Genomic insights into antimicrobial resistance in Africa: a one health scoping review (2015–2025)

Abstract Background Antimicrobial resistance (AMR) is an escalating public health threat in Africa, driven by high infectious disease burden, unregulated antimicrobial use, limited laboratory capacity, and fragmented surveillance. Conventional phenotypic methods provide limited insight into resistance evolution and cross-sectoral transmission, whereas genomic approaches such as whole-genome sequencing (WGS) and metagenomics allow high-resolution tracking of AMR genes across human, animal, and environmental reservoirs. Objectives This scoping review synthesizes genomic AMR evidence from Africa (2015–2025), evaluates sequencing capacity, resistance determinants, and cross-sectoral transmission, and identifies gaps and priorities for integrated One Health genomic surveillance. Methods Following PRISMA-ScR guidelines, 61 peer-reviewed studies and 9 programmatic reports were reviewed from PubMed, Scopus, African repositories, SeqAfrica, and the Africa CDC Pathogen Genomics Initiative. Due to heterogeneity in study designs, pathogens, and sequencing platforms, data were synthesized narratively. Results Genomic sequencing capacity was reported in 46 African countries, with major hubs in South Africa (> 10,000 isolates/year), Nigeria (3,000), Kenya (2,500), Ghana (1,200), Tanzania (800), and Uganda (1,000). Key resistance determinants—including blaCTX-M-15, blaNDM, blaOXA-48, and mcr-1—were detected across humans (~ 20–40%), animals (~ 15–25%), and the environment (~ 10–30%), indicating cross-sectoral circulation. Regional initiatives such as SeqAfrica and the Africa CDC Pathogen Genomics Initiative have strengthened workforce training and sample referral systems. Limitations include heterogeneity of study designs and platforms, preventing quantitative synthesis. Conclusion Genomic AMR research in Africa has improved understanding of resistance mechanisms within a One Health framework. However, surveillance remains fragmented, unevenly distributed, and largely dependent on short-term research efforts. Coordinated investment in laboratory capacity, workforce development, standardized data systems, and policy integration is needed to support sustainable continent-wide genomic AMR surveillance.