The ST131 Escherichia coli H22 subclone from human intestinal microbiota: Comparison of genomic and phenotypic traits with those of the globally successful H30 subclone

Abstract

BackgroundIn 2006, we found healthy subjects carrying ST131 Escherichia coli in their intestinal microbiota consisting of two populations: a subdominant population of fluoroquinolone-resistant E. coli belonging to subclone H30 (H30-R or subclade C1), the current worldwide dominant ST131 subclone, and a dominant E. coli population composed of antibiotic-susceptible E. coli belonging to subclone H22 (clade B), the precursor of subclone H30. We sequenced the whole genome of fecal H22 strain S250, compared it to the genomes of ExPEC ST131 H30-Rx strain JJ1886 and commensal ST131 H41 strain SE15, sought the H22-H30 genomic differences in our fecal strains and assessed their phenotypic consequences.ResultsWe detected 173 genes found in the Virulence Factor Database, of which 148 were shared by the three ST131 genomes, whereas some were genome-specific, notably those allowing determination of virotype (D for S250 and C for JJ1886). We found three sequences of the FimH site involved in adhesion: two in S250 and SE15 close and identical, respectively, to that previously reported to confer strong intestinal adhesion, and one in JJ1886, corresponding to that commonly present in uropathogenic E. coli. Among the genes involved in sugar metabolism, one encoding a gluconate kinase lacked in S250 and JJ1886. Although this gene was also absent in both our fecal H22 and H30-R strains, H22 strains showed a higher capacity to grow in minimal medium with gluconate. Among the genes involved in gluconate metabolism, only the ghrB gene differed between S250/H22 and JJ1886/H30-R strains, resulting in different gluconate reductases. Of the genes involved in biofilm formation, two were absent in the three genomes and one, fimB, in the JJ1886 genome. Our fecal H30-R strains lacking intact fimB displayed delayed biofilm formation relative to our fecal H22 strains. The H22 strains differed by subclade B type and plasmid content, whereas the H30-R strains were identical.ConclusionsPhenotypic analysis of our fecal strains based on observed genomic differences between S250 and JJ1886 strains suggests the presence of traits related to bacterial commensalism in our H22 strains and traits commonly found in uropathogenic E. coli in our H30-R strains.Electronic supplementary materialThe online version of this article (doi:10.1186/s12866-017-0984-8) contains supplementary material, which is available to authorized users.

Whole Genome Sequencing and Characteristics of mcr-1–Harboring Plasmids of Porcine Escherichia coli Isolates Belonging to the High-Risk Clone O25b:H4-ST131 Clade B

“…In accordance with previous studies, plasmids carrying virulence genes belong to the IncF family Nicolas-Chanoine et al, 2017). All the IncF plasmids found in this study conserved the ColV region, frequently detected among avian pathogenic E. coli (APEC) (Liu C. M. et al, 2018).…”

“…Because ST131 has once been responsible for the worldwide appearance, ESBL resistances due to the acquisition of specific IncF epidemic plasmids harboring bla CTX−M−15 gene (Nicolas-Chanoine et al, 2008, 2014Mathers et al, 2015) and therefore major therapeutic failure could come due to the association of mcr-1 gene with other broad-spectrum resistance mechanisms, such as ESBLs and/or carbapenemases (Du et al, 2016;Haenni et al, 2016;Li et al, 2016;Olaitan et al, 2016;Skov and Monnet, 2016). Further, clade B of ST131 has been signaled out as a potential foodborne uropathogen and as a stronger early biofilm producer than clade C of ST131 (Nicolas-Chanoine et al, 2017;Liu C. M. et al, 2018;Flament-Simon et al, 2019).…”

Success of Escherichia coli O25b:H4 ST131 clade C associated with a decrease in virulence

“…As previously described, our clade B strains were more frequently early biofilm producers than clade C strains (23, 24, 42). Knocking out the fimB gene in clade B strains resulted in loss of both early biofilm production capacity and early type 1 fimbriae expression.…”

“…The experiments were repeated at least three times for each strain. BHI broth without any strains was used as negative control, and strains S250 and 39, previously described with this method as strong and never biofilm producers, respectively, as control strains (24).…”

Responses of the Human Gut Escherichia coli Population to Pathogen and Antibiotic Disturbances

“…The resident populations in most subjects (001, 006, 008, 009, and 016) were dominated by the isolates of ST131. Members of this sequence type are well known for their resistance to antibiotics, particularly fluoroquinolones and beta-lactams, and are common members of resident gut communities throughout the developing world ( 33 , 34 , 36 , 37 ). While we are unable to say for certain why the subjects in this study were colonized by ST131, studies have demonstrated high rates of colonization among people who have traveled to countries of endemicity or have stayed in long-term health care facilities and that CTX-M-containing ST131 clones have spread rapidly in the United States, where it is now a dominant lineage ( 35 , 38 – 41 ).…”