Antimalarial Drug Resistance Profiling of Plasmodium falciparum Infections in Ghana Using Molecular Inversion Probes and Next-Generation Sequencing

Abstract

A key drawback to monitoring the emergence and spread of antimalarial drug resistance in sub-Saharan Africa is early detection and containment. Next-generation sequencing methods offer the resolution, sensitivity, and scale required to fill this gap by surveilling for molecular markers of drug resistance. We performed targeted sequencing using molecular inversion probes to interrogate five <i>Plasmodium falciparum</i> genes (<i>pfcrt</i>, <i>pfmdr1</i>, <i>pfdhps</i>, <i>pfdhfr</i>, and <i>pfk13</i>) implicated in chloroquine, sulfadoxine-pyrimethamine (SP), and artemisinin resistance in two sites in Ghana. A total of 803 dried blood spots from children aged between 6 months and 14 years presenting with uncomplicated <i>P. falciparum</i> malaria at the Begoro District Hospital in Begoro and the Ewim Polyclinic in Cape Coast, Ghana, from 2014 to 2017 were prepared on filter paper. Thirteen years after the removal of drug pressure, chloroquine-sensitive parasite strains with <i>pfcrt</i> K76 have increased nearly to fixation in Begoro, in the forest area (prevalence = 95%), but at a lower rate in Cape Coast, in the coastal region (prevalence = 71%, Z = -3.5, <i>P</i> < 0.001). In addition, <i>pfmdr1</i> 184F-bearing parasites are under strong selection. The <i>pfdhfr/pfdhps</i> quadruple genotype ( <b><u>IRNG</u></b> K), associated with SP resistance, is near saturation. Our study identified at a 2 to 10% prevalence <i>pfdhps</i> 581G, which is a sulfadoxine resistance marker that correlates with the failure of SP prophylaxis in pregnancy and which has not been observed in Ghana. The differences in the reexpansion of chloroquine-sensitive strains observed at the two study sites, the stronger SP resistance, and the high prevalence of <i>pfmdr1</i> 184F should be further monitored to inform malaria control strategies in Ghana.