Nontyphoidal Salmonella presents a significant threat to animal and human health as a food-borne infectious agent. This study focused on the characterization of Salmonella isolates obtained from fresh animal products consumed in Bejaia, Algeria. In total, 495 beef products, 600 chicken products, and 355 dairy products were collected from retail outlets and slaughterhouses in the region. Out of the 1450 samples collected, a Salmonella positivity rate of 3.5% (51/1450) was observed. Traditional Algerian sausages exhibited the highest prevalence of Salmonella contamination (14.1%, 36/256). Fifteen different serotypes were identified, with S. Kentucky (n = 12), S. Anatum (n = 11), and S. Bredeney (n = 9) being the most prevalent. Antimicrobial susceptibility testing showed resistance to diverse antibiotics, particularly against tetracycline, ampicillin, nalidixic acid, and sulphonamides. Whole-genome sequencing conducted on 21 isolates enabled the comparison of phylogenetic links between isolates. We notably identified clones circulating across the region in different locations and food types, suggesting contamination at the early stages of the food chain (in the herd or slaughterhouses) that disseminated to numerous butcher shops in various cities. We also identified acquired antibiotic resistance genes and point mutations in the quinolone resistance-determining region genes, contributing to the observed resistance patterns. This study describes the genomic and phylogenetic characteristics of several Salmonella clones found in diverse food samples in Algeria. It suggests potential transmission dynamics that could better understand Salmonella’s contamination routes.
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