Impressive pan-genomic diversity of E. coli from a wild animal community near urban development reflects human impacts

Human and domestic animal waste, containing bacteria such as E. coli, and other pollutants including antimicrobials, infiltrates global environments and impacts wild animal microbiomes. This promotes the spread of antibiotic resistance (ABR) and fuels the creation of better pathogens. As the human population continues to grow and encroach into wildlands, we will likely experience more frequent and possibly more severe pandemics. At the same time, we could be faced with a drastically weakened ability to cure ourselves with our current arsenal of antibiotics. Our study found that wild animals at Stanford’s Jasper Ridge Biological Preserve (JRBP) carry a huge diversity of E. coli, much of which is likely commensal, but a non-trivial amount that is human-derived, pathogenic to humans, and contains clinically relevant ABR. Furthermore, and for the first time, we show that individual wild animals carry multiple E. coli strains simultaneously, increasing the likelihood that guts of wild animals serve as melting pots of bacteria with novel combinations of pathogenic and drug resistant capabilities. We also capture multiple occurrences of probable strain-sharing among different individuals, some with predator-prey relationships, showing that transmission likely occurs readily within the wild animal community and between wild and domestic animals that frequent the preserve.These results are not expected to be unique to the JRBP animal community, but are likely reflective of human-impacted wildlife populations around the global in the Anthropocene, any one of which could be the source or sink of the next superbug. Thus, wildlife may serve as reservoirs or melting pots of pathogens, but they also host a wide diversity of commensal bacteria and themselves contribute to biodiversity that supports ecosystems, which are healthiest and most resilient when they are diverse.

Recommended citation: Lagerstrom, K. M., Scales, N. C., and Hadly, E. A. 2024. Impressive pan-genomic diversity of E. coli from a wild animal community near urban development reflects human impacts. iScience 27(3); 109072. https://doi.org/10.1016/j.isci.2024.109072
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