Genomic Diversity and Antibiotic Resistance of Escherichia coli and Salmonella from Poultry Farms in Oyo State, Nigeria

Livestock are a source of zoonotic pathogens and bacteria harbouring antimicrobial resistance (AMR) that can pose a threat to public health. This study assessed the burden of antimicrobial resistance (AMR) and genomic diversity of <i>Salmonella</i> and <i>Escherichia coli</i> at 25 poultry farms in Oyo State, Nigeria. The farm-level occurrence of <i>Salmonella</i> was 48%, with 12 serovars identified, including S. Kentucky Sequence Type 198. Notably, 70% of <i>Salmonella</i> isolates were resistant to fluoroquinolones, and multidrug resistance was observed in S. Kentucky and S. Derby. The study also found a 52% farm-level occurrence of extended-spectrum beta-lactamase-producing <i>E. coli</i>, with four bla_CTX-M variants detected (bla_CTX-M-15, bla_CTX-M-27, bla_CTX-M-55, and bla_CTX-M-65). A genomic analysis revealed the dissemination of bacterial clones between farms, indicating potential routes of transmission. The high occurrence of AMR in both <i>Salmonella</i> and <i>E. coli</i> presents a potential public health risk, mainly through the consumption of contaminated poultry products. The study highlights the need for improved farm biosecurity and appropriate antimicrobial use to reduce the spread of resistant strains and combat AMR. These findings contribute to the Nigerian National Action Plan for AMR and underscore the importance of ongoing research and interventions in the poultry sector.