Antimicrobial Resistance in Lake Victoria, Kenya

Lake Victoria, Africa’s largest freshwater lake, represents a critical yet under-studied antimicrobial resistance (AMR) hotspot where environmental contamination, aquaculture intensification, and foodborne exposure pathways converge. A cross-sectional surveillance under the FS4Africa evaluated microbial contamination and AMR risks in the Dunga Beach fish value chain. A total of 351 fish, water, and environmental samples were collected following ISO 19458 and ISO 6887-3. Bacterial isolation was performed using microbiological methods on Tryptic Soy Agar (TSA) and MacConkey agar, guided by ISO 7218. Presumptive isolates were identified by 16S rRNA gene sequencing. Antimicrobial susceptibility testing was conducted using the Kirby–Bauer disk diffusion method in accordance with CLSI M100 and EUCAST breakpoints. Cage aquaculture systems showed degraded water quality, including dissolved oxygen below 4.50 mg L⁻¹, elevated nutrient loading (ammonium 0.05 mg L⁻¹; phosphorus 0.06 mg L⁻¹; nitrogen 32.97 mg L⁻¹), high turbidity (>39.00 FTU) and pH 7.04. Molecular analysis identified 23 bacterial species across 11 genera. Microbial contamination increased along the production chain, with higher levels in Oreochromis niloticus from cage systems and informal markets, while taxa, including Aeromonas jandaei, Vibrio harveyi, and Shewanella algae, are fish pathogens associated with disease outbreaks and mortality events. Antimicrobial susceptibility testing indicated that Escherichia coli and Salmonella enterica were the most responsive isolates, exhibiting ciprofloxacin inhibition zones of 30.60 ± 0.0 mm and 31.00 ± 0.0 mm, respectively. In contrast, Pseudomonas aeruginosa exhibited a multidrug-resistant phenotype with reduced inhibition zones across tetracycline (16.80 ± 0.3 mm), ciprofloxacin (17.20 ± 0.0 mm), and trimethoprim-sulfamethoxazole (16.40 ± 0.3 mm). This study generates baseline AMR surveillance data for Lake Victoria and provides evidence of multidrug-resistant bacteria. These findings highlight the need to strengthen regional and global AMR surveillance, improve water quality management, and enhance fish handling practices to protect public health and support sustainable fisheries and blue economy.