@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{funk_davies_nichols_2001, title={Longitudinal study of Salmonella enterica in growing pigs reared in multiple-site swine production systems}, volume={83}, ISSN={["1873-2542"]}, DOI={10.1016/S0378-1135(01)00404-7}, abstractNote={Intensive longitudinal investigations of breeding and growing pig populations in two multiple-site swine production systems were conducted in NC, USA. Five cohorts of sows and individually identified growing pigs from their litters were serially sampled in order to determine the prevalence and serotypes of Salmonella enterica in each stage of production based on fecal culture. In addition to fecal samples, feed and environmental samples were obtained. Fifteen different serotypes were isolated from the two systems, the most frequently isolated serotypes were S. typhimurium var Mbandaka and S. typhimurium var Copenhagen. Pig prevalence estimates ranged from 0 to 48.1%. Environmental contamination was frequently encountered despite cleaning and disinfection. Feed was rarely (2/800, 0.25%) identified as S. enterica positive. We observed highly variable patterns of S. enterica prevalence and serotype profiles within cohorts over time and among cohorts within systems. These observations indicate that point estimates of S. enterica prevalence and serotypes cannot be considered as reliable indicators of the S. enterica status of farms, and that uncontrolled studies of interventions to control S. enterica may yield misleading results. These findings are critical to the design of epidemiological studies of S. enterica on swine farms and may suggest that cohort level, as opposed to farm or company level events or management practices, may be important as potential risk factors for S. enterica fecal shedding in market age pigs.}, number={1}, journal={VETERINARY MICROBIOLOGY}, author={Funk, JA and Davies, PR and Nichols, MA}, year={2001}, month={Oct}, pages={45–60} }
 @article{funk_davies_gebreyes_2001, title={Risk factors associated with Salmonella enterica prevalence in three-site swine production systems in North Carolina, USA}, volume={114}, number={9-10}, journal={Berliner Und Munchener Tierarztliche Wochenschrift (Berlin, Germany : 1949)}, author={Funk, J. A. and Davies, P. R. and Gebreyes, W.}, year={2001}, pages={335–338} }
 @article{gebreyes_davies_morrow_funk_altier_2000, title={Antimicrobial resistance of Salmonella isolates from swine}, volume={38}, number={12}, journal={Journal of Clinical Microbiology}, author={Gebreyes, W. A. and Davies, P. R. and Morrow, W. E. M. and Funk, J. A. and Altier, C.}, year={2000}, pages={4633–4636} }
 @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: ∼1g faeces—primary enrichments in tetrathionate and Hajna GN broths—secondary enrichment in RV broth). The effects of enrichment temperatures (37 vs 42 °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 °C was superior to 37 °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{davies_funk_morrow_2000, title={Fecal shedding of Salmonella by gilts before and after introduction to a swine breeding farm}, volume={8}, number={1}, journal={Swine Health and Production}, author={Davies, P. R. and Funk, J. A. and Morrow, W. E. M.}, year={2000}, pages={25–29} }
 @article{funk_davies_morrow_nichols_2000, title={Temporal patterns of Salmonella enterica prevalence and serotypes in breeding and growing swine populations}, journal={Proceedings of the 9th symposium of the International Society for Veterinary Epidemiology and Economics, Breckenridge, Colorado, USA, August 6-11 2000}, publisher={International Society for Veterinary Epidemiology and Economics (ISVEE)}, author={Funk, J. A. and Davies, P. R. and Morrow, W. E. M. and Nichols, M. A.}, year={2000}, pages={203} }
 @article{funk_davies_nichols_2000, title={The effect of fecal sample weight on detection of Salmonella enterica in swine feces}, volume={12}, ISSN={["1943-4936"]}, DOI={10.1177/104063870001200504}, abstractNote={The effect of different fecal sample weights on the detection of Salmonella enterica in swine feces was examined. Sample weights evaluated were rectal swabs and fecal samples weighing 1 g, 10 g, and 25 g. Comparisons were made on matched fecal samples obtained from individual pigs housed on 2 commercial swine farms in North Carolina. Relative sensitivity (number of positive pigs per fecal weight category/number positive in all weight categories) increased ( P < 0.001) with fecal sample weight, and ranged from 9% for rectal swabs to 78% for 25-g samples. Stomaching of fecal samples did not affect detection of S. enterica. These observations demonstrate that fecal sample weight can markedly influence estimates of prevalence of S. enterica in epidemiologic studies. Failure to consider the imperfect sensitivity of bacterial culture in the design and interpretation of epidemiologic studies will lead to underestimation of prevalence and reduced power to detect the presence of S. enterica-infected herds.}, number={5}, journal={JOURNAL OF VETERINARY DIAGNOSTIC INVESTIGATION}, author={Funk, JA and Davies, PR and Nichols, MA}, year={2000}, month={Sep}, pages={412–418} }
 @article{davies_funk_morrow_1999, title={Fecal shedding of Salmonella by a cohort of finishing pigs in North Carolina}, volume={7}, number={5}, journal={Swine Health and Production}, author={Davies, P. and Funk, J. and Morrow, W. E. M.}, year={1999}, pages={231–234} }
 @article{davies_bovee_funk_morrow_jones_deen_1998, title={Isolation of Salmonella serotypes from feces of pigs raised in a multiple-site production system}, volume={212}, number={12}, journal={Journal of the American Veterinary Medical Association}, author={Davies, P. R. and Bovee, F. G. E. M. and Funk, J. A. and Morrow, W. E. M. and Jones, F. T. and Deen, J.}, year={1998}, pages={1925–1929} }
 @article{funk_troutt_isaacson_fossler_1998, title={Prevalence of pathogenic Yersinia enterocolitica in groups of swine at slaughter}, volume={61}, ISSN={["1944-9097"]}, DOI={10.4315/0362-028X-61.6.677}, abstractNote={In order to estimate the prevalence of swine herds infected with pathogenic Yersinia enterocolitica, 103 lots of market swine were randomly selected at slaughter during six 1-month intervals. Pigs within each lot were sampled by swabbing the oral-pharyngeal surface, poststunning and postexsanguination but prescalding. Ninety-five lots (92.2%) contained at least one pig infected with Y. enterocolitica. Pathogenic strains were defined as those harboring the ail gene which has been identified in Y. enterocolitica that causes human clinical disease. Identification of those strains harboring the ail gene was accomplished using a polymerase chain reaction technique. Twenty-nine lots (28.2%) contained at least one pig from which ail-containing (pathogenic) Y. enterocolitica were isolated. Of the 107 pathogenic Y. enterocolitica isolates identified, 89.7% were serotype O:5 and 3.7% were serotype O:3. The results from this study will aid in the design of future epidemiological investigations concerning on-farm prevalence and associated risk factors for pathogenic Y. enterocolitica. Additionally, the results support the hypothesis that swine are a significant potential reservoir for human infections by Y. enterocolitica.}, number={6}, journal={JOURNAL OF FOOD PROTECTION}, author={Funk, JA and Troutt, HF and Isaacson, RE and Fossler, CP}, year={1998}, month={Jun}, pages={677–682} }