Abstract
Enterohemorrhagic Escherichia coli (EHEC) O26:H11, a serotype within Shiga toxin-producing E. coli (STEC) that causes severe human disease, has been considered to have evolved from attaching and effacing E. coli (AEEC) O26:H11 through the acquisition of a Shiga toxin-encoding gene. Targeted amplicon sequencing using next-generation sequencing technology of 48 phylogenetically informative single-nucleotide polymorphisms (SNPs) and three SNPs differentiating Shiga toxin-positive (stx-positive) strains from Shiga toxin-negative (stx-negative) strains were used to infer the phylogenetic relationships of 178 E. coli O26:H11 strains (6 stx-positive strains and 172 stx-negative AEEC strains) from cattle feces to 7 publically available genomes of human clinical strains. The AEEC cattle strains displayed synonymous SNP genotypes with stx2-positive sequence type 29 (ST29) human O26:H11 strains, while stx1 ST21 human and cattle strains clustered separately, demonstrating the close phylogenetic relatedness of these Shiga toxin-negative AEEC cattle strains and human clinical strains. With the exception of seven stx-negative strains, five of which contained espK, three stx-related SNPs differentiated the STEC strains from non-STEC strains, supporting the hypothesis that these AEEC cattle strains could serve as a potential reservoir for new or existing pathogenic human strains. Our results support the idea that targeted amplicon sequencing for SNP genotyping expedites strain identification and genetic characterization of E. coli O26:H11, which is important for food safety and public health.
Highlights
Shiga toxin-producing Escherichia coli (STEC) O26 strains have been associated with large food-borne outbreaks worldwide and can result in severe human illness [1,2,3]
Multilocus sequence typing has shown that this clone belongs to sequence type 29 (ST29) [8], which is associated with severe human disease, while the phylogenetically related group ST21 is associated with less-severe disease [6, 10, 19]
The evolutionary phylogenetic relationship of Escherichia coli (EHEC) O26: H11/HϪ has been investigated on strains of European origin employing whole-genome sequencing (WGS) in which four distinct clonal complexes (CCs) were observed using 48 phylogenetically informative single-nucleotide polymorphisms (SNPs) [22]
Summary
Shiga toxin-producing Escherichia coli (STEC) O26 strains have been associated with large food-borne outbreaks worldwide and can result in severe human illness [1,2,3]. A new subpopulation of pathogenic O26:H11 strains harboring stx2a or stx2d, belonging to ST29, has been identified in hemolytic-uremic syndrome (HUS) patients in France [19] These stx2-positive strains differ from the characteristic typical O26:H11 EHEC strains [20]. While they possess a stx gene and the eae-beta allele, they lack other genetic features, such as the effector translocated by the type III secretion system, espK, and contain a different allele of the aerobic respiratory control protein A (arcA) [19] They exhibit a distinct clustered regularly interspaced short palindromic repeat (CRISPR) locus. Three SNPs were identified that, when used in combination, detected all stx-positive strains; one SNP captured a subset of strains containing only stx2 [23]
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