Following both significant advances and setbacks in the past decades of fighting malaria, the end goal of malaria elimination is now once again within sight. However, this endgame may prove the most challenging yet, as there are still significant gaps in our understanding of human malaria more generally and as we know from past experience that the malaria parasite is able to rapidly overcome any challenge thrown at it. Despite the huge international endeavour to understand the genomic basis of malaria biology, the genome sequences of two of the five human malaria parasite species, Plasmodium malariae and P. ovale, have remained essentially a mystery. Consequently, the implications of these sequences on aspects such as drug resistance have eluded us. However, even for human malaria parasite species that have been sequenced at large scale, such as P. falciparum, a better understanding of the impact of genetic variation on drug resistance is needed, especially in light of multidrug resistance in Southeast Asia. In this thesis, I have, in collaboration with others, explored these different aspects of human malaria parasites, showing to what extent sequencing data can inform our understanding of human malaria and aid us in our fight against this devastating disease.

Initially I assembled reference genome sequences for both P. malariae and P. ovale, an analysis of which I present in Chapter 1. I show that the P. malariae genome is markedly different to other Plasmodium genomes and relate this to its unique biology. Using additional draft genome assemblies, I also confirm that P. ovale consists of two species that appear to have diverged millions of years ago. In Chapter 2, I use the newly assembled P. malariae reference genome in combination with clinical data to characterize a case of clinical recrudescence of a P. malariae infection, and suggest that drug resistance may have played a role. To better understand the ability of malaria parasites to acquire drug resistance, in Chapter 3 I harnessed a large dataset of P. falciparum whole genome sequences with associated phenotype data on mefloquine, an antimalarial drug. I show that the current outbreak of multidrug resistance in Southeast Asia is accompanied by a hyper-sensitization of the parasite population through the acquisition of a complex genetic architecture of mefloquine sensitivity. Finally, in Chapter 4, by incorporating phenotype data on additional drugs, including chloroquine, artemisinin and piperaquine, I identify a specific haplotype of the pfcrt gene that displays super-resistance to chloroquine and that acts as a genetic backbone to artemisinin resistance and to multidrug resistance in general. 

The approach taken in this thesis is one of extracting new information from layering on additional data. I begin by comparing genome sequences to each other in Chapter 1, I then layer on clinical metadata in Chapter 2, I add in phenotype data for one drug in Chapter 3, and finally, in Chapter 4, I harness phenotype data for multiple drugs. At each level, I identify new biology that both expands our understanding of human malaria in general and sheds light on the specifics of antimalarial drug resistance. The contributions made in this work will be of significant importance in the upcoming end game of malaria elimination.