Mapping the genomic landscape of multidrug resistance in Plasmodium falciparum and its impact on parasite fitness

Abstract

Drug-resistant Plasmodium falciparum parasites have swept across Southeast Asia and now threaten Africa. By implementing a P. falciparum genetic cross using humanized mice, we report the identification of key determinants of resistance to artemisinin (ART) and piperaquine (PPQ) in the dominant Asian KEL1/PLA1 lineage. We mapped k13 as the central mediator of ART resistance in vitro and identified secondary markers. Applying bulk segregant analysis, quantitative trait loci mapping using 34 recombinant haplotypes, and gene editing, our data reveal an epistatic interaction between mutant PfCRT and multicopy plasmepsins 2/3 in mediating high-grade PPQ resistance. Susceptibility and parasite fitness assays implicate PPQ as a driver of selection for KEL1/PLA1 parasites. Mutant PfCRT enhanced susceptibility to lumefantrine, the first-line partner drug in Africa, highlighting a potential benefit of opposing selective pressures with this drug and PPQ. We also identified that the ABCI3 transporter can operate in concert with PfCRT and plasmepsins 2/3 in mediating multigenic resistance to antimalarial agents.

Genetic surveillance ofPlasmodium falciparumreveals rapid population changes following first-line treatment policy revisions in the Greater Mekong Subregion

“…It is likely that, in the absence of piperaquine pressure, pm23 amplifications are costly in terms of parasite fitness, and lead to a survival disadvantage in the absence of piperaquine pressure. A recent in vitro study supported this notion by demonstrating that cultured C580Y parasites spontaneously de-amplify pm23 when piperaquine pressure is removed [38]. Thus, the change in policy appears to have produced two effects on KEL1/PLA1 parasites: either caused them to succumb in competition with fitter artemisinin-resistant strains, which had been circulating at low frequency during KEL1/PLA1 dominance [35]; or cause them to de-amplify pm23 , improving their fitness in the new environment.…”

SKSR1 identified as key virulence factor in Cryptosporidium by genetic crossing

“…However, traditional linkage analysis requires the comparative analysis of numerous recombinant progenies. In recent years, a more efficient linkage mapping technique, the bulked segregant analysis (BSA), has been used to characterize genetic crosses of P. falciparum isolates 15,16 . It compares the frequencies of phenotypically segregating alleles in pools of recombinant progeny, allowing the identification of SNPs associated with phenotypic traits 17 .…”

SKSR1 identified as key virulence factor inCryptosporidiumby genetic crossing

“…In recent years, a more efficient linkage mapping technique, the bulked segregant analysis (BSA), has been used to characterize genetic crosses of P. falciparum isolates. 15,16 It compares the frequencies of phenotypically segregating alleles in pools of recombinant progeny, allowing the identification of SNPs associated with phenotypic traits. 17 In this report, we describe the identification of genes underlying the virulence differences using BSA of progeny from genetic crosses of two C. parvum isolates.…”