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

Abstract

Malaria remains a health problem, with Plasmodium falciparum 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 P. falciparum samples collected from 141 patients in Brazil (2013-2023) by PCR and DNA sequencing to identify single-nucleotide polymorphisms in the pfcrt, pfmdr1, and pfk13 genes. Half of the samples carried the SVMNTMCGI haplotype in pfcrt, and none of the samples showed C350R mutations. In pfmdr1, the NYCDY haplotype was dominant (70%), with low occurrences of N86Y (4%) and no Y184F polymorphisms. No mutations linked to artemisinin partial resistance were detected in pfk13. Only one Amazonas sample exhibited wild-type haplotypes across all genes. Genetic diversity was more pronounced in pfcrt than pfmdr1, reflecting selective drug pressure. Significant linkage disequilibrium (LD) was observed within pfcrt (C72S and K76T) and pfmdr1 (S1034C and N1042D), but not between the two genes. The absence of pfk13-resistant mutations and the low prevalence of key pfmdr1 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.

Keywords: Brazilian endemic areas; Plasmodium falciparum; antimalarial drugs; resistance.

Figure 1

LD plot between SNPs of the pfcrt and pfmdr1 genes in P. falciparum isolates from the Brazilian endemic areas. Each diamond represents the r² value between two SNPs, and darker shades indicate stronger LD (r² values closer to 1 reflect stronger linkage).

Figure 2

The spatial distribution of malaria cases is classified as the following: from the Reference Center for Research, Diagnosis, and Training of Malaria in non-endemic areas (CPD-Mal) or from the endemic Brazilian regions (non-CPD-Mal). The size of the circles represents the number of samples from each municipality. Green-shaded areas indicate the locations of infection.