Whole genome sequencing of multiple Leishmania donovani clinical isolates provides insights into population structure and mechanisms of drug resistance
- Tim Downing1,10,
- Hideo Imamura2,10,
- Saskia Decuypere2,
- Taane G. Clark3,
- Graham H. Coombs4,
- James A. Cotton1,
- James D. Hilley5,
- Simonne de Doncker2,
- Ilse Maes2,
- Jeremy C. Mottram5,
- Mike A. Quail1,
- Suman Rijal6,
- Mandy Sanders1,
- Gabriele Schönian7,
- Olivia Stark7,
- Shyam Sundar8,
- Manu Vanaerschot2,
- Christiane Hertz-Fowler1,9,
- Jean-Claude Dujardin2,11 and
- Matthew Berriman1,11
- 1Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, United Kingdom;
- 2Unit of Molecular Parasitology, Department of Parasitology, Institute of Tropical Medicine, 2000 Antwerp, Belgium;
- 3London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom;
- 4Strathclyde Institute of Pharmacy and Biomedical and Sciences, University of Strathclyde, Glasgow G4 0RE, United Kingdom;
- 5Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, Scotland, United Kingdom;
- 6B.P. Koirala Institute of Health Sciences, Ghopa, Dharan, Nepal;
- 7Institut für Mikrobiologie und Hygiene, Charité Universitätsmedizin Berlin, 10117 Berlin, Germany;
- 8Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
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↵10 These authors contributed equally to this work.
Abstract
Visceral leishmaniasis is a potentially fatal disease endemic to large parts of Asia and Africa, primarily caused by the protozoan parasite Leishmania donovani. Here, we report a high-quality reference genome sequence for a strain of L. donovani from Nepal, and use this sequence to study variation in a set of 16 related clinical lines, isolated from visceral leishmaniasis patients from the same region, which also differ in their response to in vitro drug susceptibility. We show that whole-genome sequence data reveals genetic structure within these lines not shown by multilocus typing, and suggests that drug resistance has emerged multiple times in this closely related set of lines. Sequence comparisons with other Leishmania species and analysis of single-nucleotide diversity within our sample showed evidence of selection acting in a range of surface- and transport-related genes, including genes associated with drug resistance. Against a background of relative genetic homogeneity, we found extensive variation in chromosome copy number between our lines. Other forms of structural variation were significantly associated with drug resistance, notably including gene dosage and the copy number of an experimentally verified circular episome present in all lines and described here for the first time. This study provides a basis for more powerful molecular profiling of visceral leishmaniasis, providing additional power to track the drug resistance and epidemiology of an important human pathogen.
Footnotes
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↵11 Corresponding authors.
E-mail jcdujardin{at}itg.be.
E-mail matthew.berriman{at}sanger.ac.uk.
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.123430.111.
- Received March 18, 2011.
- Accepted August 23, 2011.
- Copyright © 2011 by Cold Spring Harbor Laboratory Press
Freely available online through the Genome Research Open Access option.