Analysis of Plasmodium falciparum samples from UK travellers returning from malaria endemic countries

In collaboration with Colin Sutherland and Tim Robinson, we sequenced samples obtained from travellers returning to the UK from malaria-endemic countries being treated for clinical malaria in the Hospital for Tropical Diseases, London. Malaria isolates were obtained from four patients, two of which had recently travelled to Ghana, one to Kenya and one to Mozambique. We have previously described parasite clearance dynamics in each of these patients while they were being treated (Beshir et al, 2010).

Analysis of the genome sequences obtained from these isolates resulted in the first manuscript published using data generated from the MalariaGEN Plasmodium falciparum population genomics community project: Drug-resistant genotypes and multi-clonality in Plasmodium falciparum analysed by direct genome sequencing from peripheral blood of malaria patientsRobinson T, Campino SG (co-first authors) et al.

Each patient was found to harbour multiple clone infections, and this was verified in each case using standard PCR genotyping of the original blood sample. Evidence was found for known and novel gene deletions and amplifications (see figure 1), and full–length sequence was analysed for eight known loci implicated in drug resistance. We were thus able to demonstrate that Illumina whole genome sequencing of peripheral blood P. falciparum taken directly from malaria patients provides high quality data useful for drug resistance studies, genomic structural analyses and population genetics, and also robustly represents clonal multiplicity.

Figure 1

Deletions in pfrbp2 homologues appear as areas covered by reads with significantly inflated sequence intervals.

Two isoforms of RBP2 are encoded by adjacent genes on chromosome 13, arranged head to head and thus transcribed in opposite directions. 60kb around these genes are depicted, using OX006 as an example. In this isolate, there is a ~600bp deletion in the carboxy-terminal serine-rich domain of homologue b (red elipse). In other isolates, deletions were also observed in the homololgue a.

Lead Partners

Colin Sutherland
London School of Hygiene and Tropical Medicine
Hospital for Tropical Diseases, UCLH, London

Taane Clark
London School of Hygiene and Tropical Medicine
Hospital for Tropical Diseases, UCLH, London

Tim Robinson         
London School of Hygiene and Tropical Medicine
Hospital for Tropical Diseases, UCLH, London

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

Robinson T, Campino SG, et al. 2011. Drug-resistant genotypes and multi-clonality in Plasmodium falciparum analysed by direct genome sequencing from peripheral blood of malaria patients. PLoS One 6: e23204. PMID 21853089

Beshir K, Hallett RL et al. 2010. Measuring the efficacy of anti-malarial drugs in vivo: quantitative PCR measurement of parasite clearance. Malaria J. 9: 312. PMID 21054863