Pathogenomes of Shiga Toxin Positive and Negative Escherichia coli O157:H7 Strains TT12A and TT12B: Comprehensive Phylogenomic Analysis Using Closed Genomes

• Published in: Microorganisms (Basel) 2024-03, Vol.12 (4), p.699
• Main Authors: Kalalah, Anwar A, Koenig, Sara S K, Feng, Peter, Bosilevac, Joseph M, Bono, James L, Eppinger, Mark
• Format: Article
• Language: English
• Subjects: ancestry; Annotations; bacterial isogens; bacteriophages; Bioinformatics; Chromosomes; Colitis; comparative phylogenomics; complement; E coli; enteropathogens; Escherichia coli; Escherichia coli O157; Gene sequencing; Genomes; Genomic analysis; human diseases; Inflammatory bowel disease; Inventories; multigene family; O157:H7; patients; Phages; phenotype; Phylogeny; Plasmids; Prophages; serotypes; Shiga toxin; Shiga toxin (Stx)-producing Escherichia coli (STEC); Single-nucleotide polymorphism; Stx-converting bacteriophages; Toxins; Virulence; whole genome sequencing and typing (WGST); Zoonoses
• ISSN: 2076-2607; 2076-2607
• DOI: 10.3390/microorganisms12040699

Shiga toxin-producing are zoonotic pathogens that cause food-borne human disease. Among these, the O157:H7 serotype has evolved from an enteropathogenic O55:H7 ancestor through the displacement of the somatic gene cluster and recurrent toxigenic conversion by Shiga toxin-converting bacteriophages. However, atypical strains that lack the Shiga toxin, the characteristic virulence hallmark, are circulating in this lineage. For this study, we analyzed the pathogenome and virulence inventories of the + strain, TT12A, isolated from a patient with hemorrhagic colitis, and its respective co-isolated - strain, TT12B. Sequencing the genomes to closure proved critical to the cataloguing of subtle strain differentiating sequence and structural polymorphisms at a high-level of phylogenetic accuracy and resolution. Phylogenomic profiling revealed SNP and MLST profiles similar to the near clonal outbreak isolates. Their prophage inventories, however, were notably different. The attenuated atypical non-shigatoxigenic status of TT12B is explained by the absence of both the ΦStx - and ΦStx -prophages carried by TT12A, and we also recorded further alterations in the non-Stx prophage complement. Phenotypic characterization indicated that culture growth was directly impacted by the strains' distinct lytic phage complement. Altogether, our phylogenomic and phenotypic analyses show that these intimately related isogenic strains are on divergent Stx(+/stx-) evolutionary paths.