Drug resistance profiling of asymptomatic and low-density Plasmodium falciparum malaria infections on Ngodhe island, Kenya, using custom dual-indexing next-generation sequencing

Abstract

Malaria control initiatives require rapid and reliable methods for the detection and monitoring of molecular markers associated with antimalarial drug resistance in Plasmodium falciparum parasites. Ngodhe island, Kenya, presents a unique malaria profile, with lower P. falciparum incidence rates than the surrounding region, and a high proportion of sub-microscopic and low-density infections. Here, using custom dual-indexing and Illumina next generation sequencing, we generate resistance profiles on seventy asymptomatic and low-density P. falciparum infections from a mass drug administration program implemented on Ngodhe island between 2015 and 2016. Our assay encompasses established molecular markers on the Pfcrt, Pfmdr1, Pfdhps, Pfdhfr, and Pfk13 genes. Resistance markers for sulfadoxine-pyrimethamine were identified at high frequencies, including a quintuple mutant haplotype (Pfdhfr/Pfdhps: N51I, C59R, S108N/A437G, K540E) identified in 62.2% of isolates. The Pfdhps K540E biomarker, used to inform decision making for intermittent preventative treatment in pregnancy, was identified in 79.2% of isolates. Several variants on Pfmdr1, associated with reduced susceptibility to quinolones and lumefantrine, were also identified (Y184F 47.1%; D1246Y 16.0%; N86 98%). Overall, we have presented a low-cost and extendable approach that can provide timely genetic profiles to inform clinical and surveillance activities, especially in settings with abundant low-density infections, seeking malaria elimination.

Tracing the origins of Plasmodium vivax resurgence after malaria elimination on Aneityum Island in Vanuatu

“…Low P. vivax nuclear DNA concentrations in most samples, and a lack of availability of advanced methods and analytical approaches, limited our ability to gain a more comprehensive understanding of the population genomic diversity of P. vivax parasites. Recent developments in selective whole genome amplification (sWGA) of Plasmodium species from samples stored as DBS and in amplicon deep sequencing have provided opportunities to include low-parasite density infections in malaria genomic epidemiology 46 – 50 . Nevertheless, there is some discussion that advanced malaria genomics may have several gaps for an immediate “real-world malaria control and elimination strategy” 51 and may not be necessary for malaria control or even its elimination 52 .…”