollefson_fedorka-cray_angulo_1999, title={Public health aspects of antibiotic resistance monitoring in the USA}, volume={92}, journal={Acta Veterinaria Scandinavica Supplementum}, author={Tollefson, L. and Fedorka-Cray, P.J. and Angulo, FJ}, year={1999}, pages={67–75} }
 @article{apley_brown_fedorka-cray_ferenc_house_riviere_rice_thornsberry_waddell_1998, title={AAVPT Task Force Report: Role of veterinary therapeutics in bacterial resistance development: animal and public health perspectives}, volume={212}, number={8}, journal={Journal of the American Veterinary Medical Association}, author={Apley, M.D. and Brown, S.A. and Fedorka-Cray, P.J. and Ferenc, S. and House, J.K. and Riviere, J.E. and Rice, L.B. and Thornsberry, C. and Waddell, J.}, year={1998}, pages={1209–1213} }
 @article{smith_fedorka-cray_mohan_brock_wittum_morley_hoblet_saif_1998, title={Epidemiologic herd-level assessment of causative agents and risk factors for winter dysentery in dairy cattle}, volume={59}, number={8}, journal={American Journal of Veterinary Research}, author={Smith, DR and Fedorka-Cray, PJ and Mohan, R and Brock, KV and Wittum, TE and Morley, PS and Hoblet, KH and Saif, LJ}, year={1998}, pages={994–1001} }
 @article{smith_fedorka-cray_mohan_brock_wittum_morley_hoblet_saif_1998, title={Evaluation of cow-level risk factors for the development of winter dysentery in dairy cattle}, volume={59}, number={8}, journal={American Journal of Veterinary Research}, author={Smith, DR and Fedorka-Cray, PJ and Mohan, R and Brock, KV and Wittum, TE and Morley, PS and Hoblet, KH and Saif, LJ}, year={1998}, pages={986–993} }
 @article{fedorka-cray_dargatz_wells_wineland_miller_tollefson_petersen_1998, title={Impact of antimicrobic use in veterinary medicine}, volume={213}, number={12}, journal={Journal of the American Medical Veterinary Association}, author={Fedorka-Cray, P.J. and Dargatz, D.A. and Wells, S.J. and Wineland, N.E. and Miller, M.A. and Tollefson, L. and Petersen, K.E.}, year={1998}, pages={1739–1741} }
 @article{tollefson_angulo_fedorka–cray_1998, title={National Surveillance for Antibiotic Resistance in Zoonotic Enteric Pathogens}, volume={14}, ISSN={0749-0720}, url={http://dx.doi.org/10.1016/s0749-0720(15)30285-1}, DOI={10.1016/s0749-0720(15)30285-1}, abstractNote={Treatment of food-producing animals with antimicrobial agents that are important in human therapy may present a public health risk by the transfer of resistant zoonotic pathogens from animals to humans. Resistant bacteria can diminish the effectiveness of antibiotics and demand the use of more expensive or less safe alternatives. In 1996, the Centers for Disease Control (CDC), United States Department of Agriculture (USDA), and Food and Drug Administration (FDA) established the National Antimicrobial Monitoring System to prospectively monitor changes in antimicrobial susceptibilities of zoonotic pathogens from human and animal clinical specimens, healthy farm animals, and carcasses of food-producing animals at slaughter plants. This article describes the development, implementation, and objectives of the monitoring system and presents initial data generated by the system.}, number={1}, journal={Veterinary Clinics of North America: Food Animal Practice}, publisher={Elsevier BV}, author={Tollefson, Linda and Angulo, Frederick J. and Fedorka–Cray, Paula J.}, year={1998}, month={Mar}, pages={141–150} }
 @article{fedorka cray_dargatz_thomas_gray_1998, title={Survey of Salmonella Serotypes in Feedlot Cattle}, volume={61}, ISSN={0362-028X}, url={http://dx.doi.org/10.4315/0362-028x-61.5.525}, DOI={10.4315/0362-028x-61.5.525}, abstractNote={A national study of health and management of cattle in feedlots was conducted. Within this study, the prevalence of Salmonella spp. in fecal samples was determined. Fifty fecal samples were collected from each of 100 feedlots. Within each feedlot, 25 fresh fecal samples were collected from the floor of the pens of cattle which had been on feed the shortest and 25 from those on feed the longest periods of time. The total number of samples collected was 4,977; 2,484 and 2,495 from pens of cattle on feed the shortest and longest times, respectively. Salmonella spp. were recovered from 38% (38 of 100) of the feedlots. Salmonella spp. were recovered from 5.5% (273 of 4,977) of all samples and from 3.5% (88 of 2,484) and 7.4% (185 of 2,495) of samples from pens of cattle shortest and longest on feed, respectively. The most common serotype recovered was S. anatum (27.9%), followed by S. montevideo (12.9%), S. muenster (11.8%), S. kentucky (8.2%), and S. newington (4.3%). The most common serogroups identified were E1 (39.6%), C1 (20.7%), and B (10.4%). Shedding of the serotypes most commonly associated with human illness occurred infrequently (13 of 273: 4.8%). This study provides information on the status of Salmonella spp. from cattle in feedlots and may serve as baseline information for future studies.}, number={5}, journal={Journal of Food Protection}, publisher={International Association for Food Protection}, author={Fedorka Cray, P. J. and Dargatz, D. A. and Thomas, L. A. and Gray, J. T.}, year={1998}, month={May}, pages={525–530} }
 @article{fedorka-cray_hogg_gray_lorenzen_velasquez_vonbehren_1997, title={Feed and feed trucks as sources of Salmonella contamination in swine}, volume={5}, number={5}, journal={Journal of Swine Health Production}, author={Fedorka-Cray, P.J. and Hogg, A. and Gray, J.T. and Lorenzen, K. and Velasquez, J. and VonBehren, P.}, year={1997}, pages={189–193} }
 @article{losinger_garber_smith_hurd_biehl_fedorka-cray_thomas_ferris_1997, title={Management and nutritional factors associated with the detection of Salmonella sp. from cattle fecal specimens from feedlot operations in the United States}, volume={31}, ISSN={0167-5877}, url={http://dx.doi.org/10.1016/s0167-5877(96)01143-9}, DOI={10.1016/s0167-5877(96)01143-9}, abstractNote={In a convenience sample of 100 feedlot operations (included in the United States Department of Agriculture: Animal and Plant Health Inspection Service 1994 Cattle on Feed Evaluation), up to 25 cattle fecal samples were collected and tested for the presence of Salmonella from each of two pens (the pen which contained the most-recent arrivals, and the pen with cattle that had been on feed the longest). One or more Salmonella spp. were recovered from 38 (38.0%) of the 100 feedlots, 52 (26.0%) of the 200 pens and 273 (5.5%) of the 4977 fecal samples collected. Multivariable logistic regression indicated that feeding tallow and feeding whole cottonseed or cottonseed hulls within seven days prior to fecal sample collection was associated with an increased risk of finding Salmonella in a pen. Variables not found to be significantly associated with the detection of Salmonella in a pen included region, operation size, use of sprinklers, time on feed, type of cattle in the pen, number and concentration of cattle in a pen, feeding probiotics, and various other feeds.}, number={3-4}, journal={Preventive Veterinary Medicine}, publisher={Elsevier BV}, author={Losinger, Willard C. and Garber, Lindsey P. and Smith, Marty A. and Hurd, H.Scott and Biehl, LeRoy G. and Fedorka-Cray, Paula J. and Thomas, Lee Ann and Ferris, Kathy}, year={1997}, month={Aug}, pages={231–244} }
 @article{tillotson_savage_salman_gentry-weeks_rice_fedorka-cray_hendrickson_jones_nelson_traub-dargatz_1997, title={Outbreak of Salmonella infantis infection in a large animal veterinary teaching hospital}, volume={211}, number={12}, journal={Journal of Veterinary Medicine}, author={Tillotson, K. and Savage, C.J. and Salman, M.D. and Gentry-Weeks, C.R. and Rice, D. and Fedorka-Cray, P.J. and Hendrickson, D.A. and Jones, R.L. and Nelson, W. and Traub-Dargatz, J.L.}, year={1997}, pages={1554–1557} }
 @article{harris_fedorka-cray_gray_thomas_ferris_1997, title={Prevalence of Salmonella organisms in swine feed}, volume={210}, number={3}, journal={Journal of the American Veterinary Medical Association}, author={Harris, I.T. and Fedorka-Cray, P.J. and Gray, J.T. and Thomas, L.A. and Ferris, K.}, year={1997}, pages={382–385} }
 @article{davies_morrow_jones_deen_fedorka cray_harris_1997, title={Prevalence of salmonella in finishing swine raised in different 

production systems in North Carolina, USA}, volume={119}, ISSN={0950-2688 1469-4409}, url={http://dx.doi.org/10.1017/s095026889700784x}, DOI={10.1017/s095026889700784x}, abstractNote={We compared the prevalence of salmonella in faecal samples from finishing pigs and in feed samples from swine herds in North Carolina, USA. Farms were either finishing sites using all-in/all-out management of buildings in multiple-site systems (14 farms) or farrow-to-finish systems using continuous flow management of finishing barns (15 farms). The two groups of herds differed with respect to several management variables. Salmonella were isolated from 565 of 2288 (24·6%) faecal samples and from at least 1 faecal sample on 24 of 29 (83%) farms. Predominant serotypes were S. derby , S. typhimurium (including copenhagen ), S. heidelberg , S. worthington and S. mbandaka . Fewer farrow-to-finish farms were detected as positive compared with all-in/all-out farms. Prevalence was lower for pigs raised on slotted floors compared with all other floor types, and was highest for pigs raised on dirt lots. Modern methods of raising pigs in multiple-site production systems, using all-in/all-out management of finishing pigs, appear to have no benefit in reducing the prevalence of salmonella compared with conventional farrow-to-finish systems.}, number={2}, journal={Epidemiology and Infection}, publisher={Cambridge University Press (CUP)}, author={Davies, P. R. and Morrow, W. E. M. and Jones, F. T. and Deen, J. and Fedorka Cray, P. J. and Harris, I. T.}, year={1997}, month={Oct}, pages={237–244} }
 @article{davies_morrow_jones_deen_fedorka-cray_gray_1997, title={Risk of shedding Salmonella organisms by market-age hogs in a barn with open-flush gutters}, volume={210}, number={3}, journal={Journal of the American Veterinary Medical Association}, author={Davies, P.R. and Morrow, W.E. and Jones, F.T. and Deen, J. and Fedorka-Cray, P.J. and Gray, J.T.}, year={1997}, pages={386–389} }
 @article{fedorka-cray_harris_whipp_1997, title={Using isolated weaning to raise Salmonella-free swine}, volume={92}, number={4}, journal={Veterinary Medicine}, author={Fedorka-Cray, P.J. and Harris, D.L. and Whipp, S.C.}, year={1997}, pages={375–382} }
 @article{gray_stabel_fedorka-cray_1996, title={Effect of dose on the immune response and persistence of Salmonella choleraesuis infection in swine}, volume={57}, number={3}, journal={American Journal of Veterinary Research}, author={Gray, J.T. and Stabel, T.J. and Fedorka-Cray, P.J.}, year={1996}, pages={313–319} }
 @article{gray_fedorka-cray_stabel_kramer_1996, title={Natural transmission of Salmonella choleraesuis in swine}, volume={62}, number={1}, journal={Applied and Environmental Microbiology}, author={Gray, J.T. and Fedorka-Cray, P.J. and Stabel, T.J. and Kramer, T.T.}, year={1996}, pages={141–146} }
 @inbook{hueston_fedorka-cray_1996, title={Pathogen identification on the farm and impact of farm management strategies}, publisher={USDA-Economic Research Service}, author={Hueston, W.D. and Fedorka-Cray, P.J.}, year={1996} }
 @article{fedorka-cray_collins kelly_stabel_gray_laufer_1995, title={Alternate routes of invasion may affect pathogenesis of Salmonella Typhimurium in swine}, volume={63}, number={7}, journal={Infection and Immunity}, author={Fedorka-Cray, P.J. and Collins Kelly, L. and Stabel, T.J. and Gray, J.T. and Laufer, J.A.}, year={1995}, pages={2658–2664} }
 @article{gray_fedorka-cray_stabel_ackermann_1995, title={Influence of inoculation route on the carrier state of Salmonella choleraesuis in swine}, volume={47}, ISSN={0378-1135}, url={http://dx.doi.org/10.1016/0378-1135(95)00060-n}, DOI={10.1016/0378-1135(95)00060-n}, abstractNote={This study was designed to investigate the carrier state of swine infected with Salmonella choleraesuis. Thirty-five pigs were divided into 3 groups. Groups 1 (n = 15) and 2 (n = 16) were challenged with 108 CFU of S. choleraesuis intranasally or by gastric route, respectively. Group 3 (n = 4) served as uninoculated controls. Pigs were necropsied at 2, 4, 6, and 12 weeks post inoculation. Clinical signs and microscopic lesions were more severe for group 1. Salmonella choleraesuis was recovered from a greater percentage of tissue samples for group 1 versus group 2 at 2, 4, and 6 weeks post inoculation. No differences were observed between groups at 12 weeks post inoculation. Regardless of route of inoculation, S. choleraesuis was most often recovered from the ileocolic junction, ileocolic lymph node, cecal contents, tonsil, lung and colon. Both groups shed S. choleraesuis in the feces sporadically throughout the 12 week period indicating that a carrier state is maintained for at least 12 weeks. However, group 1 shed higher numbers of S. choleraesuis initially. Serum IgG, IgM, and IgA antibody responses to S. choleraesuis lipopolysaccharide and heat extract antigens were observed for both groups. Higher serum IgG antibody titers to S. choleraesuis lipopolysaccharide were observed for group 2. Intestinal antibody responses for both groups included IgG and IgM responses but not an IgA response. Both routes of inoculation stimulated peripheral blood B-cells while the intranasal route (group 1) was more effective at stimulating peripheral blood T-cells. The reduction in levels of tissues infection and shedding observed for both groups coincided with the development of the host immune response. These data indicate that route of inoculation affects the development of humoral and cellular immunity, influences levels of Salmonella shed into the environment and the distribution of Salmonella within tissue.}, number={1-2}, journal={Veterinary Microbiology}, publisher={Elsevier BV}, author={Gray, Jeffrey T. and Fedorka-Cray, Paula J. and Stabel, Thomas J. and Ackermann, Mark R.}, year={1995}, month={Nov}, pages={43–59} }
 @article{gray_fedorka-cray_rogers_1995, title={Partial characterization of a Moraxella bovis cytolysin}, volume={43}, ISSN={0378-1135}, url={http://dx.doi.org/10.1016/0378-1135(94)00084-a}, DOI={10.1016/0378-1135(94)00084-a}, abstractNote={Moraxella bovis (M. bovis) is the etiologic agent infectious bovine keratoconjunctivitis and M. bovis hemolysin is believed to be an important virulence factor. Two strains of M. bovis were compared, Epp 63(300) (Epp), a known virulent and hemolytic strain, and IBH 63 (IBH), a known avirulent and nonhemolytic strain. Sterile 10-fold (10 ×) supernatant concentrates were obtained from cultures grown in TSB broth with 10 mM CaCl2. Supernatant hemolysin titers for Epp, were 1:1024 and 1:8192 for unconcentrated (1 ×) and 10 ×, respectively. Supernatant cytotoxin titers to bovine mononuclear cells were 1:32 and 1:128 for 1 × and 10 ×, respectively, for Epp. Cytolytic (hemolytic and cytotoxic) activities declined 10-fold but were still measurable for > 1 wk at 4°C. Both activities were inactivated by trypsin and by heating at 56°C for 20 min. A cytotoxic effect was observed on cultured bovine and ovine corneal epithelial cells with Epp. All cytolytic effects were neutralized with antiserum to 10 × Epp. No cytolytic activities were detected for 10 × IBH. SDS-PAGE electrophoresis and related immunoblots indicate a high molecular weight protein at 110 kDa for the 10 × Epp preparation when stained with silver or probed with monoclonal antibodies to the E. coli alpha hemolysin. No 110 kDa band is observed for 10 × IBH. These data suggest that hemolytic and cytotoxic activities are important in the pathogenesis of infectious bovine keratoconjunctivitis and identify the protein as a possible RTX related toxin of 110 kDa. Stability of the M. bovis cytolysin for > 1 week should allow further characterization and purification of the protein.}, number={2-3}, journal={Veterinary Microbiology}, publisher={Elsevier BV}, author={Gray, J.T. and Fedorka-Cray, P.J. and Rogers, D.G.}, year={1995}, month={Feb}, pages={183–196} }
 @article{stabel_fedorka-cray_gray_1995, title={Tumor necrosis factor-α production in swine after oral or respiratory challenge exposure with live Salmonella typhimurium or Salmonella choleraesuis}, volume={56}, number={8}, journal={American Journal of Veterinary Research}, author={Stabel, T.J. and Fedorka-Cray, P.J. and Gray, J.T.}, year={1995}, pages={1012–1018} }
 @article{fedorka-cray_cray_breisch_gray_anderson_1994, title={Actinobacillus(Haemophilus) pleuropneumoniae Part 2: Control, virulence factors, vaccines, adjuvant and immunity}, volume={16}, journal={Compendium on Continuing Education for the Practising Veterinarian}, author={Fedorka-Cray, PJ and Cray, WC, Jr. and Breisch, SA and Gray, JT and Anderson, GA}, year={1994}, pages={117–125} }
 @article{stine_fedorka-cray_huether_gentry_anderson_1994, title={Comparison of serum responses in swine after vaccination and challenge exposure with Actinobacillus pleuropneumoniae serotype 1}, volume={55}, number={9}, journal={American Journal of Veterinary Research}, author={Stine, D.L. and Fedorka-Cray, P.J. and Huether, M.J. and Gentry, M.J. and Anderson, G.A.}, year={1994}, pages={1238–1243} }
 @article{fedorka-cray_whipp_isaacson_nord_lager_1994, title={Transmission of Salmonella typhimurium to swine}, volume={41}, ISSN={0378-1135}, url={http://dx.doi.org/10.1016/0378-1135(94)90029-9}, DOI={10.1016/0378-1135(94)90029-9}, abstractNote={These studies were designed to determine the rate of transmission and the colonization pattern of Salmonella typhimurium in swine. Two experiments were conducted. In experiment 1, swine challenged per os with either S. typhimurium strain 798T + or strain 798N + were exposed to heterologous feces. Following exposure to heterologous strains, heterologous Salmonella were recovered from the feces of infected swine within 3 days and from the tonsil and ileum at necropsy. Bacterial populations in swine initially challenged with Salmonella remained constant. In experiment 2, Salmonella-free swine were commingled with a population of pigs that were shedding 2.69 log10 CFU Salmonella/gram feces. Salmonella was recovered from pooled fecal samples from the commingled swine on day 2 post-exposure to the infected group. Low numbers of Salmonella were detected in the ileocolic lymph node, ileum, cecum or spleen of all commingled swine throughout the necropsy period. These data provide a means for evaluating transmission of Salmonella to a population of swine which may be used to study the mechanisms involved in transmission and maintenance of the disease.}, number={4}, journal={Veterinary Microbiology}, publisher={Elsevier BV}, author={Fedorka-Cray, Paula J. and Whipp, Shannon C. and Isaacson, Richard E. and Nord, Nels and Lager, Kris}, year={1994}, month={Aug}, pages={333–344} }
 @article{fedorka-cray_cray_hoffman_gray_breisch_anderson_1993, title={Actinobacillus (Haemophilus) pleuropneumoniae Part 1: History, epidemiology, serotyping and treatment}, volume={15}, journal={Compendium on Continuing Education for the Practising Veterinarian}, author={Fedorka-Cray, PJ and Cray, WC, Jr. and Hoffman, L and Gray, JT and Breisch, SA and Anderson, GA}, year={1993}, pages={1447–1455} }
 @article{fedorka-cray_stine_greenwald_gray_huether_anderson_1993, title={The importance of secreted virulence factors in Actinobacillus pleuropneumoniae bacterin preparation: a comparison}, volume={37}, ISSN={0378-1135}, url={http://dx.doi.org/10.1016/0378-1135(93)90184-9}, DOI={10.1016/0378-1135(93)90184-9}, abstractNote={Current bacterins provide only partial protection against morbidity and mortality in swine following infection by Actinobacillus pleuropneumoniae. We compared the efficacy of a cell-free concentrate from mid-log phase growth cultures of Actinobacillus pleuropneumoniae (APP) serotype 1 to four commercial bacterins. This cell-free preparation contained carbohydrate, endotoxin, and protein, and had hemolytic and cytotoxic activity. Sodium dodecyl-sulfate polyacrylamide gel electrophoresis analysis indicated the presence of one major 110 000-molecular-weight protein. This protein band also stained by the periodic acid Schiff method, indicating the presence of carbohydrate. Cell-free concentrates of APP serotypes 5 and 7 had identical profiles following electrophoresis and staining with either Coomassie blue for protein or Schiff reagent for carbohydrate. Lipopolysaccharide profiles for the cell-free concentrates of serotypes 1 and 5 were semi-rough while the LPS profile for serotype 7 was smooth. Five A. pleuropneumoniae-free SPF pigs per group were vaccinated on days 0 and 21 with cell-free concentrate of serotype 1 plus adjuvant, or one of four commercial bacterins according to the manufacturer's directions. Control pigs were vaccinated with PBS mixed with adjuvant. All pigs were challenged intranasally on day 35 with serotype 1 and necropsied on day 50. Protection was greatest in the cell-free concentrate group, as compared with all other groups, in that no deaths occurred, clinical scores were less severe, and percent lung affected was significantly reduced (P < 0.05). In addition, whole-cell ELISA titers were significantly increased (P < 0.05) postvaccination in the cell-free concentrate group, and postvaccination and postchallenge sera neutralized the hemolytic activity of the cell-free concentrate from serotypes 1 and 5 (P < 0.05), as compared with all other groups. No serum neutralization to the hemolysin of serotype 7 was observed. Immunoblot analysis using antisera derived from gnotobiotic pigs indicated that the cell-free vaccine generated a response that was identical to the response observed following live challenge. Similar, but not identical, responses were observed when antisera generated against the bacterins was used. This study indicates that an acellular vaccine containing multiple virulence factors can provide complete protection from mortality and significantly reduced morbidity to homologous challenge.}, number={1-2}, journal={Veterinary Microbiology}, publisher={Elsevier BV}, author={Fedorka-Cray, Paula J. and Stine, Douglas L. and Greenwald, Janet M. and Gray, Jeffery T. and Huether, Michael J. and Anderson, Gary A.}, year={1993}, month={Oct}, pages={85–100} }
 @article{fedorka-cray_huether_stine_anderson_1990, title={Efficacy of a cell extract from Actinobacillus (Haemophilus) pleuropneumoniae serotype 1 against disease in swine}, volume={58}, number={2}, journal={Infection and Immunity}, author={Fedorka-Cray, P.J. and Huether, M.J. and Stine, D.L. and Anderson, G.A.}, year={1990}, pages={358–365} }
 @article{reddy_blecha_minocha_anderson_morrill_fedorka-cray_baker_1989, title={Bovine recombinant interleukin-2 augments immunity and resistance to bovine herpesvirus infection}, volume={23}, ISSN={0165-2427}, url={http://dx.doi.org/10.1016/0165-2427(89)90110-4}, DOI={10.1016/0165-2427(89)90110-4}, abstractNote={The in vivo administration of bovine recombinant interleukin-2 (rIL-2) was evaluated in calves vaccinated and then challenged with bovine herpesvirus-1 (BHV-1). In Experiment 1, 24 calves were allotted to four groups: control; bovine rIL-2; BHV-1 vaccine (modified-live); and bovine rIL-2+BHV-1 vaccine. Serum neutralizing antibody titers to BHV-1 were increased sixfold, and virus shedding was fourfold less in calves vaccinated and treated with rIL-2 (25 μg/kg, intramuscularly) when compared to calves that received vaccine only. Treatment with rIL-2 induced lymphokine-activated killer activity that was eliminated by pretreating effector cells with complement and a monoclonal antibody (B26A) specific for the sheep red blood cell receptor. The rIL-2 treatment in BHV-1-vaccinated calves increased the calves' ability to withstand a BHV-1 challenge. However, during treatment with rIL-2, calves developed diarrhea and mild fever that abated after IL-2 treatment was stopped. A second experiment was then conducted to determine a dose of rIL-2 that would enhance immunity to BHV-1 without causing adverse side effects. Twenty-five calves were allotted to five groups that received injections of rIL-2 at 0.0, 25.0, 2.5, 0.25, or 0.025 μg kg−1 day−1 for 5 days. All calves received a modified-live BHV-1 vaccine. Calves treated with 25.0 μg kg−1 day−1 showed similar adverse side effects as in the first experiment but all other calves were normal. Compared to control calves, those treated with 25.0, 2.5, and 0.25 μg kg−1 day−1 of rIL-2 had higher (P<0.05) serum antibody titers to BHV-1 and following challenge lower (P<0.05) BHV-1 titers in nasal secretions; additionally, clinical disease as evidenced by nasal and ocular discharge was less severe (P<0.05). In vitro cytotoxic responses against BHV-1-infected bovine kidney cells were increased (P<0.05) in calves treated with rIL-2 in a dose dependent manner. These data suggest that bovine rIL-2 at 2.5 to 0.25 μg/kg may be an effective adjuvant to immunization.}, number={1-2}, journal={Veterinary Immunology and Immunopathology}, publisher={Elsevier BV}, author={Reddy, P.G. and Blecha, F. and Minocha, H.C. and Anderson, G.A. and Morrill, J.L. and Fedorka-Cray, P.J. and Baker, P.E.}, year={1989}, month={Nov}, pages={61–74} }
 @article{flaming_blecha_fedorka-cray_anderson_1989, title={Decreased lymphocyte function associated with pseudorabies virus infection in feeder pigs: Influence of isoprinosine on lymphocyte function in virus-infected feeder pigs}, volume={50}, number={10}, journal={American Journal of Veterinary Research}, author={Flaming, K. and Blecha, F. and Fedorka-Cray, P.J. and Anderson, G.A.}, year={1989}, pages={1653–1657} }
 @article{fedorka-cray_cray_anderson_nickerson_1988, title={Bacterial tolerance of 100% dimethyl sulfoxide}, volume={34}, ISSN={0008-4166 1480-3275}, url={http://dx.doi.org/10.1139/m88-114}, DOI={10.1139/m88-114}, abstractNote={Viable bacteria were found in six bottles of dimethyl sulfoxide (DMSO) at a concentration of approximately one bacterium per 4.4 mL. The 18 bacterial isolates appeared to be tolerating the DMSO rather than metabolizing it. No fungi were detected. DMSO must be assumed to be nonsterile unless it has been previously sterilized.}, number={5}, journal={Canadian Journal of Microbiology}, publisher={Canadian Science Publishing}, author={Fedorka-Cray, Paula J. and Cray, William C., Jr. and Anderson, Gary A. and Nickerson, Kenneth W.}, year={1988}, month={May}, pages={688–689} }
 @inbook{anderson_urban_fedorka-cray_newell_nunberg_doyle_1987, place={Cold Spring Harbor, New York}, title={Interleukin-2 and protective immunity in Haemophilus pleuropneumoniae: Preliminary studies}, booktitle={Vaccines 87: Modern Approaches To New Vaccines: Prevention of aids and other viral, bacterial, and parasitic diseases}, publisher={Cold Spring Harbor Laboratory}, author={Anderson, G.A. and Urban, O. and Fedorka-Cray, P. and Newell, A. and Nunberg, J. and Doyle, M.}, editor={Chanock, R.M.Editor}, year={1987}, pages={22} }
 @article{huether_fedorka-cray_pfannenstiel_anderson_1987, title={Plasmid profiles and antibiotic susceptibility of Haemophilus pleuropneumoniae serotypes 1, 3, 5, and 7}, volume={48}, ISSN={0378-1097 1574-6968}, url={http://dx.doi.org/10.1111/j.1574-6968.1987.tb02538.x}, DOI={10.1111/j.1574-6968.1987.tb02538.x}, abstractNote={This paper describes the plasmid profiles obtained for 73 of 96 field isolates of Haemophilus pleuropneumoniae serotypes 1, 3, 5, and 7. We also characterized the antibiotic susceptibilities of these 96 isolates. Because of the high proportion of isolates resistant to some of the antibiotics, no conclusions can be drawn as to the role of plasmids in antibiotic resistance.}, number={1-2}, journal={FEMS Microbiology Letters}, publisher={Oxford University Press (OUP)}, author={Huether, Michael J. and Fedorka-Cray, Paula J. and Pfannenstiel, Mary Ann and Anderson, Gary A.}, year={1987}, month={Dec}, pages={179–182} }
 @article{gill_fedorka-cray_tweten_sleeper_1984, title={Purification and properties of the carbonic anhydrase of Rhodospirillum rubrum}, volume={138}, ISSN={0302-8933 1432-072X}, url={http://dx.doi.org/10.1007/bf00413010}, DOI={10.1007/bf00413010}, number={2}, journal={Archives of Microbiology}, publisher={Springer Nature}, author={Gill, Steven R. and Fedorka-Cray, Paula J. and Tweten, Rodney K. and Sleeper, Bayard P.}, year={1984}, month={Jun}, pages={113–118} }
 @article{spira_fedorka-cray_1984, title={Purification of enterotoxins from Vibrio mimicus that appear to be identical to cholera toxin}, volume={45}, number={3}, journal={Infection and Immunity}, author={Spira, W.M. and Fedorka-Cray, P.J.}, year={1984}, pages={679–684} }
 @article{spira_fedorka-cray_pettebone_1983, title={Colonization of the rabbit small intestine by clinical and environmental isolates of non-01 Vibrio cholerae and Vibrio mimicus}, volume={41}, number={3}, journal={Infection and Immunity}, author={Spira, W.M. and Fedorka-Cray, P.J. and Pettebone, P.}, year={1983}, pages={1175–1183} }
 @article{spira_fedorka-cray_1983, title={Enterotoxin production by Vibrio cholerae and Vibrio mimicus grown in continuous culture with microbial cell recycle}, volume={46}, number={3}, journal={Applied and Environmental Microbiology}, author={Spira, W.M. and Fedorka-Cray, P.J.}, year={1983}, pages={704–709} }
 @article{spira_fedorka-cray_1983, title={Production of cholera toxin-like toxin by Vibrio mimicus and non-0l Vibrio cholerae: Batch culture conditions for optimum yields and isolation of hypertoxigenic lincomycin-resistant mutants}, volume={42}, number={2}, journal={Infection and Immunity}, author={Spira, W.M. and Fedorka-Cray, P.J.}, year={1983}, pages={501–509} }