@article{quintana-hayashi_thakur_2012, title={Longitudinal Study of the Persistence of Antimicrobial-Resistant Campylobacter Strains in Distinct Swine Production Systems on Farms, at Slaughter, and in the Environment}, volume={78}, ISSN={["0099-2240"]}, DOI={10.1128/aem.07723-11}, abstractNote={ABSTRACT
          
            The objectives of this study were to compare and characterize the prevalence of antimicrobial-resistant (AR)
            Campylobacter
            in conventional and antimicrobial-free (ABF) production systems on farms, at slaughter, and in the environment. Fecal and environmental samples were collected from ABF farms (pigs, 1,239; environment, 797) and conventional farms (pigs, 1,650; environment, 1,325). At slaughter, we collected samples from carcasses, including postevisceration swabs, postchill swabs, and mesenteric lymph nodes from ABF systems (postevisceration swabs, 182; postchill swabs, 199; mesenteric lymph nodes, 184) and conventional systems (postevisceration swabs, 272; postchill swabs, 271; mesenteric lymph nodes, 255) at separate processing facilities. We also sampled the processing plant environment, including truck and lairage floor swab samples (ABF, 115; conventional, 90). Overall, a total of 2,908
            Campylobacter
            isolates, including
            Campylobacter coli
            (farm, 2,557, 99.8%; slaughter, 341, 98.3%) and
            Campylobacter jejuni
            (farm, 4, 0.2%; slaughter, 6, 1.7%), were isolated in the study. There was no significant difference in the prevalence of
            Campylobacter
            between ABF and conventionally raised pigs (farrowing,
            P
            = 0.20; nursery,
            P
            = 0.06; finishing,
            P
            = 0.24) and the environment (
            P
            = 0.37). At slaughter,
            Campylobacter
            was isolated from all of the stages, including postchill. The highest frequencies of resistance were exhibited against tetracycline (ABF, 48.2%; conventional, 88.3%). Ciprofloxacin-resistant
            C. coli
            isolates were observed in conventionally raised (17.1%) and ABF (1.2%) pigs (
            P
            = 0.11). Antimicrobial use data from conventional farms indicated significant associations between oxytetracycline use and tetracycline resistance in the nursery pigs (
            P
            = 0.01), between tiamulin exposure and azithromycin and erythromycin resistance in nursery (
            P
            < 0.01) and finishing (
            P
            < 0.01) pigs, and between enrofloxacin exposure and ciprofloxacin and nalidixic acid resistance in farrowing (
            P
            < 0.01) and nursery (
            P
            < 0.01) pigs. Identical antimicrobial resistance profiles were observed in the pigs and their environments on farms and at slaughter. In summary, our results highlight the persistence and dissemination of AR
            Campylobacter
            from farm to slaughter in ABF and conventionally raised pigs and their environments.
          }, number={8}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Quintana-Hayashi, Macarena P. and Thakur, Siddhartha}, year={2012}, month={Apr}, pages={2698–2705} }
 @article{quintana-hayashi_thakur_2012, title={Phylogenetic Analysis Reveals Common Antimicrobial Resistant Campylobacter coli Population in Antimicrobial-Free (ABF) and Commercial Swine Systems}, volume={7}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0044662}, abstractNote={The objective of this study was to compare the population biology of antimicrobial resistant (AR) Campylobacter coli isolated from swine reared in the conventional and antimicrobial-free (ABF) swine production systems at farm, slaughter and environment. A total of 200 C. coli isolates selected from fecal, environmental, and carcass samples of ABF (n = 100) and conventional (n = 100) swine production systems were typed by multilocus sequence typing (MLST). Sequence data from seven housekeeping genes was analyzed for the identification of allelic profiles, sequence types (STs) and clonal complex determination. Phylogenetic trees were generated to establish the relationships between the genotyped isolates. A total of 51 STs were detected including two novel alleles (glnA 424 and glyA 464) and 14 novel STs reported for the first time. The majority of the C. coli isolates belonged to ST-854 (ABF: 31, conventional: 17), and were grouped in clonal complex ST-828 (ABF: 68%, conventional: 66%). The mean genetic diversity (H) for the ABF (0.3963+/−0.0806) and conventional (0.4655+/−0.0714) systems were similar. The index of association () for the ABF ( = 0.1513) and conventional ( = 0.0991) C. coli populations were close to linkage equilibrium, indicative of a freely recombining population. Identical STs were detected between the pigs and their environment both at farm and slaughter. A minimum spanning tree revealed the close clustering of C. coli STs that originated from swine and carcass with those from the environment. In conclusion, our study reveals a genotypic diverse C. coli population that shares a common ancestry in the conventional and ABF swine production systems. This could potentially explain the high prevalence of antimicrobial resistant C. coli in the ABF system in the absence of antimicrobial selection pressure.}, number={9}, journal={PLOS ONE}, author={Quintana-Hayashi, Macarena P. and Thakur, Siddhartha}, year={2012}, month={Sep} }