Impressive pan-genomic diversity of E. coli from a wild animal community near urban development reflects human impacts
To address questions surrounding the extent of genetic diversity of Escherichia coli that exists among wild animals and assess the impact of human actions on wild animal gut microbes, we sequenced 145 whole genomes of E. coli isolated from stool samples of 14 wild and 3 domestic species that co-inhabit and occasionally interact on a preserve embedded in a landscape of human activity. We assess the pan-genomic diversity of these isolates and determine the prevalence of pathogenic and antimicrobial resistant (AMR) strains, revealing both substantial within-host diversity of E. coli at the phylogroup and sequence-type levels, as well as high prevalence of extra-intestinal pathogenic strains and the occurrence of clinically-relevant AMR. By investigating the genetic context of detected AMR genes, we inform the potential for mobilization via horizontal gene transfer. We also identify putative transmission events between different host species on the preserve using single nucleotide polymorphism (SNP) data. This work thus has implications for global public health, for agriculture, and for the unknown risks of the wildland-urban interface.