TY - JOUR
T1 - SeqAfrica
T2 - empowering Africa’s fight against antimicrobial resistance through genomics
AU - Nilsson, Pernille
AU - Gibson, Christa Twyford
AU - Thornval, Natasia R.
AU - Lacy-Roberts, Niamh
AU - Odgaard, Christina
AU - Owusu-Nyantakyi, Christian
AU - Amuasi, Grebstad Rabbi
AU - Boateng, William
AU - Mohktar, Quaneeta
AU - Bortey, Alfred
AU - Odih, Erkison Ewomazino
AU - Sunmonu, Gabriel Temitope
AU - Kumburu, Happiness H.
AU - Sonda, Tolbert
AU - Bhiman, Jinal N.
AU - Amoako, Daniel G.
AU - du Plessis, Mignon
AU - Adu, Bright
AU - van Zwetselaar, Marco
AU - von Gottberg, Anne
AU - Mmbaga, Blandina T.
AU - Okeke, Iruka N.
AU - Smith, Anthony M.
AU - Egyir, Beverly
AU - Hendriksen, Rene S.
N1 - Publisher Copyright:
Copyright © 2025 Nilsson, Gibson, Thornval, Lacy-Roberts, Odgaard, Owusu-Nyantakyi, Amuasi, Boateng, Mohktar, Bortey, Odih, Sunmonu, Kumburu, Sonda, Bhiman, Amoako, du Plessis, Adu, van Zwetselaar, von Gottberg, Mmbaga, Okeke, Smith, Egyir and Hendriksen.
PY - 2025
Y1 - 2025
N2 - 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.
AB - 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.
KW - Africa
KW - antimicrobial resistance
KW - capacity building
KW - low- and middle-income countries
KW - surveillance
KW - whole genome sequencing
UR - https://www.scopus.com/pages/publications/105026259708
U2 - 10.3389/fpubh.2025.1716498
DO - 10.3389/fpubh.2025.1716498
M3 - Article
AN - SCOPUS:105026259708
SN - 2296-2565
VL - 13
JO - Frontiers in Public Health
JF - Frontiers in Public Health
M1 - 1716498
ER -
