Fleming Fund Regional Grant ​SeqAfrica ​

A consortium of sequencing centres

SeqAfrica has established and currently supports a consortium of regional sequencing centers based in:

• Ghana (Noguchi Memorial Institute for Medical Research, NMIMR)

• Senegal (Institute Pasteur de Dakar, IPD)

• South Africa (National Institute for Communicable Diseases, NICD)
  - Center for Enteric Diseases (NICD-CED)

Former consortium partners:

• Kilimanjaro Clinical Research Institute (KCRI), Tanzania

• National Institute for Communicable diseases, Centre for Respiratory Diseases and Meningitis (NICD-CRDM), South Africa

• University of Ibadan (UI), Nigeria

Bringing WGS into AMR surveillance

SeqAfrica's main objective is to develop, expand, and support whole genome sequencing (WGS) and bioinformatics capacity for antimicrobial resistance (AMR) surveillance across Africa.
Our centers provide WGS and analysis services to surrounding countries in West, East and Southern Africa and support investigations of outbreaks, unusual resistance phenotypes, and/or delineation of the flow of organisms/genes across human, animal, agricultural and aquaculture sectors.

Submit your application for WGS services via this link. More information can be found under the Whole Genome Sequencing services page.

Building capacity and sustainably through training

Improving the surveillance of AMR in Africa does not only require building and expanding existing sequencing capacity through instrumentation, but also calls for training in the use of equipment and data analysis. In-depth training is instrumental to sustaining activities beyond the timeframe of the project, and as such SeqAfrica has developed extensive virtual training for a range of audiences going from novel and non-users to more experienced staff.

More information, details, and resources for training, including recordings of previous virtual training courses can be found at the SEQAFRICA Courses page.

In the coming year (2024) SeqAfrica will begin expanding the sequencing capacity to include long-read sequencing. To disseminate the new technology, we will  provide input and training for novel and non-users  at implementing sites for them to generate and analyse data. Read more about the democratisation of sequencing.

Funding

SEQAFRICA is led by the Research Group for Global Capacity Building at the National Food Institute, Technical University of Denmark and is funded through a Fleming Fund Regional Grant. The Fleming Fund is a £265 million UK aid investment to tackle antimicrobial resistance in low- and middle-income countries around the world. The programme is managed by the UK Department of Health and Social Care, in partnership with Mott MacDonald, the Fleming Fund Grants Management Agent for the Country and Regional.

Phase II - Expanding with sentinel surveillance sites

SeqAfrica began its second phase in October 2023. A focus of SeqAfrica Phase II will be to democratize sequencing, which will be achieved by expanding our network. We will pilot six sentinel sites focusing on ONT long-read sequencing, while still maintaining our network of regional sequencing centers. SeqAfrica will employ a solution tailored to meet the African challenges of unreliable internet and limited number of trained bioinformatics by pairing  an Oxford Nanopore Technologies MinION device with a laptop with the MinKNOW software and an approach to data analysis fit for non or novel-users. Experiences gathered during a scoping period and initial pilot phase will determine the standard operating procedures for data analysis at sentinel surveillance sites.