PS 7-91 - Understanding the eco-evolutionary dynamics of Escherichia coli in animals at the wildland-urban interface for public health and conservation

Abstract: A common and primarily commensal resident of the vertebrate gut, Escherichia coli remains starkly unexamined outside of humans and domestic animals even though wild animals are frequently blamed for pathogenic E. coli contamination in agricultural production. Here, we uncovered the genetic diversity and distribution of E. coli in wild animals in a biological preserve, used an ecological approach to determine what environmental and host factors might contribute to patterns in the distribution and diversity we found, and then assessed the potential for wild animals to act as reservoirs or even ‘melting pots’ of harmful E. coli strains. We opportunistically collected 163 fecal samples from 14 wild and 3 domestic host species at Jasper Ridge Biological Preserve in CA, USA. We plated fecal dilutions on selective media and challenged previous methods that assumed a single isolate was representative of within-host diversity by sampling an average of 20 colonies per scat. This resulted in 1756 isolates that we subsequently assigned to a phylogroup (A, B1, B2, C, D, E, F, G, or cryptic clades) using a previously developed multiplex PCR method. Whole genome sequencing was performed on a representative subset (n=145) of these isolates to investigate their pangenomic diversity, identify potential strain-sharing events within this animal community, and assess the level of human impact on the preserve.



The isolates encompassed all known phylogroups and represented substantial diversity and variation both within the individual wild animal and among host species. We showed that the maximum number of phylogroups isolated from a host species positively corresponded to the average home range and body mass of the host (p < 0.05). This suggests that within a host species, phylogroup diversity is linked not only to laboratory sampling methodologies, but also to the host’s ability to sample E. coli from its environment. ResFinder and VirulenceFinder (CGE) identified 73 clinically relevant antimicrobial resistance genes and a high diversity of virulence factors among the genomes, respectively; 41% qualified as extraintestinal pathogens, many of which were strains associated with humans. Single nucleotide polymorphism (SNP) analyses revealed 5 probable instances of strain-sharing between hosts (< 10 SNP differences). These findings suggest that in addition to providing an understanding of how E. coli moves between humans and wild animals, E. coli can potentially provide a model organism for understanding bacterial ecology and evolution in wild systems, and especially the interconnectedness between human activities and their unintended ecological impacts in the Anthropocene.