Population structure of Escherichia coli O26 : H11 with recent and repeated stx2 acquisition in multiple lineages

Abstract

A key virulence factor of enterohaemorrhagic Escherichia coli (EHEC) is the bacteriophage-encoded Shiga toxin (Stx). Stxs are classified into two types, Stx1 and Stx2, and Stx2-producing strains are thought to cause more severe infections than strains producing only Stx1. Although O26 : H11 is the second most prevalent EHEC following O157 : H7, the majority of O26 : H11 strains produce Stx1 alone. However, Stx2-producing O26 strains have increasingly been detected worldwide. Through a large-scale genome analysis, we present a global phylogenetic overview and evolutionary timescale for E. coli O26 : H11. The origin of O26 has been estimated to be 415 years ago. Sequence type 21C1 (ST21C1), one of the two sublineages of ST21, the most predominant O26 : H11 lineage worldwide, emerged 213 years ago from one of the three ST29 sublineages (ST29C2). The other ST21 lineage (ST21C2) emerged 95 years ago from ST21C1. Increases in population size occurred in the late 20th century for all of the O26 lineages, but most remarkably for ST21C2. Analysis of the distribution of stx2-positive strains revealed the recent and repeated acquisition of the stx2 gene in multiple lineages of O26, both in ST21 and ST29. Other major EHEC virulence genes, such as type III secretion system effector genes and plasmid-encoded virulence genes, were well conserved in ST21 compared to ST29. In addition, more antimicrobial-resistance genes have accumulated in the ST21C1 lineage. Although current attention is focused on several highly virulent ST29 clones that have acquired the stx2 gene, there is also a considerable risk that the ST21 lineage could yield highly virulent clones.

Nanopore sequencing for fast determination of plasmids, phages, virulence markers, and antimicrobial resistance genes in Shiga toxin-producingEscherichia coli

“…The other two STEC strains carried a single virulence plasmid albeit with different sizes and gene compositions. It was also noteworthy that none of these strains carried the etpD gene (coding for a Type II secretion protein) in the plasmid, indicative of the presence of the European clone (9,35,45,46). From the nanopore data analyzed here, the virulence profile for each strain was determined as follows: CFSAN027343 (ST21, stx 1a +, eae-beta1+, plasmid gene profile ehxA+, espP+, katP, and toxB+ ), CFSAN027346 (ST21, stx 1a +, eae-beta1+, plasmid gene profile ehxA+, espP+, katP, and toxB+), and CFSAN027350 (ST29, stx 2a +, eae-beta1+, plasmid gene profile ehxA+, espP+, and toxB+).…”

Shiga Toxin Type 1a (Stx1a) Reduces the Toxicity of the More Potent Stx2a In Vivo and In Vitro

“…HUS most often occurs in children and is characterized by thrombocytopenia, hemolytic anemia, and acute kidney failure (2). The O157:H7 serotype is most commonly associated with STEC infections and HUS in the United States (3), followed by serogroup O26 (usually O26:H11) (4)(5)(6).…”

Effective Surveillance Using Multilocus Variable-Number Tandem-Repeat Analysis and Whole-Genome Sequencing for Enterohemorrhagic Escherichia coli O157

“…Additionally, in silico typing based on WGS data can replace most conventional genotyping, including gene profiling and MLST. Certain clades (18,19) or MLST types (20)(21)(22) have been suggested to be more pathogenic than others; therefore, this genotype information could complement virulence gene data in evaluating pathogenicity of the isolates. In our analysis pipeline, the entire analysis of one isolate requires approximately 20 minutes.…”