The population genetics of pathogenic Escherichia coli


Escherichia coli is 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 during E. coli evolution, 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.

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Fig. 1: Phylogenetic history of 72 Escherichia strains.
Fig. 2: Example phylogenetic history of Escherichia coli strains of three main sequence types according to the Warwick University (WU) scheme.
Fig. 3: Modularity and mobility of acquired genomic elements.
Fig. 4: Schematic representation of various evolutionary scenarios involved in the emergence of virulent lineages within Escherichia coli species.
Fig. 5: Virulence and resistance factors of the hybrid InPEC–ExPEC pathotype O80:H2 Escherichia coli clone.


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The authors are grateful to B. Condamine for help with the figure drafts. O.C., S.B. and E.D. are partially supported by the Fondation pour la Recherche Médicale (Equipe FRM 2016, grant number DEQ20161136698).

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E.D. and D.G. conceived and wrote the main part of the Review. O.C. provided numerous reflections and epidemiologic and genomic data for the main text and the figures. S.B. wrote part of the InPEC and hybrid clones sections.

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Correspondence to Erick Denamur.

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Pathotypes (also known as pathovars)

Groups of organisms that have the same pathogenicity on a specified host.


(Also known as lineages). Groups of organisms that consist of a common ancestor and all its lineal descendants. This term has been used at different phylogenetic levels, leading to some confusion. For the cryptic clades, it corresponds to species or subspecies, whereas within the Escherichia coli species it designates groups of organisms composing a sequence type.


Groups of organisms that belong to a large phylogenetic entity within the species. There are at least eight phylogenetic groups within the Escherichia coli species, named A, B1, B2, C, D, E, F and G.


A group of organisms that have the same association of O-polysaccharide antigen (serogroup), flagellar (H) antigen and capsular (K) antigen. There are currently 53 H types and 67 K antigens. However, as few laboratories had the capability to type the K antigens, serotypes based on O and H antigens became the gold standard.


A group of organisms that have the same surface O-polysaccharide antigen. There are currently 186 different Escherichia coli O serogroups.

Sequence type

The allelic profile constituted by the alleles at each studied gene locus, usually seven. A group of organisms can be categorized according to the sequence type. Like multilocus enzyme electrophoresis, multilocus sequence typing uses the allele as the unit of comparison, rather than the nucleotide sequence. A sequence type complex (also known as a clonal group) is a simple or double-locus variant of a sequence type.

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Denamur, E., Clermont, O., Bonacorsi, S. et al. The population genetics of pathogenic Escherichia coli. Nat Rev Microbiol (2020).

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