Genomic diversity and high-risk lineages in clinical Escherichia coli from Mexico

Escherichia coli poses a significant threat to environmental, animal, and public health, mainly due to its ability to proliferate across diverse habitats, with infection prevalence and severity varying widely across countries and regions. Eleven strains of E. coli obtained from a public hospital in Culiacán, Sinaloa, were sequenced, along with 60 whole-genome sequences from Mexico reported in NCBI, to assess their genetic diversity, phylogenetic distribution, and antimicrobial resistance (AMR) profiles. Data from Mexico indicate 40 serotypes and 30 sequence types (STs), with pandemic clones ST131 and ST69 as the most prevalent, along with serotypes O25:H4 and O15:H18. Fluoroquinolone resistance genes and diverse β-lactamases, including CTX-M-15 and CTX-M-27, were detected. Virulence gene profiles revealed a predominance of genes involved in iron acquisition, adherence, and secretion systems. Notably, the genes ompA, fes, fepC, and fepA were present in all isolates. At the regional level, the strains sequenced in this study belong to STs 10, 69, 2279, 131, and three to ST1193, and contain crucial virulence genes that play a pivotal role in their infectivity, alongside a wide array of resistance genes. These findings highlight the remarkable genetic diversity of clinical E. coli in Mexico and underscore the epidemiological importance of high-risk clones. Strengthening genomic surveillance will be essential to improve disease control efforts.