The E phylogroup of Escherichia coli is highly diverse and mimics the whole E. coli species population structure

Abstract

Summary To get a global picture of the population structure of the Escherichia coli phylogroup E, encompassing the O157:H7 EHEC lineage, we analysed the whole genome of 144 strains isolated from various continents, hosts and lifestyles and representative of the phylogroup diversity. The strains possess 4331 to 5440 genes with a core genome of 2771 genes and a pangenome of 33 722 genes. The distribution of these genes among the strains shows an asymmetric U‐shaped distribution. E phylogenetic strains have the largest genomes of the species, partly explained by the presence of mobile genetic elements. Sixty‐eight lineages were delineated, some of them exhibiting extra‐intestinal virulence genes and being virulent in the mouse sepsis model. Except for the EHEC lineages and the reference EPEC, EIEC and ETEC strains, very few strains possess intestinal virulence genes. Most of the strains were devoid of acquired resistance genes, but eight strains possessed extended‐spectrum beta‐lactamase genes. Human strains belong to specific lineages, some of them being virulent and antibiotic‐resistant [sequence type complexes (STcs) 350 and 2064]. The E phylogroup mimics all the features of the species as a whole, a phenomenon already observed at the STc level, arguing for a fractal population structure of E. coli.

The Role of Mobile Genetic Elements in Virulence Factor Carriage from Symptomatic and Asymptomatic Cases of Escherichia coli Bacteriuria

“…Phylogroups B2 and D statistically carry more virulence factors than the other phylogroups, which is corroborated by other studies ( 16 , 17 , 81 ). While phylogroups E and B1 are most frequently associated with highly virulent EHEC strains ( 15 , 81 ), we identified both in our data set. Both of these traditionally highly virulent groups contained fewer virulence factors than the B2 and D phylogroups.…”

“…In ASB, a clean-catch urine sample with a high bacterial burden (typically ≥10 5 CFU/mL) is observed, but without the patient experiencing UTI-associated signs or symptoms. Strains of E. coli isolated from cases of ASB have not been distinguished from UTI-associated isolates in terms of specific defining virulence factors, and they cluster genetically in the same B2 and D clades ( 9 – 15 ). In general, B2 and D strains are known to harbor more virulence factors than other gut-commensal phylogroups, such as A, B1, and C ( 16 , 17 ).…”

High incidence of fosfomycin-resistant uropathogenic E. coli among children

“…Sixty-eight lineages were delineated, some of them exhibiting extra-intestinal virulence genes and being virulent in the mouse sepsis model. Some diarrheogenic E. coli strains are found in this phylogroup and except for the EHEC lineages and the reference EPEC, EIEC and ETEC strains, very few strains possess intestinal virulence genes [ 39 ].…”

Vaccines against extraintestinal pathogenic Escherichia coli (ExPEC): progress and challenges

“… 156 When found to be pathogenic, strains from the D lineage are usually either members of InPEC or UPEC pathotypes. 156 , 174 Phylogroup D strains can exist as harmless commensals, but like B2 strains, their pathogenicity can be difficult to predict using just genomic analysis because even commensals often carry proteins known to impact extraintestinal virulence. 63 …”