Frequencies of molecular markers of drug resistance in the context of two different Seasonal Malaria Chemoprevention (SMC) treatment regimens in the Koulikoro health district, Mali

With growing concern about parasite resistance to sulfadoxine-pyrimethamine (SP) in West Africa, the effectiveness of dihydroartemisinin-piperaquine (DHA + PQ) was assessed as an alternative drug regimen for Seasonal Malaria Chemoprevention (SMC). This study aims to determine the prevalence of molecular markers of resistance to SP + AQ and DHA + PQ in Koulikoro (Mali), where SMC has been implemented since 2014. <i>Plasmodium falciparum</i>-positive samples were analyzed by either next-generation sequencing, focusing on SNPs in genes known to be associated with resistance: <i>Pfmdr1, PfK13, Pfcrt, Pfdhfr, Pfdhps,</i> and <i>Pfexo</i> genes, and using qPCR for copy number variations (CNVs) of <i>Pfmdr1</i> and <i>Pfplasmepsin2</i>. A total of 564 PCR-positive <i>P. falciparum</i> samples were analyzed: 218 in 2019 and 346 in 2020. In both years, the <i>Pfdhfr</i> <b>51I-59R-108N</b> haplotype was highly prevalent (>93%). In both arms, the <i>Pfdhps</i> single mutant (<b>437G</b>) was the most prevalent (~60%). In 2020, the combined haplotype <i>Pfdhfr/Pfdhps</i> <b>IRN/</b>IA<b>G</b>KA<b>S</b> and <b>IRN/V</b>A<b>G</b>K<b>GS</b> was detected at 9.6% and 1.2%, respectively. The <i>Pfmdr1</i> haplotype (N86-<b>F184</b>-S1034-N1042-D1246) represented more than 52.0%, and no difference was observed between the years, while a significant increase in the <i>Pfcrt</i> wild-type haplotype (C72-V73-M74-N75-K76) from 39% in 2019 to 52% in 2020 (<i>P</i> = 0.01) was observed. Some <i>PfK13</i> non-synonymous mutations were observed in both years, including Y<b>493H</b> and C<b>580R</b>. The identification of the <b>IRN</b>I<b>/</b>IA<b>G</b>KA<b>S</b> quintuple mutant, along with emerging <i>Pfdhps</i><b>-431V</b> and non-synonymous PfK13-<b>Y493H</b> variants, underscores the importance of continued surveillance of resistance markers.