Abstract
To better understand the contribution of wildlife to the dissemination of Salmonella and antimicrobial resistance in Salmonella and Escherichia coli, we examined whole-genome sequence data from Salmonella and E. coli isolates collected from raccoons (Procyon lotor) and environmental sources on farms in southern Ontario. All Salmonella and phenotypically resistant E. coli collected from raccoons, soil, and manure pits on five swine farms as part of a previous study were included. We assessed for evidence of potential transmission of these organisms between different sources and farms utilizing a combination of population structure assessments (using core-genome multi-locus sequence typing), direct comparisons of multi-drug resistant isolates, and epidemiological modeling of antimicrobial resistance (AMR) genes and plasmid incompatibility (Inc) types. Univariable logistic regression models were fit to assess the impact of source type, farm location, and sampling year on the occurrence of select resistance genes and Inc types. A total of 159 Salmonella and 96 resistant E. coli isolates were included. A diversity of Salmonella serovars and sequence types were identified, and, in some cases, we found similar or identical Salmonella isolates and resistance genes between raccoons, soil, and swine manure pits. Certain Inc types and resistance genes associated with source type were consistently more likely to be identified in isolates from raccoons than swine manure pits, suggesting that manure pits are not likely a primary source of those particular resistance determinants for raccoons. Overall, our data suggest that transmission of Salmonella and AMR determinants between raccoons and swine manure pits is uncommon, but soil-raccoon transmission appears to be occurring frequently. More comprehensive sampling of farms, and assessment of farms with other livestock species, as well as additional environmental sources (e.g., rivers) may help to further elucidate the movement of resistance genes between these various sources.
Highlights
The rise of antimicrobial resistance (AMR) is a major global threat to the health of humans and animals alike [1, 2]
Genomic epidemiology of Salmonella and E. coli in raccoons and environmental samples from swine farms assessments of potential transmission utilizing statistical modeling, our aim was to determine the impact of source type, farm location, and sampling year on the occurrence of AMR determinants
All sources were found to Genomic epidemiology of Salmonella and E. coli in raccoons and environmental samples from swine farms contain at least one or more internationally important Salmonella sequence types which have been implicated in human illness
Summary
The rise of antimicrobial resistance (AMR) is a major global threat to the health of humans and animals alike [1, 2]. This work is part of a larger repeated cross-sectional study of wild meso-mammals (raccoons, primarily) on swine farms and conservation areas in southern Ontario, Canada between 2011 and 2013 [18,19,20]. Copenhagen DT104), serovars (e.g., Salmonella Agona) and resistance patterns appeared only in samples obtained on swine farms [18, 19]. In certain cases, it was unclear if the molecular determinants of resistance were shared or were distinct between different compartments of this environment, even when phenotypic resistance was the same
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