Climate-driven co-evolution of antimicrobial resistance and virulence in Escherichia coli on dairy farms: unraveling adaptive genetic signatures with novel SSCP-PCR

This study addresses a critical One Health challenge by investigating the epidemiological and genetic drivers of antimicrobial resistance (AMR) in E. coli from 290 clinical bovine samples. On Egyptian dairy farms, our findings revealed that while calf diarrhea peaked during the winter, a higher rate of multidrug resistance was consistently observed in isolates from the summer, directly linking seasonal pressures to AMR dissemination. Strikingly, a mastitis isolate was confirmed as the highly virulent E. coli O157:H7 serotype, harboring the Shiga toxin genes stx1 and stx2, underscoring a direct and significant public health risk. To dissect the molecular basis of these trends, we pioneered the use of a novel Single-Strand Conformation Polymorphism Polymerase Chain Reaction (SSCP-PCR) assay on 33 selected isolates. This high-throughput approach revealed prevalent mutations in resistance genes (blaTEM and gyrB) and the virulence gene (fimH). Crucially, sequencing confirmed that mutations in the highly conserved 16S rRNA gene significantly co-occurred with mutations in blaTEM, fimH, and lacI, providing compelling evidence for co-selected adaptive pathways and clonal expansion. Our research demonstrates that climate-driven environmental pressures fuel the co-evolution of AMR and virulence on farms, championing SSCP-PCR as a robust tool for tracking microbial evolution and advocating for integrated, molecularly-informed One Health strategies.