Prevalence of Molecular Markers of Resistance to Antimalarial Drugs Three Years After Perennial Malaria Chemoprevention in Sierra Leone

Background Monitoring parasite resistance to antimalarial drugs is essential for detecting potential changes in drug efficacy. This study assessed the prevalence of molecular markers of resistance to sulfadoxine-pyrimethamine (SP), chloroquine, and artemisinin in Sierra Leone, where SP is used for intermittent preventive treatment in pregnancy (IPTp) and perennial malaria chemoprevention (PMC) in young children, while artemisinin is used to treat malaria episodes. Methods A cross-sectional survey was conducted between June and August 2021 in three districts of Sierra Leone. A total of 440 febrile children aged 2-5 years attending the health facilities were screened for P. falciparum malaria using a rapid diagnostic test, and 300 participants with positive RDT were enrolled. Capillary blood samples were collected as dried blood spots, analyzed using quantitative PCR to confirm P. falciparum, and sequenced for resistance markers in pfdhfr, pfdhps, pfcrt, pfmdr1, and pfK13. Results Of 298 blood samples, 237 (79.5%) were qPCR-positive and 230 samples were successfully genotyped. The pfdhfr triple mutant (N51I/C59R/S108N) was detected in 99.5% of samples (217/218), while pfdhps mutations A437G and K540E were detected in 92.1% (211/229) and 19.1% (42/220), respectively. The pfdhfr/dhps quintuple mutant (triple mutant + A437G/K540E) prevalence was 4.6% (7/151), and no sextuple mutants (quintuple + pfdhps -A581G) were observed. Chloroquine resistance-associated mutations in pfcrt (CVIET haplotype) were detected in 36.6% of samples, while pfmdr1 mutations at codon 86, 184, 1042, and 1246 occurred in 2.3%, 71.7%, 0.9% and 1.8%, respectively. No validated pfK13 markers of artemisinin resistance were detected. Conclusion In this study, the sustained low prevalence of pfdhfr/dhps quintuple mutant justifies the continued use of SP- containing IPTp and PMC, as well as its expansion in the country into the second year of life with additional SP doses. Importantly, no validated pfK13 markers were found supporting the use of artemisinin-based combination therapies in Sierra Leone. Trial registration Clinicaltrials.gov NCT04235816. Registered on January 17, 2020