The population genetics of commensal Escherichia coli

Abstract

The primary habitat of Escherichia coli is the vertebrate gut, where it is the predominant aerobic organism, living in symbiosis with its host. Despite the occurrence of recombination events, the population structure is predominantly clonal, allowing the delineation of major phylogenetic groups. The genetic structure of commensal E. coli is shaped by multiple host and environmental factors, and the determinants involved in the virulence of the bacteria may in fact reflect adaptation to commensal habitats. A better characterization of the commensal niche is necessary to understand how a useful commensal can become a harmful pathogen. In this Review we describe the population structure of commensal E. coli, the factors involved in the spread of different strains, how the bacteria can adapt to different niches and how a commensal lifestyle can evolve into a pathogenic one.

Environmental adaptation and vertical dissemination of ESBL‐/pAmpC‐producing Escherichia coli in an integrated broiler production chain in the absence of an antibiotic treatment

“…ST‐354 isolates harboured the pap operon which was shown to be responsible for the in vitro adhesion to not only human but also animal cell lines (Stromberg et al ., 1990; Frommel et al ., 2013). But intestinal colonization is also depending on the iron uptake ability of E. coli (Nowrouzian et al ., 2006; Tenaillon et al ., 2010). On the one hand, ST‐117 strains of our study had the highest number of genes referring to iron uptake, on the other hand, these isolates had low numbers of genes which contribute to adherence factors.…”

Temporal variations in patterns ofEscherichia colistrain diversity and antimicrobial resistance in the migrant Egyptian vulture

“…While some phylogenetic groups (A and some D group strains) of E. coli are more permissive to develop resistance to third generation cephalosporins whereas group B2 strains are less likely to develop resistance compared to the other groups [51–53]. This variability influences the strain structures of E. coli in hosts frequently exposed to antimicrobials [4]. Clearly, MAR E. coli strains are surviving, persisting and propagating in the gut of the vultures.…”

“…Escherichia coli occurs widely in the intestines and faeces of all vertebrates, and its prevalence and diversity in wild species varies with host taxonomy, geography, diet, and environmental conditions particularly the degree of synanthropy of the hosts’ surroundings [1–4]. The recognition of wild vertebrate species carrying E. coli is not recent, but the number of wild species and the range of environmental conditions that have been studied to date is biased to a handful of locations globally, with notable paucity of studies from densely-populated, developing countries [5].…”

“…Also, more synanthropic bird species show increased multidrug resistance E. coli [10,11]. Wild vertebrate species, especially those that use human-dominated landscapes as part of their life history, are therefore likely to be ‘reservoirs and melting pots of bacterial resistance’ with increasing potential of resistant E. coli colonizing intestine and resulting in antimicrobial resistant infections if they end up in urinary tract or the bloodstream adding concern to human health [4,12]. …”

“…Phylogeny of E. coli of wild birds varied concomitant to exposure to humans and human-associated vertebrates such as domestic fowl underscoring the influence of anthropogenic components [5,10]. The near-absence of studies of the of E. coli in wild vertebrates in densely-populated countries is worrisome especially given the increased risk of wild species interacting with humans and domestic animals, and are urgently required [4]. In particular, documentation of the temporal and spatial patterns of antimicrobial drug resistance in different habitats and species in developing countries is essential to developing a cogent understanding of wildlife as a source of antimicrobial resistance [16,17]…”