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Antimicrobial agents and chemotherapy DOI:10.1128/AAC.05737-11

Rapid, field-deployable method for genotyping and discovery of drug-resistance single nucleotide polymorphisms in Plasmodium falciparum.

Publication TypeJournal Article
Year of Publication2012
AuthorsDaniels, R, Ndiaye, D, Wall, M, McKinney, J, Séne, PD, Sabeti, PC, Volkman, SK, Mboup, S, Wirth, DF
JournalAntimicrobial agents and chemotherapy
Date Published2012/03/19

Despite efforts to reduce malaria morbidity and mortality, drug-resistant parasites continue to evade control strategies. Recently, emphasis has shifted away from control and towards regional elimination and global eradication of malaria. Such a campaign requires tools to monitor genetic changes in the parasite that could compromise the effectiveness of anti-malarial drugs and undermine eradication programs. These tools must be fast, sensitive, unambiguous, and cost-effective to offer real-time reports of parasite drug susceptibility status across the globe. We have developed and validated a set of genotyping assays using High Resolution Melting (HRM) analysis to detect molecular biomarkers associated with drug resistance across six genes in Plasmodium falciparum. We improved on existing technical approaches by developing refinements and extensions of HRM, including the use of blocked probes (LunaProbes) and the Mutant Allele Amplification Bias (MAAB) technique. To validate the sensitivity and accuracy of our assays we compared our findings to sequence results in both culture-adapted lines and clinical isolates from Senegal. We demonstrate that our assays (1) identify both known and novel polymorphisms, (2) detect multiple genotypes indicative of mixed infections, and (3) distinguish between variants when multiple copies of a locus are present. These rapid and inexpensive assays can track drug resistance and detect emerging mutations in targeted genetic loci in P. falciparum. They provide tools for monitoring molecular changes associated with changes in drug response across populations and for determining whether parasites present after drug treatment are the result of recrudescence or re-infection in clinical settings.