Sustained high prevalence of multiple antimalarial drug resistance markers in Uganda in 2023-2024.

The emergence and spread of drug resistance threaten malaria control in Uganda. This study reports new data on key polymorphisms associated with antimalarial drug sensitivity at 32 malaria reference centers in Uganda in 2023 and 2024. Ten thousand thirty samples were collected from patients aged >6 months presenting with uncomplicated falciparum malaria and sequenced using the MAD4HatTeR panel and Illumina platforms; of these, 8,518 passed quality control and were analyzed. Multiple validated or candidate K13 mutations associated with artemisinin partial resistance were detected at ≥20% prevalence at one or more sites across multiple timepoints. The K13 mutations A675V and C469Y predominated in northern Uganda, P441L was most common in western Uganda, and R561H and C469F were confined to southwestern Uganda. After rapid increases in earlier years, prevalences of K13 mutations plateaued at most sites, with A675V, C469Y, and P441L reaching maximum site prevalences of 40%, 58%, and 46%, respectively. Prevalence of the chloroquine resistance marker CRT K76T was generally low but increased substantially at three sites in northwestern Uganda, rising to 38% at the last timepoint, with CRT H97L, newly reported in Africa, following a similar trend. The antifolate resistance quintuple mutant haplotype remained highly prevalent nationwide. In addition, DHPS A581G and DHFR I164L, markers of higher-level antifolate resistance, were most common in southwestern Uganda with prevalences up to 64% and 76%, respectively; DHFR I164L also expanded into central and eastern regions. These results highlight continued geographic heterogeneity and underscore the need for continued, nationwide molecular surveillance to guide treatment and chemoprevention policies.