Phylogenomic framework and virulence gene boundaries of emerging Shiga toxin-producing <i>Escherichia coli</i> O118 informed by the comprehensive profiling of 359 O118 genomes
Abstract
Non-O157 Shiga toxin-producing <i>Escherichia coli</i> (STEC), particularly the O118 serogroup, are emerging pathogens linked to severe foodborne illnesses, which are characterized by the production of a potent phage-borne cytotoxin. This study explores the genomic landscape, virulence factors, and resistance traits of O118 STEC. We analyzed 357 publicly available O118 genomes, all but three available only in draft stage spanning ten different H-antigen types. To enhance the availability of high-quality reference genomes, we additionally included two O118:H16 STEC strains from our collection that were sequenced to closure. Multilocus sequence typing based on the 4,160 shared genes revealed phylogenetic clustering by H-type and delineated distinct STEC-phylogroups, alongside relationships to non-STEC pathovars such as uropathogenic <i>E. coli</i> (UPEC), enteropathogenic <i>E. coli</i> (EPEC), and enterotoxigenic <i>E. coli</i> (ETEC). Identified STEC-phylogroups encompass H6, H12, H16, and H2 strains with diverse Shiga toxin profiles (<i>stx</i><sub><i>1a</i></sub>, <i>stx</i><sub><i>2a</i></sub>, <i>stx</i><sub><i>2b</i></sub>, <i>stx</i><sub><i>2c</i></sub>, <i>stx</i><sub><i>2f</i></sub>). A subset of H2-STEC lacked <i>stx</i>, suggesting potential secondary phage loss. Most STEC groups carried the locus of enterocyte effacement (LEE). Further, a strong correlation was observed between H-antigens and <i>eae</i> subtypes, with specific pairings such as H6/<i>eae-ι</i>, H16/<i>eae-β</i>, and H2/<i>eae-ε</i>. 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 their virulence potential. Our findings underscore the genetic diversity and virulence potential of O118 STEC. Understanding such phylogroup-linked virulence and resistance traits is crucial for effective surveillance and public health interventions.