Using whole-genome sequence data to examine the epidemiology of Salmonella, Escherichia coli and associated antimicrobial resistance in raccoons (Procyon lotor), swine manure pits, and soil samples on swine farms in southern Ontario, Canada

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.

Rural Raccoons (Procyon lotor) Not Likely to Be a Major Driver of Antimicrobial Resistant Human Salmonella Cases in Southern Ontario, Canada: A One Health Epidemiological Assessment Using Whole-Genome Sequence Data

“…The identification of highly similar or identical cgMLST types (<10 allelic differences) was a rare occurrence in this population of over 600 isolates and was very specific to certain sources and serovars, highlighting potential transmission only in certain contexts (i.e., S. Heidelberg between poultry and humans, S. Newport between raccoons and soil). Likely these instances represent the acquisition of Salmonella by humans through undercooked poultry [for S. Heidelberg; (45)] or as a result of frequent exchange of Salmonella between raccoons and their immediate environment, as has been previously documented (25,46). Alternatively, overlap in cgMLST types between these different sources could indicate exposure to a common source that was not identified here.…”

“…In our previous work using whole-genome sequence (WGS) data to assess the potential for transmission of Salmonella, E. coli and AMR determinants between raccoons, soil, and manure pits on swine farms in southern Ontario, the identification of similar or identical subtypes (based on core-genome multi-locus sequence typing) among isolates from these different sources and farms was consistent with potential on-farm and betweenfarm transmission (25). Our present work assesses this same subset of samples originating from raccoons, soil, and manure pits on swine farms within the context of a greater geographic region in southern Ontario, by comparing those farm isolates to other Salmonella isolates from humans, livestock, and water sources collected during the same time period as part of public health surveillance programs.…”

Using whole-genome sequence data to examine the epidemiology of antimicrobial resistance in Escherichia coli from wild meso-mammals and environmental sources on swine farms, conservation areas, and the Grand River watershed in southern Ontario, Canada

“…A strikingly similar pattern of these two tetracycline resistance genes was also documented in wild small mammals (i.e., mice, voles, shrews) captured in the same study region in 2008; tet (A)-but not tet(B)-was significantly more likely to be identified in animals captured on swine farms compared to residential areas [39]. When we previously examined the epidemiology of these two genes among E. coli in the swine farm environment in detail, no clear patterns emerged by farm location, year of sampling, or source (raccoons, soil, swine manure pits) [28]. Antimicrobial use data for these swine farms were unavailable, but tetracyclines are often used in the Canadian swine industry [44].…”

“…The aim of the present work was to build on the previous longitudinal study [19], and small-scale analysis of genomic data from swine farm isolates [28], by incorporating additional whole-genome sequencing data from E. coli isolates obtained in conservation areas, to explore the potential impact of different location types (swine farms vs. conservation areas) on the occurrence of AMR determinants in raccoons. In addition, we sought to examine phenotypically resistant E. coli water isolates obtained by routine public health surveillance in the same study region and time period alongside the isolates from the previous wildlife study, to better understand the potential role of raccoons and other meso-mammals in the ecology of AMR in a broader context.…”

“…However, a comparison of resistance phenotypes and genotypes (determined using PCR) of the resistant E. coli isolates in these different location types revealed similar phenotypes and resistance genes among isolates obtained in conservation areas that were altogether absent from isolates obtained on swine farms (e.g., blaCMY-2) [19], suggesting that there may, indeed, be differences in the types of AMR determinants carried by raccoons, depending on the local environment. Our recent epidemiologic assessment of the subset of Salmonella and E. coli isolates originating from swine farms using genomic data revealed frequent overlap, and thus, possible transmission, of AMR determinants between soil and raccoons, but there was limited overlap between isolates from raccoons and swine manure pits [28].…”