Genetic diversity of the Plasmodium falciparum GTP-cyclohydrolase 1, dihydrofolate reductase and dihydropteroate synthetase genes reveals new insights into sulfadoxine-pyrimethamine antimalarial drug resistance

Abstract

Plasmodium falciparum parasites resistant to antimalarial treatments have hindered malaria disease control. Sulfadoxine-pyrimethamine (SP) was used globally as a first-line treatment for malaria after wide-spread resistance to chloroquine emerged and, although replaced by artemisinin combinations, is currently used as intermittent preventive treatment of malaria in pregnancy and in young children as part of seasonal malaria chemoprophylaxis in sub-Saharan Africa. The emergence of SP-resistant parasites has been predominantly driven by cumulative build-up of mutations in the dihydrofolate reductase (pfdhfr) and dihydropteroate synthetase (pfdhps) genes, but additional amplifications in the folate pathway rate-limiting pfgch1 gene and promoter, have recently been described. However, the genetic make-up and prevalence of those amplifications is not fully understood. We analyse the whole genome sequence data of 4,134 P. falciparum isolates across 29 malaria endemic countries, and reveal that the pfgch1 gene and promoter amplifications have at least ten different forms, occurring collectively in 23% and 34% in Southeast Asian and African isolates, respectively. Amplifications are more likely to be present in isolates with a greater accumulation of pfdhfr and pfdhps substitutions (median of 1 additional mutations; P<0.00001), and there was evidence that the frequency of pfgch1 variants may be increasing in some African populations, presumably under the pressure of SP for chemoprophylaxis and anti-folate containing antibiotics used for the treatment of bacterial infections. The selection of P. falciparum with pfgch1 amplifications may enhance the fitness of parasites with pfdhfr and pfdhps substitutions, potentially threatening the efficacy of this regimen for prevention of malaria in vulnerable groups. Our work describes new pfgch1 amplifications that can be used to inform the surveillance of SP drug resistance, its prophylactic use, and future experimental work to understand functional mechanisms.

A computational method for predicting the most likely evolutionary trajectories in the step-wise accumulation of resistance mutations

“…The most likely first step was single mutation A437G, in agreement with previous studies which found A437G was the most frequent single mutation sulfadoxine-resistant Pf DHPS isolates [13, 47] and the data presented in [46]. Furthermore, A437G is now considered fixed in the population [48] and A437G is also the most common mutation in our isolate data, followed by S436A (Figure 5b). The most likely double mutation in our simulations was A437G/S436A, followed by A437G/K540E.…”

“…Plasmodium falciparum and vivax SNP data were sourced from recent studies [45, 48]. In those studies, paired Illumina raw sequence data was mapped to the Pf3D7 (P. falciparum) or PVP01 ( P. vivax ) reference genome using bwa-mem software (default parameters).…”

Genetic surveillance for monitoring the impact of drug use on Plasmodium falciparum populations

“…SMC may reduce the incidence in untreated age groups ( Cisse et al, 2016 ), suggesting an interruption of transmission. There is some evidence to suggest that SMC can increase the prevalence of drug resistance markers for pfdhps and pfdhfr ( Access-SMC-Partnership, 2020 ; Dieng et al, 2019 ; Maiga et al, 2016 ; Some et al, 2014 ; Turkiewicz et al, 2020 ). These data suggest that monitoring for resistance is an important consideration with repeated use of SMC.…”

Characterizing the genomic variation and population dynamics of Plasmodium falciparum malaria parasites in and around Lake Victoria, Kenya

“…However, given their close geographical proximity and the continuous movement of people between these sites, the culturing of some isolates prior to sequencing may be confounding these results 29 . The Pfdhps gene, known to be associated with resistance to SP, was found to be in the top 5% of IBD positions in island isolates from Lake Victoria, suggesting this gene is being highly conserved in this population, likely due to the continued use of SP as a method of intermittent preventative treatment in pregnancy (IPTp) 30 , 31 .…”