Pathogenomes and variations in Shiga toxin production among geographically distinct clones of Escherichia coli O113:H21

Abstract

Infections with globally disseminated Shiga toxin-producing Escherichia coli (STEC) of the O113:H21 serotype can progress to severe clinical complications, such as hemolytic uremic syndrome (HUS). Two phylogeographically distinct clonal complexes have been established by multi locus sequence typing (MLST). Infections with ST-820 isolates circulating exclusively in Australia have caused severe human disease, such as HUS. Conversely, ST-223 isolates prevalent in the US and outside Australia seem to rarely cause severe human disease but are frequent contaminants. Following a genomic epidemiology approach, we wanted to gain insights into the underlying cause for this disparity. We examined the plasticity in the genome make-up and Shiga toxin production in a collection of 20 ST-820 and ST-223 strains isolated from produce, the bovine reservoir, and clinical cases. STEC are notorious for assembly into fragmented draft sequences when using short-read sequencing technologies due to the extensive and partly homologous phage complement. The application of long-read technology (LRT) sequencing yielded closed reference chromosomes and plasmids for two representative ST-820 and ST-223 strains. The established high-resolution framework, based on whole genome alignments, single nucleotide polymorphism (SNP)-typing and MLST, includes the chromosomes and plasmids of other publicly available O113:H21 sequences and allowed us to refine the phylogeographical boundaries of ST-820 and ST-223 complex isolates and to further identify a historic non-shigatoxigenic strain from Mexico as a quasi-intermediate. Plasmid comparison revealed strong correlations between the strains’ featured pO113 plasmid genotypes and chromosomally inferred ST, which suggests coevolution of the chromosome and virulence plasmids. Our pathogenicity assessment revealed statistically significant differences in the Stx2a-production capabilities of ST-820 as compared to ST-223 strains under RecA-induced Stx phage mobilization, a condition that mimics Stx-phage induction. These observations suggest that ST-820 strains may confer an increased pathogenic potential in line with the strain-associated epidemiological metadata. Still, some of the tested ST-223 cultures sourced from contaminated produce or the bovine reservoir also produced Stx at levels comparable to those of ST-820 isolates, which calls for awareness and for continued surveillance of this lineage.

High Prevalence and Persistence of Escherichia coli Strains Producing Shiga Toxin Subtype 2k in Goat Herds

“…Among the three insertion sites in the goat-derived Stx2k-STEC strains, yecE was commonly found in Stx prophages ( 27 , 33 – 35 ), whereas the other two insertion sites were rarely reported. yccA , associated with the Sp4 prophage in O157:H7 ( 31 ), was found as the insertion site in Stx2e-, Stx2k- and Stx2a-converting prophages ( 12 , 27 , 36 ). The insertion site was usually located upstream from the phage, but in the predominate group G1, insertion site dusA was located downstream from the phage and was found in Stx2k-, Stx2a- and Stx2d-converting prophages ( 12 , 36 ).…”

“…yccA , associated with the Sp4 prophage in O157:H7 ( 31 ), was found as the insertion site in Stx2e-, Stx2k- and Stx2a-converting prophages ( 12 , 27 , 36 ). The insertion site was usually located upstream from the phage, but in the predominate group G1, insertion site dusA was located downstream from the phage and was found in Stx2k-, Stx2a- and Stx2d-converting prophages ( 12 , 36 ). This tRNA-dihydrouridine synthase also carries a phage scar in O157:H7 ( 31 ).…”

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

“…STEC genomes house an extensive and partly repetitive phage complement that hampers assembly into closed genomes ( Goldstein et al, 2019 ; Jaudou et al, 2022 ). In response, we applied a long- and short read sequencing hybrid strategy ( Nyong et al, 2020 ; Allué-Guardia et al, 2022 ) that allowed us to provide the high-quality closed genomes, including carried plasmids ( Figures 1 , 2 ; Supplementary Figures S1 , S2 ). The chromosomes have an average nucleotide identity of 98.8%, with a range from 97.6% to 99.8%, indicative of the substantial conserved chromosomal backbone of E. coli ( Rasko et al, 2008 ; Jain et al, 2018 ).…”

“…Carriage of ΦStx-prophages is a virulence hallmark of STEC; and genomes can contain multiple ΦStx-prophages in diverse stx -suballele combinations ( Huang et al, 1987 ; Eppinger et al, 2011 ; Krüger and Lucchesi, 2015 ; Rusconi et al, 2016 ; Allué-Guardia et al, 2022 ). Stx is a key virulence factor responsible for the severe symptoms associated with STEC infections such as HUS ( Karmali et al, 1983 ).…”

Escherichia cryptic clade I is an emerging source of human intestinal pathogens

“…In human and animal ETEC strains, various colonization factors (CFs) have been identified [27,28]. Although, in the ETEC-and STEC/ETEC hybrid-type C-I strains (estand/or elt-positive; n = 109), known ETEC colonization factors (CFs) were detected in only 17 strains, two types of K88-like CFs were identified in 41 C-I strains (Additional file 2: Table S1 and see Additional file 3: Supplementary text for details) [21,[27][28][29][30][31][32][33].…”