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. 2025 May 22;13(6):1174.
doi: 10.3390/microorganisms13061174.

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

Victoria Olusola Adetunji  1 , Alistair Davies  2 , Tom Chisnall  2 , Mwapu Dika Ndahi  3 , Idowu Oluwabunmi Fagbamila  4 , Eme Ekeng  5 , Ini Adebiyi  6 , Olutayo Israel Falodun  7 , Roderick M Card  2
Affiliations

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

Victoria Olusola Adetunji et al. Microorganisms. .

Abstract

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 Salmonella and Escherichia coli at 25 poultry farms in Oyo State, Nigeria. The farm-level occurrence of Salmonella was 48%, with 12 serovars identified, including S. Kentucky Sequence Type 198. Notably, 70% of Salmonella 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 E. coli, with four blaCTX-M variants detected (blaCTX-M-15, blaCTX-M-27, blaCTX-M-55, and blaCTX-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 Salmonella and E. coli 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.

Keywords: Escherichia coli; Nigeria; Salmonella; antimicrobial resistance; commercial poultry farms.

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Conflict of interest statement

The authors declare no conflicts of interest.

Figures

Figure 1
Figure 1
Maximum-likelihood phylogenetic tree generated from core genome single nucleotide polymorphisms of E. coli obtained from poultry in Oyo State, Nigeria. The Sequence Type (ST), Sample Type, and anonymised Farm Code are presented. The presence of genes and chromosomal mutations associated with antimicrobial resistance are indicated by filled squares and coloured according to antimicrobial class: green (aminoglycosides), red (beta-lactam), mauve (quinolone), blue (phenicol), purple (macrolide), black (sulphonamide), grey (tetracycline) and brown (trimethoprim). A blank square indicates gene absence. The reference strain was E. coli K12 (Accession number U00096.2).
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