Date of Award




Document Type

Master's Thesis

Degree Name

Master of Science (MS)


Department of Epidemiology and Biostatistics



Content Description

1 online resource (viii, 81 pages) : color illustrations, color maps.

Dissertation/Thesis Chair

Andrea Habura

Committee Members

Susan Madison-Antenucci, Bryon Backenson


drug resistance alleles, Malaria, pyrosequencing, Plasmodium falciparum, Drug resistance in microorganisms

Subject Categories

Biology | Epidemiology | Medicine and Health Sciences


Plasmodium falciparum is a human-infective parasite that causes the most severe form of malaria. Resistance to a wide spectrum of antimalarials has been documented in this species, and single strains may be resistant to several drugs. A new technology, pyrosequencing, has been shown to be useful for the rapid detection of SNPs involved in drug resistance. It can be used in a clinical setting and readily detects new mutants, which frequently appear in this species due to strong selection for antimalarial resistance. In this study, a pyrosequencing protocol was developed to identify mutations in the Plasmodium falciparum genes Pfcrt, Pfdhps, Pfdhfr, Pfcytb and Pfmdr1 which are thought to confer drug resistance to widely used antimalarials. In order to test the effectiveness of the method, we analyzed a set of patient samples received by the NYS Clinical Parasitology Diagnostic Laboratory between 2008-2010, and another obtained from a rural clinic in Uganda. Statistical analysis of the resistance profiles obtained was performed using SAS 9.1. The results suggest high levels of predicted resistance to many antimalarials, with the exception of atovaquone. Surprisingly, antifolate resistance was more prevalent than chloroquine resistance in our clinical samples. A comparison of the current results to data obtained from clinical samples collected in 2002-2005 suggest that fitness costs in maintaining the chloroquine resistance allele Pfcrt K76T in the context of a reduction of chloroquine use could be causing populations of the parasite to become sensitive to this drug once again. We offer evidence that antifolate resistance remains especially high in East Africa, but has in fact traveled West throughout the continent. A statistically significant anticorrelation was also found between Pfdhps S436A and Pfdhps K540E, suggesting that these two mutations are not independent of each other. Our study is advantageous in the sense that, unlike most studies which concentrate on a single locale, we look at a diverse population of pathogens and hosts. The broad geographical sampling of this study, which includes infections acquired in 23 countries, is a useful complement to previously published studies which analyze only local populations.