Phylogenetic background and habitat drive the genetic diversification of Escherichia coli

PLoS Genetics
Marie TouchonE P C Rocha

Abstract

Escherichia coli is mostly a commensal of birds and mammals, including humans, where it can act as an opportunistic pathogen. It is also found in water and sediments. We investigated the phylogeny, genetic diversification, and habitat-association of 1,294 isolates representative of the phylogenetic diversity of more than 5,000 isolates from the Australian continent. Since many previous studies focused on clinical isolates, we investigated mostly other isolates originating from humans, poultry, wild animals and water. These strains represent the species genetic diversity and reveal widespread associations between phylogroups and isolation sources. The analysis of strains from the same sequence types revealed very rapid change of gene repertoires in the very early stages of divergence, driven by the acquisition of many different types of mobile genetic elements. These elements also lead to rapid variations in genome size, even if few of their genes rise to high frequency in the species. Variations in genome size are associated with phylogroup and isolation sources, but the latter determine the number of MGEs, a marker of recent transfer, suggesting that gene flow reinforces the association of certain genetic backgrounds with spec...Continue Reading

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Citations

Sep 19, 2020·Microbiology Resource Announcements·Georgia Breckell, Olin K Silander
Aug 23, 2020·Nature Reviews. Microbiology·Erick DenamurDavid Gordon
Jan 9, 2021·Microbial Genomics·Gal HoreshNicholas R Thomson
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Jan 8, 2021·MSphere·Robert MurphyDanesh Moradigaravand
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Dec 17, 2021·The Science of the Total Environment·Diana DiasSónia Mendo

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Methods Mentioned

BETA
PCA
biopsies

Software Mentioned

Virsorter
R
infernal
Mash
stats
R package
mafft
bionj
ISfinder
igraph

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