Genomic Epidemiology and Evolution of Escherichia coli in Wild Animals in Mexico.

MSphere
Robert MurphyDanesh Moradigaravand

Abstract

Escherichia coli is a common bacterial species in the gastrointestinal tracts of warm-blooded animals and humans. Pathogenicity and antimicrobial resistance in E. coli may emerge via host switching from animal reservoirs. Despite its potential clinical importance, knowledge of the population structure of commensal E. coli within wild hosts and the epidemiological links between E. coli in nonhuman hosts and E. coli in humans is still scarce. In this study, we analyzed the whole-genome sequencing data of a collection of 119 commensal E. coli strains recovered from the guts of 55 mammal and bird species in Mexico and Venezuela in the 1990s. We observed low concordance between the population structures of E. coli isolates colonizing wild animals and the phylogeny, taxonomy, and ecological and physiological attributes of the host species, with distantly related E. coli strains often colonizing the same or similar host species and distantly related host species often hosting closely related E. coli strains. We found no evidence for recent transmission of E. coli genomes from wild animals to either domesticated animals or humans. However, multiple livestock- and human-related virulence factor genes were present in E. coli of wild anim...Continue Reading

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Datasets Mentioned

BETA
PRJEB23294

Methods Mentioned

BETA
Illumina sequencing

Software Mentioned

ape package
R
VirulenceFinder
iTOL
lite
ade4 package
Roary
Figtree
ResFinder
fsm

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