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

The Fleming Fund has awarded SEQAFRICA, an AMR surveillance project, a grant investment extension of £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.

The grant extension will support:

• Core WGS equipment installations to reach the sequencing target of 31k genomes.

• Ongoing sequencing and data analysis support for SARS-CoV-2 to assist the global surveillance efforts providing early detection of further variants emerging, working with SEQAfrica partner NICD in South Africa, and neighbouring states (Eswatini, Lesotho, Namibia, Mauritius, Sudan and Mozambique).

• AMR data analysis and dissemination of WGS results on a national and global scientific level.

• Strengthening the sequencing centre’s workforce through continued bioinformatics training.

• Development of training in portable, real-time sequencing using a handheld device, the Oxford Nanopore MinION, for AMR data surveillance analysis and equipping scientists to identify possible new COVID variants.

The Department of Health and Social Care's Fleming Fund is a UK aid-funded programme supporting up to 25 countries across Africa and Asia to tackle antimicrobial resistance (AMR), a leading contributor to deaths from infectious diseases worldwide. The Fleming Fund invests in strengthening surveillance systems through a portfolio of country grants, regional grants and fellowships managed by Mott MacDonald, and global projects managed by DHSC.

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.

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.

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

The WGS network of lab teams and advanced genomics, high-throughput platforms for antimicrobial screening 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, 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.

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 interconnected.

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 as the genomic data was collected from both animal and environmental sources to understand pathogens in circulation. This has allowed us to investigate the antimicrobial transmission and extent of AMR resistance.”

For example, Fleming Fund fellow Alumnus Mabel Aworh, 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.”

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.”

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 steppingstone for future surveillance work.”