Longitudinal genomic surveillance of Plasmodium falciparum malaria parasites reveals complex genomic architecture of emerging artemisinin resistance

Abstract

BackgroundArtemisinin-based combination therapies are the first line of treatment for Plasmodium falciparum infections worldwide, but artemisinin resistance has risen rapidly in Southeast Asia over the past decade. Mutations in the kelch13 gene have been implicated in this resistance. We used longitudinal genomic surveillance to detect signals in kelch13 and other loci that contribute to artemisinin or partner drug resistance. We retrospectively sequenced the genomes of 194 P. falciparum isolates from five sites in Northwest Thailand, over the period of a rapid increase in the emergence of artemisinin resistance (2001–2014).ResultsWe evaluate statistical metrics for temporal change in the frequency of individual SNPs, assuming that SNPs associated with resistance increase in frequency over this period. After Kelch13-C580Y, the strongest temporal change is seen at a SNP in phosphatidylinositol 4-kinase, which is involved in a pathway recently implicated in artemisinin resistance. Furthermore, other loci exhibit strong temporal signatures which warrant further investigation for involvement in artemisinin resistance evolution. Through genome-wide association analysis we identify a variant in a kelch domain-containing gene on chromosome 10 that may epistatically modulate artemisinin resistance.ConclusionsThis analysis demonstrates the potential of a longitudinal genomic surveillance approach to detect resistance-associated gene loci to improve our mechanistic understanding of how resistance develops. Evidence for additional genomic regions outside of the kelch13 locus associated with artemisinin-resistant parasites may yield new molecular markers for resistance surveillance, which may be useful in efforts to reduce the emergence or spread of artemisinin resistance in African parasite populations.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-017-1204-4) contains supplementary material, which is available to authorized users.

Fitness Costs and the Rapid Spread of kelch13 -C580Y Substitutions Conferring Artemisinin Resistance

“…The ART-S parasite used in this work has 2/4 of these variants ( pfcrt -N326S and pfarps 10-V127M). Cerqueira et al (23) noted that the frequencies of some P. falciparum SNPs are increased on the Thai-Myanmar border at rates similar to those of kelch13 , suggesting the involvement of other loci.…”

Estimating relatedness between malaria parasites

“…, m) single nucleotide polymorphism (SNP) data from monoclonal P. falciparum samples ( Table 1). All data are published [50,51,29,30,52,8]. They were obtained either from sparse genome-wide panels of select markers, called barcodes, or from dense whole genome sequencing (WGS) data sets (reviewed in [53]); full details of sample collection and data generation can be found via the citations above and references therein.…”

Mapping malaria by combining parasite genomic and epidemiologic data

“…Nonetheless, the development of a tool box of genotyping methods tailored to answering questions relevant for transmission on different spatial scales is an important goal. To this end, several ambitious sequencing studies have begun, and over 4,000 Plasmodium falciparum genomes sequenced from different transmission settings around the globe (such as the Pf3K Project -https://www.malariagen.net/data/pf3k-pilot-datarelease-3) [41][42][43]. These genetic data are all publicly available, providing a crucial framework to build upon when designing more local, sequence-based epidemiological studies that balance the trade-off between the number of genetic loci evaluated with the quality of the data (e.g.…”