Tracking Drug Resistance in Plasmodium falciparum: Genetic Diversity of Key Resistance Markers in Brazilian Malaria Hotspots

Malaria remains a health problem, with <i>Plasmodium falciparum</i> accounting for 96% of cases in Africa and 15% in Brazil. The growing threat of drug resistance to artemisinin-based combination therapies (ACTs) jeopardizes progress toward elimination. This study examined <i>P. falciparum</i> samples collected from 141 patients in Brazil (2013-2023) by PCR and DNA sequencing to identify single-nucleotide polymorphisms in the <i>pfcrt</i>, <i>pfmdr1</i>, and <i>pfk13</i> genes. Half of the samples carried the <b>S</b>VMN<b>T</b>MCGI haplotype in <i>pfcrt</i>, and none of the samples showed C350<b>R</b> mutations. In <i>pfmdr1</i>, the NY<b>CDY</b> haplotype was dominant (70%), with low occurrences of N86<b>Y</b> (4%) and no Y184<b>F</b> polymorphisms. No mutations linked to artemisinin partial resistance were detected in <i>pfk13</i>. Only one Amazonas sample exhibited wild-type haplotypes across all genes. Genetic diversity was more pronounced in <i>pfcrt</i> than <i>pfmdr1</i>, reflecting selective drug pressure. Significant linkage disequilibrium (LD) was observed within <i>pfcrt</i> (C72S and K76T) and <i>pfmdr1</i> (S1034C and N1042D), but not between the two genes. The absence of <i>pfk13</i>-resistant mutations and the low prevalence of key <i>pfmdr1</i> markers support the efficacy of ACTs. The persistence of diverse haplotypes and intragenic LD reflects ongoing drug pressure, underscoring the need for continuous genetic surveillance to anticipate emerging resistance.