Phylogenetic analysis reveals common antimicrobial resistant Campylobacter coli population in antimicrobial-free (ABF) and commercial swine systems

Abstract

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 (I(A)(S)) for the ABF (I(A)(S)= 0.1513) and conventional (I(A)(S) = 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.

Figure 1. Radial neighbor-joining tree of the unique ABF and conventional C. coli STs.

ABF and conventional STs are represented by red and blue circles, respectively.

Figure 2. Minimum spanning tree (MST) of C. coli isolates from ABF and conventional production systems.

Each ST is represented by a node. The size of each node is proportional to the number of strains that comprise that ST. Pie charts with differential colors represent C. coli sources: ABF pigs and carcass (purple), ABF environment at farm and slaughter (yellow), conventional pigs and carcass (red), and conventional environment at farm and slaughter (green). Allele differences are represented by thick bold branch lines (single locus variants), thin continuous lines (double locus variants), and dashed lines (three allele differences). Unique STs of the pigs, carcass, and environment at farm and slaughter from ABF and conventional systems were distinguished by single colored nodes.