The Technical University of Denmark (DTU), Fleming Fund regional grantee, presented on the SEQAFRICA project at the symposium ‘Beyond COVID-19: Pathogen Genomics and Bioinformatics for Health Security in Africa’, hosted at the African Union Commission in Addis Ababa, Ethiopia.
'SeqAfrica' enters next phase to expand AMR genomics sequencing across continent
SeqAfrica has launched the second phase of its work in Sub-Saharan Africa with a £3.6 million (DKK 31 million) regional grant from the UK government’s Fleming Fund. SeqAfrica’s focus on increasing surveillance data will allow governments to monitor and analyse antimicrobial resistance (AMR), informing healthcare actions and policy change throughout the African region.
Through SeqAfrica, the Technical University of Denmark (DTU) National Food Institute − in collaboration with the Institut Pasteur de Dakar in Senegal , Noguchi Memorial Institute for Medical Research in Ghana, and the National Institute for Communicable Diseases in South Africa − are supporting African countries to strengthen AMR surveillance through the introduction and expansion of whole genome sequencing (WGS) technologies and skills.
The SeqAfrica team based at the Noguchi Memorial Institute for Medical Research
The burden of bacterial antimicrobial resistance in the WHO African region in 2019: a cross-country systematic analysis estimated over one million deaths associated with bacterial AMR and 250K deaths attributable to bacterial AMR. The largest fatal AMR burden was attributed to lower respiratory and thorax or intra-abdominal infections, with seven leading pathogens collectively responsible for 821K deaths associated with resistance in this region.
The Fleming Fund partners with global organisations to establish and strengthen AMR surveillance systems, improving laboratory infrastructure, staff capacity, and data collection and analysis capability.
The SeqAfrica project has worked to strengthen and equip a network of five regional sequencing centres across Africa, sequencing over 20,000 bacterial and 10,000 SARS-CoV-2 genomes from 22 African countries.
Some of this data was recently used to inform healthcare actions at the Eastern Regional Hospital in Koforidua, Ghana. Consortium Partner Noguchi Memorial Institute for Medical Research held an interactive session where they shared results from the SeqAfrica-supported National AMR surveillance project with healthcare workers at the facility.
The session highlighted the importance of combining genomic and phenotypic methods to strengthen AMR surveillance. The healthcare workers and SeqAfrica team explored strategies to address the challenges posed by AMR and to tackle drug resistance in hospitals and Ghana at large. The project has additional interactive data-sharing sessions planned for other hospitals in Ghana in phase 2 of the Fleming Fund regional grant.
Dr Beverly Egyir, SeqAfrica Project Lead at the Noguchi Memorial Institute for Medical Research shares findings from Ghana’s national whole genome sequencing surveillance pilot to the Eastern Regional Hospital.
In its first phase, SeqAfrica created a series of training programmes to build expertise in WGS for AMR surveillance, which saw animal and human health professionals from over 18 countries participating. This data was used to produce over 25 research publications, which have informed scientific and policy developments in AMR surveillance.
The project’s second phase will use the AMR surveillance expertise developed at regional sequencing centres during phase I to expand into pilot surveillance sites. This aims to democratise WGS and build momentum for policy action.
SeqAfrica helps African countries build laboratory capacity and reliable data on the extent of antibiotic resistance. The second phase is about democratisation, where we will strengthen the monitoring of AMR and disseminate and anchor data locally. We are setting up local facilities in addition to regional so that AMR and trends in drug resistance can be quickly identified and handled locally
explains Professor Rene S. Hendriksen, Programme Director of SeqAfrica at DTU National Food Institute.
The grant from the Fleming Fund means that antibiotic resistance monitoring can now be extended, and that the data collected can be translated into public health actions driving greater investment in AMR surveillance.
"It will be easier to pave the way for national policies in Africa that mandate the reduction and prevention of antibiotic resistance from building resistance surveillance capacity deep down the surveillance pyramid and the health system; involving general practitioners in countries and sectors,”
says Hendriksen.
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The Fleming Fund has awarded an AMR surveillance project, ‘SEQAFRICA’, with an additional £2.4 million. SEQAFRICA uses the innovative technology whole genome sequencing (WGS) to improve antimicrobial resistance (AMR) surveillance and invests in training African scientists to help triple the capacity for gene sequencing across the continent.