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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.

Phylogenetic Analysis Reveals Common Antimicrobial Resistant Campylobacter coli Population in Antimicrobial-Free (ABF) and Commercial Swine Systems