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

Authors: ALLUE-GUARDIA, ANNA - University Of Texas At San Antonio; KOENIG, SARA - University Of Texas At San Antonio; MARTINEZ, RICARDO - University Of Texas At San Antonio; RODRIGUEZ, ARMANDO - University Of Texas At San Antonio; Bosilevac, Joseph - Mick; FENG, PETER - Food And Drug Administration(FDA); EPPINGER, MARK - University Of Texas At San Antonio

Submitted to: Microbial Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/7/2022
Publication Date: 4/8/2022
Citation: Allué-Guardia, A., Koenig, S.S., Martinez, R.A., Rodriguez, A.L., Bosilevac, J.M., Feng, P., Eppinger, M. 2022. Pathogenomes and variations in Shiga toxin production among geographically distinct clones of Escherichia coli O113:H21. Microbial Genomics. 8. Article 000796. https://doi.org/10.1099/mgen.0.000796.
DOI: https://doi.org/10.1099/mgen.0.000796

Interpretive Summary: Escherichia coli of serotype O113:H21 are found around the globe and can be divided into two groups. One group called ST-820 is found in Australia and can cause very severe disease while the other group called ST-223 is found outside Australia and does not cause severe illness. To investigate why these two groups differ in their ability to cause disease, 20 strains (eight ST-820’s and twelve ST-223’s) were whole genome sequenced and compared to one another and other E. coli O113:H21 sequences in public databases. Results revealed the evolutionary relatedness of the strains and identified many virulence markers that set the ST-820’s apart from the ST-223’s. Whole genome sequencing provided new information about pathogenic E. coli that will improve risk assessment, surveillance, and public health.

Technical 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 seems 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 carried plasmids for two representative ST-820 and ST-223 strains. The established high-resolution framework, based on whole genome alignments, SNP-and MLST-typing, 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 the Stx-phage induction in the gastrointestinal tract during human infection. 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.