Whole genome sequencing reveals antimicrobial resistance, virulence determinants, and stress adaptation traits of Escherichia coli from informal dairy sector

In Zimbabwe, the informal dairy sector supplies a large proportion of milk that is frequently sold raw or spontaneously fermented, raising concerns about foodborne pathogens and antimicrobial resistance (AMR). This study presents the first whole-genome sequencing (WGS) characterization of E. coli from raw and culture milk in this sector, examining pathogenicity, genetic diversity, stress adaptation, and AMR profiles. Fifty-five isolates were confirmed as E. coli, with five selected for WGS analysis. The sequenced isolates belonged to sequence types ST10, ST410, ST6636, and ST7036, lineages previously associated with human and animal infections, indicating potential foodborne transmission risks. Virulence profiling revealed genes associated with adhesion, toxin production, and iron acquisition, while stress-response genes linked to acid resistance and general stress tolerance suggested survival in fermented dairy environments. Overall, the findings underscore public health risks linked to raw milk consumption and highlight the need for improved hygiene, consumer education, affordable pasteurization options, strengthened AMR surveillance, and integrated One Health interventions.