Genomic and phenotypic characterization of non-O157 Shiga toxin-producing Escherichia coli from Bangladeshi cattle reveals diverse virulence and resistance profiles.

UNLABELLED: Shiga toxin-producing Escherichia coli (STEC) are important zoonotic pathogens that cause diarrheal diseases and hemolytic uremic syndrome in humans, but data from Bangladesh remain limited. We collected 352 rectal swabs and 2 retail meat samples from cattle at the Gabtoli Hat livestock market (Dhaka, Banglades) in 2017-2018 and recovered 1 E. coli isolate per sample (n = 354). PCR screening detected stx1 and/or stx2 in 228/354 isolates (64.4%): 77 carried stx1 only, 68 carried stx2 only, and 83 carried both genes. Antimicrobial susceptibility testing revealed frequent resistance to mecillinam, tetracyclines, macrolides, and piperacillin, while resistance to ciprofloxacin, gentamicin, and colistin was uncommon, and no isolate displayed imipenem resistance. To explore the genetic diversity, eleven non-O157 isolates (including five stx-positive representatives stratified by toxin profiles, phylogroups, and resistance phenotypes) were sequenced with Illumina MiSeq. All genomes lacked the canonical intimin gene eae; however, they universally encoded eaeH, type 1 fimbrial genes, and rpoS. Comparative phylogenomics against 212 publicly available stx-positive genomes placed several cattle isolates near human and food-associated lineages, suggesting shared lineage relationships rather than direct transmission. Phenotypically, all sequenced isolates formed weak-to-moderate biofilms, and only two showed marked survival in normal human serum, indicating virulence-associated heterogeneity independent of iss copy number. Collectively, these results show that cattle in Bangladesh carry a notable reservoir of virulence and resistance-associated traits relevant to public health. These findings underscore the need for integrated One Health-based genomic surveillance, limited antibiotic use in livestock, and targeted public health interventions to reduce human transmission risk.

IMPORTANCE: Genomic surveillance of non-O157 Shiga toxin-producing Escherichia coli in cattle from a livestock market in Dhaka, Bangladesh, is limited. By screening cattle-derived E. coli isolates, we found that nearly two-thirds of isolates carried Shiga toxin genes and that resistance to commonly used antibiotics was common. Whole-genome sequencing of 11 selected isolates revealed diverse non-O157 lineages that lacked the classical intimin gene but carried alternative adhesion factors, stress-response genes, and diverse plasmid and prophage content. Several cattle-derived isolates showed genetic relatedness to lineages observed in human and food-associated strains, although direct transmission cannot be inferred without matched epidemiological and temporal data. These findings highlight the value of urban livestock markets within an integrated One Health approach, supporting genomic surveillance, prudent antibiotic use in livestock, and targeted public health interventions to reduce the risk of human transmission.