Dynamic changes in genetic diversity, drug resistance mutations, and treatment outcomes of falciparum malaria from the low-transmission to the pre-elimination phase on the isolated islands of São Tomé and Príncipe

Abstract

Background With effective vector control and case management, substantial progress has been made in the elimination of malaria on the islands of São Tomé and Príncipe (STP). During the critical period from the low-transmission to the pre-elimination phase, this study tracked the dynamic changes in the genetic diversity in Plasmodium falciparum, the distribution of antimalarial drug-resistance genes, and the treatment outcomes in patients to provide insights for the prevention of rebounded malaria in STP. Methods Dried blood spots (DBSs) and case follow-up data were collected from malaria patients who had visited the Central Hospital between 2010 and 2016. Genomic DNA of P. falciparum was extracted from DBSs. The polymorphic regions on the genes for merozoite surface proteins 1 and 2 (msp1 and msp2) were amplified in 118 pre-treatment samples to identify the genetic diversity of the infected parasites. Anti-malarial drug resistance mutations in the multi-drug resistance (pfmdr1), chloroquine resistance transporter (pfcrt), and kelch 13 (pfK13) genes were genotyped using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and DNA sequencing in 111 samples. Treatment outcomes were categorized based on the parasitological results from microscopy during the 28-day follow-up after treatment. Factors related to malaria recurrence were characterized by logistic regression models using case follow-up data (total number = 7,482). Results The circulating parasite strains in STP showed significant changes at the recent peak incidence in 2012, during which the prevalent allelic type in MSP1 changed from K1 to MAD20, and that in MSP2 changed from 3D7/IC to FC27. Genotyping results for antimalarial drug-resistance markers showed that the dominant alleles of pfmdr1 86 + 184 + 1246-pfcrt 76 were YFD-T (51.4%). Logistic regression models showed that significant factors related to parasitological failure after treatment were age (protective factor, OR = 0.97–0.98), log10-transformed parasite density (OR = 1.07–1.44), and treatment (quinine vs. artemisinin-based combination therapy, OR = 1.91–1.96). Overall, younger patients, those with higher parasitemia levels at enrollment, and those treated with quinine had a higher risk of recurrence during follow-up. Conclusions Although malaria treatment efficacy remained acceptable in STP, this study showed temporal changes in the dominant strains and the development of drug resistance mutations in the local parasite population. Therapeutic efficacy should be carefully monitored to adequately adjust the policy in the future.