Genomic analysis of shiga toxin-containing Escherichia coli O157:H7 isolated from Argentinean cattle

Whole-Genome Sequence Reveals Genetic Determinants of the Colonization of Shiga Toxin-Producing Escherichia coli O22:H8 Isolates in Cattle

Shiga toxin-producing Escherichia coli (STEC) is a zoonotic foodborne pathogen responsible for different cases and outbreaks of severe enteric diseases in humans worldwide. Our group previously showed that Argentine O22:H8 isolates (155 and 182) interfere with the colonization of O157:H7 in an experimental infection bovine model. In this study, we applied a comparative genomic and genome-wide association study (GWAS) analysis to explore the differences between the genetic bases of O22:H8 and O157:H7 strains isolated from cattle. The whole-genome sequence of O22:H8 155 and 182 isolates was compared with 33 O22:H8 and 156 O157:H7 isolates from bovine. Our results showed that O22:H8 isolates harbor genes associated with specific metabolic pathways related to the metabolism of products of vegetal origin, which are absent in O157:H7 isolates. These O22:H8 isolates also carry classical genes of the locus of adhesion and autoaggregation related to the adhesion of non-O157 isolates. In addition, we showed that the T6SS-1 cluster related to bacterial competition predicted in the Argentine O22:H8 isolates is absent both in O157:H7 and other O22:H8 isolates. We also predicted for the first time the locus of type VI secretion system 1 (LT6SS-T1), a genomic island that harbors both T6SS-1 cluster genes and genes related to STEC pathogenesis. This study reveals a subset of genes present in the Argentine O22:H8 isolates that could confer an advantage over O157:H7 during the colonization process in the bovine intestinal tract.

Pathogenomes and virulence profiles of representative big six non-O157 serogroup Shiga toxin-producing Escherichia coli

Shiga toxin (Stx)-producing Escherichia coli (STEC) of non-O157:H7 serotypes are responsible for global and widespread human food-borne disease. Among these serogroups, O26, O45, O103, O111, O121, and O145 account for the majority of clinical infections and are colloquially referred to as the "Big Six." The "Big Six" strain panel we sequenced and analyzed in this study are reference type cultures comprised of six strains representing each of the non-O157 STEC serogroups curated and distributed by the American Type Culture Collection (ATCC) as a resource to the research community under panel number ATCC MP-9. The application of long- and short-read hybrid sequencing yielded closed chromosomes and a total of 14 plasmids of diverse functions. Through high-resolution comparative phylogenomics, we cataloged the shared and strain-specific virulence and resistance gene content and established the close relationship of serogroup O26 and O103 strains featuring flagellar H-type 11. Virulence phenotyping revealed statistically significant differences in the Stx-production capabilities that we found to be correlated to the strain's individual stx-status. Among the carried Stx1a, Stx2a, and Stx2d phages, the Stx2a phage is by far the most responsive upon RecA-mediated phage mobilization, and in consequence, stx2a + isolates produced the highest-level of toxin in this panel. The availability of high-quality closed genomes for this "Big Six" reference set, including carried plasmids, along with the recorded genomic virulence profiles and Stx-production phenotypes will provide a valuable foundation to further explore the plasticity in evolutionary trajectories in these emerging non-O157 STEC lineages, which are major culprits of human food-borne disease.