Polymorphisms in Plasmodium falciparum Chloroquine Resistance Transporter and Multidrug Resistance 1 Genes: Parasite Risk Factors That Affect Treatment Outcomes for P. falciparum Malaria After Artemether-Lumefantrine and Artesunate-Amodiaquine

Abstract

Adequate clinical and parasitologic cure by artemisinin combination therapies relies on the artemisinin component and the partner drug. Polymorphisms in the Plasmodium falciparum chloroquine resistance transporter (pfcrt) and P. falciparum multidrug resistance 1 (pfmdr1) genes are associated with decreased sensitivity to amodiaquine and lumefantrine, but effects of these polymorphisms on therapeutic responses to artesunate-amodiaquine (ASAQ) and artemether-lumefantrine (AL) have not been clearly defined. Individual patient data from 31 clinical trials were harmonized and pooled by using standardized methods from the WorldWide Antimalarial Resistance Network. Data for more than 7,000 patients were analyzed to assess relationships between parasite polymorphisms in pfcrt and pfmdr1 and clinically relevant outcomes after treatment with AL or ASAQ. Presence of the pfmdr1 gene N86 (adjusted hazards ratio = 4.74, 95% confidence interval = 2.29 – 9.78, P < 0.001) and increased pfmdr1 copy number (adjusted hazards ratio = 6.52, 95% confidence interval = 2.36–17.97, P < 0.001) were significant independent risk factors for recrudescence in patients treated with AL. AL and ASAQ exerted opposing selective effects on single-nucleotide polymorphisms in pfcrt and pfmdr1. Monitoring selection and responding to emerging signs of drug resistance are critical tools for preserving efficacy of artemisinin combination therapies; determination of the prevalence of at least pfcrt K76T and pfmdr1 N86Y should now be routine.

Pooled Amplicon Deep Sequencing of Candidate Plasmodium falciparum Transmission-Blocking Vaccine Antigens

“…Consistent with past reports, African pools were comprised exclusively of the 3D7 allele, while the Asian pools were composed primarily of the G131A allele (> 80%). 15 In fact, our allele frequencies were nearly identical to those determined from genome sequencing databases-G131A has a reported allele frequency of 0.807 in south Asia and 0.840 in eastern southeast Asia. 15 A higher number of non-synonymous polymorphisms have been reported for Pfs48/45, with 14 occurring within the amplified region.…”

“…15 In fact, our allele frequencies were nearly identical to those determined from genome sequencing databases-G131A has a reported allele frequency of 0.807 in south Asia and 0.840 in eastern southeast Asia. 15 A higher number of non-synonymous polymorphisms have been reported for Pfs48/45, with 14 occurring within the amplified region. Pfs48/45 mutant allele frequencies tend to be higher, and high frequencies occur in a more diverse geographic range than with Pfs25.…”

“…15 In this study, we identified two pfs25 variants-the 3D7 allele and an allele with the G131A polymorphism. Consistent with past reports, African pools were comprised exclusively of the 3D7 allele, while the Asian pools were composed primarily of the G131A allele (> 80%).…”

“…Four of the nonsynonymous polymorphisms have not been described previously in genome data (gray in Table 2). 15 Parasite populations harbored between 0 and 5 polymorphisms, ranging from 1% to 86% frequency. The number of polymorphisms did not correlate with the number of parasites in a pool (correlation coefficient = 0.28).…”

“…13,14 Our deep-sequencing data, as well as previously published whole-genome sequencing data, show that these antigens are more conserved than preerythrocytic-and erythrocytic-stage antigens, but can still show significant antigenic diversity. 15 In this study, DNA was extracted from 329 dried blood spots of P. falciparum field isolates collected in previous studies across six countries, four in Africa and two in Asia (Supplemental Table 1). All participants provided informed consent as approved by national institutional review boards (IRBs).…”