ArticlePLoS neglected tropical diseases2019
Genomes of Leishmania parasites directly sequenced from patients with visceral leishmaniasis in the Indian subcontinent.
Article in PLoS neglected tropical diseases, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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Who cites it
45 citing papers in PubMed, 72 citations in OpenAlex.
- Beyond resistance: Emerging methods to dissect drug responses in Leishmania.PLoS pathogens · 2026Review
- From dogma to data: charting a path forward for clinico-immunological research in Ethiopian cutaneous leishmaniasis.Infectious diseases of poverty · 2026Review
- Direct sequencing of Leishmania donovani from patients in Garissa County, Northern Kenya, reveals a newly emerging intra-specific hybrid genotype.PLoS neglected tropical diseases · 2026Article
- Spatial mapping of Ethiopian cutaneous leishmaniasis lesions reveals distinct tissue level immune programs.Frontiers in immunology · 2026Article
- Enrichment of Helminth Mitochondrial Genomes From Faecal Samples Using Hybridisation Capture.Molecular ecology resources · 2025Article
- Genomic Characterization of Leishmania tropica in Cutaneous Leishmaniasis, Somali Region, Ethiopia, 2023.Emerging infectious diseases · 2025Article
- Metagenomic next-generation sequencing assists in the diagnosis of visceral leishmaniasis in non-endemic areas of China.Frontiers in cellular and infection microbiology · 2025Article
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- Far-East Asian Toxoplasma isolates share ancestry with North and South/Central American recombinant lineages.Nature communications · 2024Article
- Ancestral aneuploidy and stable chromosomal duplication resulting in differential genome structure and gene expression control in trypanosomatid parasites.Genome research · 2024Article
- Phylogenomic reconstruction ofbioRxiv : the preprint server for biology · 2024Article
- Hybrid-Capture Target Enrichment in Human Pathogens: Identification, Evolution, Biosurveillance, and Genomic Epidemiology.Pathogens (Basel, Switzerland) · 2024Review
- Genomic Insight of Leishmania Parasite: In-Depth Review of Drug Resistance Mechanisms and Genetic Mutations.ACS omega · 2024Review
- Source Tracing of Leishmania donovani in Emerging Foci of Visceral Leishmaniasis, Western Nepal.Emerging infectious diseases · 2024Article
- Analytic Approaches in Genomic Epidemiological Studies of Parasitic Protozoa.Transboundary and emerging diseases · 2024Review
- Diversity and dissemination of viruses in pathogenic protozoa.Nature communications · 2023Article
- The adaptive roles of aneuploidy and polyclonality in Leishmania in response to environmental stress.EMBO reports · 2023Article
- A Rare Case of Imported Cutaneous Leishmaniasis Caused byTropical medicine and infectious disease · 2023Article
- Selective whole-genome amplification reveals population genetics of Leishmania braziliensis directly from patient skin biopsies.PLoS pathogens · 2023Article
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Authors and funding
13 authors at 4 institutions in 3 countries.
Funding
Abstract
Whole genome sequencing (WGS) is increasingly used for molecular diagnosis and epidemiology of infectious diseases. Current Leishmania genomic studies rely on DNA extracted from cultured parasites, which might introduce sampling and biological biases into the subsequent analyses. Up to now, direct analysis of Leishmania genome in clinical samples is hampered by high levels of human DNA and large variation in parasite load in clinical samples. Here, we present a method, based on target enrichment of Leishmania donovani DNA with Agilent SureSelect technology, that allows the analysis of Leishmania genomes directly in clinical samples. We validated our protocol with a set of artificially mixed samples, followed by the analysis of 63 clinical samples (bone marrow or spleen aspirates) from visceral leishmaniasis patients in Nepal. We were able to identify genotypes using a set of diagnostic SNPs in almost all of these samples (97%) and access comprehensive genome-wide information in most (83%). This allowed us to perform phylogenomic analysis, assess chromosome copy number and identify large copy number variants (CNVs). Pairwise comparisons between the parasite genomes in clinical samples and derived in vitro cultured promastigotes showed a lower aneuploidy in amastigotes as well as genomic differences, suggesting polyclonal infections in patients. Altogether our results underline the need for sequencing parasite genomes directly in the host samples.
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