MOLECULAR EPIDEMIOLOGY AND PHYLOGENETIC TRACKING OF MULTIDRUG-RESISTANT SALMONELLA STRAINS IN INTEGRATED LIVESTOCK PRODUCTION SYSTEMS

Abstract

The emergence of multidrug-resistant (MDR) Salmonella strains within livestock environments poses a major threat to global food safety and public health. This study employed a mixed-method experimental design to isolate and characterize Salmonella from poultry and swine production chains. A total of 180 isolates were subjected to antimicrobial susceptibility testing, molecular characterization, and biofilm assays. The results revealed that 68% of isolates were resistant to Ampicillin, 54% to Tetracycline, and 42% to Ciprofloxacin. Whole-genome sequencing uncovered widespread carriage of resistance genes including bla_TEM, tetA, qnrB, and efflux pump genes like acrAB. Biofilm formation was notably stronger among MDR strains, suggesting a link between environmental persistence and resistance. Integrons and plasmid-mediated genes were detected in 84% of MDR strains, highlighting the role of horizontal gene transfer. Minimum inhibitory concentration (MIC) testing confirmed elevated resistance levels with over 60% of isolates surpassing clinical breakpoints. Advanced data visualizations including heatmaps, pie charts, and cluster plots supported the phenotypic-genotypic integration. This comprehensive analysis underscores the urgent need for antimicrobial stewardship in livestock sectors and advocates for the implementation of genomic surveillance to mitigate MDR Salmonella risks. The study offers a critical contribution to the One Health approach by linking microbiological, genetic, and environmental dimensions of antimicrobial resistance.