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bioRxiv · 10.1101/2025.04.29.651274

Phylogenomic framework and virulence gene boundaries of emerging Shiga toxin producing Escherichia coli O118 informed by the comprehensive profiling of 359 O118 genomes

Rivera, I.·Konig, S. S. K.·Rodriguez, A. L.·Bosilevac, J. M.·Eppinger, M.
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Abstract

Non-O157 Shiga toxin-producing Escherichia coli (STEC), particularly the O118 serogroup, are emerging pathogens linked to severe foodborne illnesses, including hemolytic uremic syndrome. The hallmark of STEC virulence is the production of a potent phage-borne cytotoxin, often accompanied by the locus of enterocyte effacement (LEE). This study explores the genomic landscape, virulence factors, and resistance traits of O118 STEC. We analyzed 357 publicly available O118 genomes across ten H-antigens and included two clinically significant O118:H16 STEC strains sequenced to closure. Pangenome assessment and core genome multilocus sequence typing (MLST) based on 4,160 shared genes revealed phylogenetic clustering by H-type and delineated distinct STEC-phylogroups, alongside relationships to non-STEC pathovars such as uropathogenic E. coli (UPEC), enteropathogenic E. coli (EPEC), and enterotoxigenic E. coli (ETEC). Identified STEC phylogroups encompassed H6, H12, H16, and H2 strains with diverse Shiga toxin (stx) profiles (stx1a, stx2a, stx2b, stx2c, stx2f). A subset of H2-STEC lacked stx, suggesting potential secondary phage loss. Most STEC groups harbored the locus of enterocyte effacement (LEE). Further, a strong correlation was observed between H-antigens and eae subtypes, with specific pairings such as H6/eae-{iota}, H16/eae-{beta}, and H2/eae-{varepsilon}. Horizontally acquired pathogenicity islands--including O-island 122 in H16 strains and a novel pathogenicity-associated island carrying antibiotic resistance--along with other loci related to colonization and interbacterial competition, further enhance these strains virulence potential. Our findings underscore the genetic diversity and virulence potential of O118 STEC. Understanding phylogroup-specific traits and resistance markers is crucial for effective surveillance and public health interventions. ImportanceShiga toxin-producing Escherichia coli (STEC) are a major public health concern, responsible for illnesses ranging from diarrhea to life-threatening kidney damage. Among non-O157 STEC, serogroup O118 is increasingly recognized as an emerging STEC lineage. This study provides the most comprehensive genomic analysis to date of O118 STEC, offering critical insights into their pathogenome, virulence traits, and antimicrobial resistance inventories. Notably, we identified a novel 74 kb pathogenicity island in clinical strain H16-12089 that encodes a combination of multidrug resistance genes, virulence factors, and interbacterial competition systems. Understanding the genetic makeup and virulence potential of these pathogens is essential for improving surveillance, risk assessment, and public health interventions.

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Rivera, I., Konig, S. S. K., Rodriguez, A. L., Bosilevac, J. M., Eppinger, M.. 2025-05-01. Phylogenomic framework and virulence gene boundaries of emerging Shiga toxin producing Escherichia coli O118 informed by the comprehensive profiling of 359 O118 genomes. https://doi.org/10.1101/2025.04.29.651274

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