Abstract

Background Antimalarial drug efficacy is threatened by the development of drug resistance. In Rwanda, high levels of resistance have been reported in the past, including mutations in the Pfk13 gene associated with partial resistance to artemisinin, leading to delayed parasite clearance of Artemether-Lumefantrine (AL). Therefore, continuous molecular surveillance of drug resistance markers is required. Here, we report polymorphisms in the Pfcrt, Pfdhps, and Pfdhfr genes in samples collected in Rwanda in 2018. Methods Samples from three sites (Masaka, Rukara, and Bugarama) were collected during a therapeutic efficacy study (TES) conducted in 2018. Targeted amplification of resistance genes of interest was performed by PCR, and products were sequenced by Sanger sequencing. Results The K76T Pfcrt mutation was found in 10% of the samples, only in Bugarama. For Pfdhps, the A437G, K540E and A581G mutations were detected in 94%, 94% and 55% of the samples, respectively. For Pfdhfr, the N51I, S198N, C59R and I164L mutations were found in 99%, 99%, 88% and 16% of samples, respectively. The latter was only detected in Masaka and Rukara. Conclusions We confirm the slow and partial recovery of chloroquine susceptibility in the country. All previously reported Pfk13 mutants were Pfcrt wild type, thus possibly selected by AL. The prevalence of Pfdhps and Pfdhfr mutants, including those with the highly resistant I164L mutation, is high and increasing, despite the absence of drug pressure. It is imperative to closely monitor resistance and efficacy of AL and other treatment options as part of the malaria surveillance program and resistance mitigation strategy in the country.