Temporal trends in artemisinin partial resistance and other antimalarial drug mutations in Plasmodium falciparum from Kagera region, Northwestern Tanzania, 2021-2023.

Artemisinin-based combination therapies (ACTs) remain the cornerstone of malaria treatment, yet the emergence of artemisinin partial resistance (ART-R) in Africa threatens their efficacy. ART-R is primarily associated with mutations in Plasmodium falciparum kelch13 (K13), notably R561H, which has been linked to delayed parasite clearance in East Africa. We genotyped 2,866 P. falciparum isolates from seven districts in Tanzania's Kagera region (2021-2023) using 121 molecular inversion probes (MIP) targeting key resistance loci to characterize trends in ART-R and other resistance markers. The WHO-validated K13 mutation R561H persisted in border districts of Karagwe and Kyerwa, with prevalence ranging from 14% to 26%, and appeared for the first time in Muleba in 2022 (10.0%) and Bukoba rural district (0.7%) in 2023, indicating eastward spread toward Lake Victoria. Regional prevalence of R561H rose from 5.5% in 2021 to 6.9% in 2023. Additional validated (A675V) and candidate (V568G, P441L) mutations were detected at low frequencies. Markers associated with reduced sensitivity to partner drugs showed minimal change. Early DHFR and DHPS mutations were near fixation and high-level resistance markers (DHFR I164L and DHPS A581G) exhibited marked gradients. These latest mutations are significantly spatially colocalized (weighted spearman R2 = 0.58, P = 0.045) and co-occur within a number of individual genomes. These results highlight notable variation in mutation prevalence and underscore the importance of high-resolution surveillance to identify emerging hotspots and guide targeted interventions. Sustained molecular monitoring is critical to inform treatment policy, preserve ACT efficacy, and mitigate the risk of widespread resistance across East Africa.