Mapping Plasmodium falciparum sequence variants associated with antimalarial drug resistance across the Democratic Republic of Congo using ‘MOSAIC’ a high throughput methodology

Geographical differences in antimalarial drug efficacy are known to exist in the Democratic Republic of Congo (DRC), and so accurate mapping of resistance is required to inform and optimise the sub-national tailoring of treatment and chemoprevention. Therapeutic efficacy studies (TES) are the gold standard for monitoring clinical and parasitological response to treatment but to perform them with adequate coverage and regularity is costly. A further limitation of efficacy studies is that resistance to one drug in a combination treatment is masked by the antiparasitic effects of its partner. Genetic surveillance for the sequence determinants of parasite resistance is therefore a useful addition to efficacy studies, enabling an affordable expansion of coverage and actionable warnings of resistance before it becomes apparent in the clinic. We used a sampling framework based upon national sentinel surveillance sites, sampling between 100–200 patients from a single clinic location in 16 of the 26 provinces in DRC. We employed a high-throughput low-cost genotyping methodology pipeline to characterize molecular determinants of resistance and generate maps of the distribution of artemisinin and partner drug resistance across the Country. There were few observations of Pfk13 validated or candidate markers of artemisinin resistance in any part of the DRC but genotype profiles for resistance to partner drugs were regionally distinct. In Eastern provinces bordering the Great Lakes Region, we found high prevalence of Pfcrt and Pfmdr1 markers linked to 4-aminoquinoline resistance; and associated with a significant risk of ASAQ treatment failure. By contrast, parasite populations in the North and South of DRC predominantly carried Pfmdr1 and Pfcrt haplotypes which are associated with risk of ALU treatment failure. We extended the coverage of national drug resistance surveillance by TES, by using supplementary sampling and then used high throughput genotyping to describe drug resistance profiles of parasites sampled in 16 of the 26 Provinces. We demonstrate the operational utility of this approach to inform subnational tailoring of malaria treatment and chemoprevention to administrative level 1.