Plasmodium falciparum drug resistance profile, Ngodhe island, KE

Difficulties in malaria control have highlighted the need for rapid and reliable methods for the detection and monitoring of molecular markers associated with antimalarial drug resistance in Plasmodium falciparum. Advancements in low-cost sequencing-based approaches that target molecular markers for drug resistance offer a new high throughput and robust method of parasite surveillance. Due to the high proportion of sub-microscopic, low-density, P. falciparum infections on Ngodhe island (population size 600–1,000) in Lake Victoria, Kenya, there was no genetic information available from the island's parasite population. Here we demonstrate the use of custom dual-indexing and Illumina next generation sequencing-technology to generate a resistance profile of the low-density P. falciparum infections in Lake Victoria, including molecular markers of resistance on the Pfcrt, Pfmdr1, Pfdhps, Pfdhfr, and Pfk13 genes. Resistance markers for sulfadoxine-pyrimethamine were identified at high frequencies. The quintuple mutant haplotype, encompassing the Pfdhfr N51I, C59R, and S108N variants alongside the Pfdhps G437A and K540E resistance biomarkers, was identified in 68% of screened isolates. The Pfdhps K540E biomarker, used to inform decision making by the World Health Organization surrounding intermittent preventative treatment in pregnancy, was identified in 76% of the Ngodhe island isolates, suggesting there may be reduced efficacy of IPTp-SP therapies within the region. Although there were no mutations observed on Pfk13 believed to be able to confer resistance to artemisinin combination therapies, there were 3 SNPs identified on Pfmdr1 associated with resistance to partner drugs, such as lumefantrine. Overall, our work demonstrates the effectiveness of sequencing-based, high throughput, surveillance in a low resource setting on asymptomatic, low-density, P. falciparum infections.