Phenotypic and molecular characterization of Salmonella enterica isolated from retail beef in Peshawar, Pakistan

Salmonella enterica is a major foodborne pathogen associated with beef contamination and increasing antimicrobial resistance, particularly in low- and middle-income countries. This study investigated the prevalence, antimicrobial resistance patterns, and genetic diversity of S. enterica isolated from retail beef samples in Peshawar, Pakistan, using combined phenotypic and molecular approaches. A total of 250 beef samples were collected from urban, rural, and peri-urban retail markets. Salmonella enterica was isolated using standard culture and biochemical methods and confirmed by PCR targeting the invA gene. Antimicrobial susceptibility was determined by the Kirby-Bauer disk diffusion method, and genetic diversity was assessed using randomly amplified polymorphic DNA PCR (RAPD-PCR). Overall, S. enterica was detected in 150 samples (60.0%), with higher prevalence in rural markets (77.5%) compared with urban (52.5%) and peri-urban (50.0%) locations. A high percentage of isolates were resistant to azithromycin (94.0%), tetracycline (68.7%), and streptomycin (52.0%), indicating widespread multidrug resistance among isolates. Five isolates (3.3%) were identified as extended-spectrum β-lactamase (ESBL) producers and carried blaTEM-1, blaCTX-M-15, or blaSHV-12 genes. RAPD-PCR analysis revealed substantial genetic heterogeneity, with isolates distributed across multiple phylogenetic clusters, suggesting diverse contamination sources rather than clonal dissemination. These findings indicate that retail beef in Peshawar represents a significant reservoir of genetically diverse and antimicrobial-resistant S. enterica. The combined use of phenotypic methods with targeted molecular and low-cost genotyping approaches provides a practical framework for surveillance of foodborne Salmonella in resource-limited settings.