Selective whole-genome sequencing of <i>Plasmodium</i> parasites directly from blood samples by nanopore adaptive sampling

Abstract

Malaria is caused by parasites of the genus <i>Plasmodium</i>, and reached a global disease burden of 247 million cases in 2021. To study drug resistance mutations and parasite population dynamics, whole-genome sequencing of patient blood samples is commonly performed. However, the predominance of human DNA in these samples imposes the need for time-consuming laboratory procedures to enrich <i>Plasmodium</i> DNA. We used the Oxford Nanopore Technologies' adaptive sampling feature to circumvent this problem and enrich <i>Plasmodium</i> reads directly during the sequencing run. We demonstrate that adaptive nanopore sequencing efficiently enriches <i>Plasmodium</i> reads, which simplifies and shortens the timeline from blood collection to parasite sequencing. In addition, we show that the obtained data can be used for monitoring genetic markers, or to generate nearly complete genomes. Finally, owing to its inherent mobility, this technology can be easily applied on-site in endemic areas where patients would benefit the most from genomic surveillance.