Barcoding Genetically Distinct Plasmodium falciparum Strains for Comparative Assessment of Fitness and Antimalarial Drug Resistance

Abstract

The complex interplay between antimalarial resistance and parasite fitness has important implications for understanding the development and spread of drug resistance alleles and the impact of genetic background on transmission. One limitation with current methodologies to measure parasite fitness is the ability to scale this beyond simple head-to-head competition experiments between a wildtype control line and test line, with a need for a scalable approach that allows tracking of parasite growth in complex mixtures. In our study, we have used CRISPR editing to insert unique DNA barcodes into a safe-harbor genomic locus to tag multiple parasite strains and use next-generation sequencing to read out strain dynamics. We observe inherent fitness differences between the strains, as well as sensitive modulation of responses to challenge with clinically relevant antimalarials, including artemisinin.