Phylogenetic and genomic diversity of human bacteremic Escherichia coli strains

Abstract

BackgroundExtraintestinal pathogenic Escherichia coli (ExPEC) strains represent a huge public health burden. Knowledge of their clonal diversity and of the association of clones with genomic content and clinical features is a prerequisite to recognize strains with a high invasive potential. In order to provide an unbiased view of the diversity of E. coli strains responsible for bacteremia, we studied 161 consecutive isolates from patients with positive blood culture obtained during one year in two French university hospitals. We collected precise clinical information, multilocus sequence typing (MLST) data and virulence gene content for all isolates. A subset representative of the clonal diversity was subjected to comparative genomic hybridization (CGH) using 2,324 amplicons from the flexible gene pool of E. coli.ResultsRecombination-insensitive phylogenetic analysis of MLST data in combination with the ECOR collection revealed that bacteremic E. coli isolates were highly diverse and distributed into five major lineages, corresponding to the classical E. coli phylogroups (A+B1, B2, D and E) and group F, which comprises strains previously assigned to D. Compared to other strains of phylogenetic group B2, strains belonging to MLST-derived clonal complexes (CCs) CC1 and CC4 were associated (P < 0.05) with a urinary origin. In contrast, no CC appeared associated with severe sepsis or unfavorable outcome of the bacteremia. CGH analysis revealed genomic characteristics of the distinct CCs and identified genomic regions associated with CC1 and/or CC4.ConclusionOur results demonstrate that human bacteremia strains distribute over the entire span of E. coli phylogenetic diversity and that CCs represent important phylogenetic units for pathogenesis and comparative genomics.

Phylo-typing of clinicalEscherichia coliisolates originating from bovine mastitis and canine pyometra and urinary tract infection by means of quadruplex PCR

“…Nevertheless, the increase in genome research and multi-locus sequence data put forward eight new phylo-groups of E. coli, assigned as A, B1, B2, C, D, E and F which belong to E. coli sensu stricto and one correspond to the Escherichia cryptic clade I (Jaureguy et al 2008;Moissenet et al 2010;Tenaillon et al 2010;Clermont et al 2011;Luo et al 2011). Group E is recognized as a new group that was formerly comprised unassigned strains; group F designated as sister group of B2; group C includes strains closely related but distinct from group B1 and an Escherichia clade I which is considered to be a new phylo-group that is phenotypically indistinguishable but genotypically different from E. coli (Clermont et al 2013).…”

The importance of the “V”-Factor:Escherichia colibacteremia and sepsis

“…Mortality caused by E. coli bacteremia and sepsis remains high and is now one the top 10 causes of death in the western world. 2,3 Representing a significant health burden, E.coli is the gram-negative bacteria most often associated with sepsis and infection by uropathogenic E. coli account for 70-95% of community acquired and 50% of hospital acquired urinary tract infections. 2,3 The high degree of intra-strain genetic diversity represents a challenge in correct clinical management of patients.…”

“…2,3 Representing a significant health burden, E.coli is the gram-negative bacteria most often associated with sepsis and infection by uropathogenic E. coli account for 70-95% of community acquired and 50% of hospital acquired urinary tract infections. 2,3 The high degree of intra-strain genetic diversity represents a challenge in correct clinical management of patients. Coupled with this the level of patient risk factor diversity confounds this issue, highlighting the need for studies such as this to increase treatment options and survival outcomes for affected individuals.…”

E. coli Bacteremia Strains - High diversity and Associations with Agerelated Clinical Phenomena

“…However, this study did not look into patient outcomes [32]. A French study of the genetics of 161 consecutive E. coli bacteremia isolates showed that bacteremia strains are distributed over the entire span of E. coli phylogenetic diversity and that clonal complex, in spite of not being associated with severe sepsis or unfavorable outcomes represent important direction for future research in pathogenesis and comparative genomics [33]. A selection of 60 of the 161 strains was used to induce sepsis in genetically identical mice, and the authors found strong associations between phylogenetic group, virulence factor content and observed virulence, but this did not translate into severity of infection in the patients from whom the isolates originated from in the first place.…”