Understanding the delicate balance of drug resistance and evolutionary fitness in malaria

Malaria is caused by the mosquito-borne parasite Plasmodium falciparum and causes hundreds of thousands of deaths globally, almost all in children under five. Despite improvements in public health measures, cases have increased in the past decade, partly due to increasing drug resistance. Current first-line treatments are artemisinin-based combination therapies (ACTs), combining artemisinin-based compounds (ART) with a second longer-lasting drug. ART resistance has emerged in Asia and parts of Eastern Africa; spread of resistance across the rest of Africa would lead to a public health catastrophe. ART resistance is driven by alterations in the k13 gene, yet different parasite strains show variable levels of resistance when expressing the same k13 allele. This suggests that other regions of the parasite genome (i.e. the genetic background) also play a critical role in generating ART resistance as a functional outcome. Moreover, in many African strains, parasites with mutant k13 replicate less well, which is called having a "fitness cost". The same fitness cost is not seen in Asian strains that have shown artemisinin resistance for 10-15 years longer. This suggests that for ART resistance to become widespread, fitness costs must be overcome, and that the genetic background of the parasite must play a role. Parasite genetic differences could act by enabling further resistance or compensating for the fitness cost of mutant k13. This “supportive” genetic background appears to be present in Asian strains, but less so in African strains. Resistance to piperaquine (PPQ), a partner drug in ACT, has also been described in South-East Asia, driven by mutations in pfcrt (Plasmodium falciparum chloroquine resistance transporter), a gene also associated with chloroquine resistance. As with ART, studies from the Lee (University of Dundee) and Fidock labs (Columbia University) have shown that PPQ-resistance-associated pfcrt mutations are more likely to cause resistance in Asian strains compared to African strains. This suggests that, like ART resistance, genetic background plays an important role in PPQ resistance. My fellowship aims to leverage traditional genetic approaches from the Fidock lab with state-of-the-art genomic methods from the Lee lab to quantitatively determine how parasite genetic background influences both the fitness cost of drug-resistance mutations and susceptibility to multiple anti-malarial drugs. An improved understanding of the relationship between drug resistance and fitness will provide fundamental insights into the evolutionary biology of malaria parasites, and is vital to design accurate surveillance systems for malaria drug resistance. Currently, surveillance programmes monitor for k13 mutations, but knowing which other genes contribute to fitness in the context of drug selective pressure would mean that these can also be monitored. Because ART resistance in Africa is currently confined to small areas, understanding which areas provide a “hospitable” genetic environment for ART resistance mutations will enable better geographic focusing of resources for malaria control. The major aims of this project are to: Aim 1: Identify P. falciparum genes co-inherited with mutations in k13 or pfcrt that either complement drug resistance or compensate for fitness costs incurred by those mutations. Aim 2: Determine the function of specific genes that are co-inherited with ART-resistant k13 mutations, to identify variants that are necessary or sufficient for increased parasite fitness or resistance. Aim 3: Explore the effect of PPQ-resistance-associated pfcrt mutations on African and Asian strains of P. falciparum, and clarify the role of non-pfcrt genes in PPQ resistance and/or compensatory fitness.