Characterization of Antimicrobial-Resistant Non-Typhoidal Salmonella and Other Bacteria in Integrated Fish Farming Environments in Nyeri County

Aim: This study aimed to characterize antimicrobial resistant non-typhoidal Salmonella and other bacteria in integrated fish farming environments in Nyeri County. Study Design: Integrated fish farming systems utilizing animal manure were investigated across three sub-counties: Tetu East, Nyeri Town, and Mathira. Methodology: Samples from fish, pond water, and manure were collected and processed for microbial analysis. Fish intestinal contents, water, and manure were incubated in nutrient broth and cultured on nutrient agar. Bacterial identification was done using MALDI-ToF mass spectrometry. Non-typhoidal Salmonella (NTS) was identified using selective culture media and confirmed through 16S rDNA typing. Antimicrobial susceptibility was tested via broth micro dilution, and Plasmid DNA of resistant isolates were screened through PCR and gel electrophoresis. Results: Multiple pathogens were detected, including Escherichia coli, Shigella spp., Staphylococcus spp., Aeromonas hydrophila, Serratia. NTS was found in 42.3% of all samples. Over 88% of Salmonella isolates showed MIC ≤1 µg/ml for ciprofloxacin, while 75% had MIC ≥3.125 µg/ml for azithromycin. High resistance was observed for oxacillin (54% with MIC 300–6000 µg/ml) and streptomycin (50% with MIC ≥24,000 µg/ml). Resistance rates were 60.6% for ciprofloxacin, 100% for oxacillin and streptomycin, and 23.1% for azithromycin. Resistance genes detected included parC, gyrA, msrA, strA, and strB, though mecA was absent. Discussion and Conclusion: The findings suggest that integrated fish farming poses a risk of transmitting antimicrobial-resistant pathogens from animal manure to aquatic environments. This not only threatens aquatic animal health but also poses a serious risk to human health through potential transmission via direct contact, environmental exposure, or consumption of contaminated fish products.