Escherichia coli in Kisumu Fish Markets, Kenya

This study investigated microbial contamination across the fish supply chain in Kisumu County, Kenya, with a focus on wild fish, cage aquaculture, and market environments within the Lake Victoria region. A cross-sectional design was applied under the FS4Africa project, integrating microbiological analysis of Escherichia coli (E. coli), physicochemical water quality assessment, and stratified sampling across landing sites, aquaculture cages, processing environments, and informal markets. A total of 351 samples comprising fish, water, and surface swabs were analyzed using ISO 16649-2 protocols with MacConkey agar and IMViC confirmation. Results revealed a clear contamination gradient across the fish value chain. Wild fish from Dunga, showed generally low contamination, with omena consistently testing negative (0%), confirming a strong natural safety baseline at harvest. Cage water analysis identified contamination hotspots in Cage 5 (66.7%) and Cage 6 (33.3%), associated with dissolved oxygen below 4.50 mg L⁻¹, elevated ammonium up to 0.0486 mg L⁻¹, total phosphorus up to 0.0606 mg L⁻¹, total nitrogen up to 32.97 mg L⁻¹, and turbidity exceeding 39 FTU. Although pH remained largely within acceptable limits, slight acidification in affected cages (pH 7.04) coincided with microbial presence. Market analysis revealed the highest risks in informal markets, with prevalence reaching 100% in Obunga, 80% in Fish Market, 66.7% in Kondele, and 60% in Nyalenda, while Dunga (3.4%) and Star Market (0%) demonstrated safer outcomes. Processing methods further influenced contamination, with fried and heat-treated fish remaining safe under controlled conditions, while post-cooking recontamination was a major risk in informal settings. Microbial contamination was driven by environmental stressors and post-harvest hygiene rather than fish species. The findings support policy actions on aquaculture water quality surveillance and strengthened market hygiene standards. Scalable interventions including hygienic processing, vendor training, hybrid solar drying, and IoT-enabled traceability can enhance fish safety, consumer confidence, and sustainable Blue Economy growth in Kenya.

Key words

Cage aquaculture, Escherichia coli, Fish safety, Fish value chain, Water quality