Antibiotic sensitivity of bacterial isolates from farmed fish in Uasin Gishu County, Kenya

Abstract

The study was conducted with the aim of investigating the antibiotic sensitivity of bacterial isolates from farmed fish to commonly used antibiotics in Uasin Gishu County, Kenya, a region experiencing rapid aquaculture growth. Despite no direct antibiotic use in local fish farms, concerns over antimicrobial resistance (AMR) have emerged due to indirect exposure from integrated livestock-crop systems. A longitudinal study design was used to evaluate microbial infestations. Over a 12-month period, 468 fish samples from 13 ponds across five farms were examined, yielding 154 bacterial isolates representing 12 species, including Escherichia coli, Aeromonas species, Pseudomonas aeruginosa, Vibrio species and Flavobacterium columnare. Antibiotic susceptibility testing was conducted using six commonly used antibiotics: amoxicillin (AMX), erythromycin (ERY), cotrimoxazole (CT), doxycycline (DO), streptomycin (STR), and ciprofloxacin (CIP). Statistical analysis using Fisher’s exact test revealed significant interspecies resistance variation for AMX and ERY (p = 0.0005), while the other antibiotics showed consistent susceptibility across species. Principal Component Analysis (PCA) and heatmap analyses confirmed AMX and ERY as the primary drivers of resistance variation, particularly in E. coli, Aeromonas hydrophila and Streptococcus species, which showed resistance rates above 35 to 50%. Conversely, CIP, DO, and STR exhibited high effectiveness, with over 80% susceptibility in most isolates. The results suggest that indirect exposure through runoff, manure application, and effluent from livestock farming is likely promoting resistance. The findings of this study reveal that antibiotic use in surrounding agricultural systems, although not directly applied to fish, may be contributing to the development of resistant bacterial populations within aquaculture environments. This highlights a critical link between terrestrial and aquatic ecosystems, reinforcing the need for a One Health approach to antimicrobial stewardship. The results emphasize the importance of regular monitoring of antibiotic resistance patterns and adopting tailored antibiotic selection based on local data. Furthermore, the study underscores the necessity of improved waste management, enhanced farmer education, and strengthened biosecurity practices to curb the spread of resistant bacteria. Continued surveillance of antibiotic resistance in aquaculture is essential to ensure food safety, safeguard public health, and promote the sustainability of fish farming systems.