Genomics of parasite clearance in response to artemisinins in Cambodia

Since 2005, Rick Fairhurst and his colleagues have been working in Cambodia, where they have established three clinical field sites to collect parasite and patient samples from epidemiologically unique regions of the country. Rick’s collaborative work in Cambodia aims to identify the parasite genetic determinants of parasite clearance rate in response to artemisinins and parasite susceptibility to antimalarial drugs, and to define the relationships between single clone parasite genotypes. His team also investigates the putative host contributions of acquired immunity and erythrocyte polymorphisms to parasite clearance rates.

Rick’s team established their first field site in Pursat province, western Cambodia, to investigate the role of haemoglobin E and other common erythrocyte polymorphisms in protection from severe falciparum malaria. In this province, malaria is acquired predominantly by adult males who are occupationally exposed to parasites as they work in the forests where Anopheles vectors breed; therefore, age-associated acquired immunity was not expected to significantly confound any protective effects of erythrocyte polymorphisms. In 2009, his team began to investigate the artemisinin-resistance phenotype of slow parasite clearance in response to the artemisinin treatment. In particular, Rick became interested in the natural variation in parasite clearance rates, investigating putative contributions from parasite population structure, host immunity and erythrocyte polymorphisms.

In 2010, Rick’s team opened up a second field site in Ratanakiri province, eastern Cambodia, to investigate whether age-associated acquired immunity accelerates parasite clearance rates. Here, in the most malaria-endemic province of Cambodia, parasite genetics was not expected to significantly confound measurements of parasite clearance rates. This is because the artemisinins and the latest generation of its partner drugs have only recently been introduced to this region. Indeed, his team has now confirmed that the in vitro IC50s to almost all antimalarial drugs tested are lower for parasite isolates in Ratanakiri than in Pursat.

As a founder and principal investigator of the Tracking Resistance to Artemisinins Collaboration (TRAC), Rick’s team established a third study site in Preah Vihear, central Cambodia, to study parasite clearance rates in an epidemiological setting believed to be intermediate between Pursat and Ratanakiri. All three sites are now up and running indefinitely and continue to provide the Wellcome Trust Sanger Centre with large numbers of high quality P. falciparum DNA samples for whole-genome sequencing. Genotype-phenotype analyses are now underway, with an emphasis on elucidating the mechanisms underlying the artemisinin resistance phenotype and ex vivo parasite resistance to a battery of antimalarial drugs.

Lead partner

 
  Rick M. Fairhurst
  rfairhurst@niaid.nih.gov
  NIAID/NIH

Key partners

Chanaki Amaratunga
amaratungac@niaid.nih.gov
NIAID/NIH

Pharath Lim
limp@niaid.nih.gov
NIAID/NIH
Cambodia’s National Malaria Centre

Publications

Manske M, Miotto O. et al. Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing. Nature.
DOI: 10.1038/nature11174.
ePrint version of article

Fairhurst RM. et al. Artemisinin-Resistant Malaria: Research Challenges, Opportunities and Public Health Implications. Am J Trop Med Hyg. In press.

Venkatesan M. et al. Using CF11 cellulose columns to inexpensively and effectively remove human DNA from Plasmodium falciparum-infected whole blood samples. Malar J. 2012;11:41. PMID 22321373

Campino S, Auburn S. et al. Population genetic analysis of Plasmodium falciparum parasites using a customized Illumina GoldenGate genotyping assay. PLoS One. 2011;6:e20251. PMID 21673999