Two decades of molecular surveillance in Kenya reveal shifting Plasmodium falciparum drug resistance mutations linked to frontline drug changes

This study provides a longitudinal genomic record of Plasmodium falciparum across 719 archived peripheral blood DNA samples collected from eleven sites in Kenya between 1998 and 2021. Samples were collected from clinical malaria patients (microscopy or RDT confirmed) at outpatient departments in Nairobi, Kisumu, Alupe, Mumias, Kombewa, Kericho, Kisii, Marigat, Busia, Entasopia, and Isiolo. Following species confirmation via qPCR, total genomic DNA was captured using a Molecular Inversion Probe (MIP) panel targeting 14 known antimalarial drug resistance genes. Libraries were sequenced (150bp paired-end) on an Illumina NextSeq 550. Data processing was performed using the MIPTools pipeline, utilizing Unique Molecular Identifiers (UMIs) for error correction and consensus sequence construction. This dataset is intended to support the spatiotemporal monitoring of parasite evolution in response to shifting drug pressures in East Africa.