High Prevalence of Molecular Markers Associated with Artemisinin, Sulfadoxine, and Pyrimethamine Resistance in Northern Namibia

Artemisinin-based combination therapies are a cornerstone of Namibia’s efforts to eliminate malaria. Namibia has experienced a greater than 90% reduction in malaria cases since the introduction of these therapies in 2005. However, their efficacy has not been routinely monitored, with malaria outbreaks regularly reported since 2016. The recent emergence of artemisinin partial resistance in Africa has highlighted the role of malaria molecular surveillance in complementing efficacy studies. This cross-sectional genomic surveillance study was nested within Namibia’s routine surveillance system and aimed to determine the prevalence of antimalarial drug resistance markers in northern Namibia. Dried blood spots (DBS) and epidemiological data were collected from patients with confirmed Plasmodium falciparum cases who presented at health facilities in the highest malaria-burden regions (Zambezi, Kavango East, Kavango West, Ohangwena, and Omusati) from April to September 2023. Twelve genes associated with resistance to seven antimalarial drugs were genotyped from 264 DBS using multiplexed targeted amplicon sequencing. Multiple kelch 13 mutations associated with artemisinin partial resistance were identified: the P441L candidate marker was the most abundant, at 33.2%, and the P574L and A675V validated markers were observed in 1.2% of samples. The chloroquine resistance transporter C72/V73/M74I/N75E/K76T haplotype was observed in 1% of samples, whereas the multidrug resistance protein 1 N86 genotype, which is associated with reduced susceptibility to lumefantrine, was found in all samples. Although sulfadoxine–pyrimethamine is not used in Namibia, a high proportion of sulfadoxine–pyrimethamine resistance-associated mutations in the dihydropteroate synthase and dihydrofolate reductase genes were observed. In this study, we underscore the need for routine genomic surveillance to monitor emerging drug resistance markers and call for further research to define their clinical implications.