Comparison of Antimicrobial-Resistant Escherichia coli Isolates from Urban Raccoons and Domestic Dogs

Abstract

Wildlife can be exposed to antimicrobial-resistant bacteria (ARB) via multiple pathways. Spatial overlap with domestic animals is a prominent exposure pathway. However, most studies of wildlife-domestic animal interfaces have focused on livestock and little is known about the wildlife-companion animal interface. Here, we investigated the prevalence and phylogenetic relatedness of extended-spectrum cephalosporin-resistant (ESC-R) Escherichia coli from raccoons (Procyon lotor) and domestic dogs (Canis lupus familiaris) in the metropolitan area of Chicago, IL, USA. To assess the potential importance of spatial overlap with dogs, we explored whether raccoons sampled at public parks (i.e., parks where people and dogs could enter) differed in prevalence and phylogenetic relatedness of ESC-R E. coli to raccoons sampled at private parks (i.e., parks where people and dogs could not enter). Raccoons had a significantly higher prevalence of ESC-R E. coli (56.9%) than dogs (16.5%). However, the richness of ESC-R E. coli did not vary by host species. Further, core single-nucleotide polymorphism (SNP)-based phylogenetic analyses revealed that isolates did not cluster by host species, and in some cases displayed a high degree of similarity (i.e., differed by less than 20 core SNPs). Spatial overlap analyses revealed that ESC-R E. coli were more likely to be isolated from raccoons at public parks than raccoons at private parks, but only for parks located in suburban areas of Chicago, not urban areas. That said, ESC-R E. coli isolated from raccoons did not genetically cluster by park of origin. Our findings suggest that domestic dogs and urban/suburban raccoons can have a diverse range of ARB, some of which display a high degree of genetic relatedness (i.e., differ by less than 20 core SNPs). Given the differences in prevalence, domestic dogs are unlikely to be an important source of exposure for mesocarnivores in urbanized areas. IMPORTANCE Antimicrobial-resistant bacteria (ARB) have been detected in numerous wildlife species across the globe, which may have important implications for human and animal health. Wildlife can be exposed to ARB via numerous pathways, including via spatial overlap with domestic animals. However, the interface with domestic animals has mostly been explored for livestock and little is known about the interface between wild animals and companion animals. Our work suggests that urban and suburban wildlife can have similar ARB to local domestic dogs, but local dogs are unlikely to be a direct source of exposure for urban-adapted wildlife. This finding is important because it underscores the need to incorporate wildlife into antimicrobial resistance surveillance efforts, and to investigate whether certain urban wildlife species could act as additional epidemiological pathways of exposure for companion animals, and indirectly for humans.

Keywords: Escherichia coli; cephalosporin; dog; interface; phylogenetic; raccoon; urban.

FIG 1

Sampling sites in the northwestern portion of the Chicago metropolitan area. Small dark red and yellow polygons depict sites where raccoons were sampled. The four small dark red polygons are private sites (i.e., sites where people and domestic dogs were not allowed to enter) and the three yellow polygons are public sites (i.e., sites where people and dogs were allowed to enter). Blue stars represent dog parks and pink polygons are dog home ZIP codes. Four shapefiles were used to create the map: (i) a street shapefile for Cook County (https://hub-cookcountyil.opendata.arcgis.com/datasets/4569d77e6d004c0ea5fada54640189cf_5), (ii) a street shapefile for DuPage County (https://gisdata-dupage.opendata.arcgis.com/datasets/roadtypecenterline?geometry=-89.010%2C41.659%2C-87.158%2C42.017), (iii) a Lake Michigan shapefile (https://gis-michigan.opendata.arcgis.com/datasets/5e2911231fe246128d0ff8495935ee85_12), and (iv) a U.S. shapefile (https://hub.arcgis.com/datasets/1b02c87f62d24508970dc1a6df80c98e_0?geometry=118.842%2C29.346%2C-4.029%2C67.392).

FIG 2

Prevalence and phylogenetic associations of ESC-R E. coli isolated from raccoons and domestic dogs. (A) Prevalence of ESC-R E. coli. Whiskers represent 95% confidence intervals and numbers above whiskers are sample sizes. (B) Minimum spanning tree of ESC-R E. coli sequence types (STs) detected in raccoons (blue) and domestic dogs (orange). The size of nodes represents the number of isolates and the length of lines connecting nodes represents the number of allelic differences. ST numbers preceded by a tilde were unknown. (C) Core SNP-based maximum likelihood phylogenetic tree of the 152 ESC-R E. coli and heatmap of isolates classified based on host species (i.e., raccoon, blue; dog, orange). The reference is E. coli K-12 strain MG1655.

FIG 3

Mean number of core SNP differences between pairs of ESC-R E. coli isolates by sequence type (ST) based on whether pairs of isolates were from different animal species (“between”) or the same animal species (“within”). Numbers next to raccoon and dog silhouettes are the number of isolates belonging to each animal species by ST. NA indicates that no comparison could be done.

FIG 4

Prevalence of antimicrobial resistance genes (ARG) in ESC-R E. coli isolated from raccoons (blue) (n = 123) and domestic dogs (orange) (n = 29).

FIG 5

Raw prevalence of ESC-R E. coli in raccoons by urban-suburban context and dog presence (yellow, public park [i.e., people and domestic dogs can enter], red, private parks [i.e., people and domestic dogs cannot enter]). Whiskers are 95% confidence intervals. Raccoons were sampled in two public (n = 78) and two private (n = 52) suburban parks and one public (n = 56) and two private (n = 25) urban parks.