National genomic profiling of Plasmodium falciparum antimalarial resistance in Zambian children participating in the 2018 malaria indicator survey.

UNLABELLED: The emergence of antimalarial drug resistance is a major threat to malaria control and elimination. Using whole genome sequencing of 282 P. falciparum samples collected during the 2018 Zambia National Malaria Indicator Survey, we determined the prevalence and spatial distribution of known and candidate antimalarial drug resistance mutations in key genes, including kelch13 (Pfk13), chloroquine resistance transporter (Pfcrt), multidrug resistance protein 1 (mdr1), dihydropteroate synthase (Pfdhps), and dihydrofolate reductase (Pfdhfr) and 8 other genes. High levels of genotypic resistance were found across Zambia to pyrimethamine, > 94% (n = 266) of samples carried the Pfdhfr triple mutant (N51I, C59R, and S108N), and sulfadoxine, > 84% (n = 238) carried the Pfdhps double mutant (A437G and K540E). In northern Zambia 5.3% (n = 15) of samples additionally harbored the Pfdhps A581G mutation. While a total of 29 non-synonymous mutations were identified in Pfkelch13, these mutations were present at low frequency (< 2.5%), and only three were WHO-validated artemisinin partial resistance mutations, P441L (n = 1, 0.35%), V568M (n = 2, 0.7%) and R622T (n = 1, 0.35%). However, 91 (32%) of samples carried the E431K mutation, a candidate artemisinin resistance marker in the Pfatpase6 gene. Finally, no specimens carried any known mutations associated with chloroquine resistance in the Pfcrt gene (codons 72–76). In conclusion, P. falciparum strains circulating in Zambia appear highly resistant to sulfadoxine and pyrimethamine but remain susceptible to chloroquine and artemisinin. While this is encouraging, there are early genetic signs of artemisinin resistance developing underlining the crucial need to remain vigilant and to expand routine genomic surveillance to track these changes.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-45996-y.