@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{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{binkley_deressa_shi_jara_escobar_mauldin_matheny_o'quin_pieracci_kling_et al._2021, title={Use of partial N-gene sequences as a tool to monitor progress on rabies control and elimination efforts in Ethiopia}, volume={221}, ISSN={["1873-6254"]}, DOI={10.1016/j.actatropica.2021.106022}, abstractNote={Ethiopia is one of the African countries most affected by rabies. A coarse catalog of rabies viruses (RABV) was created as a benchmark to assess the impact of control and elimination activities. We evaluated a 726 bp amplicon at the end of the N-gene to infer viral lineages in circulation using maximum likelihood and Bayesian methods for phylogenetic reconstruction. We sequenced 228 brain samples from wild and domestic animals collected in five Ethiopian regions during 2010-2017. Results identified co-circulating RABV lineages that are causing recurrent spillover infections into wildlife and domestic animals. We found no evidence of importation of RABVs from other African countries or vaccine-induced cases in the area studied. A divergent RABV lineage might be involved in an independent rabies cycle in jackals. This investigation provides a feasible approach to assess rabies control and elimination efforts in resource-limited countries.}, journal={ACTA TROPICA}, author={Binkley, Laura and Deressa, Asefa and Shi, Mang and Jara, Manuel and Escobar, Luis E. and Mauldin, Mathew R. and Matheny, Audrey and O'Quin, Jeanette and Pieracci, Emily G. and Kling, Chantal and et al.}, year={2021}, month={Sep} }
 @article{gebreyes_jackwood_bruno de oliveira_lee_hoet_thakur_2020, title={Molecular Epidemiology of Infectious Zoonotic and Livestock Diseases}, volume={8}, ISSN={["2165-0497"]}, DOI={10.1128/microbiolspec.AME-0011-2019}, abstractNote={ABSTRACT}, number={2}, journal={MICROBIOLOGY SPECTRUM}, author={Gebreyes, Wondwossen A. and Jackwood, Daral and Bruno De Oliveira, Celso Jose and Lee, Chang-Won and Hoet, Armando E. and Thakur, Siddhartha}, year={2020}, month={Mar} }
 @article{smith_gebreyes_abley_harper_forshey_male_martin_molla_sreevatsan_thakur_et al._2013, title={Methicillin-Resistant Staphylococcus aureus in Pigs and Farm Workers on Conventional and Antibiotic-Free Swine Farms in the USA}, volume={8}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0063704}, abstractNote={Much uncertainty remains about the origin and public health implications of livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA). This study aimed to investigate the occurrence and prevalence of MRSA in general and LA-MRSA in particular in pigs and farm workers in five states. We collected nasal swabs from pigs and farm workers at 45 swine herds (21 antibiotic-free herds; 24 conventional herds) in Illinois, Iowa, Minnesota, North Carolina and Ohio. MRSA was isolated from 50 of 1085 pigs (4.6%) and 31 of 148 (20.9%) of farm workers. MRSA-positive pigs and people were clustered in four conventional swine farms in Iowa and Illinois. Based on genotyping, spa type t034, a common livestock associated variant, was predominant among both human and swine isolates. These results confirm the presence of LA-MRSA in pigs and swine farm workers in the USA, but the prevalence found is relatively low compared with European studies.}, number={5}, journal={PLOS ONE}, author={Smith, Tara C. and Gebreyes, Wondwossen A. and Abley, Melanie J. and Harper, Abby L. and Forshey, Brett M. and Male, Michael J. and Martin, H. Wayne and Molla, Bayleyegn Z. and Sreevatsan, Srinand and Thakur, Siddhartha and et al.}, year={2013}, month={May} }
 @article{alali_thakur_berghaus_martin_gebreyes_2010, title={Prevalence and Distribution of Salmonella in Organic and Conventional Broiler Poultry Farms}, volume={7}, ISSN={["1556-7125"]}, DOI={10.1089/fpd.2010.0566}, abstractNote={The objective of this cross-sectional study was to compare the prevalence of Salmonella and antimicrobial-resistant Salmonella, as well as investigate the distribution of this pathogen in organic and conventional broiler poultry farms. Fecal (n = 420), feed (n = 140), and drinking water (n = 140) samples were collected from birds at 3 and 8 weeks of age for 2-flock cycles. One house was sampled per farm at three organic and four conventional broiler farms from the same company in North Carolina. All samples were analyzed for the presence of Salmonella using selective enrichment techniques. Further phenotypic (antimicrobial susceptibility) and genotypic (pulsed-field gel electrophoresis [PFGE]) testing were performed. Salmonella prevalences in fecal samples were 5.6% (10/180) and 38.8% (93/240) from organic and conventional farms, respectively. From feed, 5.0% (3/60) and 27.5% (22/80) of the samples were positive for Salmonella from organic and conventional farms, respectively. None of the water samples were positive for Salmonella. Seventy isolates were characterized by antimicrobial susceptibility and PFGE types. The two most common resistance phenotypes were single resistance to streptomycin (36.2% [25/58]: conventional; 25% [3/12] organic), and multidrug resistance to six antimicrobial agents: ampicillin-streptomycin-amoxicillin/clavulanic acid-cephalothin-ceftiofur-cefoxitin (AmStAxChCfFx; 39.7%: conventional only). Genotypic analysis using PFGE showed clonality among isolates within and between the two types of farms. The results of our study suggest that within this poultry company, the prevalence of fecal Salmonella was lower in certified-organic birds than in conventionally raised birds, and the prevalence of antimicrobial-resistant Salmonella was also higher in conventionally raised birds than in certified-organic birds.}, number={11}, journal={FOODBORNE PATHOGENS AND DISEASE}, author={Alali, Walid Q. and Thakur, Siddhartha and Berghaus, Roy D. and Martin, Michael P. and Gebreyes, Wondwossen A.}, year={2010}, month={Nov}, pages={1363–1371} }
 @article{thakur_putnam_fry_abley_gebreyes_2010, title={Prevalence of antimicrobial resistance and association with toxin genes in Clostridium difficile in commercial swine}, volume={71}, ISSN={["0002-9645"]}, DOI={10.2460/ajvr.71.10.1189}, abstractNote={Abstract}, number={10}, journal={AMERICAN JOURNAL OF VETERINARY RESEARCH}, author={Thakur, Siddhartha and Putnam, Michelle and Fry, Pamela R. and Abley, Melanie and Gebreyes, Wondwossen A.}, year={2010}, month={Oct}, pages={1189–1194} }
 @article{gebreyes_thakur_dorr_tadesse_post_wolf_2009, title={Occurrence of spvA Virulence Gene and Clinical Significance for Multidrug-Resistant Salmonella Strains}, volume={47}, ISSN={["0095-1137"]}, DOI={10.1128/JCM.01660-08}, abstractNote={
            Nontyphoidal
            Salmonella
            strains are important reservoirs of antimicrobial resistance. An important issue that has not been investigated is whether the multiresistant
            Salmonella
            strains are more virulent than their susceptible counterparts.
            Salmonella
            isolates collected from clinical human (
            n
            = 888) and porcine (
            n
            = 2,120) cases at the same time period and geographic location were investigated. Antimicrobial susceptibility, PCR analysis for the
            spvA
            virulence gene, and pulsed-field gel electrophoresis (PFGE) genotyping were done. Carriage of
            spvA
            was associated with multidrug-resistant (MDR) type ACSSuT strains (odds ratio, 7.1;
            P
            < 0.05), a type often implicated in bacteremic human cases. PFGE revealed that clinical isolates from pigs were more clonally related to those of human origin than the nonclinical porcine isolates. The findings suggest that MDR strains that also carry specific virulence factors are more likely to be of clinical significance.
          }, number={3}, journal={JOURNAL OF CLINICAL MICROBIOLOGY}, author={Gebreyes, Wondwossen A. and Thakur, Siddhartha and Dorr, Paul and Tadesse, Daniel A. and Post, Karen and Wolf, Leslie}, year={2009}, month={Mar}, pages={777–780} }
 @article{thakur_morrow_funk_bahnson_gebreyes_2008, title={Molecular epidemiologic investigation of Campylobacter coli in swine production systems, using multilocus sequence typing (vol 72, pg 5666, 2006)}, volume={74}, ISSN={["0099-2240"]}, DOI={10.1128/aem.02326-07}, abstractNote={Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, 4700 Hillsborough St., Raleigh, North Carolina 27606; Department of Animal Science, North Carolina State University, Raleigh, North Carolina 27606; Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio; and Department of Medical Sciences, University of Wisconsin, Madison, Wisconsin}, number={1}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Thakur, Siddhartha and Morrow, W. E. Morgan and Funk, Julie A. and Bahnson, Peter B. and Gebreyes, Wondwossen A.}, year={2008}, month={Jan}, pages={342–342} }
 @article{dorr_baker_almond_wayne_gebreyes_2007, title={Epidemiologic assessment of porcine circovirus type 2 coinfection with other pathogens in swine}, volume={230}, ISSN={["1943-569X"]}, DOI={10.2460/javma.230.2.244}, abstractNote={Abstract}, number={2}, journal={JAVMA-JOURNAL OF THE AMERICAN VETERINARY MEDICAL ASSOCIATION}, author={Dorr, Paul M. and Baker, Rodney B. and Almond, Glen W. and Wayne, Spencer R. and Gebreyes, Wondwossen A.}, year={2007}, month={Jan}, pages={244–250} }
 @article{thakur_tadesse_morrow_gebreyes_2007, title={Occurrence of multidrug resistant Salmonella in antimicrobial-free (ABF) swine production systems}, volume={125}, ISSN={["0378-1135"]}, DOI={10.1016/j.vetmic.2007.05.025}, abstractNote={This cross-sectional study was conducted to determine the prevalence and antimicrobial resistance of Salmonella species in swine reared in the intensive (indoor) and extensive (outdoor) ABF production systems at farm and slaughter in North Carolina, U.S.A. We sampled a total of 279 pigs at farm (extensive 107; intensive 172) and collected 274 carcass swabs (extensive 124; intensive 150) at slaughter. Salmonella species were tested for their susceptibility against 12 antimicrobial agents using the Kirby-Bauer disk diffusion method. Serogrouping was done using polyvalent and group specific antisera. A total of 400 salmonellae were isolated in this study with a significantly higher Salmonella prevalence from the intensive (30%) than the extensive farms (0.9%) (P<0.001). At slaughter, significantly higher Salmonella was isolated at the pre- and post-evisceration stages from extensively (29% pre-evisceration and 33.3% post-evisceration) than the intensively (2% pre-evisceration and 6% post-evisceration) reared swine (P<0.001). The isolates were clustered in six serogroups including B, C, E1, E4, G and R. Highest frequency of antimicrobial resistance was observed against tetracycline (78.5%) and streptomycin (31.5%). A total of 13 antimicrobial resistance patterns were observed including the pentaresistant strains with ampicillin, chloramphenicol, streptomycin, sulfamethoxazole, tetracycline resistance pattern observed only among isolates from the intensive farms (n=28) and all were serotype Salmonella typhimurium var. Copenhagen. In conclusion, this study shows that multidrug resistant Salmonella are prevalent in ABF production systems despite the absence of antimicrobial selection pressure. In addition, it also highlights the possible role played by slaughterhouse and other environmental factors in the contamination and dissemination of antimicrobial resistant Salmonella in ABF production systems.}, number={3-4}, journal={VETERINARY MICROBIOLOGY}, author={Thakur, Siddhartha and Tadesse, Daniel A. and Morrow, Morgan and Gebreyes, Wondwossen A.}, year={2007}, month={Dec}, pages={362–367} }
 @article{miller_fuller_gebreyes_lewbart_shchelkunov_shivappa_joiner_woolford_stone_dixon_et al._2007, title={Phylogenetic analysis of spring virema of carp virus reveals distinct subgroups with common origins for recent isolates in North America and the UK}, volume={76}, ISSN={["1616-1580"]}, DOI={10.3354/dao076193}, abstractNote={Genetic relationships between 35 spring viremia of carp virus (SVCV) genogroup Ia isolates were determined based on the nucleotide sequences of the phosphoprotein (P) gene and glycoprotein (G) genes. Phylogenetic analysis based on P gene sequences revealed 2 distinct subgroups within SVCV genogroup Ia, designated SVCV Iai and Iaii, and suggests at least 2 independent introductions of the virus into the USA in 2002. Combined P- and G-sequence data support the emergence of SVCV in Illinois, USA, and in Lake Ontario, Canada, from the initial outbreak in Wisconsin, USA, and demonstrate a close genetic link to viruses isolated during routine import checks on fish brought into the UK from Asia. The data also showed a genetic link between SVCV isolations made in Missouri and Washington, USA, in 2004 and the earlier isolation made in North Carolina, USA, in 2002. However, based on the close relationship to a 2004 UK isolate, the data suggest than the Washington isolate represents a third introduction into the US from a common source, rather than a reemergence from the 2002 isolate. There was strong phylogenetic support for an Asian origin for 9 of 16 UK viruses isolated either from imported fish, or shown to have been in direct contact with fish imported from Asia. In one case, there was 100% nucleotide identity in the G-gene with a virus isolated in China.}, number={3}, journal={DISEASES OF AQUATIC ORGANISMS}, author={Miller, O. and Fuller, F. J. and Gebreyes, W. A. and Lewbart, G. A. and Shchelkunov, I. S. and Shivappa, R. B. and Joiner, C. and Woolford, G. and Stone, D. M. and Dixon, P. F. and et al.}, year={2007}, month={Jul}, pages={193–204} }
 @article{dorr_gebreyes_almond_2007, title={Porcine reproductive and respiratory syndrome virus: Age and management system disease modeling for pathogenic co-infection}, volume={15}, number={5}, journal={Journal of Swine Health and Production}, author={Dorr, P. M. and Gebreyes, W. A. and Almond, G. W.}, year={2007}, pages={258–263} }
 @article{gebreyes_thakur_morrow_2006, title={Comparison of prevalence, antimicrobial resistance, and occurrence of multidrug-resistant Salmonella in antimicrobial-free and conventional pig production}, volume={69}, ISSN={["1944-9097"]}, DOI={10.4315/0362-028x-69.4.743}, abstractNote={Conventional swine production evolved to routinely use antimicrobials, and common occurrence of antimicrobial-resistant Salmonella has been reported. There is a paucity of information on the antimicrobial resistance of Salmonella in swine production in the absence of antimicrobial selective pressure. Therefore, we compared the prevalence and antimicrobial resistance of Salmonella isolated from antimicrobial-free and conventional production systems. A total of 889 pigs and 743 carcasses were sampled in the study. Salmonella prevalence was significantly higher among the antimicrobial-free systems (15.2%) than the conventional systems (4.2%) (odds ratio [OR] = 4.23; P < 0.05). Antimicrobial resistance was detected against 10 of the 12 antimicrobials tested. The highest frequency of resistance was found against tetracycline (80%), followed by streptomycin (43.4%) and sulfamethoxazole (36%). Frequency of resistance to most classes of antimicrobials (except tetracycline) was significantly higher among conventional farms than antimicrobial-free farms, with ORs ranging from 2.84 for chloramphenicol to 23.22 for kanamycin at the on-farm level. A total of 28 antimicrobial resistance patterns were detected. A resistance pattern with streptomycin, sulfamethoxazole, and tetracycline (n = 130) was the most common multidrug resistance pattern. There was no significant difference in the proportion of isolates with this pattern between the conventional (19.5%) and the antimicrobial-free systems (18%) (OR = 1.8; P > 0.05). A pentaresistance pattern with ampicillin, chloramphenicol, streptomycin, sulfamethoxazole, and tetracycline was strongly associated with antimicrobial-free groups (OR = 5.4; P = 0.01). While showing the higher likelihood of finding antimicrobial resistance among conventional herds, this study also implies that specific multidrug-resistant strains may occur on antimicrobial-free farms. A longitudinal study with a representative sample size is needed to reach more conclusive results of the associations detected in this study.}, number={4}, journal={JOURNAL OF FOOD PROTECTION}, author={Gebreyes, WA and Thakur, S and Morrow, WEM}, year={2006}, month={Apr}, pages={743–748} }
 @article{thakur_morrow_funk_bahnson_gebreyes_2006, title={Molecular epidemiologic investigation of Campylobacter coli in swine production systems, using multilocus sequence typing}, volume={72}, ISSN={["1098-5336"]}, DOI={10.1128/AEM.00658-06}, abstractNote={ABSTRACT}, number={8}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Thakur, Siddhartha and Morrow, W. E. Morgan and Funk, Julie A. and Bahnson, Peter B. and Gebreyes, Wondwossen A.}, year={2006}, month={Aug}, pages={5666–5669} }
 @article{gebreyes_altier_thakur_2006, title={Molecular epidemiology and diversity of Salmonella serovar Typhimurium in pigs using phenotypic and genotypic approaches}, volume={134}, ISSN={["1469-4409"]}, DOI={10.1017/S0950268805004723}, abstractNote={SUMMARY}, number={1}, journal={EPIDEMIOLOGY AND INFECTION}, author={Gebreyes, WA and Altier, C and Thakur, S}, year={2006}, month={Feb}, pages={187–198} }
 @article{thakur_gebreyes_2005, title={Campylobacter coli in swine production: Antimicrobial resistance mechanisms and molecular epidemiology}, volume={43}, ISSN={["1098-660X"]}, DOI={10.1128/JCM.43.11.5705-5714.2005}, abstractNote={ABSTRACT}, number={11}, journal={JOURNAL OF CLINICAL MICROBIOLOGY}, author={Thakur, S and Gebreyes, WA}, year={2005}, month={Nov}, pages={5705–5714} }
 @article{gebreyes_thakur_morrow_2005, title={Campylobacter coli: prevalence and antimicrobial resistance in antimicrobial-free (ABF) swine production systems}, volume={56}, ISSN={["1460-2091"]}, DOI={10.1093/jac/dki305}, abstractNote={OBJECTIVES
To determine the prevalence and antimicrobial resistance of Campylobacter species in swine reared in the intensive and extensive antimicrobial-free (ABF) production systems at farm and slaughter. In the ABF system, antimicrobials are neither used for growth promotion nor therapeutic purposes.


METHODS
Swine faecal and carcass swabs were collected from 10 groups of pigs (five each from intensive and extensive ABF farms) at the finishing farm and the slaughter plant. A total of 292 pigs at farm (extensive 118; intensive 174) and 254 carcass swabs (extensive 134; intensive 120) were collected during the study. Campylobacter species were isolated under microaerobic conditions and confirmed by biochemical testing. Up to three presumptive Campylobacter colonies per positive pig/carcass were further characterized. Speciation was done by PCR, targeting ceuE and hipO genes for Campylobacter coli and Campylobacter jejuni, respectively. The isolates were tested for their antimicrobial resistance profile using the agar dilution method against six antimicrobials.


RESULTS
A total of 526 Campylobacter isolates were cultured from 292 pigs and 254 carcasses sampled. All the isolates were found to be C. coli. Overall prevalence of C. coli was 55.8% on farm (55% extensive and 56.3% intensive) and 26% at slaughter (32.8% extensive and 18.3% intensive). There was no significant difference in C. coli between the intensive and extensive systems on the finishing farms (P = 0.83). At post-chill stage, C. coli were isolated only from the extensively reared ABF pigs. Antimicrobial resistance against ciprofloxacin (MIC > 4 mg/L) was found at the farm level in both the intensive- and extensive-reared groups. The erythromycin/nalidixic acid/tetracycline resistance pattern (3%) was the most common pattern in multidrug-resistant C. coli.


CONCLUSIONS
This study highlights the high prevalence of diverse and antimicrobial-resistant C. coli in the ABF production systems of swine. This is the first study reporting the isolation of ciprofloxacin-resistant strains from ABF pigs in the USA and warrants concern.}, number={4}, journal={JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY}, author={Gebreyes, WA and Thakur, S and Morrow, WEM}, year={2005}, month={Oct}, pages={765–768} }
 @article{gebreyes_thakur_2005, title={Multidrug-resistant Salmonella enterica serovar Muenchen from pigs and humans and potential interserovar transfer of antimicrobial resistance}, volume={49}, ISSN={["1098-6596"]}, DOI={10.1128/AAC.49.2.503-511.2005}, abstractNote={ABSTRACT}, number={2}, journal={ANTIMICROBIAL AGENTS AND CHEMOTHERAPY}, author={Gebreyes, WA and Thakur, S}, year={2005}, month={Feb}, pages={503–511} }
 @article{kong_shea_gebreyes_xia_2005, title={Novel hydrophobicity ruler approach for determining the octanol/water partition coefficients of very hydrophobic compounds via their polymer/solvent solution distribution coefficients}, volume={77}, ISSN={["1520-6882"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-14744281423&partnerID=MN8TOARS}, DOI={10.1021/ac048847r}, abstractNote={A novel hydrophobicity ruler approach for determining the octanol/water partition coefficients of very hydrophobic compounds is proposed, which is an indirect method that measures the polymer/solvent solution distribution coefficients (log Kp/s) of reference and unknown compounds. The log Kp/s values of the unknown compounds can be calibrated to their log Ko/w values via the correlation of the log Kp/s values of the reference compounds with their log Ko/w values. An organic solvent was used to increase the solubility of the very hydrophobic compounds in the aqueous solution, so that their concentrations and absorption amounts were high enough to be measured precisely. The solvent also reduced the hydrophobicity scale of the very hydrophobic compounds and controlled the amounts absorbed into the polymer phase, so that compounds spanning a very wide range of log Ko/w values could be measured in a single measurement and the coexisting compounds would not interfere each other. Poly(dimethylsiloxane) (PDMS), aqueous methanol solutions, and a series of 21 PCB (polychlorinated biphenyl) compounds were used to demonstrate the principle of the hydrophobicity ruler approach. The PCB compounds with known experimental log Ko/w values served as reference compounds, whereas the PCB compounds without known log Ko/w values were determined. The log Ko/w values determined for PCB126, PCB187, PCB197, PCB180, PCB170, and PCB195 were 6.94, 7.84, 8.33, 8.17, 7.92, and 8.49, respectively. The correlation of the log Kp/s values of the reference PCB compounds with their log Ko/w values was linear (log Ko/w=2.56 log Kp/s+1.08, R2=0.95). The hydrophobicity ruler approach is also a valuable tool for validating the experimental and theoretical log Ko/w values and identifying outliers in log Ko/w databases.}, number={5}, journal={ANALYTICAL CHEMISTRY}, author={Kong, XQ and Shea, D and Gebreyes, WA and Xia, XR}, year={2005}, month={Mar}, pages={1275–1281} }
 @article{thakur_gebreyes_2005, title={Prevalence and antimicrobial resistance of Campylobacter in antimicrobial-free and conventional pig production systems}, volume={68}, ISSN={["1944-9097"]}, DOI={10.4315/0362-028X-68.11.2402}, abstractNote={The objectives of this study were to determine and compare the prevalence and antimicrobial resistance of Campylobacter species in swine reared in conventional and antimicrobial-free (ABF) production systems. Campylobacter coli was the predominant species, with 1,459 isolates (99%) in the study. We found significantly higher prevalence of C. coli on the ABF farms (77.3%) than on the conventional farms (27.6%) among pigs at the nursery stage (P < 0.001). At slaughter, we found significantly higher prevalence at the postevisceration than at the preevisceration stage (P < 0.001) in both production systems. The 1,459 C. coli isolates were tested with the agar dilution method for their susceptibility to six antimicrobials: chloramphenicol, ciprofloxacin, erythromycin, gentamicin, nalidixic acid, and tetracycline. Resistance was most prevalent against tetracycline (66.2% of isolates) followed by erythromycin (53.6% of isolates). Frequency of resistance to these two antimicrobials was significantly higher among conventional herds (83.4% for tetracycline and 77% for erythromycin) than among ABF herds (56.2% for tetracycline and 34.5% for erythromycin). Resistance to ciprofloxacin at the MIC (> 4 mg/liter) was also found on farms in both systems. Multidrug-resistant C. coli strains were detected in both the conventional (7%) and ABF (4%) herds. This is the first report of ciprofloxacin-resistant strains of C. coli in ABF pigs in the United States. These findings highlight the high prevalence of antimicrobial-resistant C. coli in both conventional and ABF pig production systems and have significant implications for the persistence of antimicrobial-resistant Campylobacter in the pig production environment regardless of levels of antimicrobial use.}, number={11}, journal={JOURNAL OF FOOD PROTECTION}, author={Thakur, S and Gebreyes, WA}, year={2005}, month={Nov}, pages={2402–2410} }
 @article{gebreyes_davies_turkson_morgan morrow_funk_altier_thakur_2004, title={Characterization of Antimicrobial-Resistant Phenotypes and Genotypes among Salmonella enterica Recovered from Pigs on Farms, from Transport Trucks, and from Pigs after Slaughter}, volume={67}, ISSN={0362-028X}, url={http://jfoodprotection.org/doi/abs/10.4315/0362-028X-67.4.698}, DOI={10.4315/0362-028X-67.4.698}, abstractNote={The main objectives of this study were to determine antimicrobial resistance patterns among Salmonella serotypes and to evaluate the role of transport trucks in dissemination of antimicrobial-resistant strains of Salmonella. Salmonella from groups of nursery and finishing pigs on farms, from trucks, and from pigs after slaughter were compared using serotyping, patterns of antimicrobial resistance, and pulsed-field gel electrophoresis patterns. The five farms included in the study yielded 858 isolates representing 27 Salmonella serovars. The most common resistance observed (80% of all isolates) was to tetracycline; resistance to ampicillin (42%), chloramphenicol (31%), amoxicillin/clavulanic acid (30%), and piperacillin (31%) also were common. We found a correlation between serovar and antimicrobial resistance. High correlation was found between Salmonella Typhimurium var. Copenhagen and chloramphenicol resistance (Spearman rank correlation, rho = 0.7). Multidrug resistance was observed primarily in Salmonella Typhimurium var. Copenhagen (94%) and Salmonella Typhimurium (93%) and was much less common in the other common serovars, including Salmonella Derby (7%) and Salmonella Heidelberg (8%). Of the 225 isolates exhibiting the most common pentaresistance pattern in this study, amoxicillin/clavulanic acid-ampicillin-chloramphenicol-piperacillin-tetracycline, 220 (98%) were Salmonella Typhimurium var. Copenhagen, and 86% of the isolates of this serovar had this pattern. Isolates from the trucks were similar, based on pulsed-field gel electrophoresis patterns, to those from the cecum and mesenteric lymph nodes of pigs on two of the farms, suggesting the probable infection of pigs during transport. Class I integrons were also common among various serovars.}, number={4}, journal={Journal of Food Protection}, author={Gebreyes, Wondwossen A. and Davies, Peter R. and Turkson, Paa-Kobina and Morgan Morrow, W. E. and Funk, Julie A. and Altier, Craig and Thakur, Siddhartha}, year={2004}, month={Apr}, pages={698–705} }
 @article{funk_gebreyes_2004, title={Risk factors associated with Salmonella prevalence on swine farms}, volume={12}, number={5}, journal={Journal of Swine Health and Production}, author={Funk, J. and Gebreyes, W. A.}, year={2004}, pages={246–251} }
 @article{gebreyes_davies_turkson_morrow_funk_altier_2004, title={Salmonella enterica serovars from pigs on farms and after slaughter and validity of using bacteriologic data to define herd Salmonella status}, volume={67}, ISSN={["1944-9097"]}, DOI={10.4315/0362-028X-67.4.691}, abstractNote={The primary objective of this study was to evaluate the validity of using data obtained from slaughtered pigs for farm-level epidemiologic studies of Salmonella. The study involved groups of pigs from five farms. Salmonella isolates were obtained from on-farm samples, and a total of 370 on-farm and an additional 486 isolates from samples collected after commercial slaughter were subsequently tested. Preharvest samples included feces of individual animals from defined groups of nursery and finishing pigs on commercial farms and swabs from trucks. Postslaughter samples were cecal contents and mesenteric lymph node samples. The concordance between Salmonella serovars isolated from on-farm samples and those serovars isolated after slaughter varied widely among farms. Results of paired lymph node and cecal cultures were strongly associated (odds ratio, 7.0), but the agreement between on-farm and postslaughter results at the pig level was poor (kappa = 0.34). The results support recent findings that risk of exposure to Salmonella during transport and lairage remains a concern under contemporary industry conditions. The findings further imply that slaughter plant studies based on phenotyping of Salmonella alone (such as serovars) may not reliably indicate the Salmonella status of commercial swine farms.}, number={4}, journal={JOURNAL OF FOOD PROTECTION}, author={Gebreyes, WA and Davies, PR and Turkson, PK and Morrow, WEM and Funk, JA and Altier, C}, year={2004}, month={Apr}, pages={691–697} }
 @article{gebreyes_thakur_davies_funk_altier_2004, title={Trends in antimicrobial resistance, phage types and integrons among Salmonella serotypes from pigs, 1997-2000}, volume={53}, ISSN={["1460-2091"]}, DOI={10.1093/jac/dkh247}, abstractNote={OBJECTIVES
The objectives of this study were to determine antimicrobial resistance and to identify phage types and class 1 integrons among non-typhoidal Salmonella isolates from 24 pig farms in North Carolina collected between 1997 and 2000.


METHODS
A total of 1314 isolates of 30 serotypes from pig faecal samples were collected and analysed over a 3 year period. The isolates were characterized using antimicrobial susceptibility testing, phage typing, PCR and DNA sequencing for class 1 integrons.


RESULTS
A high frequency of resistance to antimicrobial agents including tetracycline (85%), ampicillin (47%), co-amoxiclav (23%) and chloramphenicol (21%) was detected. Two multidrug resistance patterns were common in Typhimurium (including variant Copenhagen): isolates with co-amoxiclav, ampicillin, chloramphenicol, streptomycin, sulfamethoxazole and tetracycline (R-type AxACSSuT) [36%] and isolates with ampicillin, kanamycin, streptomycin, sulfamethoxazole and tetracycline (R-type AKSSuT) [45%] resistance patterns. Definitive Type 104 (DT104) was the most common (34%) among eight phage types identified. AKSSuT was found among non-DT104 phage types, particularly DT21 and DT193. Class 1 integrons were detected among various serotypes including Typhimurium, Derby, Muenchen, Worthington, Bere and Muenster. aadA was the most common resistance gene insert, and the oxa30 beta-lactamase resistance gene was also identified among serovar Muenchen.


CONCLUSIONS
In this study, two most important multidrug resistance patterns (AxACSSuT and AKSSuT) and phage types of public health significance (DT104 and DT193) constituted two-thirds of the serotype Typhimurium isolates. The findings imply that pigs raised in the commercial production system may pose a risk in serving as reservoirs of resistant Salmonella.}, number={6}, journal={Journal of Antimicrobial Chemotherapy}, author={Gebreyes, W.A. and Thakur, S. and Davies, P.R. and Funk, J.A. and Altier, C.}, year={2004}, month={Jun}, pages={997–1003} }
 @article{gebreyes_2003, title={Pre-harvest food safety diagnostics for Salmonella serovars. Part 2: Molecular diagnostics}, volume={11}, number={3}, journal={Journal of Swine Health and Production}, author={Gebreyes, W. A.}, year={2003}, pages={141–145} }
 @article{gebreyes_altier_2002, title={Molecular characterization of multidrug-resistant Salmonella enterica subsp enterica serovar Typhimurium isolates from swine}, volume={40}, ISSN={["0095-1137"]}, DOI={10.1128/JCM.40.8.2813-2822.2002}, abstractNote={ABSTRACT}, number={8}, journal={JOURNAL OF CLINICAL MICROBIOLOGY}, author={Gebreyes, WA and Altier, C}, year={2002}, month={Aug}, pages={2813–2822} }