Genomic and Pharmacodynamic Characterisation of Multidrug-Resistant Salmonella Isolates from Poultry and Humans in the South West Poultry Belt

Salmonella represents a critical priority zoonotic pathogen at the human-animal-food interface in Nigeria, and the South West poultry belt spanning Ogun, Oyo, and Lagos states is one of the highest-density commercial poultry regions in sub-Saharan Africa. The genomic epidemiology of multidrug-resistant Salmonella and the pharmacodynamic consequences of resistance acquisition have not been characterised in this high-risk regional context. This study conducted whole-genome sequencing and comparative pharmacodynamic characterisation of Salmonella isolates recovered from broiler farms, abattoir carcasses, and clinical human cases in the South West poultry belt. Three hundred isolates were subjected to Illumina short-read whole-genome sequencing. Resistome analysis, multilocus sequence typing, pangenome reconstruction, and plasmid mobilisation profiling were performed bioinformatically. Pharmacodynamic parameters including MIC, MBC, and time-kill kinetics were generated for ciprofloxacin, cefotaxime, and azithromycin against representative resistant isolates. Phylogenomic analysis revealed clonal transmission of sequence type 198 and sequence type 313 between poultry and human clinical isolates, establishing direct epidemiological linkage. Multiple integrative conjugative elements carrying blaCTX-M-15, qnrS, and aadA genes were identified on IncI and IncFIB plasmids shared between poultry and clinical strains. Extended-spectrum beta-lactamase-producing isolates showed dramatically elevated cefotaxime MIC values above 64 micrograms per millilitre. These findings demonstrate genomic convergence and pharmacodynamic equivalence between poultry and human resistant Salmonella in South West Nigeria, establishing a compelling One Health rationale for integrated surveillance and antibiotic stewardship at the animal-human interface. Keywords: Salmonella, whole genome sequencing, antimicrobial resistance, One Health, South West Nigeria.