Harnessing genomic and bioinformatics for surveillance of pathogens in Africa: a scoping review of existing training and gaps in training

BACKGROUND: Pathogen surveillance is vital for managing infectious diseases in Africa, where high disease burdens necessitate advanced tools like genomics and bioinformatics. While these technologies enable early detection, resistance monitoring, and targeted interventions, yet their adoption is hindered by limited training and educational resources. This scoping review maps existing training programmes in genomics and bioinformatics for pathogen surveillance in Africa, identifying gaps and opportunities to enhance capacity-building. METHODS: Following PRISMA-ScR guidelines, we systematically searched databases (PubMed, Embase, Scopus, etc.) and grey literature for articles which described the design, implementation, delivery, or evaluation of a specific genomics/bioinformatics training programme or discussed training needs or status published between November 2014 and December 2025. Eligible articles focused on genomics or bioinformatics training for pathogen surveillance in Africa. Data were extracted on programme characteristics, outcomes, challenges, and recommendations, with findings synthesised narratively and thematically. RESULTS: Of 2491 identified articles, 40 were included, spanning 2014-2025. These comprised case studies (45%), opinion pieces (27.5%), reviews (15%), cross-sectional studies (10%), and a methodological study (2.8%). Twenty-three articles detailed specific training programmes, predominantly short-term (e.g., 2-14 days), with 60.9% of the training programmes covering both genomics and bioinformatics. Training programmes were mostly carried out in African countries (91.3%), often funded by external agencies like NIH (26.1%) and Wellcome Trust (13%). Key outcomes included enhanced technical skills (21.7%) and career development (17.4%). Challenges included inadequate infrastructure, skill gaps, and theoretical-heavy curricula, while opportunities encompassed virtual delivery, collaborative networks, and open-access resources. Seventeen studies were included as they examined training status and deficiencies in Africa, highlighting limited expertise and brain drain, and recommending investment in infrastructure, expansion of curricula, and development of local trainers. CONCLUSION: Genomics and bioinformatics training in Africa is growing but remains fragmented, donor-dependent, and resource-constrained. Sustainable capacity-building requires institutionalising training within academic systems, increasing government investment, and leveraging open-access and regional networks. These findings provide a foundation for policymakers and educators to develop targeted, inclusive programmes, strengthening Africa's pathogen surveillance capabilities. CLINICAL TRIAL NUMBER: N/A.