Democratising AMR genomics surveillance across Africa to target resistant pathogens

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The Fleming Fund-supported Regional Grant, SeqAfrica’s pilot project in South Africa, analyses local laboratories’ capacity for whole genome sequencing (WGS) to improve the accessibility, cost and efficiency of genomics analysis for antimicrobial resistance (AMR) data in-country.

SeqAfrica, led by the Technical University of Denmark (DTU), works to strengthen genomic surveillance of antimicrobial resistance (AMR) in Africa by training scientists and expanding sequencing capacity across the continent.

The process of WGS determines the complete genetic makeup of an organism by reading its DNA. For AMR surveillance, WGS helps scientists and public health professionals identify genetic changes in bacteria that cause drug resistance.

Providing a high-resolution picture of the organism, WGS allows researchers to track the spread of resistant strains, detect new resistance genes, and improve infection control strategies. This information is crucial for monitoring AMR trends and guiding public health interventions to combat the growing threat of antibiotic resistance.

Local African laboratories

In phase 1, the SeqAfrica project introduced WGS technology to several regional laboratories, which are now using it to conduct regional and national AMR surveillance. The recently completed pilot project was designed to expand this AMR surveillance capacity in local labs in Africa.

In phase 2 of the project, the pilot, launched by DTU PhD candidate, Natasia Rebekka Thornval, trained three Fleming Fund-supported laboratories in South Africa – the University of Pretoria, Lancet Laboratories, and the Centre for Enteric Diseases at the South African National Institute for Communicable Diseases (NICD) – integrating the new sequencing technology and simplified analytical tools into their research.

Natasia introduced Oxford Nanopore Technology’s MinION sequencing platform, a palm-sized device that can be more affordable for smaller laboratories than traditional sequencing technologies. “Our team developed easy-to-use sample-to-analysis protocols, using consumables available in Africa, which were designed to use minimal non-standard equipment for cost-effectiveness, both in procurement and time,” said Natasia.

AMR data validation

By introducing these tools to pilot sites, the SeqAfrica project hopes to contribute to the democratisation of sequencing capabilities across the African continent.

From the SeqAfrica laboratory training, the sites can now conduct regular analysis of Salmonella isolates of AMR concern using the new MinION technology. “The isolates analysed were sent to the National Reference Laboratory (NRL) at the NICD, for parallel testing of the pilot sites’ data and analysis, to validate the new results,” added Natasia.

Preliminary comparison of the pilot site’s WGS data with the NRL analysis of the same isolate indicated an issue with Citrobacter freundii ─ a pathogen bacterium susceptible to AMR, previously misidentified as Salmonella spp ─ at one of the pilot sites. Despite past species’ confirmation with phenotypic and PCR (polymerase chain reaction)-based laboratory methods, widely used for rapid DNA sequence analysis at NRLs.

Natasia further explains the impact: “This result underscores how WGS enhances AMR surveillance by resolving species-level misidentification not detected through routine-based methods, enabling more accurate resistance profiling while also providing a critical quality-control checkpoint to refine and strengthen local WGS data generation and analysis processes.”

Equitable AMR surveillance

Throughout the pilot project, Natasia kept track of what worked well for training and implementation, as well as glitches and technical issues. The sites' feedback provided valuable experience, knowledge, and insight for improving the workflow and methods to suit the specific on-site settings and analysing local pathogen bacterial strains.

All of which, Natasia said will be valuable lessons to carry forward at future WGS sites: "The lessons learned, for example, were used by the SeqAfrica consortium partners at Noguchi Memorial Institute in Ghana to train two additional local surveillance sites. As a result of the pilot, the sites now feel confident about their ability to use WGS for their ongoing surveillance".

Martie Ehlers-van der Zel, Professor and Principal Medical Scientist in the Department of Medical Microbiology at the University of Pretoria in South Africa, shared: “My department is grateful for the Fleming Fund’s generous support, which facilitated technology transfer and implementation within the department. This collaboration offered invaluable learning experiences, equipping students with the tools and skills necessary for future endeavours.”

DTU Professor Rene Hendrkisen, SeqAfrica Project Director, said on the pilot: “Making sequencing accessible to all laboratories and not just national reference centres is a critical step toward equitable AMR surveillance. When frontline diagnostics are placed directly in the hands of local scientists, it empowers countries to respond rapidly to emerging threats and strengthens public health from the ground up.”