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

Katherine M Lagerstrom; Nicholas C Scales; Elizabeth A Hadly

doi:10.1016/j.isci.2024.109072

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

iScience. 2024 Feb 1;27(3):109072. doi: 10.1016/j.isci.2024.109072. eCollection 2024 Mar 15.

Authors

Katherine M Lagerstrom¹, Nicholas C Scales², Elizabeth A Hadly^{1

3

4

5}

Affiliations

¹ Department of Biology, Stanford University, Stanford, CA, USA.
² Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA, USA.
³ Stanford Woods Institute for the Environment, Stanford University, Stanford, CA, USA.
⁴ Center for Innovation in Global Health, Stanford University, Stanford, CA, USA.
⁵ Department of Earth Systems Science, Stanford University, Stanford, CA, USA.

Abstract

Human and domesticated animal waste infiltrates global freshwater, terrestrial, and marine environments, widely disseminating fecal microbes, antibiotics, and other chemical pollutants. Emerging evidence suggests that guts of wild animals are being invaded by our microbes, including Escherichia coli, which face anthropogenic selective pressures to gain antimicrobial resistance (AMR) and increase virulence. However, wild animal sources remain starkly under-represented among genomic sequence repositories. We sequenced whole genomes of 145 E. coli isolates from 55 wild and 13 domestic animal fecal samples, averaging 2 (ranging 1-7) isolates per sample, on a preserve imbedded in a human-dominated landscape in California Bay Area, USA, to assess AMR, virulence, and pan-genomic diversity. With single nucleotide polymorphism analyses we predict potential transmission routes. We illustrate the usefulness of E. coli to aid our understanding of and ability to surveil the emergence of zoonotic pathogens created by the mixing of human and wild bacteria in the environment.

Keywords: Microbiology; Wildlife microbiology.