A scoping review of antimicrobial use, residues, and resistance in African aquaculture: evidence, gaps, and emerging interventions (2020–2025)

Abstract

African aquaculture is characterized by the prevalent use of antimicrobials and no clear guidelines on their use. The common drugs used include tetracyclines, penicillins, sulfonamides, and fluoroquinolones. Excessive misuse of antimicrobial agents can drive antimicrobial resistance (AMR), which can endanger human health, ecosystems, and economic productivity. The current work aimed at synthesizing recent evidence on antimicrobial use, residues, and resistance in African aquaculture published between 2020 and 2025. A scoping review was conducted following Prisma-ScR guidelines with six databases (PubMed, Scopus, Embase, Web of Science, Cochrane Library, and African Index Medicus) searched, which yielded 482 records. After the screening process, 41 studies were finally selected. Data extracted from these studies included drug use patterns, concentrations of residues, types and genes of resistance, the prevalence of multidrug- or extensively drug-resistant bacteria. Variability in study design, farm species and farm production systems precluded meta-analysis, and the findings narratively. Antimicrobial resistance was pervasive, with a high prevalence of multidrug-resistant Escherichia coli (43%) and Salmonella (40%). Resistance was particularly against ampicillin and co-trimoxazole, which, although are of lower-priority for human health, remain widely used in Africa. Residues in fish tissues and pond environments ranged from 70 to 450 µg/kg, with 12% exceeding regulatory limits (e.g., EU). Resistance was most common against drugs most frequently used, like ampicillin and co-trimoxazole. Antimicrobial use for disease prevention or promoting growth was observed in only few farms. Major drivers of resistance included weak regulation enforcement, limited laboratory capacity, inadequate extension services, and low incorporation of aquaculture into the national AMR surveillance and response systems. Intervention measures such as vaccination, probiotics, plant-based immunostimulants, and biosecurity measures provided opportunities to reduce disease risk and antimicrobial reliance. The use of antimicrobials and drive resistance in practically every sector of African aquaculture pose significant One Health challenges. We recommend strengthening AMR surveillance, standardization of metrics for antimicrobial use and AMR, improving laboratory capacity, enforcement of regulations, and adoption of alternative disease control measures to improve sustainability of the sector.