Rising prevalence of Plasmodium falciparum artemisinin resistance mutations in Ethiopia

Ethiopia is striving to eliminate local malaria transmission by 2030, despite a recent resurgence of malaria cases due to multiple factors. A significant contributor to this resurgence could be drug resistance, particularly the emergence of partial resistance to artemisinin (ArtR) in Ethiopia and other regions of Eastern Africa. This situation highlights the necessity for genomic surveillance to monitor relevant drug resistance markers. This study reports sentinel site-based genomic surveillance results for P. falciparum antimalarial drug resistance mutations. From 2019 to 2022, dried blood spots (DBS) were collected from febrile outpatients ≥1 year of age with microscopically confirmed falciparum malaria at 12 sentinel sites across 5 regions. Molecular inversion probe (MIP) sequencing targeted mutations associated with artemisinin and partner drug resistance, including k13 , mdr1, crt, dhfr, and dhps genes, along with genome-wide markers to assess the complexity of infection (COI) and parasite relatedness. A total of 1,199 falciparum - positive patients were assessed, with a median age of 20 years (IQR: 14-30) and including 463 (38.6%) females. The WHO-validated K13 R622I mutation had a high but regionally variable prevalence (15.7%, range 0-58.8%). The validated K13 A675V mutation was detected for the first time in Ethiopia in the Gambella Region (4.5%), as well as P441L and P574L mutations were detected at low frequencies in Southern and Oromia Regions, respectively. Several partner drug resistance markers were identified, with mutations in MDR1(184F), DHPS, DHFR, and CRT nearly fixed across the country. Most samples (87.2%) were monogenic infections (COI=1) and showed high genetic relatedness, particularly within the health facilities. Principal component analysis revealed regional clustering of parasites, particularly in Gambella. The prevalence of K13 R622I across the country and the presence of multiple additional ArtR markers emphasizes the urgent need for rigorous monitoring of artemisinin combination therapy (ACT) efficacy to detect partner drug resistance and ACT failure early and its impact on malaria resurgence in Ethiopia.