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Abstract
Shiga toxin-producing Escherichia coli of serotype O26:H11/H- constitute a diverse group of strains and several clones with distinct genetic characteristics have been identified and characterized. Whole genome sequencing was performed using Illumina and PacBio technologies on eight stx2-positive O26:H11 strains circulating in France. Comparative analyses of the whole genome of the stx2-positive O26:H11 strains indicate that several clones of EHEC O26:H11 are co-circulating in France. Phylogenetic analysis of the French strains together with stx2-positive and stx-negative E. coli O26:H11 genomes obtained from Genbank indicates the existence of four clonal complexes (SNP-CCs) separated in two distinct lineages, one of which comprises the “new French clone” (SNP-CC1) that appears genetically closely related to stx-negative attaching and effacing E. coli (AEEC) strains. Interestingly, the whole genome SNP (wgSNP) phylogeny is summarized in the cas gene phylogeny, and a simple qPCR assay targeting the CRISPR array specific to SNP-CC1 (SP_O26-E) can distinguish between the two main lineages. The PacBio sequencing allowed a detailed analysis of the mobile genetic elements (MGEs) of the strains. Numerous MGEs were identified in each strain, including a large number of prophages and up to four large plasmids, representing overall 8.7–19.8% of the total genome size. Analysis of the prophage pool of the strains shows a considerable diversity with a complex history of recombination. Each clonal complex (SNP-CC) is characterized by a unique set of plasmids and phages, including stx-prophages, suggesting evolution through separate acquisition events. Overall, the MGEs appear to play a major role in O26:H11 intra-serotype clonal diversification.
Highlights
Shiga toxin-producing Escherichia coli (STEC) of serotype O26:H11/H- have been recognized for several years as public health threats
Previous studies have determined that strains of this O26:H11 clone belong to sequence type 21 (ST21), are associated with allelic type 14 of the arcA gene, possess the espK gene, and react with the CRISPR-specific qPCR assays SP_O26-C and/or –D (Miko et al, 2010; Bugarel et al, 2011; Delannoy et al, 2012)
The eight new E. coli O26:H11 genomes were compared to each other as well as to previously reported O26:H11 genomes derived from patients with diarrhea and hemolytic uremic syndrome (HUS), including: the O26:H11 reference strain 11368, a set of strains (FHI4, FHI24, FHI27) isolated from HUS patients in Norway and carrying the stx2a gene only (Haugum et al, 2014), and a set of stx-negative strains (DEC9A, DEC9B, DEC9C, DEC9D, DEC9E and DEC10D) isolated from diarrheagenic patients and selected according to their CRISPR profiles (Hazen et al, 2012)
Summary
Shiga toxin-producing Escherichia coli (STEC) of serotype O26:H11/H- have been recognized for several years as public health threats. Previous studies have determined that strains of this O26:H11 clone belong to sequence type 21 (ST21), are associated with allelic type 14 of the arcA gene, possess the espK gene, and react with the CRISPR-specific qPCR assays SP_O26-C and/or –D (Miko et al, 2010; Bugarel et al, 2011; Delannoy et al, 2012) This clone possesses the plasmid gene combination ehxA+ / katP+ / espP+ / etpD− (Zhang et al, 2000; Bielaszewska et al, 2013; Delannoy et al, 2015a)
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