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These bacterial pathogens cause human illnesses characterized by hemorrhagic colitis, vomiting, nausea, and other agent-related symptoms. The increasing occurrence of antimicrobial resistance in these pathogens is also a serious public health concern globally. Regular surveillance of phenotypes and genotypes of<jats:italic>Salmonella<\/jats:italic>spp. and<jats:italic>Escherichia coli<\/jats:italic>from animal-derived foods is necessary for effective reduction and control of these foodborne pathogens. This study was conducted to assess the occurrence, antimicrobial resistance, virulence genes and genetic diversity of<jats:italic>Salmonella<\/jats:italic>spp. and<jats:italic>E. coli<\/jats:italic>isolates from fresh Nile tilapia obtained from retail markets in Nairobi, Kenya.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>A total of 68 fresh Nile tilapia fish samples were collected from retail markets and used for isolation of<jats:italic>Salmonella<\/jats:italic>spp. and<jats:italic>E. coli<\/jats:italic>. Antimicrobial susceptibilities of the isolates weretested by Kirby-Bauer agar disc diffusion method. According to the antimicrobial resistance profiles, the multi-drug resistant isolates were identified by 16\u00a0S rRNA sequencing and phylogenetic analysis using the Bayesian inference method. The MDR<jats:italic>Salmonella<\/jats:italic>spp. and<jats:italic>E. coli<\/jats:italic>isolates were subjected to PCR-based screening for the detection virulence and antibiotic resistance genes.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>The prevalence of contamination of the fish samples with<jats:italic>Salmonella<\/jats:italic>spp. and<jats:italic>E.coli<\/jats:italic>was 26.47% and 35.29% respectively. Overall phenotypic resistance among the<jats:italic>Salmonella<\/jats:italic>spp. ranged from 5.5% for ceftazidime, chloramphenicol, meropenem, nitrofurantoin and streptomycin and 22.2% for penicillin-G. For<jats:italic>E. coli<\/jats:italic>phenotypic resistance ranged from 4.2% for ceftazidime and chloramphenicol and 25% for rifampicin. Multi-drug resistance was observed in three<jats:italic>Salmonella<\/jats:italic>spp. and two<jats:italic>E. coli<\/jats:italic>isolates. Results of 16\u00a0S rRNA sequences, sequence alignment and phylogenic trees confirmed the identified MDR isolates as<jats:italic>S. typhymurium<\/jats:italic>WES-09,<jats:italic>S. typhymurium<\/jats:italic>MAK-22,<jats:italic>S. typhimurium<\/jats:italic>EMB-32 and<jats:italic>E. coli<\/jats:italic>MAK-26 and<jats:italic>E. coli<\/jats:italic>LAN-35. The presence of antibiotic-resistance genes belonging to \u03b2-lactamases, tetracycline, sulfonamide, trimethoprim and aminoglycosides-resistant genes were detected in all the identified MDR isolates.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>The findings from this study indicate that Nile tilapia (<jats:italic>Oreochromis niloticus<\/jats:italic>) sold in retail markets can acts as reservoirs of<jats:italic>Salmonella<\/jats:italic>spp. and<jats:italic>E<\/jats:italic>.<jats:italic>coli<\/jats:italic>pathogens linked to human disease, some of which were multidrug resistance to critically important antimicrobials. Both microorganisms are of zoonotic significance and represent a significant public health risk to the society.<\/jats:p><\/jats:sec>","DOI":"10.1186\/s12866-023-03049-8","type":"journal-article","created":{"date-parts":[[2023,10,26]],"date-time":"2023-10-26T02:02:14Z","timestamp":1698285734000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":41,"title":["Antimicrobial resistance profiles of salmonella spp. and escherichia coli isolated from fresh nile tilapia (oreochromis niloticus) fish marketed for human consumption"],"prefix":"10.1186","volume":"23","author":[{"given":"Millicent T.","family":"Mumbo","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Evans N.","family":"Nyaboga","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Johnson K.","family":"Kinyua","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Edward K.","family":"Muge","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Scholastica G. 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