Molecular Characterization and Comparative Genomics of Clinical Hybrid Shiga Toxin-Producing and Enterotoxigenic Escherichia coli (STEC/ETEC) Strains in Sweden

Abstract

Hybrid E. coli pathotypes are representing emerging public health threats with enhanced virulence from different pathotypes. Hybrids of Shiga toxin-producing and enterotoxigenic E. coli (STEC/ETEC) have been reported to be associated with diarrheal disease and hemolytic uremic syndrome (HUS) in humans. Here, we identified and characterized four clinical STEC/ETEC hybrids from diarrheal patients with or without fever or abdominal pain and healthy contact in Sweden. Rare stx2 subtypes were present in STEC/ETEC hybrids. Stx2 production was detectable in stx2a and stx2e containing strains. Different copies of ETEC virulence marker, sta gene, were found in two hybrids. Three sta subtypes, namely, sta1, sta4 and sta5 were designated, with sta4 being predominant. The hybrids represented diverse and rare serotypes (O15:H16, O187:H28, O100:H30, and O136:H12). Genome-wide phylogeny revealed that these hybrids exhibited close relatedness with certain ETEC, STEC/ETEC hybrid and commensal E. coli strains, implying the potential acquisition of Stx-phages or/and ETEC virulence genes in the emergence of STEC/ETEC hybrids. Given the emergence and public health significance of hybrid pathotypes, a broader range of virulence markers should be considered in the E. coli pathotypes diagnostics, and targeted follow up of cases is suggested to better understand the hybrid infection.

Figure 1

Phylogenetic tree of sta alleles by the neighbour-joining method. The neighbour-joining tree was inferred from nucleotide sequences of all sta alleles using a p distance matrix. Strain designations and GenBank accession numbers (or WGS prefixes) are given at the branch tips. Bootstrap values based on 1000 replications (>50%) are given at the internal nodes. sta subtypes are given next to the outer brackets. The four STEC/ETEC hybrid strains in this study were highlighted in bold.

Figure 2

Phylogenetic relationships of STEC/ETEC hybrid strains in this study to other E. coli/Shigella reference strains. The phylogenetic positions of the four hybrid strains in relative to the other 41 reference strains were studied with three different approaches: panel (A) 80% consensus tree generated from three runs of 55 ribosomal protein subunits (rps) gene ClonalFrame analysis; panel (B), Neighbor-Net phylogeny inferred from the allele profiles of the 2181 loci that shared by the 45 isolates; and panel (C) Gubbins tree of the concatenated sequences of the shared loci that found in the wgMLST analysis. The four hybrid isolates were highlighted with red letter.