Preharvest antibiotic use influences antibiotic resistance in Salmonella species from commercial poultry and swine farms in Lagos, Southwestern Nigeria

Introduction The widespread use of antibiotics in commercial food animal production for growth promotion and prophylaxis is a primary driver of antimicrobial resistance (AMR) globally. This study provides a systematic characterization of the drivers of pre-harvest AMR in Salmonella spp. across farms in Lagos, southwestern Nigeria. Methods We evaluated 3,600 fecal samples from animals on commercial poultry and swine farms for Salmonella spp. and for antimicrobial and virulence determinants, using established microbiological, biochemical, and molecular protocols. We further assessed farm management practices and antimicrobial use through structured questionnaires and correlated these data with antimicrobial resistance phenotypes and determinants in Salmonella strains recovered from fecal samples across the farms. Results Overall, we observed a 1.5% (54/3,600) prevalence of Salmonella spp. across the sampled animals, with 0.67, 1.67, and 2.2% in layers, broilers, and pigs, respectively. While most Salmonella strains showed multidrug resistance, high rates of erythromycin (80–100%) and tetracycline (75–92.3%) resistance were observed across animal species, with multiple antibiotic resistance indices (MARI) ranging from 0.2 to 0.9. Molecular analysis revealed widespread distribution of major resistance determinants - tetA (70–100%), ant (3”)- Ia (80.8–100%), and sul1 (65.4–80%), and high prevalence of Salmonella -associated virulence factors, including iroB (62.5–75%), pipD (37.5–92.3%), and orfL (65–88.5%). Furthermore, we found extensive preharvest antibiotic use [as growth promoters (53.8–85.7%) and prophylaxis (71.4–81.3%)] as well as weak positive correlations ( r = 0.058–0.487, p = 0.327–0.913) between antibiotic use and AMR phenotypes across animal species. Discussion Our study reveals widespread AMR and virulence determinants in Salmonella spp. from commercial farms, suggesting a potential public health risk and the need for enhanced investigation, antimicrobial stewardship, and a concerted One Health mitigation strategy.