Pocket-Sized DNA Sequencers Track Malaria Drug Resistance in Near Real-Time

Despite ongoing control efforts, malaria continues to be a major global health challenge, claiming over 600,000 lives annually, predominantly among young children in sub-Saharan Africa. A major hurdle in combating malaria has been the parasite’s ability to quickly develop resistance to antimalarial drugs. Genomic surveillance – the continuous monitoring of changes in the parasite’s DNA – enables the analysis of genomic data related to parasite drug resistance. However, until now, this has been performed mostly in distant labs in high-income, non-endemic countries, away from the affected regions. Now, researchers have developed a new method for rapid and reliable detection of genetic mutations in malaria parasites, utilizing just a gaming laptop and a portable sequencer.

This groundbreaking approach developed by researchers from the Wellcome Sanger Institute (Cambridgeshire, UK) and University of Ghana (Accra, Ghana) allows for end-to-end, real-time pathogen monitoring directly in rural, malaria-prone areas with limited resources. The focus of their research was to identify crucial drug resistance markers in the malaria parasite and to examine the diversity within the vaccine target gene. This development is a significant step towards enabling local regions to monitor drug resistance and evaluate the effectiveness of new malaria vaccines.

For their study, the researchers collected parasites from clinical blood samples using standard molecular biology tools and a simple finger prick method. They then sequenced the malaria parasite DNA using the portable MinION sequencer from Oxford Nanopore (Oxford, UK) and a laptop. This allowed them to swiftly identify known drug resistance markers, emerging mutations, and targets of new malaria vaccines, with sequencing information available within just 48 hours after sample collection. The cost of this process was kept low, at approximately GBP 27 per sample for batches of 96.

The study's findings indicated that current frontline treatments are largely effective against the prevalent strains of malaria in Ghana. However, it also highlighted the importance of continuous monitoring, especially to safeguard high-risk groups receiving targeted treatments. The researchers identified several genetic variances between the circulating malaria strains and the protein targeted by new malaria vaccines. Importantly, no evidence of resistance to artemisinins, the best available treatment for P. falciparum malaria, was found. Although mutations related to resistance to sulfadoxine and pyrimethamine (SP) were detected, the more severe mutations leading to high-level resistance to SP were not present. These findings could have implications for the effectiveness of recent vaccine rollouts across Africa and underscore the need for further investigation.

“By taking sequencing to the source, insights arrive in days rather than years — enabling rapid, localized responses,” said Edem Adika, co-first author of the study at University of Ghana. “This unprecedented speed promises to be a powerful game-changer against infectious diseases outpacing our countermeasures. We hope this on-site approach is soon applied here to other pathogens.”

“The repeated evolution and spread of resistance to key antimalarial drugs has thwarted efforts to eliminate malaria over the last 70 years,” added Dr. William Hamilton, senior author of the study at the Wellcome Sanger Institute. “Expanding molecular surveillance in Africa is now critical for tracking emerging drug and diagnostic test resistance, and informing interventions like new vaccines.”

Related Links:
Wellcome Sanger Institute
University of Ghana
Oxford Nanopore 

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