Accelerated evolution and spread of multidrug-resistant Plasmodium falciparum takes down the latest first-line antimalarial drug in southeast Asia
Authors: Didier Ménard, David A Fidock
Journal: The Lancet Infectious Diseases (2019)

The global fight against malaria has, over the decades, repeatedly been compromised by multidrug-resistant Plasmodium falciparum strains that first emerged in southeast Asia.1White NJ Pukrittayakamee S Hien TT Faiz MA Mokuolu OA Dondorp AM Malaria.Lancet. 2014; 383: 723-735Summary Full Text Full Text PDF PubMed Scopus (656) Google Scholar Successively, these parasites have acquired resistance to chloroquine, sulphadoxine-pyrimethamine, mefloquine, and more recently the artemisinins through point mutations or amplification in genes (crt, dhps, dhfr, mdr1, and kelch13).2Ariey F Witkowski B Amaratunga C et al.A molecular marker of artemisinin-resistant Plasmodium falciparum malaria.Nature. 2014; 505: 50-55Crossref PubMed Scopus (1103) Google Scholar, 3Ashley EA Dhorda M Fairhurst RM et al.Spread of artemisinin resistance in Plasmodium falciparum malaria.N Engl J Med. 2014; 371: 411-423Crossref PubMed Scopus (1230) Google Scholar, 4Phyo AP Ashley EA Anderson TJC et al.Declining efficacy of artemisinin combination therapy against P. falciparum malaria on the Thai-Myanmar border (2003-2013): the role of parasite genetic factors.Clin Infect Dis. 2016; 63: 784-791Crossref PubMed Scopus (108) Google Scholar, 5Ross LS Fidock DA Elucidating mechanisms of drug-resistant Plasmodium falciparum.Cell Host Microbe. 2019; 26: 35-47Summary Full Text Full Text PDF PubMed Scopus (28) Google Scholar, 6Menard D Dondorp A Antimalarial drug resistance: a threat to malaria elimination.Cold Spring Harb Perspect Med. 2017; 7a025619Crossref PubMed Scopus (127) Google Scholar Following increased resistance to artesunate plus mefloquine,7Price RN Uhlemann AC Brockman A et al.Mefloquine resistance in Plasmodium falciparum and increased pfmdr1 gene copy number.Lancet. 2004; 364: 438-447Summary Full Text Full Text PDF PubMed Scopus (603) Google Scholar, 8Alker AP Lim P Sem R et al.pfmdr1 and in vivo resistance to artesunate-mefloquine in falciparum malaria on the Cambodian-Thai border.Am J Trop Med Hyg. 2007; 76: 641-647Crossref PubMed Scopus (145) Google Scholar an early artemisinin-based combined therapy, regional authorities turned increasingly to dihydroartemisinin plus piperaquine. This drug combination was officially adopted in the western provinces of Cambodia in 2008 and the rest of the country in 2010, in Thailand in 2015, and in Vietnam in 2016 (although this artemisinin-based combined therapy was available previously). Warning signs came in 2009 with reports of emerging resistance to artemisinins,9Dondorp AM Nosten F Yi P et al.Artemisinin resistance in Plasmodium falciparum malaria.N Engl J Med. 2009; 361: 455-467Crossref PubMed Scopus (2282) Google Scholar manifesting clinically as delayed rates of parasite clearance3Ashley EA Dhorda M Fairhurst RM et al.Spread of artemisinin resistance in Plasmodium falciparum malaria.N Engl J Med. 2014; 371: 411-423Crossref PubMed Scopus (1230) Google Scholar and placing increased selective pressure on the partner drug piperaquine.10Leang R Taylor WR Bouth DM et al.Evidence of Plasmodium falciparum malaria multidrug resistance to artemisinin and piperaquine in western Cambodia: dihydroartemisinin-piperaquine open-label multicenter clinical assessment.Antimicrob Agents Chemother. 2015; 59: 4719-4726Crossref PubMed Scopus (180) Google Scholar In The Lancet Infectious Diseases, two studies illustrate the accelerated pace at which resistance of P falciparum to dihydroartemisinin plus piperaquine has evolved and spread across southeast Asia, decimating the efficacy of this drug combination. The first report from Rob van der Pluijm and colleagues11van der Pluijm RW Imwong M Chau NH et al.Determinants of dihydroartemisinin-piperaquine treatment failure in Plasmodium falciparum malaria in Cambodia, Thailand, and Vietnam: a prospective clinical, pharmacological, and genetic study.Lancet Infect Dis. 2019; (published online July 22.)http://dx.doi.org/10.1016/S1473-3099(19)30391-3Summary Full Text Full Text PDF Scopus (103) Google Scholar presents interim clinical data from a multicentre, open-label, randomised controlled trial (TRAC2; NCT02453308) that was done to assess the efficacy, safety, and tolerability of experimental triple artemisinin-based combined therapies compared with two-agent artemisinin-based combined therapies in areas with multidrug-resistant P falciparum malaria. Clinical, pharmacological, and genetic data were reported for a cohort of 140 patients with acute P falciparum malaria who were treated in 2015–18 with dihydroartemisinin plus piperaquine in sites in Cambodia, Thailand, and Vietnam. PCR-corrected clinical efficacy rates at day 42 were 12·7% in northeastern Thailand, 38·2% in western Cambodia, 73·4% in northeastern Cambodia, and 47·1% in southwestern Vietnam, averaging to a 50·0% treatment failure rate across the region. Treatment failures were far more common than reported a few years ago.10Leang R Taylor WR Bouth DM et al.Evidence of Plasmodium falciparum malaria multidrug resistance to artemisinin and piperaquine in western Cambodia: dihydroartemisinin-piperaquine open-label multicenter clinical assessment.Antimicrob Agents Chemother. 2015; 59: 4719-4726Crossref PubMed Scopus (180) Google Scholar, 12Phuc BQ Rasmussen C Duong TT et al.Treatment failure of dihydroartemisinin/piperaquine for Plasmodium falciparum malaria, Vietnam.Emerg Infect Dis. 2017; 23: 715-717Crossref PubMed Scopus (55) Google Scholar Significant increases were also observed across the region in the prevalence of P falciparum markers of artemisinin resistance (with the kelch13 Cys580Tyr [C580Y] variant now at 88%) and piperaquine resistance (plasmepsin 2 and plasmepsin 3 amplifications and crt mutations, both at 74%), compared with prevalence data from 2011–13 (from the earlier TRAC project). The most striking result was the rapid increase in crt mutations, present at a combined prevalence of only 5% in the 2011–13 samples. The risk of treatment failure was strongly associated with the individual crt mutations Thr93Ser (T93S), His97Tyr (H97Y), Phe145Ile (F145I), or Ile218Phe (I218F), as well as with plasmepsin 2 and plasmepsin 3 amplification. These data, supported by recent clinical, genetic epidemiology, and gene-editing results,13Agrawal S Moser KA Morton L et al.Association of a novel mutation in the Plasmodium falciparum chloroquine resistance transporter with decreased piperaquine sensitivity.J Infect Dis. 2017; 216: 468-476Crossref PubMed Scopus (60) Google Scholar, 14Ross LS Dhingra SK Mok S et al.Emerging Southeast Asian PfCRT mutations confer Plasmodium falciparum resistance to the first-line antimalarial piperaquine.Nat Commun. 2018; 93314Crossref PubMed Scopus (84) Google Scholar provide compelling evidence that these new crt mutations can mediate high-grade piperaquine resistance and are driving the increased rates of treatment failure with dihydroartemisinin plus piperaquine. The second, complementary study by William Hamilton and colleagues15Hamilton WL Amato R van der Pluijm RW et al.Evolution and expansion of multidrug resistant malaria in southeast Asia: a genomic epidemiology study.Lancet Infect Dis. 2019; (published online July 22.)http://dx.doi.org/10.1016/S1473-3099(19)30392-5Summary Full Text Full Text PDF Scopus (85) Google Scholar provides detailed insight into the molecular epidemiology of P falciparum and the evolution of the artemisinin-resistant and piperaquine-resistant KEL1/PLA1 co-lineage, first identified in samples from 2008 in western Cambodia.16Amato R Pearson RD Almagro-Garcia J et al.Origins of the current outbreak of multidrug-resistant malaria in southeast Asia: a retrospective genetic study.Lancet Infect Dis. 2018; 18: 337-345Summary Full Text Full Text PDF PubMed Scopus (73) Google Scholar Genome data were analysed from 1673 P falciparum clinical samples collected between 2007 and 2018 from patients with malaria in Cambodia, Laos, northeastern Thailand, and Vietnam, combining the TRAC2 and the Genetic Reconnaissance in the Greater Mekong Subregion (GenRe-Mekong) projects. Results showed that KEL1/PLA1 parasites had spread across all the surveyed countries, in several areas exceeding 80% of the local parasite population. Genetic similarity between KEL1/PLA1-type parasites across borders was greater than overall within-country parasite diversity, implying strong selective pressures favouring KEL1/PLA1. Their aggressive expansion across the region was accompanied by the diversification of the KEL1/PLA1 co-lineage into six different subgroups. The three most abundant subgroups carried the mutually exclusive crt mutations T93S, H97Y, F145I, or I218F, which had emerged on the crt Dd2 haplotype.15Hamilton WL Amato R van der Pluijm RW et al.Evolution and expansion of multidrug resistant malaria in southeast Asia: a genomic epidemiology study.Lancet Infect Dis. 2019; (published online July 22.)http://dx.doi.org/10.1016/S1473-3099(19)30392-5Summary Full Text Full Text PDF Scopus (85) Google Scholar This founder haplotype had earlier swept across the region as the primary determinant of chloroquine resistance, and harbours eight point mutations compared with the chloroquine-sensitive wild-type crt isoform.17Wootton JC Feng X Ferdig MT et al.Genetic diversity and chloroquine selective sweeps in Plasmodium falciparum.Nature. 2002; 418: 320-323Crossref PubMed Scopus (571) Google Scholar These new variant isoforms were found to co-exist simultaneously in Cambodia, Laos, and Vietnam, suggesting they have a strong selective advantage over the other subgroups (harbouring mostly the piperaquine-sensitive Dd2 isoform). An earlier study reported that the F145I mutation conferred high-level piperaquine resistance in cultured parasites yet had a substantially reduced growth rate in vitro.14Ross LS Dhingra SK Mok S et al.Emerging Southeast Asian PfCRT mutations confer Plasmodium falciparum resistance to the first-line antimalarial piperaquine.Nat Commun. 2018; 93314Crossref PubMed Scopus (84) Google Scholar Further studies will provide insight into how resistance and fitness contribute to this evolving landscape of soft sweeps that often coalesce around a few isoforms or only one, and will show how quickly this will change as countries move to alternative first-line treatments and whether these new resistance traits expose vulnerabilities in terms of other antimalarial drugs becoming more potent. In the Greater Mekong Subregion, P falciparum parasite populations are highly structured in fragmented forest areas (considered as hotspots of malaria transmission), yet remain interconnected because of intensive human migration and parasite population flow. This epidemiological context, wherein major changes can rapidly occur—for example, following the introduction of new antimalarial drugs, and subsequent extinction or adaptation and recolonisation by the relatively fittest parasite populations—could explain the recent emergence and expansion of new KEL1/PLA1 subgroups flowing across borders. In this regard, findings from these two studies highlight the urgent need to adopt new and effective treatments (such as the triple artemisinin-based combined therapies or the artemisinin-based combined therapy artesunate plus pyronaridine18Bui Quang P Huynh Hong Q Tran Thanh D et al.Pyronaridine-artesunate efficacy and safety in uncomplicated Plasmodium falciparum malaria in areas of artemisinin-resistant falciparum in Viet Nam (2017–2018).Clin Infect Dis. 2019; (published online June 28.)DOI:10.1093/cid/ciz580Crossref PubMed Scopus (9) Google Scholar). These findings also demonstrate the advantages of implementing a regional strategy rather than country-specific programmes to address population movements and to integrate regional clinical and genetic surveillance systems into a coordinated campaign, with the goal of achieving malaria elimination in southeast Asia. We declare no competing interests. Determinants of dihydroartemisinin-piperaquine treatment failure in Plasmodium falciparum malaria in Cambodia, Thailand, and Vietnam: a prospective clinical, pharmacological, and genetic studyDihydroartemisinin-piperaquine is not treating malaria effectively across the eastern Greater Mekong subregion. A highly drug-resistant P falciparum co-lineage is evolving, acquiring new resistance mechanisms, and spreading. Accelerated elimination of P falciparum malaria in this region is needed urgently, to prevent further spread and avoid a potential global health emergency. Full-Text PDF Open AccessEvolution and expansion of multidrug-resistant malaria in southeast Asia: a genomic epidemiology studyAfter emerging and circulating for several years within Cambodia, the P falciparum KEL1/PLA1 co-lineage diversified into multiple subgroups and acquired new genetic features, including novel crt mutations. These subgroups have rapidly spread into neighbouring countries, suggesting enhanced fitness. These findings highlight the urgent need for elimination of this increasingly drug-resistant parasite co-lineage, and the importance of genetic surveillance in accelerating malaria elimination efforts. Full-Text PDF Open Access