1
|
de Vrij N, Pollmann J, Rezende AM, Ibarra-Meneses AV, Pham TT, Hailemichael W, Kassa M, Bogale T, Melkamu R, Yeshanew A, Mohammed R, Diro E, Maes I, Domagalska MA, Landuyt H, Vogt F, van Henten S, Laukens K, Cuypers B, Meysman P, Beyene H, Sisay K, Kibret A, Mersha D, Ritmeijer K, van Griensven J, Adriaensen W. Persistent T cell unresponsiveness associated with chronic visceral leishmaniasis in HIV-coinfected patients. Commun Biol 2024; 7:524. [PMID: 38702419 PMCID: PMC11068874 DOI: 10.1038/s42003-024-06225-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 04/22/2024] [Indexed: 05/06/2024] Open
Abstract
A large proportion of HIV-coinfected visceral leishmaniasis (VL-HIV) patients exhibit chronic disease with frequent VL recurrence. However, knowledge on immunological determinants underlying the disease course is scarce. We longitudinally profiled the circulatory cellular immunity of an Ethiopian HIV cohort that included VL developers. We show that chronic VL-HIV patients exhibit high and persistent levels of TIGIT and PD-1 on CD8+/CD8- T cells, in addition to a lower frequency of IFN-γ+ TIGIT- CD8+/CD8- T cells, suggestive of impaired T cell functionality. At single T cell transcriptome and clonal resolution, the patients show CD4+ T cell anergy, characterised by a lack of T cell activation and lymphoproliferative response. These findings suggest that PD-1 and TIGIT play a pivotal role in VL-HIV chronicity, and may be further explored for patient risk stratification. Our findings provide a strong rationale for adjunctive immunotherapy for the treatment of chronic VL-HIV patients to break the recurrent disease cycle.
Collapse
Affiliation(s)
- Nicky de Vrij
- Clinical Immunology Unit, Department of Clinical Sciences, Institute of Tropical Medicine, 2000, Antwerp, Belgium
- Adrem Data Lab, Department of Computer Science, University of Antwerp, 2020, Antwerp, Belgium
| | - Julia Pollmann
- Department of Medical Oncology, University Hospital Heidelberg, National Center for Tumor Diseases (NCT) Heidelberg, 69120, Heidelberg, Germany
| | - Antonio M Rezende
- Department of Microbiology, Aggeu Magalhães Institute-FIOCRUZ/PE, Recife, Brazil
| | - Ana V Ibarra-Meneses
- Département de Pathologie et Microbiologie, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, QC, Canada
| | - Thao-Thy Pham
- Clinical Immunology Unit, Department of Clinical Sciences, Institute of Tropical Medicine, 2000, Antwerp, Belgium
| | - Wasihun Hailemichael
- Department of Immunology and Molecular Biology, Faculty of Biomedical Sciences, University of Gondar, Gondar, Ethiopia
| | - Mekibib Kassa
- Leishmaniasis Research and Treatment Centre, University of Gondar, Gondar, Ethiopia
| | - Tadfe Bogale
- Leishmaniasis Research and Treatment Centre, University of Gondar, Gondar, Ethiopia
| | - Roma Melkamu
- Leishmaniasis Research and Treatment Centre, University of Gondar, Gondar, Ethiopia
| | - Arega Yeshanew
- Leishmaniasis Research and Treatment Centre, University of Gondar, Gondar, Ethiopia
| | - Rezika Mohammed
- Leishmaniasis Research and Treatment Centre, University of Gondar, Gondar, Ethiopia
| | - Ermias Diro
- Leishmaniasis Research and Treatment Centre, University of Gondar, Gondar, Ethiopia
| | - Ilse Maes
- Molecular Parasitology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, 2000, Antwerp, Belgium
| | - Malgorzata A Domagalska
- Molecular Parasitology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, 2000, Antwerp, Belgium
| | - Hanne Landuyt
- Clinical Trial Unit, Department of Clinical Sciences, Institute of Tropical Medicine, 2000, Antwerp, Belgium
| | - Florian Vogt
- National Centre for Epidemiology and Population Health, The Australian National University, Canberra, 2601, Australia
- The Kirby Institute, University of New South Wales, Sydney, 2052, Australia
- Unit of Neglected Tropical Diseases, Department of Clinical Sciences, Institute of Tropical Medicine, 2000, Antwerp, Belgium
| | - Saskia van Henten
- Unit of Neglected Tropical Diseases, Department of Clinical Sciences, Institute of Tropical Medicine, 2000, Antwerp, Belgium
| | - Kris Laukens
- Adrem Data Lab, Department of Computer Science, University of Antwerp, 2020, Antwerp, Belgium
| | - Bart Cuypers
- Adrem Data Lab, Department of Computer Science, University of Antwerp, 2020, Antwerp, Belgium
| | - Pieter Meysman
- Adrem Data Lab, Department of Computer Science, University of Antwerp, 2020, Antwerp, Belgium
| | | | | | | | | | | | - Johan van Griensven
- Unit of Neglected Tropical Diseases, Department of Clinical Sciences, Institute of Tropical Medicine, 2000, Antwerp, Belgium
| | - Wim Adriaensen
- Clinical Immunology Unit, Department of Clinical Sciences, Institute of Tropical Medicine, 2000, Antwerp, Belgium.
| |
Collapse
|
2
|
Heeren S, Maes I, Sanders M, Lye LF, Adaui V, Arevalo J, Llanos-Cuentas A, Garcia L, Lemey P, Beverley SM, Cotton JA, Dujardin JC, Van den Broeck F. Diversity and dissemination of viruses in pathogenic protozoa. Nat Commun 2023; 14:8343. [PMID: 38102141 PMCID: PMC10724245 DOI: 10.1038/s41467-023-44085-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 11/29/2023] [Indexed: 12/17/2023] Open
Abstract
Viruses are the most abundant biological entities on Earth and play a significant role in the evolution of many organisms and ecosystems. In pathogenic protozoa, the presence of viruses has been linked to an increased risk of treatment failure and severe clinical outcome. Here, we studied the molecular epidemiology of the zoonotic disease cutaneous leishmaniasis in Peru and Bolivia through a joint evolutionary analysis of Leishmania braziliensis and their dsRNA Leishmania virus 1. We show that parasite populations circulate in tropical rainforests and are associated with single viral lineages that appear in low prevalence. In contrast, groups of hybrid parasites are geographically and ecologically more dispersed and associated with an increased prevalence, diversity and spread of viruses. Our results suggest that parasite gene flow and hybridization increased the frequency of parasite-virus symbioses, a process that may change the epidemiology of leishmaniasis in the region.
Collapse
Affiliation(s)
- Senne Heeren
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Ilse Maes
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | | | - Lon-Fye Lye
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Vanessa Adaui
- Laboratory of Biomolecules, Faculty of Health Sciences, Universidad Peruana de Ciencias Aplicadas, Lima, Peru
| | - Jorge Arevalo
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Alejandro Llanos-Cuentas
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Lineth Garcia
- Instituto de Investigación Biomédicas e Investigación Social, Universidad Mayor de San Simon, Cochabamba, Bolivia
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Stephen M Beverley
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - James A Cotton
- Welcome Sanger Institute, Hinxton, UK
- School of Biodiversity, One Health and Comparative Medicine, Wellcome Centre for Integrative Parasitology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Jean-Claude Dujardin
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium.
| | - Frederik Van den Broeck
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium.
| |
Collapse
|
3
|
Negreira GH, de Groote R, Van Giel D, Monsieurs P, Maes I, de Muylder G, Van den Broeck F, Dujardin J, Domagalska MA. The adaptive roles of aneuploidy and polyclonality in Leishmania in response to environmental stress. EMBO Rep 2023; 24:e57413. [PMID: 37470283 PMCID: PMC10481652 DOI: 10.15252/embr.202357413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/15/2023] [Accepted: 06/30/2023] [Indexed: 07/21/2023] Open
Abstract
Aneuploidy is generally considered harmful, but in some microorganisms, it can act as an adaptive mechanism against environmental stress. Here, we use Leishmania-a protozoan parasite with remarkable genome plasticity-to study the early steps of aneuploidy evolution under high drug pressure (using antimony or miltefosine as stressors). By combining single-cell genomics, lineage tracing with cellular barcodes, and longitudinal genome characterization, we reveal that aneuploidy changes under antimony pressure result from polyclonal selection of pre-existing karyotypes, complemented by further and rapid de novo alterations in chromosome copy number along evolution. In the case of miltefosine, early parasite adaptation is associated with independent point mutations in a miltefosine transporter gene, while aneuploidy changes only emerge later, upon exposure to increased drug levels. Therefore, polyclonality and genome plasticity are hallmarks of parasite adaptation, but the scenario of aneuploidy dynamics depends on the nature and strength of the environmental stress as well as on the existence of other pre-adaptive mechanisms.
Collapse
Affiliation(s)
- Gabriel H Negreira
- Molecular Parasitology UnitInstitute of Tropical Medicine AntwerpAntwerpBelgium
| | - Robin de Groote
- Molecular Parasitology UnitInstitute of Tropical Medicine AntwerpAntwerpBelgium
| | - Dorien Van Giel
- Molecular Parasitology UnitInstitute of Tropical Medicine AntwerpAntwerpBelgium
| | - Pieter Monsieurs
- Molecular Parasitology UnitInstitute of Tropical Medicine AntwerpAntwerpBelgium
| | - Ilse Maes
- Molecular Parasitology UnitInstitute of Tropical Medicine AntwerpAntwerpBelgium
| | | | - Frederik Van den Broeck
- Molecular Parasitology UnitInstitute of Tropical Medicine AntwerpAntwerpBelgium
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical ResearchKatholieke Universiteit LeuvenLeuvenBelgium
| | - Jean‐Claude Dujardin
- Molecular Parasitology UnitInstitute of Tropical Medicine AntwerpAntwerpBelgium
- Department of Biomedical SciencesUniversity of AntwerpAntwerpBelgium
| | | |
Collapse
|
4
|
Van den Broeck F, Heeren S, Maes I, Sanders M, Cotton JA, Cupolillo E, Alvarez E, Garcia L, Tasia M, Marneffe A, Dujardin JC, Van der Auwera G. Genome Analysis of Triploid Hybrid Leishmania Parasite from the Neotropics. Emerg Infect Dis 2023; 29:1076-1078. [PMID: 37081624 PMCID: PMC10124652 DOI: 10.3201/eid2905.221456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023] Open
Abstract
We discovered a hybrid Leishmania parasite in Costa Rica that is genetically similar to hybrids from Panama. Genome analyses demonstrated the hybrid is triploid and identified L. braziliensis and L. guyanensis-related strains as parents. Our findings highlight the existence of poorly sampled Leishmania (Viannia) variants infectious to humans.
Collapse
|
5
|
Heeren S, Maes I, Sanders M, Lye LF, Arevalo J, Llanos-Cuentas A, Garcia L, Lemey P, Beverley SM, Cotton JA, Dujardin JC, den Broeck FV. Parasite hybridization promotes spreading of endosymbiotic viruses. bioRxiv 2023:2023.03.24.534103. [PMID: 36993291 PMCID: PMC10055345 DOI: 10.1101/2023.03.24.534103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Viruses are the most abundant biological entities on Earth and play a significant role in the evolution of many organisms and ecosystems. In pathogenic protozoa, the presence of endosymbiotic viruses has been linked to an increased risk of treatment failure and severe clinical outcome. Here, we studied the molecular epidemiology of the zoonotic disease cutaneous leishmaniasis in Peru and Bolivia through a joint evolutionary analysis of Leishmania braziliensis parasites and their endosymbiotic Leishmania RNA virus. We show that parasite populations circulate in isolated pockets of suitable habitat and are associated with single viral lineages that appear in low prevalence. In contrast, groups of hybrid parasites were geographically and ecologically dispersed, and commonly infected from a pool of genetically diverse viruses. Our results suggest that parasite hybridization, likely due to increased human migration and ecological perturbations, increased the frequency of endosymbiotic interactions known to play a key role in disease severity.
Collapse
Affiliation(s)
- Senne Heeren
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Ilse Maes
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Mandy Sanders
- Parasite Genomics Group, Welcome Sanger Institute, Hinxton, United Kingdom
| | - Lon-Fye Lye
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, United States
| | - Jorge Arevalo
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Alejandro Llanos-Cuentas
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Lineth Garcia
- Instituto de Investigación Biomédicas e Investigación Social, Universidad Mayor de San Simon, Cochabamba, Bolivia
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Stephen M Beverley
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, United States
| | - James A Cotton
- Parasite Genomics Group, Welcome Sanger Institute, Hinxton, United Kingdom
| | - Jean-Claude Dujardin
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Frederik Van den Broeck
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
| |
Collapse
|
6
|
Hadermann A, Heeren S, Maes I, Dujardin JC, Domagalska MA, Van den Broeck F. Genome diversity of Leishmania aethiopica. Front Cell Infect Microbiol 2023; 13:1147998. [PMID: 37153154 PMCID: PMC10157169 DOI: 10.3389/fcimb.2023.1147998] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 03/27/2023] [Indexed: 05/09/2023] Open
Abstract
Leishmania aethiopica is a zoonotic Old World parasite transmitted by Phlebotomine sand flies and causing cutaneous leishmaniasis in Ethiopia and Kenya. Despite a range of clinical manifestations and a high prevalence of treatment failure, L. aethiopica is one of the most neglected species of the Leishmania genus in terms of scientific attention. Here, we explored the genome diversity of L. aethiopica by analyzing the genomes of twenty isolates from Ethiopia. Phylogenomic analyses identified two strains as interspecific hybrids involving L. aethiopica as one parent and L. donovani and L. tropica respectively as the other parent. High levels of genome-wide heterozygosity suggest that these two hybrids are equivalent to F1 progeny that propagated mitotically since the initial hybridization event. Analyses of allelic read depths further revealed that the L. aethiopica - L. tropica hybrid was diploid and the L. aethiopica - L. donovani hybrid was triploid, as has been described for other interspecific Leishmania hybrids. When focusing on L. aethiopica, we show that this species is genetically highly diverse and consists of both asexually evolving strains and groups of recombining parasites. A remarkable observation is that some L. aethiopica strains showed an extensive loss of heterozygosity across large regions of the nuclear genome, which likely arose from gene conversion/mitotic recombination. Hence, our prospection of L. aethiopica genomics revealed new insights into the genomic consequences of both meiotic and mitotic recombination in Leishmania.
Collapse
Affiliation(s)
- Amber Hadermann
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Senne Heeren
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Ilse Maes
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Jean-Claude Dujardin
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Malgorzata Anna Domagalska
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- *Correspondence: Frederik Van den Broeck, ; Malgorzata Anna Domagalska,
| | - Frederik Van den Broeck
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
- *Correspondence: Frederik Van den Broeck, ; Malgorzata Anna Domagalska,
| |
Collapse
|
7
|
Jara M, Barrett M, Maes I, Regnault C, Imamura H, Domagalska MA, Dujardin JC. Transcriptional Shift and Metabolic Adaptations during Leishmania Quiescence Using Stationary Phase and Drug Pressure as Models. Microorganisms 2022; 10:97. [PMID: 35056546 PMCID: PMC8781126 DOI: 10.3390/microorganisms10010097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 12/28/2021] [Accepted: 12/30/2021] [Indexed: 11/16/2022] Open
Abstract
Microorganisms can adopt a quiescent physiological condition which acts as a survival strategy under unfavorable conditions. Quiescent cells are characterized by slow or non-proliferation and a deep downregulation of processes related to biosynthesis. Although quiescence has been described mostly in bacteria, this survival skill is widespread, including in eukaryotic microorganisms. In Leishmania, a digenetic parasitic protozoan that causes a major infectious disease, quiescence has been demonstrated, but the molecular and metabolic features enabling its maintenance are unknown. Here, we quantified the transcriptome and metabolome of Leishmania promastigotes and amastigotes where quiescence was induced in vitro either, through drug pressure or by stationary phase. Quiescent cells have a global and coordinated reduction in overall transcription, with levels dropping to as low as 0.4% of those in proliferating cells. However, a subset of transcripts did not follow this trend and were relatively upregulated in quiescent populations, including those encoding membrane components, such as amastins and GP63, or processes like autophagy. The metabolome followed a similar trend of overall downregulation albeit to a lesser magnitude than the transcriptome. It is noteworthy that among the commonly upregulated metabolites were those involved in carbon sources as an alternative to glucose. This first integrated two omics layers afford novel insight into cell regulation and show commonly modulated features across stimuli and stages.
Collapse
Affiliation(s)
- Marlene Jara
- Molecular Parasitology Unit, Institute of Tropical Medicine Antwerp, 2000 Antwerp, Belgium; (I.M.); (M.A.D.)
| | - Michael Barrett
- Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK; (M.B.); (C.R.)
- Glasgow Polyomics, Wolfson Wohl Cancer Research Centre, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Ilse Maes
- Molecular Parasitology Unit, Institute of Tropical Medicine Antwerp, 2000 Antwerp, Belgium; (I.M.); (M.A.D.)
| | - Clement Regnault
- Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK; (M.B.); (C.R.)
- Glasgow Polyomics, Wolfson Wohl Cancer Research Centre, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Hideo Imamura
- Centre for Medical Genetics, Universitair Ziekenhuis Brussel, 1090 Brussels, Belgium;
| | - Malgorzata Anna Domagalska
- Molecular Parasitology Unit, Institute of Tropical Medicine Antwerp, 2000 Antwerp, Belgium; (I.M.); (M.A.D.)
| | - Jean-Claude Dujardin
- Molecular Parasitology Unit, Institute of Tropical Medicine Antwerp, 2000 Antwerp, Belgium; (I.M.); (M.A.D.)
- Department of Biomedical Sciences, University of Antwerp, 2000 Antwerp, Belgium
| |
Collapse
|
8
|
Negreira GH, Monsieurs P, Imamura H, Maes I, Kuk N, Yagoubat A, Van den Broeck F, Sterkers Y, Dujardin JC, Domagalska MA. High throughput single-cell genome sequencing gives insights into the generation and evolution of mosaic aneuploidy in Leishmania donovani. Nucleic Acids Res 2021; 50:293-305. [PMID: 34893872 PMCID: PMC8886908 DOI: 10.1093/nar/gkab1203] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 11/17/2021] [Accepted: 11/23/2021] [Indexed: 11/14/2022] Open
Abstract
Leishmania, a unicellular eukaryotic parasite, is a unique model
for aneuploidy and cellular heterogeneity, along with their potential role in
adaptation to environmental stresses. Somy variation within clonal populations
was previously explored in a small subset of chromosomes using fluorescence
hybridization methods. This phenomenon, termed mosaic aneuploidy (MA), might
have important evolutionary and functional implications but remains
under-explored due to technological limitations. Here, we applied and validated
a high throughput single-cell genome sequencing method to study for the first
time the extent and dynamics of whole karyotype heterogeneity in two clonal
populations of Leishmania promastigotes representing different
stages of MA evolution in vitro. We found that drastic changes
in karyotypes quickly emerge in a population stemming from an almost euploid
founder cell. This possibly involves polyploidization/hybridization at an early
stage of population expansion, followed by assorted ploidy reduction. During
further stages of expansion, MA increases by moderate and gradual karyotypic
alterations, affecting a defined subset of chromosomes. Our data provide the
first complete characterization of MA in Leishmania and pave
the way for further functional studies.
Collapse
Affiliation(s)
- Gabriel H Negreira
- Molecular Parasitology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Pieter Monsieurs
- Molecular Parasitology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Hideo Imamura
- Molecular Parasitology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Ilse Maes
- Molecular Parasitology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Nada Kuk
- MiVEGEC, University of Montpellier, CNRS, IRD, Montpellier, France
| | - Akila Yagoubat
- MiVEGEC, University of Montpellier, CNRS, IRD, Montpellier, France
| | - Frederik Van den Broeck
- Molecular Parasitology Unit, Institute of Tropical Medicine, Antwerp, Belgium.,Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Yvon Sterkers
- MiVEGEC, University of Montpellier, CNRS, IRD, Montpellier, France
| | - Jean-Claude Dujardin
- Molecular Parasitology Unit, Institute of Tropical Medicine, Antwerp, Belgium.,Department of Biomedical Sciences, University of Antwerp, Belgium
| | | |
Collapse
|
9
|
Imamura H, Monsieurs P, Jara M, Sanders M, Maes I, Vanaerschot M, Berriman M, Cotton JA, Dujardin JC, Domagalska MA. Evaluation of whole genome amplification and bioinformatic methods for the characterization of Leishmania genomes at a single cell level. Sci Rep 2020; 10:15043. [PMID: 32929126 PMCID: PMC7490275 DOI: 10.1038/s41598-020-71882-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 08/19/2020] [Indexed: 02/07/2023] Open
Abstract
Here, we report a pilot study paving the way for further single cell genomics studies in Leishmania. First, the performances of two commercially available kits for Whole Genome Amplification (WGA), PicoPLEX and RepliG were compared on small amounts of Leishmania donovani DNA, testing their ability to preserve specific genetic variations, including aneuploidy levels and SNPs. We show here that the choice of WGA method should be determined by the planned downstream genetic analysis, PicoPLEX and RepliG performing better for aneuploidy and SNP calling, respectively. This comparison allowed us to evaluate and optimize corresponding bio-informatic methods. As PicoPLEX was shown to be the preferred method for studying single cell aneuploidy, this method was applied in a second step, on single cells of L. braziliensis, which were sorted by fluorescence activated cell sorting (FACS). Even sequencing depth was achieved in 28 single cells, allowing accurate somy estimation. A dominant karyotype with three aneuploid chromosomes was observed in 25 cells, while two different minor karyotypes were observed in the other cells. Our method thus allowed the detection of aneuploidy mosaicism, and provides a solid basis which can be further refined to concur with higher-throughput single cell genomic methods.
Collapse
Affiliation(s)
- Hideo Imamura
- Institute of Tropical Medicine Antwerp, Molecular Parasitology Unit, Antwerp, Belgium
| | - Pieter Monsieurs
- Institute of Tropical Medicine Antwerp, Molecular Parasitology Unit, Antwerp, Belgium
| | - Marlene Jara
- Institute of Tropical Medicine Antwerp, Molecular Parasitology Unit, Antwerp, Belgium
| | | | - Ilse Maes
- Institute of Tropical Medicine Antwerp, Molecular Parasitology Unit, Antwerp, Belgium
| | - Manu Vanaerschot
- Institute of Tropical Medicine Antwerp, Molecular Parasitology Unit, Antwerp, Belgium
| | | | | | - Jean-Claude Dujardin
- Institute of Tropical Medicine Antwerp, Molecular Parasitology Unit, Antwerp, Belgium.
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium.
| | | |
Collapse
|
10
|
Domagalska MA, Imamura H, Sanders M, Van den Broeck F, Bhattarai NR, Vanaerschot M, Maes I, D’Haenens E, Rai K, Rijal S, Berriman M, Cotton JA, Dujardin JC. Genomes of Leishmania parasites directly sequenced from patients with visceral leishmaniasis in the Indian subcontinent. PLoS Negl Trop Dis 2019; 13:e0007900. [PMID: 31830038 PMCID: PMC6932831 DOI: 10.1371/journal.pntd.0007900] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 12/26/2019] [Accepted: 11/01/2019] [Indexed: 12/02/2022] Open
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 Visceral leishmaniasis (VL) is caused by parasitic protozoa of the Leishmania donovani complex and is lethal in the absence of treatment. Whole Genome Sequencing (WGS) of L. donovani clinical isolates revealed hitherto cryptic population structure in the Indian Sub-Continent and provided insights into the epidemiology and potential mechanisms of drug resistance. However, several biases are likely introduced during the culture step. We report here the development of a method that allows determination of parasite genomes directly in clinical samples, and validate it on bone marrow and splenic aspirates of VL patients in Nepal. Our study sheds a new light on the biology of Leishmania in the human host: we found that intracellular parasites of the patients had very low levels of aneuploidy, in sharp contrast to the situation in cultivated isolates. Moreover, the observed differences in genomes between intracellular amastigotes of the patient and the derived cultured parasites suggests polyclonality of infections, with different clones dominating in clinical samples and in culture, likely due to fitness differences. We believe this method is most suitable for clinical studies and for molecular tracking in the context of elimination programs.
Collapse
Affiliation(s)
- Malgorzata A. Domagalska
- Institute of Tropical Medicine Antwerp, Molecular Parasitology Unit, Antwerp, Belgium
- * E-mail: (MAD); (JAC); (JC-D)
| | - Hideo Imamura
- Institute of Tropical Medicine Antwerp, Molecular Parasitology Unit, Antwerp, Belgium
| | | | | | | | - Manu Vanaerschot
- Institute of Tropical Medicine Antwerp, Molecular Parasitology Unit, Antwerp, Belgium
| | - Ilse Maes
- Institute of Tropical Medicine Antwerp, Molecular Parasitology Unit, Antwerp, Belgium
| | - Erika D’Haenens
- Institute of Tropical Medicine Antwerp, Molecular Parasitology Unit, Antwerp, Belgium
| | - Keshav Rai
- BP Koirala Institute of Health Sciences, Dharan, Nepal
| | - Suman Rijal
- BP Koirala Institute of Health Sciences, Dharan, Nepal
| | | | - James A. Cotton
- Wellcome Sanger Institute, Hinxton, United Kingdom
- * E-mail: (MAD); (JAC); (JC-D)
| | - Jean-Claude Dujardin
- Institute of Tropical Medicine Antwerp, Molecular Parasitology Unit, Antwerp, Belgium
- University of Antwerp, Department of Biomedical Sciences, Antwerp, Belgium
- * E-mail: (MAD); (JAC); (JC-D)
| |
Collapse
|
11
|
Cuypers B, Berg M, Imamura H, Dumetz F, De Muylder G, Domagalska MA, Rijal S, Bhattarai NR, Maes I, Sanders M, Cotton JA, Meysman P, Laukens K, Dujardin JC. Integrated genomic and metabolomic profiling of ISC1, an emerging Leishmania donovani population in the Indian subcontinent. Infect Genet Evol 2018; 62:170-178. [PMID: 29679745 PMCID: PMC6261844 DOI: 10.1016/j.meegid.2018.04.021] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 04/14/2018] [Accepted: 04/17/2018] [Indexed: 01/06/2023]
Abstract
Leishmania donovani is the responsible agent for visceral leishmaniasis (VL) in the Indian subcontinent (ISC). The disease is lethal without treatment and causes 0.2 to 0.4 million cases each year. Recently, reports of VL in Nepalese hilly districts have increased as well as VL cases caused by L. donovani from the ISC1 genetic group, a new and emerging genotype. In this study, we perform for the first time an integrated, untargeted genomics and metabolomics approach to characterize ISC1, in comparison with the Core Group (CG), main population that drove the most recent outbreak of VL in the ISC. We show that the ISC1 population is very different from the CG, both at genome and metabolome levels. The genomic differences include SNPs, CNV and small indels in genes coding for known virulence factors, immunogens and surface proteins. Both genomic and metabolic approaches highlighted dissimilarities related to membrane lipids, the nucleotide salvage pathway and the urea cycle in ISC1 versus CG. Many of these pathways and molecules are important for the interaction with the host/extracellular environment. Altogether, our data predict major functional differences in ISC1 versus CG parasites, including virulence. Therefore, particular attention is required to monitor the fate of this emerging ISC1 population in the ISC, especially in a post-VL elimination context.
Collapse
Affiliation(s)
- Bart Cuypers
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium; Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium
| | - Maya Berg
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Hideo Imamura
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Franck Dumetz
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Géraldine De Muylder
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | | | - Suman Rijal
- BP Koirala Institute of Health Sciences, Dharan, Nepal
| | | | - Ilse Maes
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Mandy Sanders
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - James A Cotton
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Pieter Meysman
- Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium
| | - Kris Laukens
- Department of Mathematics and Computer Science, University of Antwerp, Antwerp, Belgium
| | - Jean-Claude Dujardin
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium; Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium.
| |
Collapse
|
12
|
Maes I, Van Braeckel D, Michielsen K. Knowledge, attitudes and practices of East Flemish general practitioners towards subscribing LARCs for adolescents. Facts Views Vis Obgyn 2018; 10:39-44. [PMID: 30510666 PMCID: PMC6260670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
OBJECTIVE While long acting reversible contraceptives (LARCs) offer a more reliable protection against unintended pregnancies than short acting reversible methods (SARCs), their uptake among adolescents in Flanders (Belgium) is low. This study assesses to what degree general practitioners constitute a barrier for the uptake of LARCs by adolescents. METHODS We did an online survey among 79 general practitioners in East Flanders to assess their knowledge, attitudes and behaviours related to advising and prescribing LARCs to adolescents. RESULTS Almost one third (31,6%) of respondents does not discuss LARCs with adolescents and a vast majority (87.3%) indicates to only recommend SARCs. Uncertainty of their own technical skills is among the main barriers, next to the perceived need to transfer the patient to a gynaecologist. Half of the respondents indicate that their practice is equipped to place implants and hormonal IUDs, one in four to place copper IUDs. Furthermore, responses indicate that prejudices and traditions play a role in the reluctance of general practitioners to recommend LARCs to adolescents. DISCUSSION These results indicate that adolescents are not always offered the necessary information to make an informed choice between a full range of modern contraceptives. Another worrying finding is that most of the main reasons for hesitating to recommend LARCs to adolescents are provider-related barriers rather than reasons related to the well-being of the patients. CONCLUSION Based on the data, we can say that (lack of) knowledge, skills and equipment of general practitioners constitute a barrier to uptake of LARCs by adolescents.
Collapse
|
13
|
Jara M, Berg M, Caljon G, de Muylder G, Cuypers B, Castillo D, Maes I, Orozco MDC, Vanaerschot M, Dujardin JC, Arevalo J. Macromolecular biosynthetic parameters and metabolic profile in different life stages of Leishmania braziliensis: Amastigotes as a functionally less active stage. PLoS One 2017; 12:e0180532. [PMID: 28742826 PMCID: PMC5526552 DOI: 10.1371/journal.pone.0180532] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Accepted: 05/26/2017] [Indexed: 12/04/2022] Open
Abstract
It was recently hypothesized that Leishmania amastigotes could constitute a semi-quiescent stage characterized by low replication and reduced metabolic activity. This concept developed with Leishmania (Leishmania) mexicana and Leishmania (Leishmania) major models might explain numerous clinical and sub-clinical features of Leishmania (Viannia) braziliensis infections, like reactivation of the disease, non-response to chemotherapy or asymptomatic infections. We compared here in vitro the proliferative capability of L. (V.) braziliensis amastigotes and promastigotes, assessed the expression of key molecular parameters and performed metabolomic analysis. We found that contrary to the highly proliferative promastigotes, amastigotes (axenic and intracellular) do not show evidence of extensive proliferation. In parallel, amastigotes showed a significant decrease of (i) the kDNA mini-circle abundance, (ii) the intracellular ATP level, (iii) the ribosomal components: rRNA subunits 18S and 28S α and ribosomal proteins RPS15 and RPL19, (iv) total RNA and protein levels. An untargeted metabolomic study identified clear differences between the different life stages: in comparison to logarithmic promastigotes, axenic amastigotes showed (a) a strong decrease of 14 essential and non-essential amino acids and eight metabolites involved in polyamine synthesis, (b) extensive changes in the phospholipids composition and (c) increased levels of several endogenous and exogenous sterols. Altogether, our results show that L. (V.) braziliensis amastigotes can show a phenotype with negligible rate of proliferation, a lower capacity of biosynthesis, a reduced bio-energetic level and a strongly altered metabolism. Our results pave the way for further exploration of quiescence among amastigotes of this species.
Collapse
Affiliation(s)
- Marlene Jara
- Instituto de Medicina Tropical “Alexander von Humboldt”, Universidad Peruana Cayetano Heredia, Lima, Perú
- Institute of Tropical Medicine Antwerp, Molecular Parasitology Unit, Antwerp, Belgium
| | - Maya Berg
- Institute of Tropical Medicine Antwerp, Molecular Parasitology Unit, Antwerp, Belgium
| | - Guy Caljon
- Institute of Tropical Medicine Antwerp, Molecular Parasitology Unit, Antwerp, Belgium
| | - Geraldine de Muylder
- Institute of Tropical Medicine Antwerp, Molecular Parasitology Unit, Antwerp, Belgium
| | - Bart Cuypers
- Institute of Tropical Medicine Antwerp, Molecular Parasitology Unit, Antwerp, Belgium
- University of Antwerp, Antwerp, Belgium
| | - Denis Castillo
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Ilse Maes
- Institute of Tropical Medicine Antwerp, Molecular Parasitology Unit, Antwerp, Belgium
| | - María del Carmen Orozco
- Instituto de Medicina Tropical “Alexander von Humboldt”, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Manu Vanaerschot
- Institute of Tropical Medicine Antwerp, Molecular Parasitology Unit, Antwerp, Belgium
| | - Jean-Claude Dujardin
- Institute of Tropical Medicine Antwerp, Molecular Parasitology Unit, Antwerp, Belgium
- University of Antwerp, Antwerp, Belgium
| | - Jorge Arevalo
- Instituto de Medicina Tropical “Alexander von Humboldt”, Universidad Peruana Cayetano Heredia, Lima, Perú
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| |
Collapse
|
14
|
Fraga J, Fernández-Calienes A, Montalvo AM, Maes I, Deborggraeve S, Büscher P, Dujardin JC, Van der Auwera G. Phylogenetic analysis of the Trypanosoma genus based on the heat-shock protein 70 gene. Infect Genet Evol 2016; 43:165-72. [PMID: 27180897 DOI: 10.1016/j.meegid.2016.05.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 05/10/2016] [Accepted: 05/11/2016] [Indexed: 11/20/2022]
Abstract
Trypanosome evolution was so far essentially studied on the basis of phylogenetic analyses of small subunit ribosomal RNA (SSU-rRNA) and glycosomal glyceraldehyde-3-phosphate dehydrogenase (gGAPDH) genes. We used for the first time the 70kDa heat-shock protein gene (hsp70) to investigate the phylogenetic relationships among 11 Trypanosoma species on the basis of 1380 nucleotides from 76 sequences corresponding to 65 strains. We also constructed a phylogeny based on combined datasets of SSU-rDNA, gGAPDH and hsp70 sequences. The obtained clusters can be correlated with the sections and subgenus classifications of mammal-infecting trypanosomes except for Trypanosoma theileri and Trypanosoma rangeli. Our analysis supports the classification of Trypanosoma species into clades rather than in sections and subgenera, some of which being polyphyletic. Nine clades were recognized: Trypanosoma carassi, Trypanosoma congolense, Trypanosoma cruzi, Trypanosoma grayi, Trypanosoma lewisi, T. rangeli, T. theileri, Trypanosoma vivax and Trypanozoon. These results are consistent with existing knowledge of the genus' phylogeny. Within the T. cruzi clade, three groups of T. cruzi discrete typing units could be clearly distinguished, corresponding to TcI, TcIII, and TcII+V+VI, while support for TcIV was lacking. Phylogenetic analyses based on hsp70 demonstrated that this molecular marker can be applied for discriminating most of the Trypanosoma species and clades.
Collapse
Affiliation(s)
- Jorge Fraga
- Parasitology Department, Institute of Tropical Medicine Pedro Kouri, La Havana, Cuba
| | | | | | - Ilse Maes
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Stijn Deborggraeve
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Philippe Büscher
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Jean-Claude Dujardin
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium; Department of Biomedical Sciences, Antwerp University, Antwerp, Belgium
| | - Gert Van der Auwera
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.
| |
Collapse
|
15
|
Imamura H, Downing T, Van den Broeck F, Sanders MJ, Rijal S, Sundar S, Mannaert A, Vanaerschot M, Berg M, De Muylder G, Dumetz F, Cuypers B, Maes I, Domagalska M, Decuypere S, Rai K, Uranw S, Bhattarai NR, Khanal B, Prajapati VK, Sharma S, Stark O, Schönian G, De Koning HP, Settimo L, Vanhollebeke B, Roy S, Ostyn B, Boelaert M, Maes L, Berriman M, Dujardin JC, Cotton JA. Evolutionary genomics of epidemic visceral leishmaniasis in the Indian subcontinent. eLife 2016; 5. [PMID: 27003289 PMCID: PMC4811772 DOI: 10.7554/elife.12613] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 02/15/2016] [Indexed: 12/25/2022] Open
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. DOI:http://dx.doi.org/10.7554/eLife.12613.001 The parasite Leishmania donovani causes a disease called visceral leishmaniasis that affects many of the world's poorest people. Around half a million new cases develop every year, but health authorities lack safe and effective drugs to treat them. Up to 80% of these cases occur in the Indian subcontinent, where devastating epidemics have occurred in the last decades. One reason these epidemics continue to occur is that the parasites develop genetic mutations allowing them to adapt to and resist the drugs used to kill them. As there are few existing drugs that can kill L. donovani, it is crucial to understand how drug resistance emerges and spreads among parasite populations. Imamura, Downing, Van den Broeck et al. have now investigated the history of visceral leishmaniasis epidemics by characterising the complete genetic sequence – or genome – of 204 L. donovani parasite samples. This revealed that the majority of parasites in the Indian subcontinent first appeared in the nineteenth century, matching the first historical records of visceral leishmaniasis epidemics. The genomes show that most of the parasites are genetically similar and can be clustered into several closely related groups. These groups first appeared in the 1960s following the end of a regional campaign to eradicate malaria. The most common parasite group is particularly resistant to drugs called antimonials, which were the main treatment for leishmaniasis until recently. These parasites have a small genetic change that scrambles most of a protein known to be involved in the uptake of antimonials. Parasites may also be able to develop resistance to drugs through additional mechanisms that allow them to produce many copies of the same gene. These mechanisms could allow the parasites to rapidly adapt to new drugs or changes in the populations it infects. The work of Imamura et al. looks only at parasites isolated from patients then grown in the laboratory, so further research is now needed to explore how variable the Leishmania genome is in both of the parasite’s hosts: humans and sandflies. Imamura et al.’s study reveals how L. donovani has spread throughout the Indian subcontinent in fine detail. The genome data can be used to create simple molecular tools that could form an "early warning system" to track the success of disease control programs and to determine how well the current drugs are working. DOI:http://dx.doi.org/10.7554/eLife.12613.002
Collapse
Affiliation(s)
- Hideo Imamura
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Tim Downing
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom.,School of Maths, Applied Maths and Statistics, National University of Ireland Galway, Galway, Ireland
| | | | | | - 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
| | | | - Saskia Decuypere
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.,Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - Keshav Rai
- 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
- 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
- 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
- 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
| | | | - 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
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| |
Collapse
|
16
|
Adaui V, Lye LF, Akopyants NS, Zimic M, Llanos-Cuentas A, Garcia L, Maes I, De Doncker S, Dobson DE, Arevalo J, Dujardin JC, Beverley SM. Association of the Endobiont Double-Stranded RNA Virus LRV1 With Treatment Failure for Human Leishmaniasis Caused by Leishmania braziliensis in Peru and Bolivia. J Infect Dis 2015; 213:112-21. [PMID: 26123565 DOI: 10.1093/infdis/jiv354] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 06/08/2015] [Indexed: 11/14/2022] Open
Abstract
Cutaneous and mucosal leishmaniasis, caused in South America by Leishmania braziliensis, is difficult to cure by chemotherapy (primarily pentavalent antimonials [Sb(V)]). Treatment failure does not correlate well with resistance in vitro, and the factors responsible for treatment failure in patients are not well understood. Many isolates of L. braziliensis (>25%) contain a double-stranded RNA virus named Leishmaniavirus 1 (LRV1), which has also been reported in Leishmania guyanensis, for which an association with increased pathology, metastasis, and parasite replication was found in murine models. Here we probed the relationship of LRV1 to drug treatment success and disease in 97 L. braziliensis-infected patients from Peru and Bolivia. In vitro cultures were established, parasites were typed as L. braziliensis, and the presence of LRV1 was determined by reverse transcription-polymerase chain reaction, followed by sequence analysis. LRV1 was associated significantly with an increased risk of treatment failure (odds ratio, 3.99; P = .04). There was no significant association with intrinsic Sb(V) resistance among parasites, suggesting that treatment failure arises from LRV1-mediated effects on host metabolism and/or parasite survival. The association of LRV1 with clinical drug treatment failure could serve to guide more-effective treatment of tegumentary disease caused by L. braziliensis.
Collapse
Affiliation(s)
- Vanessa Adaui
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia Unidad de Pathoantigenos
| | - Lon-Fye Lye
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri
| | - Natalia S Akopyants
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri
| | - Mirko Zimic
- Unidad de Bioinformática, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | | | - Lineth Garcia
- Laboratorio de Biología Molecular-IIBISMED, Facultad de Medicina, Universidad Mayor de San Simón, Cochabamba, Bolivia
| | - Ilse Maes
- Molecular Parasitology Unit, Institute of Tropical Medicine Antwerp
| | | | - Deborah E Dobson
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri
| | - Jorge Arevalo
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia Unidad de Pathoantigenos
| | - Jean-Claude Dujardin
- Molecular Parasitology Unit, Institute of Tropical Medicine Antwerp Department of Biomedical Sciences, University of Antwerp, Belgium
| | - Stephen M Beverley
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri
| |
Collapse
|
17
|
Fraga J, Fernandez-Calienes A, Montalvo AM, Maes I, Dujardin JC, Van der Auwera G. Differentiation betweenTrypanosoma cruziandTrypanosoma rangeliusing heat-shock protein 70 polymorphisms. Trop Med Int Health 2013; 19:195-206. [DOI: 10.1111/tmi.12222] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Jorge Fraga
- Parasitology Department; Institute of Tropical Medicine Pedro Kouri; La Havana Cuba
| | | | | | - Ilse Maes
- Department of Biomedical Sciences; Institute of Tropical Medicine; Antwerp Belgium
| | - Jean-Claude Dujardin
- Department of Biomedical Sciences; Institute of Tropical Medicine; Antwerp Belgium
- Department of Biomedical Sciences; University of Antwerp; Antwerp Belgium
| | - Gert Van der Auwera
- Department of Biomedical Sciences; Institute of Tropical Medicine; Antwerp Belgium
| |
Collapse
|
18
|
Berg M, Vanaerschot M, Jankevics A, Cuypers B, Maes I, Mukherjee S, Khanal B, Rijal S, Roy S, Opperdoes F, Breitling R, Dujardin JC. Metabolic adaptations of Leishmania donovani in relation to differentiation, drug resistance, and drug pressure. Mol Microbiol 2013; 90:428-42. [PMID: 24020363 DOI: 10.1111/mmi.12374] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/20/2013] [Indexed: 12/31/2022]
Abstract
Antimonial (sodium stibogluconate, SSG) resistance and differentiation have been shown to be closely linked in Leishmania donovani, with SSG-resistant strains showing an increased capacity to generate infectious (metacyclic) forms. This is the first untargeted LC-MS metabolomics study which integrated both phenomena in one experimental design and provided insights into metabolic differences between three clinical L. donovani strains with a similar genetic background but different SSG-susceptibilities. We performed this analysis at different stages during promastigote growth and in the absence or presence of drug pressure. When comparing SSG-resistant and SSG-sensitive strains, a number of metabolic changes appeared to be constitutively present in all growth stages, pointing towards a clear link with SSG-resistance, whereas most metabolic changes were only detected in the stationary stage. These changes reflect the close intertwinement between SSG-resistance and an increased metacyclogenesis in resistant parasites. The metabolic changes suggest that SSG-resistant parasites have (i) an increased capacity for protection against oxidative stress; (ii) a higher fluidity of the plasma membrane; and (iii) a metabolic survival kit to better endure infection. These changes were even more pronounced in a resistant strain kept under Sb(III) drug pressure.
Collapse
Affiliation(s)
- Maya Berg
- Unit of Molecular Parasitology, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Van der Auwera G, Maes I, De Doncker S, Ravel C, Cnops L, Van Esbroeck M, Van Gompel A, Clerinx J, Dujardin JC. Heat-shock protein 70 gene sequencing for Leishmania species typing in European tropical infectious disease clinics. ACTA ACUST UNITED AC 2013; 18:20543. [PMID: 23929181 DOI: 10.2807/1560-7917.es2013.18.30.20543] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We describe Leishmania species determination on clinical samples on the basis of partial sequencing of the heat-shock protein 70 gene (hsp70), without the need for parasite isolation. The method is especially suited for use in non-endemic infectious disease clinics dealing with relatively few cases on an annual basis, for which no fast high throughput diagnostic tests are needed. We show that the results obtained from this gene are in nearly perfect agreement with those from multilocus enzyme electrophoresis, which is still considered by many clinicians and the World Health Organization (WHO) as the gold standard in Leishmania species typing. Currently, 203 sequences are available that cover the entire hsp70 gene region analysed here, originating from a total of 41 leishmaniasis endemic countries, and representing 15 species and sub-species causing human disease. We also provide a detailed laboratory protocol that includes a step-by-step procedure of the typing methodology, to facilitate implementation in diagnostic laboratories.
Collapse
Affiliation(s)
- G Van der Auwera
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.
| | | | | | | | | | | | | | | | | |
Collapse
|
20
|
Odiwuor S, Muia A, Magiri C, Maes I, Kirigi G, Dujardin JC, Wasunna M, Mbuchi M, Auwera GVD. Identification of Leishmania tropica from micro-foci of cutaneous leishmaniasis in the Kenyan Rift Valley. Pathog Glob Health 2013; 106:159-65. [PMID: 23265373 DOI: 10.1179/2047773212y.0000000015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
We performed diagnosis and species identification of parasites in lesion samples from suspected cutaneous leishmaniasis patients in four villages, three of which are in a known Leishmania tropica endemic region in Kenya. Samples were analyzed both by microscopy and PCR for Leishmania, and typed by an assay using four ribosomal DNA-based species-identification PCRs. The lesions were demonstrated to be caused by L. tropica, which confirms the re-emergence of cutaneous leishmaniasis from this species after a period of reduced incidence in the endemic zone. Our report highlights the importance of an intervention and sustained Leishmania control program.
Collapse
Affiliation(s)
- Samwel Odiwuor
- Centre for Clinical Research, Kenya Medical Research Institute, Nairobi, Kenya
| | | | | | | | | | | | | | | | | |
Collapse
|
21
|
Odiwuor S, De Doncker S, Maes I, Dujardin JC, Van der Auwera G. Natural Leishmania donovani/Leishmania aethiopica hybrids identified from Ethiopia. Infection, Genetics and Evolution 2011; 11:2113-8. [DOI: 10.1016/j.meegid.2011.04.026] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Revised: 04/11/2011] [Accepted: 04/12/2011] [Indexed: 11/26/2022]
|
22
|
Downing T, Stark O, Vanaerschot M, Imamura H, Sanders M, Decuypere S, de Doncker S, Maes I, Rijal S, Sundar S, Dujardin JC, Berriman M, Schönian G. Genome-wide SNP and microsatellite variation illuminate population-level epidemiology in the Leishmania donovani species complex. Infect Genet Evol 2011; 12:149-59. [PMID: 22119748 PMCID: PMC3315668 DOI: 10.1016/j.meegid.2011.11.005] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Revised: 10/28/2011] [Accepted: 11/10/2011] [Indexed: 11/23/2022]
Abstract
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.
Collapse
Affiliation(s)
- Tim Downing
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK.
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
23
|
Downing T, Imamura H, Decuypere S, Clark TG, Coombs GH, Cotton JA, Hilley JD, de Doncker S, Maes I, Mottram JC, Quail MA, Rijal S, Sanders M, Schönian G, Stark O, Sundar S, Vanaerschot M, Hertz-Fowler C, Dujardin JC, Berriman M. Whole genome sequencing of multiple Leishmania donovani clinical isolates provides insights into population structure and mechanisms of drug resistance. Genome Res 2011; 21:2143-56. [PMID: 22038251 DOI: 10.1101/gr.123430.111] [Citation(s) in RCA: 311] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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.
Collapse
Affiliation(s)
- Tim Downing
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, United Kingdom
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Adaui V, Maes I, Huyse T, Van den Broeck F, Talledo M, Kuhls K, De Doncker S, Maes L, Llanos-Cuentas A, Schönian G, Arevalo J, Dujardin JC. Multilocus genotyping reveals a polyphyletic pattern among naturally antimony-resistant Leishmania braziliensis isolates from Peru. Infect Genet Evol 2011; 11:1873-80. [PMID: 21871584 DOI: 10.1016/j.meegid.2011.08.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2011] [Revised: 07/29/2011] [Accepted: 08/01/2011] [Indexed: 10/17/2022]
Abstract
In order to understand the epidemiological dynamics of antimonial (Sb(V)) resistance in zoonotic tegumentary leishmaniasis and its link with treatment outcome, we analyzed the population structure of 24 Peruvian Leishmania braziliensis clinical isolates with known in vitro antimony susceptibility and clinical phenotype by multilocus microsatellite typing (14 microsatellite loci). The genetic variability in the Peruvian isolates was high and the multilocus genotypes were strongly differentiated from each other. No correlation was found between the genotypes and in vitro drug susceptibility or clinical treatment outcome. The finding of a polyphyletic pattern among the Sb(V)-resistant L. braziliensis might be explained by (i) independent events of drug resistance emergence, (ii) sexual recombination and/or (iii) other phenomena mimicking recombination signals. Interestingly, the polyphyletic pattern observed here is very similar to the one we observed in the anthroponotic Leishmania donovani (Laurent et al., 2007), hereby questioning the role of transmission and/or chemotherapeutic drug pressure in the observed population structure.
Collapse
Affiliation(s)
- Vanessa Adaui
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
25
|
Odiwuor SOC, Saad AA, De Doncker S, Maes I, Laurent T, El Safi S, Mbuchi M, Büscher P, Dujardin JC, Van der Auwera G. Universal PCR assays for the differential detection of all Old World Leishmania species. Eur J Clin Microbiol Infect Dis 2010; 30:209-18. [PMID: 20936316 DOI: 10.1007/s10096-010-1071-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2010] [Accepted: 09/19/2010] [Indexed: 12/01/2022]
Abstract
For the epidemiological monitoring and clinical case management of leishmaniasis, determination of the causative Leishmania species gains importance. Current assays for the Old World often suffer from drawbacks in terms of validation on a geographically representative sample set and the ability to recognize all species complexes. We want to contribute to standardized species typing for Old World leishmaniasis. We determined the ribosomal DNA internal transcribed spacer 1 sequence of 24 strains or isolates, and validated four species-specific polymerase chain reactions (PCRs) amplifying this target. They discriminate L. aethiopica, L. tropica, L. major, and the L. donovani complex, use the same cycling conditions, and include an internal amplification control. Our PCRs amplify 0.1 pg of Leishmania DNA, while being 100% specific for species identification on an extensive panel of geographically representative strains and isolates. Similar results were obtained in an endemic reference laboratory in Kenya. Species could also be identified in clinical specimens. The presented PCRs require only agarose gel detection, and have several other advantages over many existing assays. We outline potential problems, suggest concrete solutions for transferring the technique to other settings, and deliver the proof-of-principle for analyzing clinical samples.
Collapse
Affiliation(s)
- S Ogado Ceasar Odiwuor
- Department of Parasitology, Institute of Tropical Medicine Antwerp, Nationalestraat 155, 2000, Antwerp, Belgium
| | | | | | | | | | | | | | | | | | | |
Collapse
|
26
|
Vanaerschot M, Maes I, Ouakad M, Adaui V, Maes L, De Doncker S, Rijal S, Chappuis F, Dujardin JC, Decuypere S. Linking in vitro and in vivo survival of clinical Leishmania donovani strains. PLoS One 2010; 5:e12211. [PMID: 20808916 PMCID: PMC2923181 DOI: 10.1371/journal.pone.0012211] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2010] [Accepted: 07/24/2010] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Leishmania donovani is an intracellular protozoan parasite that causes a lethal systemic disease, visceral leishmaniasis (VL), and is transmitted between mammalian hosts by phlebotomine sandflies. Leishmania expertly survives in these 'hostile' environments with a unique redox system protecting against oxidative damage, and host manipulation skills suppressing oxidative outbursts of the mammalian host. Treating patients imposes an additional stress on the parasite and sodium stibogluconate (SSG) was used for over 70 years in the Indian subcontinent. METHODOLOGY/PRINCIPAL FINDINGS We evaluated whether the survival capacity of clinical L. donovani isolates varies significantly at different stages of their life cycle by comparing proliferation, oxidative stress tolerance and infection capacity of 3 Nepalese L. donovani strains in several in vitro and in vivo models. In general, the two strains that were resistant to SSG, a stress encountered in patients, attained stationary phase at a higher parasite density, contained a higher amount of metacyclic parasites and had a greater capacity to cause in vivo infection in mice compared to the SSG-sensitive strain. CONCLUSIONS/SIGNIFICANCE The 2 SSG-resistant strains had superior survival skills as promastigotes and as amastigotes compared to the SSG-sensitive strain. These results could indicate that Leishmania parasites adapting successfully to antimonial drug pressure acquire an overall increased fitness, which stands in contrast to what is found for other organisms, where drug resistance is usually linked to a fitness cost. Further validation experiments are under way to verify this hypothesis.
Collapse
Affiliation(s)
- Manu Vanaerschot
- Unit of Molecular Parasitology, Department of Parasitology, Institute of Tropical Medicine, Antwerp, Belgium
- Laboratory for Microbiology, Parasitology and Hygiene, Department of Biomedical Sciences, Antwerp University, Antwerp, Belgium
| | - Ilse Maes
- Unit of Molecular Parasitology, Department of Parasitology, Institute of Tropical Medicine, Antwerp, Belgium
| | - Meriem Ouakad
- Unit of Molecular Parasitology, Department of Parasitology, Institute of Tropical Medicine, Antwerp, Belgium
| | - Vanessa Adaui
- Unit of Molecular Parasitology, Department of Parasitology, Institute of Tropical Medicine, Antwerp, Belgium
- Institute of Tropical Medicine ‘Alexander von Humboldt’, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Louis Maes
- Laboratory for Microbiology, Parasitology and Hygiene, Department of Biomedical Sciences, Antwerp University, Antwerp, Belgium
| | - Simonne De Doncker
- Unit of Molecular Parasitology, Department of Parasitology, Institute of Tropical Medicine, Antwerp, Belgium
| | - Suman Rijal
- Department of Internal Medicine, B.P. Koirala Institute of Health Sciences, Dharan, Nepal
| | - François Chappuis
- Division of International and Humanitarian Medicine, Geneva University Hospitals and University of Geneva, Geneva, Switzerland
| | - Jean-Claude Dujardin
- Unit of Molecular Parasitology, Department of Parasitology, Institute of Tropical Medicine, Antwerp, Belgium
- Laboratory for Microbiology, Parasitology and Hygiene, Department of Biomedical Sciences, Antwerp University, Antwerp, Belgium
- * E-mail:
| | - Saskia Decuypere
- Unit of Molecular Parasitology, Department of Parasitology, Institute of Tropical Medicine, Antwerp, Belgium
| |
Collapse
|
27
|
Abstract
INTRODUCTION Smoking is an independent risk factor for periodontal disease and tooth loss. STATE OF THE ART Smoking impairs inflammatory and immune responses to periodontal pathogens, and exerts both systemic and local effects. Periodontal disease is increased both in prevalence and severity in smokers. Smoking is a predisposing factor to acute necrotizing ulcerative gingivitis and is associated with an increased rate of periodontal disease in terms of pocket formation and attachment loss, as well as alveolar bone loss. Cigar, pipe, water-pipe and cannabis smoking have similar adverse effects on periodontal health as cigarette smoking. Passive smoking is also an independent periodontal disease risk factor. Smokeless tobacco is associated with localized periodontal disease. Smokers respond less favourably to both non-surgical and surgical treatments and have higher failure rates and complications following dental implantation. Smoking cessation may halt the disease progression and improve the outcome of periodontal treatment. CONCLUSION Smoking cessation counselling should be an integral part of periodontal therapy and prevention.
Collapse
Affiliation(s)
- M Underner
- Unité de Tabacologie, Service de Pneumologie, Pavillon René Beauchant, CHU la Milétrie, BP 577, 86021 Poitiers cedex.
| | | | | | | |
Collapse
|
28
|
Jordt F, Maes I. Effizienteres Prozess-Management mit innovativen Prozessanalysenmethoden und Automatisierungskonzepten. CHEM-ING-TECH 2005. [DOI: 10.1002/cite.200590328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
29
|
De Schrijver K, Maes I, Van Damme P, Tersago J, Moës E, Van Ranst M. An outbreak of nosocomial hepatitis B virus infection in a nursing home for the elderly in Antwerp (Belgium). Acta Clin Belg 2005; 60:63-9. [PMID: 16082990 DOI: 10.1179/acb.2005.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
After notification of a case of fulminant hepatitis B virus (HBV) infection in a 83-year-old female resident of a nursing home to the Flemish Health Inspectorate, a seroepidemiological study and a retrospective cohort study were conducted among the 94 residents and 47 nursing staff to assess the extent of HBV transmission and to identify risk factors. Susceptible residents were vaccinated against HBV and their serological response to hepatitis B vaccination determined. From December 2002 to April 2003, five residents with acute hepatitis B infection were identified with an attack rate of 5.5% and a case fatality rate of 40%. Three other residents were identified as HBV surface antigen and e-antigen positive carrier. None of the nursing staff tested positive for acute HBV infection or HBV carriage. Diabetic patients who were exposed to a shared finger-stick device for blood sampling were 10.7 times more likely to contract an acute HBV infection (RR 10.7; 95% CI 1.3-91.3). Other potential risk factors were undergoing podiatric care and being exposed to the shared razor blade of the hairdresser. The transmission of the infection could be controlled by restricting the use of finger-stick capillary sampling devices to individual patients, assigning separate glucometers to individual patients and, implementation of standard infection-control recommendations like wearing gloves and performing hand hygiene by the nursing staff, assigning separate podiatric sets to individual patients. HBV vaccination of the residents with three doses of HBV vaccine has not induced a sufficient degree of protection. The outbreak stresses the need for appropriate and generally applied standard procedures in nursing homes to prevent bloodborne pathogens.
Collapse
Affiliation(s)
- K De Schrijver
- Flemish Community Health Inspectorate, Antwerp, Belgium.
| | | | | | | | | | | |
Collapse
|
30
|
Abstract
In Antwerp, Belgium, 403 cases of diarrhoeic shellfish poisoning were reported after consumption of blue mussels. Symptoms included diarrhoea, vomiting, abdominal pain, and nausea. The analysis of faecal specimens from patients allowed diagnosis exclusions for bacteria and viruses. Mouse-assays revealed the presence of biotoxins specific of dinoflagellates, which were identified and quantified by LC-MS. The mussels were imported from Denmark, and were part of a batch presenting high concentrations of okadaic acid above the regulatory limits.
Collapse
Affiliation(s)
- K De Schrijver
- Gezondheidsinspectie Copernicuslaan 1 Antwerpen, Belgium
| | | | | | | |
Collapse
|