A Novel Plasmodium falciparum Kelch13 A675T Mutation and High Levels of Chloroquine and Sulfadoxine-Pyrimethamine Resistance in Burundi

Antimalarial resistance, including failure of artemisinin combination therapy, is increasing in Africa. Molecular surveillance of markers of drug resistance is essential to monitoring drug resistance. Plasmodium falciparum isolates from Cibitoke Province, Burundi were sequenced for ten markers of resistance (including potential background markers conferring kelch13-mediated artemisinin partial resistance) by Illumina or Nanopore sequencing. Plasmepsin-2 and mdr1 copy number variations were typed by digital PCR. Among 157 isolates, no validated pfkelch13 mutations linked to artemisinin partial resistance (ART-R) were detected. However, a novel pfkelch13 mutation, A675T, was identified. A mutation in the same position (A675V) had been found and validated in neighboring Rwanda previously. Background mutations were frequent, including pffd D193Y (45.9%) and pfarps10 V127M (11.5%). Sulfadoxine-pyrimethamine (SP) resistance was widespread, with quintuple haplotypes detected in 82.3% and sextuple haplotypes in 12.3% of mono-infections. The pfcrt IET triple mutant haplotype (94.9%) and pfmdr1 N-F-D mutant haplotype (57.9%) indicate sustained CQ resistance and efficacy of artemether-lumefantrine (AL). No pfpm2 duplications but rare pfmdr1 amplifications (1.8%) were identified. These findings indicate substantial SP resistance, posing a threat to the efficacy of IPTp and SMC strategies in Burundi. The findings also show potential ART-R and partner drug resistance in Burundi, highlighting the need for strengthened surveillance and coordinated regional efforts to mitigate resistance and sustain malaria control.