Selective sweeps and genetic lineages of Plasmodium falciparum drug -resistant alleles in Ghana

Abstract

Background: In 2005, Ghana adopted artemisinin-based combination therapy (ACT) for primary treatment of falciparum malaria. A comprehensive study of the drug-resistance-associated mutations and their genetic lineages will lead to a better understanding of the evolution of antimalarial drug resistance in this region.

Methods: The pfcrt, pfmdr1, dhps, and dhfr mutations associated with chloroquine (CQ) and sulfadoxine-pyrimethamine (SP) resistance and the microsatellite loci flanking these genes were genotyped in Plasmodium falciparum isolates from Ghana.

Results: The prevalence of mutations associated with both CQ and SP resistance was high in Ghana. However, we observed a decrease in prevalence of the pfcrt K76T mutation in northern Ghana after the change in drug policy from CQ to ACT. Analysis of genetic diversity and differentiation at microsatellite loci flanking all 4 genes indicated that they have been under strong selection, because of CQ and SP use. The triple-mutant pfcrt and dhfr alleles in Ghana were derived from Southeast Asia, whereas the double-mutant dhfr, dhps, and pfmdr1 alleles were of African lineage.

Conclusion: Because of the possible role of pfmdr1 in amodiaquine and mefloquine resistance, demonstrating selection on pfmdr1 and defining lineages of resistant alleles in an African population holds great importance.

Figure 1.

Map of Ghana showing the 4 sites (solid black circles) from which Plasmodium falciparum isolates were collected for this study.

Figure 2.

The expected heterozygosity (H_e) at microsatellite loci flanking (A) pfcrt, (B) pfmdr1, (C) dhfr, and (D) dhps alleles. The dashed line crossing the y-axis indicates the mean H_e at 8 neutral microsatellite loci on chromosomes 2 and 3. Mutant amino acids are underlined. Error bars indicate standard deviation (SD).

Figure 3.

Median-joining network diagrams showing genetic lineages of (A) pfmdr1 and (B) dhps alleles in Ghana. The multilocus microsatellite haplotype profiles (using −9.3, −4.2, −3.3, 0, .16, .45, 3.6, and 9.1 kb loci flanking pfmdr1; and −7.5, −2.9, −1.5, −.13, .03, .5, 1.4, and 6.4 kb flanking dhps) were constructed for each gene to generate networks. The 63 Plasmodium falciparum isolates analyzed for pfmdr1 formed 50 unique 8-loci microsatellite haplotypes, whereas the 66 isolates analyzed for dhps formed 57 haplotypes. For allele sizes and other details please refer to Figures S2B and S2D, available online as supplementary material. Each circle in the network represents a unique microsatellite haplotype with the size of the circle being proportional to the number of isolates showing that particular haplotype, and color of the circle indicating the pfmdr1 or dhps allele. The red dots are hypothetical median vectors generated by the software to connect existing haplotypes within the network with maximum parsimony.