The population genetics of pathogenicEscherichia coli

Escherichia coliis a commensal of the vertebrate gut as well as an opportunistic pathogen. In this Review, Denamur and colleagues explore the emergence of virulence during the evolution ofE. coli, with a focus on the main ExPEC, InPEC and hybrid clones. Escherichia coliis a commensal of the vertebrate gut that is increasingly involved in various intestinal and extra-intestinal infections as an opportunistic pathogen. Numerous pathotypes that represent groups of strains with specific pathogenic characteristics have been described based on heterogeneous and complex criteria. The democratization of whole-genome sequencing has led to an accumulation of genomic data that render possible a population phylogenomic approach to the emergence of virulence. Few lineages are responsible for the pathologies compared with the diversity of commensal strains. These lineages emerged multiple times duringE. colievolution, mainly by acquiring virulence genes located on mobile elements, but in a specific chromosomal phylogenetic background. This repeated emergence of stable and cosmopolitan lineages argues for an optimization of strain fitness through epistatic interactions between the virulence determinants and the remaining genome.