Microbial Profiling, Antibiotic Susceptibility, and Residue Detection in Market-Ready Tilapia from Key Aquaculture Regions in Zambia

Aquaculture is a rapidly expanding sector that plays a critical role in global food security. However, intensive fish farming practices can lead to increased bacterial infections and antimicrobial resistance (AMR). This study investigated microbial profiles, antibiotic susceptibility, and antibiotic residues in market-ready Nile tilapia (Oreochromis niloticus) from key aquaculture production regions in Zambia. A total of 118 fish samples were collected from small-, medium-, and large-scale farms in Kafue and Siavonga districts, covering both cage and pond culture systems. Bacterial isolates were identified using selective media, biochemical tests, and molecular methods. The antibiotic susceptibility of Vibrio spp., Lactococcus garvieae, Escherichia coli, Salmonella spp., and Aeromonas spp. was determined using the disk diffusion method. Residue analysis was conducted using ultra-high-performance liquid chromatography tandem mass spectrometry (UHPLC-MS/MS). The results revealed significant bacterial contamination, with E. coli detected in 6.78% of samples, Salmonella spp. in 17.8%, and Aeromonas spp. in 3.39% in large-scale commercial operations. Vibrio spp. prevalence was highest in pond culture at 22.88%, while L. garvieae was most prevalent in large-scale pond farms at 10.17%. Antibiotic resistance was widespread, with 100% resistance to ampicillin in E. coli across all farm scales and 100% resistance to imipenem and erythromycin in L. garvieae from cage culture. Minimal antibiotic residues were detected, except for a single instance of penicillin residue in small-scale cage culture. These findings underscore the need for enhanced biosecurity measures, and robust monitoring systems to mitigate AMR risks and ensure food safety in Zambia’s aquaculture industry.