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.

大肠杆菌是脊椎动物肠道的共生菌，作为机会性病原体越来越多地参与各种肠道和肠外感染。已经根据异质性和复杂的标准描述了代表具有特定致病特征的菌株组的许多致病型。全基因组测序的大众化导致了基因组数据的积累，使群体系统基因组学方法有可能出现毒力。与共生菌株的多样性相比，很少有谱系对病理负责。这些谱系在大肠杆菌中出现多次进化，主要是通过获得位于移动元件上的毒力基因，但在特定的染色体系统发育背景中。这种稳定和世界性谱系的反复出现主张通过毒力决定因素和剩余基因组之间的上位相互作用来优化菌株适应性。