SeqAfrica: Empowering Africa's fight against antimicrobial resistance through genomics

Pernille Nilsson^1*Christa Twyford Gibson¹Natasia Rebekka Thornval¹Niamh Lacy-Roberts¹Christina Odgaard¹Christian Owusu-Nyantakyi²Grebstad Rabbi Amuasi²William Boateng²Quaneeta Mohktar²Alfred Bortey²Erkison Ewomazino Odih³Gabriel Temitope Sunmonu³Happiness Houka Kumburu⁴Tolbert Sonda⁴Jinal N Bhiman^5,6,7,8Daniel Gyamfi Amoako^10,5,9Mignon du Plessis^11,5Bright Adu²Marco van Zwetselaar^12,4Anne von Gottberg^11,5Blandina Theophil Mmbaga^13,4Iruka N Okeke³Anthony Smith^14,15Beverly Egyir²Rene S Hendriksen¹

• ¹Technical University of Denmark, National Food Institute, Research Group for Global Capacity Building, Kgs. Lyngby, Denmark
• ²University of Ghana Noguchi Memorial Institute for Medical Research, Accra, Ghana
• ³Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Oyo State, Ibadan, Nigeria
• ⁴Kilimanjaro Clinical Research Institute, Moshi, Tanzania
• ⁵Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Division of the National Health Laboratories Service, Johannesburg, South Africa
• ⁶SAMRC Antibody Immunity Research Unit, School of Pathology, University of Witwatersrand, Johannesburg, South Africa
• ⁷National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa
• ⁸Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
• ⁹Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
• ¹⁰Department of Pathobiology, University of Guelph, ON N1G 2W1, Guelph, Canada
• ¹¹Department of Clinical Microbiology and Infectious Diseases (CMID), School of Pathology, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa
• ¹²Zwets IT, Harskamp, Netherlands
• ¹³School of Medicine, KCMC University, Moshi, Tanzania
• ¹⁴Centre for Enteric Diseases, National Institute for Communicable Diseases, Division of the National Health Laboratories Service, Johannesburg, South Africa
• ¹⁵Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa

The ongoing threat of antimicrobial resistance (AMR) demands capacity strengthening in Africa for improved pathogen surveillance. The high-resolution picture of AMR provided by pathogen whole genome sequencing (WGS) can help close data gaps and inform disease prevention strategies, interventions and public health actions. Here, we report on phase 1 of the Fleming Fund-supported SeqAfrica project (2019-2023), one of the first genomic AMR surveillance networks in Africa. SeqAfrica established five regional sequencing hubs across West, East, and Southern Africa, expanded infrastructure, and delivered hybrid training programs to strengthen workforce capacity. During phase 1, the network generated 29,269 pathogen genomes (18,264 bacterial, 300 fungal, and 10,705 SARS-CoV-2) from 21 African countries, contributing to 40 scientific publications and substantial genomic data for national and global surveillance efforts, supporting outbreak investigations and antimicrobial stewardship initiatives. The median turnaround time from sample receipt to data release was 12 weeks (range: 3-104 weeks), demonstrating the feasibility of genomic AMR surveillance despite logistical challenges. By nurturing a community of practice, expanding the workforce, and translating data into actionable insights, SeqAfrica has advanced the integration of pathogen genomics into national and regional surveillance frameworks. However, sustaining this capacity remains a challenge amid global funding constraints, procurement bottlenecks, and workforce retention issues. Lessons learned from implementation include successes in regional collaboration and persistent challenges in procurement, workforce retention, and metadata completeness, which informed the design of phase 2. As Africa continues to invest in genomic health infrastructure, SeqAfrica provides a proven model for embedding pathogen genomics into public health strategies and strengthening AMR surveillance across the continent.