Comparative distribution of antimicrobial resistance genes in non-typhoidal Salmonella from chicken and aquaculture production systems, 2010–2025: a systematic review and meta-analysis

To compare the prevalence and distribution of antimicrobial resistance (AMR) genes in non-typhoidal Salmonella from chicken and aquaculture production systems and assess regional and temporal patterns of resistance genes, six databases were searched for studies published between 2010 and 2025 reporting AMR genes in non-typhoidal Salmonella. Seventy-six studies met the inclusion criteria, including 68 from chicken and eight from aquaculture. Random-effects meta-analysis was used to estimate pooled prevalence. Pooled Salmonella prevalence was 21.0% (95% CI 15.3-28.2) in chicken and 44.3% (95% CI 22.6-68.4) in aquaculture, although aquaculture estimates were based on fewer studies. Resistance genes associated with tetracyclines, β-lactams and sulfonamides were frequently detected, particularly tet(A), blaTEM, blaCTX and sul2. Chicken isolates showed substantial regional heterogeneity, with higher prevalence in the Eastern Mediterranean and South-East Asia regions. Prevalence of selected genes, including tet(A), sul2, aadA and qnrS, increased across sampling periods. Overlapping AMR gene profiles across chicken and aquaculture suggest interconnected resistance reservoirs that may increase opportunities for human exposure through the food chain, highlighting the importance of integrated AMR surveillance and antimicrobial stewardship strategies.