Characterization and rapid identification of phylogroup G in Escherichia coli, a lineage with high virulence and antibiotic resistance potential

Abstract

Summary The phylogeny of the Escherichia coli species, with the identification of seven phylogroups (A, B1, B2, C, D, E and F), is linked to the lifestyle of the strains. With the accumulation of whole genome sequence data, it became clear that some strains belong to a group intermediate between the F and B2 phylogroups, designated as phylogroup G. Here, we studied the complete sequences of 112 strains representative of the G phylogroup diversity and showed that it is composed of one main sequence type complex (STc)117 and four other STcs (STc657, STc454, STc738 and STc174). STc117, which phylogeny is characterized by very short internal branches, exhibits extensive O diversity, but little H‐type and fimH allele diversity, whereas the other STcs are characterized by a main O, H and fimH type. STc117 strains possess many traits associated with extra‐intestinal virulence, are virulent in a mouse sepsis model and exhibit multi‐drug resistance such as CTX‐M production. Epidemiologic data on 4,524 Australian and French strains suggest that STc117 is a poultry‐associated lineage that can also establish in humans and cause extra‐intestinal diseases. We propose an easy identification method that will help to trace this potentially virulent and resistant phylogroup in epidemiologic studies.

Phylogenetic background and habitat drive the genetic diversification of Escherichia coli

“…Studies on E. coli were seminal in the development of bacterial population genetics 16 . They showed moderate levels of recombination in the species 3, 17–19 , and a strong phylogenetic structure with eight main phylogroups, among which four (A, B1, B2 and D) represent the majority of the strains and four others (C, E, F and G) are rarer 20–22 . Strains differ in their phenotypic and genotypic characteristics within and across phylogroups 2, 3, 23, 24 , and their isolation frequency depends on factors such as host species, diet, sex, age 25–27 , body mass 28 , but also climate 29, 30 , and geographic location 31 .…”

Unique k-mers as Strain-Specific Barcodes for Phylogenetic Analysis and Natural Microbiome Profiling

“…Probably the most important is the detection of 10 strains with complete genomes that form a clade between groups F and B2. Recently, this clade was classified into the separate phylogroup G based on shotgun sequences [46]. Another example is the phylogroup C. Previously, it was represented by only three strains with complete genomes (ACN002, APEC O78 and str.…”

“…In 2016, two new isolates of intestinal E. coli of Marmota himalayana were characterized [53]. Together with other bacteria with partially assembled genomes, they formed a branch on the phylogenetic tree between groups F and B2 and were assigned to phylogroup G [46]. Therefore, the modern version of the classification includes eight phylogroups.…”

“…This would be of particular importance for intraspecies taxonomy, where pathogenic strains are often very difficult to distinguish from non-pathogenic. Therefore, in this study, we updated the previously developed UniSeq software [44] for a more accurate search for unique k-mers in bacterial genomes and for the first time applied them to distinguish between eight phylogroups of Escherichia coli, classified by Clermont et al [45,46].Initially, this classification included only phylogroups A, B1, B2, and D [47]. In 2004, seven strains with serotypes O157:H7 and O55:H7 were transferred from group D into a separate group E [48], and this was accepted in later works [49,50].…”

“…This would be of particular importance for intraspecies taxonomy, where pathogenic strains are often very difficult to distinguish from non-pathogenic. Therefore, in this study, we updated the previously developed UniSeq software [44] for a more accurate search for unique k-mers in bacterial genomes and for the first time applied them to distinguish between eight phylogroups of Escherichia coli, classified by Clermont et al [45,46].…”