Changes in susceptibility of Plasmodium falciparum to antimalarial drugs in Uganda over time: 2019-2024

BackgroundThe treatment and control of malaria in Africa is challenged by drug resistance, including Plasmodium falciparum transporter, folate pathway, and PfK13 mutations that mediate resistance to aminoquinolines, antifolates, and artemisinins, respectively. Characterization of drug susceptibility informs optimal control strategies. MethodsWe characterized ex vivo susceptibilities to nine drugs of isolates collected from individuals presenting with uncomplicated falciparum malaria in eastern (2019-2024) and northern (2021-2024) Uganda using a growth inhibition assay and the dihydroartemisinin (DHA) ring survival assay (RSA). Genetic polymorphisms were characterized by molecular inversion probe and dideoxy sequencing. We assessed drug susceptibilities over time and evaluated associations between susceptibilities and potential resistance markers for samples studied since 2016. ResultsOf 1,297 collected, 724/828 eastern and 390/469 northern Uganda isolates were successfully evaluated for ex vivo drug susceptibilities. Median half-maximal inhibitory concentrations (IC50s) were low-nanomolar for chloroquine, monodesethylamodiaquine, piperaquine, pyronaridine, lumefantrine, mefloquine, and DHA, but higher for quinine and pyrimethamine. Over time, susceptibilities improved for chloroquine, decreased for lumefantrine, mefloquine, and DHA, and were unchanged for other drugs. Changes in prevalences of known markers of altered drug susceptibility followed the same patterns. Genotypes associated with drug susceptibility were those previously identified for aminoquinolines and pyrimethamine. For lumefantrine, susceptibility was decreased with wild-type PfCRT K76T or PfMDR1 N86Y, mutant PfK13 C469Y or A675V, the newly identified PfCARL D611N mutation, which increased in prevalence over time, and a number of other polymorphisms. For DHA, RSA results were not associated with PfK13 mutations, but susceptibilities based on IC50s were decreased in parasites with the PfK13 C469Y or A675V mutations and the newly identified PfMDR1 Y500N mutation. InterpretationSusceptibilities to antimalarial drugs were mostly excellent, but decreased activities of lumefantrine and DHA over time suggest potential loss of efficacies of leading regimens. FundingNational Institutes of Health, Medicines for Malaria Venture, Gates Foundation. Research in ContextO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed for combinations of the terms "antimalarial resistance", "malaria", "Plasmodium", "Africa", "ex vivo", "pfmdr1", "pfcrt", "kelch", or "K13" and identified papers published between Jan 1, 2020, and Dec 30, 2024 on antimalarial drug sensitivity and resistance in Africa. A prior identical search was conducted for papers published from Jan 1, 2000 to Dec 31, 2020 in preparation for an earlier publication. We reviewed and included any relevant articles cited in those references. Our search identified many studies on antimalarial drugs and molecular markers of resistance, but few combining ex vivo drug susceptibility with genotyping results. Added value of this studyThis study provides a comprehensive assessment of ex vivo susceptibility of Ugandan Plasmodium falciparum parasites to nine antimalarial drugs from July, 2019 to June, 2024. It also characterized genotype-phenotype associations based on these ex vivo data and sequencing of 80 genes identified as potential resistance mediators. Our findings add value to the existing literature by providing comprehensive data on antimalarial drug susceptibility in Uganda, including ex vivo drug susceptibilities for >1100 isolates from two regions of the country, description of changes in drug susceptibilities over time, and characterisation of genotype-phenotype associations, considering genetic polymorphisms previously associated with resistance to various antimalarials and potential novel resistance mediators. Implication of all the available evidenceMalaria parasites circulating in eastern and northern Uganda over the past five years were mostly sensitive to commonly used antimalarial drugs. However, parasite genotypes and phenotypes have changed over time. Most importantly, susceptibilities to dihydroartemisinin and lumefantrine, the components of the first-line antimalarial therapy in Uganda, have decreased over time, although the magnitudes of these decreases are modest, and the clinical implications of the results are uncertain. Continued performance of parasitological and genomic surveillance for evidence of antimalarial drug resistance and institution of policy changes to limit resistance selection and treatment failure should be high priorities.