Browsing by Author "Hideo Imamura"

Now showing 1 - 5 of 5

Evolutionary genomics of epidemic visceral leishmaniasis in the Indian subcontinent
(eLife Sciences Publications Ltd, 2016) 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
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. © Imamura et al.
Genetic markers for SSG resistance in leishmania donovani and SSG treatment failure in visceral leishmaniasis patients of the Indian subcontinent
(2012) Manu Vanaerschot; Saskia Decuypere; Tim Downing; Hideo Imamura; Olivia Stark; Simonne De Doncker; Syamal Roy; Bart Ostyn; Louis Maes; Basudha Khanal; Marleen Boelaert; Gabriele Schönian; Matthew Berriman; François Chappuis; Jean-Claude Dujardin; Shyam Sundar; Suman Rijal
The current standard to assess pentavalent antimonial (SSG) susceptibility of Leishmania is a laborious in vitro assay of which the result has little clinical value because SSG-resistant parasites are also found in SSG-cured patients. Candidate genetic markers for clinically relevant SSG-resistant parasites identified by full genome sequencing were here validated on a larger set of clinical strains. We show that 3 genomic locations suffice to specifically detect the SSG-resistant parasites found only in patients experiencing SSG treatment failure. This finding allows the development of rapid assays to monitor the emergence and spread of clinically relevant SSG-resistant Leishmania parasites. © The Author 2012.
Genome-wide SNP and microsatellite variation illuminate population-level epidemiology in the Leishmania donovani species complex
(2012) Tim Downing; Olivia Stark; Manu Vanaerschot; Hideo Imamura; Mandy Sanders; Saskia Decuypere; Simonne de Doncker; Ilse Maes; Suman Rijal; Shyam Sundar; Jean-Claude Dujardin; Matthew Berriman; Gabriele Schönian
The species of the Leishmania donovani species complex cause visceral leishmaniasis, a debilitating infectious disease transmitted by sandflies. Understanding molecular changes associated with population structure in these parasites can help unravel their epidemiology and spread in humans. In this study, we used a panel of standard microsatellite loci and genome-wide SNPs to investigate population-level diversity in L. donovani strains recently isolated from a small geographic area spanning India, Bihar and Nepal, and compared their variation to that found in diverse strains of the L. donovani complex isolates from Europe, Africa and Asia. Microsatellites and SNPs could clearly resolve the phylogenetic relationships of the strains between continents, and microsatellite phylogenies indicated that certain older Indian strains were closely related to African strains. In the context of the anti-malaria spraying campaigns in the 1960s, this was consistent with a pattern of episodic population size contractions and clonal expansions in these parasites that was supported by population history simulations. In sharp contrast to the low resolution provided by microsatellites, SNPs retained a much more fine-scale resolution of population-level variability to the extent that they identified four different lineages from the same region one of which was more closely related to African and European strains than to Indian or Nepalese ones. Joining results of in vitro testing the antimonial drug sensitivity with the phylogenetic signals from the SNP data highlighted protein-level mutations revealing a distinct drug-resistant group of Nepalese and Indian L. donovani. This study demonstrates the power of genomic data for exploring parasite population structure. Furthermore, markers defining different genetic groups have been discovered that could potentially be applied to investigate drug resistance in clinical Leishmania strains. © 2011 Elsevier B.V.
Refining wet lab experiments with in silico searches: A rational quest for diagnostic peptides in visceral leishmaniasis
(Public Library of Science, 2019) Bruno Cesar Bremer Hinckel; Tegwen Marlais; Stephanie Airs; Tapan Bhattacharyya; Hideo Imamura; Jean-Claude Dujardin; Sayda El-Safi; Om Prakash Singh; Shyam Sundar; Andrew Keith Falconar; Bjorn Andersson; Sergey Litvinov; Michael A. Miles; Pascal Mertens
Background The search for diagnostic biomarkers has been profiting from a growing number of high quality sequenced genomes and freely available bioinformatic tools. These can be combined with wet lab experiments for a rational search. Improved, point-of-care diagnostic tests for visceral leishmaniasis (VL), early case detection and surveillance are required. Previous investigations demonstrated the potential of IgG1 as a biomarker for monitoring clinical status in rapid diagnostic tests (RDTs), although using a crude lysate antigen (CLA) as capturing antigen. Replacing the CLA by specific antigens would lead to more robust RDTs. Methodology Immunoblots revealed L. donovani protein bands detected by IgG1 from VL patients. Upon confident identification of these antigens by mass spectrometry (MS), we searched for evidence of constitutive protein expression and presence of antigenic domains or high accessibility to B-cells. Selected candidates had their linear epitopes mapped with in silico algorithms. Multiple high-scoring predicted epitopes from the shortlisted proteins were screened in peptide arrays. The most promising candidate was tested in RDT prototypes using VL and nonendemic healthy control (NEHC) patient sera. Results Over 90% of the proteins identified from the immunoblots did not satisfy the selection criteria and were excluded from the downstream epitope mapping. Screening of predicted epitope peptides from the shortlisted proteins identified the most reactive, for which the sensitivity for IgG1 was 84% (95% CI 60—97%) with Sudanese VL sera on RDT prototypes. None of the sera from NEHCs were positive. Conclusion We employed in silico searches to reduce drastically the output of wet lab experiments, focusing on promising candidates containing selected protein features. By predicting epitopes in silico we screened a large number of peptides using arrays, identifying the most promising one, for which IgG1 sensitivity and specificity, with limited sample size, supported this proof of concept strategy for diagnostics discovery, which can be applied to the development of more robust IgG1 RDTs for monitoring clinical status in VL. © 2019 Bremer Hinckel et al.
Whole genome sequencing of multiple Leishmania donovani clinical isolates provides insights into population structure and mechanisms of drug resistance
(2011) Tim Downing; Hideo Imamura; Saskia Decuypere; Taane G. Clark; Graham H. Coombs; James A. Cotton; James D. Hilley; Simonne De Doncker; Ilse Maes; Jeremy C. Mottram; Mike A. Quail; Suman Rijal; Mandy Sanders; Gabriele Schönian; Olivia Stark; Shyam Sundar; Manu Vanaerschot; Christiane Hertz-Fowler; Jean-Claude Dujardin; Matthew Berriman
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 wholegenome 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. © 2011 by Cold Spring Harbor Laboratory Press.