eLife (Mar 2016)
Evolutionary genomics of epidemic visceral leishmaniasis in the Indian subcontinent
- Hideo Imamura,
- Tim Downing,
- Frederik Van den Broeck,
- Mandy J Sanders,
- Suman Rijal,
- Shyam Sundar,
- An Mannaert,
- Manu Vanaerschot,
- Maya Berg,
- Géraldine De Muylder,
- Franck Dumetz,
- Bart Cuypers,
- Ilse Maes,
- Malgorzata Domagalska,
- Saskia Decuypere,
- Keshav Rai,
- Surendra Uranw,
- Narayan Raj Bhattarai,
- Basudha Khanal,
- Vijay Kumar Prajapati,
- Smriti Sharma,
- Olivia Stark,
- Gabriele Schönian,
- Harry P De Koning,
- Luca Settimo,
- Benoit Vanhollebeke,
- Syamal Roy,
- Bart Ostyn,
- Marleen Boelaert,
- Louis Maes,
- Matthew Berriman,
- Jean-Claude Dujardin,
- James A Cotton
Affiliations
- Hideo Imamura
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Tim Downing
- ORCiD
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom; School of Maths, Applied Maths and Statistics, National University of Ireland Galway, Galway, Ireland
- Frederik Van den Broeck
- ORCiD
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Mandy J Sanders
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- Suman Rijal
- BP Koirala Institute of Health Sciences, Dharan, Nepal
- Shyam Sundar
- Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
- An Mannaert
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Manu Vanaerschot
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Maya Berg
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Géraldine De Muylder
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Franck Dumetz
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Bart Cuypers
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Ilse Maes
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Malgorzata Domagalska
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Saskia Decuypere
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium; Telethon Kids Institute, University of Western Australia, Perth, Australia
- Keshav Rai
- ORCiD
- BP Koirala Institute of Health Sciences, Dharan, Nepal
- Surendra Uranw
- BP Koirala Institute of Health Sciences, Dharan, Nepal
- Narayan Raj Bhattarai
- BP Koirala Institute of Health Sciences, Dharan, Nepal
- Basudha Khanal
- BP Koirala Institute of Health Sciences, Dharan, Nepal
- Vijay Kumar Prajapati
- Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
- Smriti Sharma
- Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
- Olivia Stark
- Institut für Mikrobiologie und Hygiene, Charité Universitätsmedizin Berlin, Berlin, Germany
- Gabriele Schönian
- Institut für Mikrobiologie und Hygiene, Charité Universitätsmedizin Berlin, Berlin, Germany
- Harry P De Koning
- ORCiD
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- Luca Settimo
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom; Department of Chemistry and Chemical Biology, Northeastern University, Boston, United States
- Benoit Vanhollebeke
- ORCiD
- Laboratory of Molecular Parasitology, Université Libre de Bruxelles, Gosselies, Belgium
- Syamal Roy
- Department of Infectious Diseases and Immunology, Council of Scientific and Industrial Research, Indian Institute of Chemical Biology, Kolkata, India
- Bart Ostyn
- Department of Public Health, Institute of Tropical Medicine, Antwerp, Belgium
- Marleen Boelaert
- ORCiD
- Department of Public Health, Institute of Tropical Medicine, Antwerp, Belgium
- Louis Maes
- Department of Biomedical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
- Matthew Berriman
- ORCiD
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- Jean-Claude Dujardin
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium; Department of Biomedical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
- James A Cotton
- ORCiD
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- DOI
- https://doi.org/10.7554/eLife.12613
- Journal volume & issue
-
Vol. 5
Abstract
Leishmania donovani causes visceral leishmaniasis (VL), the second most deadly vector-borne parasitic disease. A recent epidemic in the Indian subcontinent (ISC) caused up to 80% of global VL and over 30,000 deaths per year. Resistance against antimonial drugs has probably been a contributing factor in the persistence of this epidemic. Here we use whole genome sequences from 204 clinical isolates to track the evolution and epidemiology of L. donovani from the ISC. We identify independent radiations that have emerged since a bottleneck coincident with 1960s DDT spraying campaigns. A genetically distinct population frequently resistant to antimonials has a two base-pair insertion in the aquaglyceroporin gene LdAQP1 that prevents the transport of trivalent antimonials. We find evidence of genetic exchange between ISC populations, and show that the mutation in LdAQP1 has spread by recombination. Our results reveal the complexity of L. donovani evolution in the ISC in response to drug treatment.
Keywords
