Comparative genomics of diverse Escherichia coli O157:H7 strains to characterize plasmids, prophages, virulence, and antimicrobial resistance genes

Abstract

Plasmids play a critical role in bacterial evolution and represent major drivers of the emergence and dissemination of antimicrobial resistance. As primary mobile genetic elements (MGEs), plasmids facilitate the horizontal transfer of resistance determinants alongside genes associated with virulence, metabolic functions, and broader adaptive advantages. Recent studies have further highlighted the importance of conjugative plasmids, such as IncI1-like elements, in mediating the spread of extended-spectrum β-lactamase (ESBL) genes and other clinically relevant traits across diverse bacterial populations. Whether the recurrent detection of these plasmids is coincidental or reflects unique genetic features that enhance their capacity for transmission remains an important question in microbial genomics. In this context, the present study analyses complete genome sequences and whole-genome maps of Escherichia coli O157:H7 strains to characterize their antimicrobial resistance genes, virulence-associated loci, prophage content, and plasmid profiles. Publicly available sequences from the NCBI GenBank repository were examined using comparative genomic tools, including BRIG, VirulenceFinder, ResFinder, PlasmidFinder, and PHASTEST. This work also underscores the limited availability of whole-genome data for E. coli O157:H7 and O157:H7NM in developing regions, particularly within African countries, highlighting the need for expanded genomic surveillance. Comparative analyses revealed that most strains displayed high genomic similarity to the reference Sakai strain, with relatively few missing regions, although a subset exhibited reduced homology marked by numerous gaps. Prophages, bacteriophages integrated into the bacterial genome, were found to contribute substantially to genomic diversity, influencing virulence potential, antimicrobial resistance, and patterns of horizontal gene transfer. These findings emphasize the complex role of mobile genetic elements in shaping the evolution of E. coli O157:H7 and reinforce the importance of continued genomic sequencing to further elucidate the pathogen's diversity and adaptive mechanisms.

HIGHLIGHTS • Comparative genomics was used to analyze diverse E. coli O157:H7 strains. • Plasmid, prophage, virulence, and antimicrobial resistance profiles were characterized. • IncI1-like and other plasmids carrying key AMR and virulence genes were identified. • Prophages contributed substantially to genomic diversity and adaptive potential.