African genomics project receives additional funding to map AMR transmission patterns across continent


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.

Led by the Technical University of Denmark (DTU), SEQAFRICA has established a network of WGS clients in 15 countries across Africa with innovative WGS and bioinformatics capabilities to sequence and analyse AMR genomic data. The data is collected from humans, animals, and the environment - providing insight into AMR transmission under a One Health remit.

Map of SEQAFRICA's partners.

The grant was launched in 2019, at which time the National Institute for Communicable Diseases (NICD) in South Africa was the only centre in sub-Saharan Africa that could carry out this essential genomics surveillance.

The original SEQAFRICA grant of £4.3 million to DTU has now established three additional regional AMR sequencing centres: the University of Ibadan (UI) in Nigeria; the Noguchi Memorial Institute for Medical Research (NMIMR) based in Ghana; and the Kilimanjaro Clinical Research Institute (KCRI) in Tanzania.

WGS Network

The grant also provided essential technology and support for surveillance of COVID-19 variants. The additional £2.4 million will continue to support this vital work by providing additional equipment, training and logistics support to widen the WGS service.

The WGS network have sequenced the genomes of over 16,000 samples, of which 87% are uploaded to publicly available databases to aid further AMR analysis.

The SEQAFRICA team has also developed training modules to upskill life scientists and practitioners in WGS AMR surveillance and workflows, sequencing of the COVID virus - SARS-CoV-2, and advanced bioinformatics.

Dr Toby Leslie, Global Technical Lead at Mott MacDonald, the Fleming Fund’s Management Agent, said:

“The grant has provided access for African countries to the vital WGS service using the latest technologies, which reduces the country costs for genome sequencing previously conducted outside the continent. This was identified as a specific need to improve AMR surveillance in sub-Saharan Africa.”

One Health, AMR and COVID-19

As COVID-19 became a worldwide pandemic, SEQAFRICA was able to begin pivoting to SARS-CoV-2 sequencing through NICD in South Africa. They provided essential input into the global response, increasing awareness and understanding of the benefits of WGS for pathogen surveillance.

The NICD COVID team was involved in the detection and analysis of new SARS-CoV-2 virus variants of concern, including the Omicron strain.

The Fleming Fund grant has also demonstrated the importance of using WGS in One Health surveillance showing that bacteria from human, animal and environmental origins are linked.

Grant lead Prof Rene S. Hendriksen at DTU, said:

“Although most genomes sequenced in the SEQAFRICA project were sourced in a human health clinical setting, multiple contributions came from animals and the environment.”

“This has led to wider interest in AMR surveillance in the scientific community, particularly the connection to One Health. Collecting the samples from multiple sources has allowed us to investigate the antimicrobial transmission and extent of AMR resistance.”

For example, Fleming Fund fellow Alumnus Mabel Aworh, who has recently published a paper using findings from the SEQAFRICA grant, explains:

“With WGS, we have detected the same antimicrobial resistant genes in abattoir workers and beef cattle in Nigeria.”

“This is possibly the result of AMR genes spreading between humans and animals through direct contact with the cattle or contaminated abattoir surfaces. One of the recommendations and preventative measures could be as simple as the abattoir workers washing their hands before eating.”

Open Science

In addition to providing genomics data to the grant’s partners, SEQAFRICA also held workshops on data quality and analysis, including demonstrations on publicly available tools for the research community.

“We are delighted with DTU’s outstanding performance to date and excited to support the next phase of this important technical grant”, said DHSC.

“The extension enables the SEQAFRICA team to continue their vital work exploring AMR transmission through genes. This valuable insight helps us to better understand and tackle the growing threat of AMR.”

The grant investment extension will support:

Prof Hendriksen, added: “Data generation and analysis is ongoing and as it advances and is disseminated through clients and SEQAFRICA, understanding of the impact and extent of data use will also evolve and provide a stepping stone for future surveillance work.”

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The Fleming Fund and the Open University have released new modules on the Tackling Antimicrobial Resistance course, meaning 23 modules are now available. The course is completely free and available world-wide, regardless of whether participants are affiliated with the Fleming Fund.

In 2017, the researchers of the Institute for Health Metrics and Evaluation (IHME) and the University of Oxford developed a partnership to establish the human cost (burden) of AMR. This partnership gave birth to the Global Research on Antimicrobial Resistance (GRAM) project. Fast forward four years, 434 million individual records and 12,582 study-location-years' worth of data, and GRAM has become a household name for anyone in the industry.