Evolving patterns of antimalarial drug resistance markers in symptomatic infections in Kenya, 2013–2022

Abstract Background Ongoing antimalarial drug resistance surveillance is essential to guide effective treatment strategies. Historically, resistance to chloroquine and sulfadoxine-pyrimethamine (SP) has been associated with well-characterized mutations in the chloroquine resistance transporter ( Pfcrt ; K76T) and antifolate pathway genes, including dihydrofolate reductase ( Pfdhfr ; N51I, C59R, S108N) and dihydropteroate synthase ( Pfdhps; A437G, K540E, A581G). Since the introduction of artemisinin-based combination therapies (ACTs), 13 mutations in the kelch 13 (PfK13) propeller domain have emerged as World Health Organization (WHO) validated markers of partial artemisinin resistance. This study aimed to characterize temporal trends in both established, Pfcrt and Pfk13, and less well-described potential markers, cysteine desulfurase ( Pfnfs) and Pfcoronin , using febrile malaria samples collected across diverse regions of Kenya between 2013 and 2022. Methods The temporal trend of these markers of resistance were assessed by screening archived P. falciparum -positive dried blood spots (DBS). A total of 1750 DBS samples were collected from therapeutic efficacy studies (TES) conducted across distinct malaria transmission settings in Kenya, including coastal Kenya (Kwale 2013, n = 350; 2018, n = 150), the lake endemic region of Western Kenya (Kisumu 2015, n = 314; Busia 2016, n = 334), and the highland epidemic region of western Kenya (Kisii 2017, n = 314). Additional samples were obtained from an hrp2 study conducted in Kisii in 2022, ( n = 288). Parasite genomic DNA was extracted using the Chelex-saponin method and confirmed by a Pf 18S real-time polymerase chain reaction (RT-PCR). Pfk13, Pfcrt, Pfnfs , and Pfcoronin PCR amplicons were sequenced using capillary electrophoresis, Illumina Miseq or Oxford Nanopore (GridION) platforms. Results The prevalence of Pfcrt mutations declined over time and no WHO-validated Pfk13 mutations associated with artemisinin resistance were detected. However, synonymous substitutions at WHO-validated codons C469C and P553P were identified. In the Pfcoronin gene, nonsynonymous mutations distinct from those reported in West Africa were observed at high frequencies (> 75%). Notably, the Pfnfs -K65Q mutation, previously associated with reduced lumefantrine sensitivity in West Africa, was detected in more than 80% of the samples. Conclusions Our findings reveal no WHO-validated k13 mutations up until 2022 and confirm previous findings of a reduction in the Pfcrt resistance genotypes over time. This study underscores the importance of continued molecular surveillance and suggests that resistance may evolve through different pathways in East compared with West Africa and Southeast Asia. Graphical Abstract