Imported malaria predominates in near-elimination settings in Southwestern Uganda

Malaria transmission in southwestern Uganda is low, but persists despite control efforts. Identifying whether infections are locally sustained or imported by travelers is critical for guiding interventions. We integrated epidemiologic surveillance with parasite genomics to characterize imported malaria episodes at three health facilities in southwestern Uganda. Between January 2023 and June 2024, we enrolled microscopy-confirmed malaria cases at three health facilities, Maziba and Muko (very low transmission) and Kamwezi (low-to-moderate transmission), administered travel history questionnaires, and collected dried blood spots for genotyping. 348 Plasmodium falciparum infections were genotyped using MAD4HatTeR, a multiplex amplicon sequencing panel targeting 165 diversity markers and 38 drug resistance loci. Complexity of infection and pairwise relatedness were estimated using MOIRE and Dcifer, respectively. Plasmotrack, a transmission network framework, was used to infer transmission networks and importation rates. Amongst malaria cases, travel was common in Maziba (87%) and Muko (96%) but infrequent in Kamwezi (12%). Most travel in Maziba and Muko was from high-transmission regions in northern and eastern Uganda. Parasites in Maziba and Muko exhibited higher within-host diversity and lower within-site relatedness compared to those in Kamwezi, with the proportion of significant related infection pairs substantially lower in Maziba (0.59%) and Muko (0.17%) than in Kamwezi (6.36%). Transmission network inference identified most infections in Maziba and Muko as imported, with the majority of inferred secondary transmission linked to recent travelers. In contrast, Kamwezi showed multiple highly related clusters, indicating sustained local transmission. Validated markers of artemisinin resistance (K13 P441L and R561H) were more prevalent in Kamwezi. Malaria in Maziba and Muko was driven largely by importation from other parts of Uganda, while local transmission predominated in Kamwezi. Tailored interventions addressing travel-associated risks and local transmission, supported by travel histories and genetic data will be valuable to advance malaria elimination in this region.