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 programs 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 on training and training materials published between November 2014 and October 2024. Eligible training focused on genomics or bioinformatics training for pathogen surveillance in Africa. Data were extracted on program characteristics, outcomes, challenges, and recommendations, with findings synthesised narratively and thematically. Results : Of 2464 identified articles, 35 were included, spanning 2014–2024. These comprised case studies (48.6%), opinion pieces (25.7%), reviews (17.1%), and cross-sectional studies (8.6%). Twenty-two articles detailed specific training programs, predominantly short-term (e.g., 2–14 days) and in-person (59.1%), with 59.1% covering both genomics and bioinformatics. Training programs were mostly carried out in African countries (94%), often funded by external agencies like NIH (27.3%) and Wellcome Trust (13.6%). Key outcomes included enhanced technical skills (22.7%) and career development (18.2%). Challenges included inadequate infrastructure, skill gaps, and theoretical-heavy curricula, while opportunities encompassed virtual delivery, collaborative networks, and open-access resources. 13 studies highlighted deficiencies like limited expertise and brain drain, recommending infrastructure investment, expanded curricula, and local trainer development. 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 programs, strengthening Africa’s pathogen surveillance capabilities.