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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] [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.
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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.
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2
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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 : THE PREPRINT SERVER FOR BIOLOGY 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] [Abstract] [Grants] [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.
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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
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3
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Hoyos J, Rosales-Chilama M, León C, González C, Gómez MA. Sequencing of hsp70 for discernment of species from the Leishmania (Viannia) guyanensis complex from endemic areas in Colombia. Parasit Vectors 2022; 15:406. [PMID: 36329517 PMCID: PMC9635106 DOI: 10.1186/s13071-022-05438-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 08/11/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Colombia is ranked very high among countries with the highest numbers of endemic Leishmania species (n = 9) causing human disease. Although much effort has been devoted to generating simple and specific tools for Leishmania species identification, challenges remain in the discrimination of species belonging to the Leishmania (Viannia) guyanensis complex: L. (V.) guyanensis and L. (V.) panamensis. METHODS A set of seven reference strains of species belonging to the L. (Leishmania) and L. (Viannia) subgenera, clinical strains from human cases of cutaneous leishmaniasis (CL; n = 26) and samples collected from sylvatic mammals and sand flies (n = 7) from endemic areas in Colombia were analyzed in this study. The heat-shock protein 70 gene (hsp70) was amplified by PCR from DNA extracted from logarithmic-phase promastigotes or tissue samples, and the PCR products were sequenced. Sequence alignment was performed against a set of previously published and curated sequences, and phylogenetic analysis based on the maximum-likelihood and Bayesian inference approaches was conducted. Haplotype diversity among strains and species of the L. (V.) guyanensis complex was explored using a median-joining network. RESULTS Sequencing of the hsp70 gene for L. (Viannia) spp. typing was comparable to species identification using isoenzyme electrophoresis or monoclonal antibodies. Complete species matching was found, except for one sylvatic sample with an identity yet unsolved. Among the L. (V.) panamensis clinical strains, two distinctive phylogenetic clusters were found to correlate with two different zymodemes: L. (V.) panamensis Z2.2 and Z2.3. Analysis of samples from sylvatic environments identified novel records of naturally infected wild mammal and sand fly species. CONCLUSIONS Our results support the adequacy of hsp70 gene sequencing as a single-locus approach for discrimination of L. (Viannia) spp., as well as for exploring the genetic diversity within the L. (V.) guyanensis complex.
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Affiliation(s)
- Juliana Hoyos
- Departamento de Ciencias Biológicas, Centro de Investigaciones en Microbiología Y Parasitología Tropical (CIMPAT), Universidad de los Andes, Bogota, D.C Colombia
- Centro Internacional de Entrenamiento E Investigaciones Médicas (CIDEIM), Campus de la Universidad Icesi (Edificio O), Cali, Colombia
- Present Address: Odum School of Ecology, University of Georgia, Athens, GA 30602 USA
| | - Mariana Rosales-Chilama
- Centro Internacional de Entrenamiento E Investigaciones Médicas (CIDEIM), Campus de la Universidad Icesi (Edificio O), Cali, Colombia
- Universidad Icesi, Cali, Colombia
| | - Cielo León
- Departamento de Ciencias Biológicas, Centro de Investigaciones en Microbiología Y Parasitología Tropical (CIMPAT), Universidad de los Andes, Bogota, D.C Colombia
| | - Camila González
- Departamento de Ciencias Biológicas, Centro de Investigaciones en Microbiología Y Parasitología Tropical (CIMPAT), Universidad de los Andes, Bogota, D.C Colombia
| | - María Adelaida Gómez
- Centro Internacional de Entrenamiento E Investigaciones Médicas (CIDEIM), Campus de la Universidad Icesi (Edificio O), Cali, Colombia
- Universidad Icesi, Cali, Colombia
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Llanes A, Cruz G, Morán M, Vega C, Pineda VJ, Ríos M, Penagos H, Suárez JA, Saldaña A, Lleonart R, Restrepo CM. Genomic diversity and genetic variation of Leishmania panamensis within its endemic range. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 103:105342. [PMID: 35878820 DOI: 10.1016/j.meegid.2022.105342] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 07/15/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
Species belonging to the Leishmania (Viannia) subgenus are important causative agents of cutaneous and mucocutaneous leishmaniasis in Central and South America. These parasites possess several distinctive biological features that are influenced by their genetics, population structure, and genome instability. To date, several studies have revealed varying degrees of genetic diversity within Leishmania species. Particularly, in species of the L. (Viannia) subgenus, a generalized high intraspecific genetic diversity has been reported, although, conflicting conclusions have been drawn using different molecular techniques. Despite being the most common Leishmania species circulating in Panama and Colombia, few studies have analyzed clinical samples of Leishmania panamensis using whole-genome sequencing, and their restricted number of samples has limited the information they can provide to understand the population structure of L. panamensis. Here, we used next generation sequencing (NGS) to explore the genetic diversity of L. panamensis within its endemic range, analyzing data from 43 isolates of Colombian and Panamanian origin. Our results show the occurrence of three well-defined geographically correlated groups, and suggests the possible occurrence of additional phylogeographic groups. Furthermore, these results support the existence of a mixed mode of reproduction in L. panamensis, with varying frequencies of events of genetic recombination occurring primarily within subpopulations of closely related strains. This study offers important insights into the population genetics and reproduction mode of L. panamensis, paving the way to better understand their population structure and the emergence and maintenance of key eco-epidemiological traits.
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Affiliation(s)
- Alejandro Llanes
- Centro de Biología Celular y Molecular de Enfermedades, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama City, Panama, Panama
| | - Génesis Cruz
- Escuela de Biología, Facultad de Ciencias Naturales, Exactas y Tecnología, Universidad de Panamá, Panama City, Panama, Panama
| | - Mitchelle Morán
- Centro de Biología Celular y Molecular de Enfermedades, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama City, Panama, Panama
| | - Carlos Vega
- Escuela de Biología, Facultad de Ciencias Naturales, Exactas y Tecnología, Universidad de Panamá, Panama City, Panama, Panama
| | - Vanessa J Pineda
- Instituto Conmemorativo Gorgas de Estudios de la Salud (ICGES), Panama City, Panama, Panama
| | - Margarita Ríos
- Instituto Conmemorativo Gorgas de Estudios de la Salud (ICGES), Panama City, Panama, Panama
| | - Homero Penagos
- Hospital Regional Dr. Rafael Hernández, Caja de Seguro Social, David, Chiriquí, Panama; Sistema Nacional de Investigación-Secretaría Nacional de Ciencia, Tecnología e Innovación (SNI-SENACYT), Panama City, Panama, Panama
| | - José A Suárez
- Instituto Conmemorativo Gorgas de Estudios de la Salud (ICGES), Panama City, Panama, Panama; Sistema Nacional de Investigación-Secretaría Nacional de Ciencia, Tecnología e Innovación (SNI-SENACYT), Panama City, Panama, Panama
| | - Azael Saldaña
- Instituto Conmemorativo Gorgas de Estudios de la Salud (ICGES), Panama City, Panama, Panama; Sistema Nacional de Investigación-Secretaría Nacional de Ciencia, Tecnología e Innovación (SNI-SENACYT), Panama City, Panama, Panama
| | - Ricardo Lleonart
- Centro de Biología Celular y Molecular de Enfermedades, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama City, Panama, Panama; Sistema Nacional de Investigación-Secretaría Nacional de Ciencia, Tecnología e Innovación (SNI-SENACYT), Panama City, Panama, Panama.
| | - Carlos M Restrepo
- Centro de Biología Celular y Molecular de Enfermedades, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama City, Panama, Panama; Sistema Nacional de Investigación-Secretaría Nacional de Ciencia, Tecnología e Innovación (SNI-SENACYT), Panama City, Panama, Panama.
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5
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De los Santos MB, Ramírez IM, Rodríguez JE, Beerli P, Valdivia HO. Genetic diversity and population structure of Leishmania (Viannia) braziliensis in the Peruvian jungle. PLoS Negl Trop Dis 2022; 16:e0010374. [PMID: 35605021 PMCID: PMC9126394 DOI: 10.1371/journal.pntd.0010374] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 03/30/2022] [Indexed: 11/23/2022] Open
Abstract
Background Human cutaneous leishmaniasis caused by Leishmania (Viannia) braziliensis is highly prevalent in the Peruvian jungle, where it affects military forces deployed to fight against drug trafficking and civilian people that migrate from the highland to the lowland jungle for economic activities such as mining, agriculture, construction, and chestnut harvest. We explored the genetic diversity and population structure of 124 L. (V.) braziliensis isolates collected from the highland (Junín, Cusco, and Ayacucho) and lowland Peruvian jungle (Loreto, Ucayali, and Madre de Dios). All samples were genotyped using Multilocus Microsatellite Typing (MLMT) of ten highly polymorphic markers. Principal findings High polymorphism and genetic diversity were found in Peruvian isolates of L. (V.) braziliensis. Most markers are not in Hardy-Weinberg equilibrium; this deviation is most likely caused by local inbreeding, as shown by the positive FIS values. Linkage Disequilibrium in subpopulations was not strong, suggesting the reproduction was not strictly clonal. Likewise, for the first time, two genetic clusters of this parasite were determined, distributed in both areas of the Peruvian jungle, which suggested a possible recent colonization event of the highland jungle from the lowland jungle. Conclusions L. (V.) braziliensis exhibits considerable genetic diversity with two different clusters in the Peruvian jungle. Migration analysis suggested a colonization event between geographical areas of distribution. Although no human migration was observed at the time of sampling, earlier displacement of humans, reservoirs, or vectors could have been responsible for the parasite spread in both regions. L. (V.) braziliensis is widespread in the Peruvian jungle region. In this region, the departments of Cusco and Madre de Dios account for a large number of patients that get infected while working in the virgin forest. For the first time, we described ample genetic diversity among Peruvian L. (V.) braziliensis isolates with new alleles that were not previously reported in South America. In addition, two different genetic clusters or subpopulations of L. (V.) braziliensis in the Amazon Rainforest of Peru were described. This finding reveals the important distribution of parasite populations and suggests a possible colonization event between ecoregions of the highland and lowland Peruvian jungle independently of recent human migration.
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Affiliation(s)
| | | | - Jorge E. Rodríguez
- Unidad de Biotecnología Molecular, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Peter Beerli
- Department of Scientific Computing, Florida State University, Tallahassee, Florida, United States of America
| | - Hugo O. Valdivia
- Department of Parasitology, U.S. Naval Medical Research Unit 6, Lima, Peru
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6
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Leishmania and the Model of Predominant Clonal Evolution. Microorganisms 2021; 9:microorganisms9112409. [PMID: 34835534 PMCID: PMC8620605 DOI: 10.3390/microorganisms9112409] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 11/18/2021] [Accepted: 11/20/2021] [Indexed: 01/23/2023] Open
Abstract
As it is the case for other pathogenic microorganisms, the respective impact of clonality and genetic exchange on Leishmania natural populations has been the object of lively debates since the early 1980s. The predominant clonal evolution (PCE) model states that genetic exchange in these parasites’ natural populations may have a high relevance on an evolutionary scale, but is not sufficient to erase a persistent phylogenetic signal and the existence of bifurcating trees. Recent data based on high-resolution markers and genomic polymorphisms fully confirm the PCE model down to a microevolutionary level.
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Travi BL, Delos Santos MB, Shelite TR, Santos RP, Rosales LA, Castellanos-Gonzalez A, Saldarriaga O, Melby PC. Diagnostic Efficacy of Recombinase-Polymerase-Amplification Coupled with Lateral Flow Strip Reading in Patients with Cutaneous Leishmaniasis from the Amazonas Rainforest of Perú. Vector Borne Zoonotic Dis 2021; 21:941-947. [PMID: 34665665 DOI: 10.1089/vbz.2021.0038] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Cutaneous leishmaniasis (CL) is highly prevalent in rural and sylvatic regions of Latin America, with an estimated 55,000 annual cases. Diagnosis in resource-limited areas still relies on microscopy of dermal scrapings, while more sensitive methods like PCR are not attainable due to costs and lack of adequate health infrastructure. Isothermal amplification of Leishmania DNA can be performed without sophisticated equipment and training and may become a point of care (POC) test for health care centers with scarce resources. We evaluated the efficacy of recombinase-polymerase-amplification (RPA-LF) to diagnose CL in 226 patients attending a clinic in Puerto Maldonado within the Peruvian Amazon basin. Conventional PCR targeting kinetoplast DNA (kDNA-PCR) was used as the gold standard. Eight of 226 patients were considered true negatives (microscopy, kDNA-PCR, and RPA-LF negative), while RPA-LF resulted positive in 186 of 204 kDNA-PCR positive patients, yielding 91.2% (confidence interval [CI] = 86.5-94.4%) sensitivity and 93% (CI 88.6-95.8%) positive predictive value. There were 14% (32/226) discrepant samples alternating positive and negative results in similar proportions between both tests. Quantitative PCR used to resolve the discrepancies suggested that they occurred in samples with scarce parasite numbers as determined by high cycle threshold (Ct) values (≥32; cutoff 35.5). Microscopy had the lowest sensitivity of all methods (45.4%). Nested real-time PCR performed in 71 samples determined that Leishmania (Viannia) braziliensis was highly prevalent (69/71), and Leishmania (Viannia) lainsoni was present in only two isolates. Results indicated that RPA-LF has POC potential for CL endemic areas, yet further simplification and optimization coupled with field validation will be necessary to confirm its broad applicability.
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Affiliation(s)
- Bruno L Travi
- Division of Infectious Diseases, Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas, USA.,Center for Tropical Diseases, University of Texas Medical Branch, Galveston, Texas, USA
| | - Maxy B Delos Santos
- Department of Parasitology, U.S. Naval Medical Research Unit 6 (NAMRU-6), Lima, Peru
| | - Thomas R Shelite
- Division of Infectious Diseases, Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas, USA
| | - Rocio P Santos
- Department of Parasitology, U.S. Naval Medical Research Unit 6 (NAMRU-6), Lima, Peru
| | - Luis A Rosales
- Department of Parasitology, U.S. Naval Medical Research Unit 6 (NAMRU-6), Lima, Peru
| | - Alejandro Castellanos-Gonzalez
- Division of Infectious Diseases, Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas, USA.,Center for Tropical Diseases, University of Texas Medical Branch, Galveston, Texas, USA
| | - Omar Saldarriaga
- Division of Infectious Diseases, Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas, USA
| | - Peter C Melby
- Division of Infectious Diseases, Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas, USA.,Center for Tropical Diseases, University of Texas Medical Branch, Galveston, Texas, USA
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8
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Torrico MC, Fernández-Arévalo A, Ballart C, Solano M, Rojas E, Ariza E, Tebar S, Lozano D, Abras A, Gascón J, Picado A, Muñoz C, Torrico F, Gállego M. Tegumentary leishmaniasis by Leishmania braziliensis complex in Cochabamba, Bolivia including the presence of L. braziliensis outlier: Tegumentary leishmaniasis in Cochabamba, Bolivia. Transbound Emerg Dis 2021; 69:2242-2255. [PMID: 34232559 DOI: 10.1111/tbed.14228] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 06/27/2021] [Accepted: 07/05/2021] [Indexed: 01/07/2023]
Abstract
Leishmaniasis is caused by protozoans of the Leishmania genus, which includes more than 20 species capable of infecting humans worldwide. In the Americas, the most widespread specie is L. braziliensis, present in 18 countries including Bolivia. The taxonomic position of the L. braziliensis complex has been a subject of controversy, complicated further by the recent identification of a particular subpopulation named L. braziliensis atypical or outlier. The aim of this study was to carry out a systematic analysis of the L. braziliensis complex in Bolivia and to describe the associated clinical characteristics. Forty-one strains were analyzed by sequencing an amplified 1245 bp fragment of the hsp70 gene, which allowed its identification as: 24 (59%) L. braziliensis, 16 (39%) L. braziliensis outlier, and one (2%) L. peruviana. In a dendrogram constructed, L. braziliensis and L. peruviana are grouped in the same cluster, whilst L. braziliensis outlier appears in a separate branch. Sequence alignment allowed the identification of five non-polymorphic nucleotide positions (288, 297, 642, 993, and 1213) that discriminate L. braziliensis and L. peruviana from L. braziliensis outlier. Moreover, nucleotide positions 51 and 561 enable L. peruviana to be discriminated from the other two taxa. A greater diversity was observed in L. braziliensis outlier than in L. braziliensis-L. peruviana. The 41 strains came from 32 patients with tegumentary leishmaniasis, among which 22 patients (69%) presented cutaneous lesions (11 caused by L. braziliensis and 11 by L. braziliensis outlier) and 10 patients (31%) mucocutaneous lesions (eight caused by L. braziliensis, one by L. braziliensis outlier, and one by L. peruviana). Nine patients (28%) simultaneously provided two isolates, each from a separate lesion, and in each case the same genotype was identified in both. Treatment failure was observed in six patients infected with L. braziliensis and one patient with L. peruviana.
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Affiliation(s)
- Mary Cruz Torrico
- Facultad de Medicina, Universidad Mayor de San Simón, Cochabamba, Bolivia.,Fundación CEADES y Medio Ambiente, Cochabamba, Bolivia.,Secció de Parasitología, Departament de Biologia, Sanitat i Medi Ambient, Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de Barcelona, Barcelona, Spain
| | - Anna Fernández-Arévalo
- Secció de Parasitología, Departament de Biologia, Sanitat i Medi Ambient, Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de Barcelona, Barcelona, Spain.,Institut de Recerca Biomèdica Sant Pau, Barcelona, Spain
| | - Cristina Ballart
- Secció de Parasitología, Departament de Biologia, Sanitat i Medi Ambient, Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de Barcelona, Barcelona, Spain.,Instituto de Salud Global de Barcelona (ISGlobal), Barcelona, Spain
| | - Marco Solano
- Facultad de Medicina, Universidad Mayor de San Simón, Cochabamba, Bolivia
| | - Ernesto Rojas
- Facultad de Medicina, Universidad Mayor de San Simón, Cochabamba, Bolivia
| | - Eva Ariza
- Secció de Parasitología, Departament de Biologia, Sanitat i Medi Ambient, Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de Barcelona, Barcelona, Spain.,Institut de Recerca Biomèdica Sant Pau, Barcelona, Spain
| | - Silvia Tebar
- Secció de Parasitología, Departament de Biologia, Sanitat i Medi Ambient, Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de Barcelona, Barcelona, Spain
| | - Daniel Lozano
- Facultad de Medicina, Universidad Mayor de San Simón, Cochabamba, Bolivia.,Fundación CEADES y Medio Ambiente, Cochabamba, Bolivia
| | - Alba Abras
- Secció de Parasitología, Departament de Biologia, Sanitat i Medi Ambient, Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de Barcelona, Barcelona, Spain.,Institut de Recerca Biomèdica Sant Pau, Barcelona, Spain.,Laboratori d'Ictiologia Genètica, Departament de Biologia, Universitat de Girona, Girona, Spain
| | - Joaquim Gascón
- Instituto de Salud Global de Barcelona (ISGlobal), Barcelona, Spain
| | - Albert Picado
- Instituto de Salud Global de Barcelona (ISGlobal), Barcelona, Spain.,Foundation for Innovative New Diagnostics (FIND), Geneva, Switzerland
| | - Carmen Muñoz
- Institut de Recerca Biomèdica Sant Pau, Barcelona, Spain.,Servei de Microbiologia, Hospital de la Santa Creu i Sant Pau Barcelona, Barcelona, Spain.,Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Faustino Torrico
- Facultad de Medicina, Universidad Mayor de San Simón, Cochabamba, Bolivia.,Fundación CEADES y Medio Ambiente, Cochabamba, Bolivia
| | - Montserrat Gállego
- Secció de Parasitología, Departament de Biologia, Sanitat i Medi Ambient, Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de Barcelona, Barcelona, Spain.,Instituto de Salud Global de Barcelona (ISGlobal), Barcelona, Spain
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9
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The Maze Pathway of Coevolution: A Critical Review over the Leishmania and Its Endosymbiotic History. Genes (Basel) 2021; 12:genes12050657. [PMID: 33925663 PMCID: PMC8146029 DOI: 10.3390/genes12050657] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 04/01/2021] [Accepted: 04/05/2021] [Indexed: 01/10/2023] Open
Abstract
The description of the genus Leishmania as the causative agent of leishmaniasis occurred in the modern age. However, evolutionary studies suggest that the origin of Leishmania can be traced back to the Mesozoic era. Subsequently, during its evolutionary process, it achieved worldwide dispersion predating the breakup of the Gondwana supercontinent. It is assumed that this parasite evolved from monoxenic Trypanosomatidae. Phylogenetic studies locate dixenous Leishmania in a well-supported clade, in the recently named subfamily Leishmaniinae, which also includes monoxenous trypanosomatids. Virus-like particles have been reported in many species of this family. To date, several Leishmania species have been reported to be infected by Leishmania RNA virus (LRV) and Leishbunyavirus (LBV). Since the first descriptions of LRVs decades ago, differences in their genomic structures have been highlighted, leading to the designation of LRV1 in L. (Viannia) species and LRV2 in L. (Leishmania) species. There are strong indications that viruses that infect Leishmania spp. have the ability to enhance parasitic survival in humans as well as in experimental infections, through highly complex and specialized mechanisms. Phylogenetic analyses of these viruses have shown that their genomic differences correlate with the parasite species infected, suggesting a coevolutionary process. Herein, we will explore what has been described in the literature regarding the relationship between Leishmania and endosymbiotic Leishmania viruses and what is known about this association that could contribute to discussions about the worldwide dispersion of Leishmania.
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10
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Miranda ADC, González KA, Samudio F, Pineda VJ, Calzada JE, Capitan-Barrios Z, Jiménez A, Castillo J, Mendoza Y, Suárez JA, Ortiz B, Méndez J, Pascale JM, Grögl M, Sosa N, Saldaña A. Molecular Identification of Parasites Causing Cutaneous Leishmaniasis in Panama. Am J Trop Med Hyg 2021; 104:1326-1334. [PMID: 33432903 DOI: 10.4269/ajtmh.20-1336] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 11/27/2020] [Indexed: 02/03/2023] Open
Abstract
Isolates from 475 cutaneous leishmaniasis (CL) patients from three endemic regions were studied by three typing techniques. The molecular analysis from lesion scrapings based on hsp70 PCR-RFLP showed that 78.1% (371/475) restriction patterns corresponded to Leishmania (Viannia) panamensis, 19% (90/475) to Leishmania (Viannia) guyanensis, and 3.0% (14/475) to Leishmania (Viannia) braziliensis. Promastigotes isolated by culture from lesions of 228 patients (48.0%, 228/475) were identified by multi-locus enzyme electrophoresis. Of them, 95.2% (217/228) were typified as L. (V.) panamensis, 1.3% (3/228) as L. (V.) guyanensis, 2.2% (5/228) as L. (V.) braziliensis, and 1.3% (3/228) as hybrids (L. [V.] braziliensis/L. [V.] panamensis). However, a partial sequencing analysis of the hsp70 gene from 77 selected samples showed 16.9% (13/77) typified as L. (V.) panamensis, 68.8% (53/77) as Leishmania (V.) sp., 1, 3.9% (3/77) as L. (V.) guyanensis, 1.3% (1/77) as L. (V.) braziliensis outlier, 2.6% (2/77) as Leishmania (Viannia) naiffi, 2.6% as (2/77) Leishmania (V.) sp., and 2 and 3.9% (3/77) hybrid isolates of L. (V.) braziliensis/L. (V.) guyanensis. These results confirm L. (V.) panamensis as the predominant species and cause of CL lesions in Panama and that L. (V.) guyanensis, L. (V.) braziliensis, and L. (V.) naiffi are circulating to a lower degree. Furthermore, the determination of parasite isolates belonging to atypical clusters and hybrid isolates suggests the circulation of genetic variants with important implications for the epidemiology and clinical follow-up of CL in Panama. No evidence of the existence of parasites of the Leishmania (Leishmania) mexicana complex in Panamanian territory was found in this study.
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Affiliation(s)
| | - Kadir A González
- Instituto Conmemorativo Gorgas de Estudios de la Salud (ICGES), Panama, Panama
| | - Franklyn Samudio
- Facultad de Ciencias Naturales, Exactas y Tecnología, Universidad de Panamá, Panama, Panama.,Instituto Conmemorativo Gorgas de Estudios de la Salud (ICGES), Panama, Panama
| | - Vanessa J Pineda
- Instituto Conmemorativo Gorgas de Estudios de la Salud (ICGES), Panama, Panama
| | - José E Calzada
- Facultad de Medicina Veterinaria, Universidad de Panamá, Panama, Panama.,Instituto Conmemorativo Gorgas de Estudios de la Salud (ICGES), Panama, Panama
| | | | - Ana Jiménez
- Instituto Conmemorativo Gorgas de Estudios de la Salud (ICGES), Panama, Panama
| | - Juan Castillo
- Instituto Conmemorativo Gorgas de Estudios de la Salud (ICGES), Panama, Panama
| | - Yaxelis Mendoza
- Instituto Conmemorativo Gorgas de Estudios de la Salud (ICGES), Panama, Panama
| | - José A Suárez
- Instituto Conmemorativo Gorgas de Estudios de la Salud (ICGES), Panama, Panama
| | - Betsi Ortiz
- Instituto Conmemorativo Gorgas de Estudios de la Salud (ICGES), Panama, Panama
| | - Juan Méndez
- Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Juan M Pascale
- Instituto Conmemorativo Gorgas de Estudios de la Salud (ICGES), Panama, Panama
| | - Max Grögl
- U.S. Naval Medical Research Unit No. 6, Lima, Peru
| | - Néstor Sosa
- Instituto Conmemorativo Gorgas de Estudios de la Salud (ICGES), Panama, Panama
| | - Azael Saldaña
- Instituto Conmemorativo Gorgas de Estudios de la Salud (ICGES), Panama, Panama.,Centro de Investigación y Diagnóstico de Enfermedades Parasitarias (CIDEP), Facultad de Medicina, Universidad de Panamá, Panama, Panama
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11
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Correa-Cárdenas CA, Pérez J, Patino LH, Ramírez JD, Duque MC, Romero Y, Cantillo-Barraza O, Rodríguez O, Alvarado MT, Cruz C, Méndez C. Distribution, treatment outcome and genetic diversity of Leishmania species in military personnel from Colombia with cutaneous leishmaniasis. BMC Infect Dis 2020; 20:938. [PMID: 33297972 PMCID: PMC7724885 DOI: 10.1186/s12879-020-05529-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 10/20/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Leishmaniasis is one of the most important infectious diseases affecting the Colombian National Army due to the high number of reported cases and exposure throughout military operations in endemic areas. The main aim of this study was to estimate the geographical distribution along with the genetic diversity and treatment outcome of Leishmania species in Colombian military personnel. METHODS Skin lesion samples by smear and aspirate were collected in 136 patients having parasitological cutaneous leishmaniasis (CL) diagnosis. DNA was extracted, the nuclear marker heat shock protein 70 (HSP70) was amplified by PCR and sequenced. Leishmania species were identified by BLASTn. The geo-spatial distribution of the identified parasites was determined according to the possible site of infection. Gene tree was constructed by maximum likelihood (ML), diversity indices (π, h) were estimated and haplotype network was constructed under the Templeton-Crandall-Sing algorithm in order to determine the geographic relationships of the genetic variants of Leishmania species circulating in Colombian military population. RESULTS The species were identified in 77.94% of the samples, with a predominance of L. braziliensis (65.09%), followed by L. panamensis (31.13%), L. naiffi by the first time reported in Colombia in two patients (1.89%) as well as L. lindenbergi in a single patient (0.945%) with possible infection in the municipality of Miraflores, Guaviare and L. infantum in a single patient (0.945%) notified with CL in the municipality of Tumaco, Nariño. The phylogenetic analysis was consistent according to bootstrap, showing four strongly differentiated clades. CONCLUSIONS The geo-spatial distribution suggested that L. braziliensis has a greater abundance, while L. panamensis has a greater dispersion. The phylogenetic relationships of Leishmania species in Colombian military personnel was estimated with the confirmation of two new species circulating without prior report in the country and a species with no background for CL in the Colombian army. A substantial genetic diversity of Leishmania braziliensis was defined. This study contributes through the understanding of the molecular epidemiology to the CL transmission in Colombia.
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Affiliation(s)
- Camilo A Correa-Cárdenas
- Grupo de Investigación en Enfermedades Tropicales del Ejército (GINETEJ), Laboratorio de Referencia e Investigación, Dirección de Sanidad Ejército, Bogotá, Colombia
| | - Julie Pérez
- Grupo de Investigación en Enfermedades Tropicales del Ejército (GINETEJ), Laboratorio de Referencia e Investigación, Dirección de Sanidad Ejército, Bogotá, Colombia
| | - Luz H Patino
- Grupo de Investigaciones Microbiológicas - UR (GIMUR), Departamento de Biología, Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Juan David Ramírez
- Grupo de Investigaciones Microbiológicas - UR (GIMUR), Departamento de Biología, Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Maria Clara Duque
- Grupo de Investigación en Enfermedades Tropicales del Ejército (GINETEJ), Laboratorio de Referencia e Investigación, Dirección de Sanidad Ejército, Bogotá, Colombia
| | - Yanira Romero
- Grupo de Investigación en Enfermedades Tropicales del Ejército (GINETEJ), Laboratorio de Referencia e Investigación, Dirección de Sanidad Ejército, Bogotá, Colombia
| | - Omar Cantillo-Barraza
- Grupo de Investigación en Enfermedades Tropicales del Ejército (GINETEJ), Laboratorio de Referencia e Investigación, Dirección de Sanidad Ejército, Bogotá, Colombia
| | - Omaira Rodríguez
- Grupo de Investigación en Enfermedades Tropicales del Ejército (GINETEJ), Laboratorio de Referencia e Investigación, Dirección de Sanidad Ejército, Bogotá, Colombia
| | - Maria Teresa Alvarado
- Grupo de Investigación en Enfermedades Tropicales del Ejército (GINETEJ), Laboratorio de Referencia e Investigación, Dirección de Sanidad Ejército, Bogotá, Colombia
| | - Claudia Cruz
- Grupo de Investigación en Enfermedades Tropicales del Ejército (GINETEJ), Laboratorio de Referencia e Investigación, Dirección de Sanidad Ejército, Bogotá, Colombia
| | - Claudia Méndez
- Grupo de Investigación en Enfermedades Tropicales del Ejército (GINETEJ), Laboratorio de Referencia e Investigación, Dirección de Sanidad Ejército, Bogotá, Colombia.
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12
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Abstract
Parasites are interesting models for studying speciation processes because they have a high potential for specialization, thanks to the intimate ecological association with their hosts and vectors. Yet little is known about the circumstances under which new parasite lineages emerge. Here we studied the genome diversity of parasites of the Leishmania braziliensis species complex that inhabit both Amazonian and Andean biotas in Peru. We identify three major parasite lineages that occupy particular ecological niches and show that these emerged during forestation changes over the past 150,000 y. We furthermore discovered that meiotic recombination between Amazonian and Andean lineages resulted in full-genome hybrids presenting mixed mitochondrial genomes, providing insights into the genetic consequences of hybridization in parasitic protozoa. The tropical Andes are an important natural laboratory to understand speciation in many taxa. Here we examined the evolutionary history of parasites of the Leishmania braziliensis species complex based on whole-genome sequencing of 67 isolates from 47 localities in Peru. We first show the origin of Andean Leishmania as a clade of near-clonal lineages that diverged from admixed Amazonian ancestors, accompanied by a significant reduction in genome diversity and large structural variations implicated in host–parasite interactions. Within the Andean species, patterns of population structure were strongly associated with biogeographical origin. Molecular clock and ecological niche modeling suggested that the history of diversification of the Andean lineages is limited to the Late Pleistocene and intimately associated with habitat contractions driven by climate change. These results suggest that changes in forestation over the past 150,000 y have influenced speciation and diversity of these Neotropical parasites. Second, genome-scale analyses provided evidence of meiotic-like recombination between Andean and Amazonian Leishmania species, resulting in full-genome hybrids. The mitochondrial genome of these hybrids consisted of homogeneous uniparental maxicircles, but minicircles originated from both parental species. We further show that mitochondrial minicircles—but not maxicircles—show a similar evolutionary pattern to the nuclear genome, suggesting that compatibility between nuclear-encoded mitochondrial genes and minicircle-encoded guide RNA genes is essential to maintain efficient respiration. By comparing full nuclear and mitochondrial genome ancestries, our data expand our appreciation on the genetic consequences of diversification and hybridization in parasitic protozoa.
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13
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Ducharme O, Simon S, Ginouves M, Prévot G, Couppie P, Demar M, Blaizot R. Leishmania naiffi and lainsoni in French Guiana: Clinical features and phylogenetic variability. PLoS Negl Trop Dis 2020; 14:e0008380. [PMID: 32797078 PMCID: PMC7449503 DOI: 10.1371/journal.pntd.0008380] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 08/26/2020] [Accepted: 05/11/2020] [Indexed: 11/19/2022] Open
Abstract
In French Guiana, five species are associated with Cutaneous Leishmaniasis (CL). Though infections with Leishmania guyanensis, L. (V.) braziliensis and L. (L.) amazonensis have been extensively described, there are few available clinical and genetic data on L. (V.) lainsoni and L. (V.) naiffi. We determined the clinical and epidemiological features of all cases of CL due to L. (V.) naiffi and L. (V.) lainsoni diagnosed in French Guiana between 2003 and 2019. Phylogenetic analysis was performed by sequencing a portion of HSP70 and cyt b genes. Five cases of L. naiffi and 25 cases of L. lainsoni were reported. Patients infected by L. (V.) lainsoni were usually infected on gold camps, mostly along the Maroni river (60%), while L. naiffi was observed in French patients infected on the coast (100%). A high number of pediatric cases (n = 5; 20%) was observed for L. (V.) lainsoni. A mild clinical course was observed for all cases of L. (V.) naiffi. HSP70 and cyt b partial nucleotide sequence analysis revealed different geographical clusters within L. (V.) naiffi and L. (V.) lainsoni but no association were found between phylogenetic and clinical features. Our data suggest distinct socio-epidemiological features for these two Leishmania species. Patients seem to get infected with L. (V.) naiffi during leisure activities in anthropized coastal areas, while L. (V.) lainsoni shares common features with L. (V.) guyanensis and braziliensis and seems to be acquired during professional activities in primary forest regions. Phylogenetic analysis has provided information on the intraspecific genetic variability of L. (V.) naiffi and L. (V.) lainsoni and how these genotypes are distributed at the geographic level.
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Affiliation(s)
- Océane Ducharme
- Service de Dermatologie, Hôpital Andrée Rosemon, Cayenne, French Guiana
| | - Stéphane Simon
- Equipe EA3593, Ecosystèmes Amazoniens et Pathologie Tropicale, Université de la Guyane, Cayenne, French Guiana
| | - Marine Ginouves
- Equipe EA3593, Ecosystèmes Amazoniens et Pathologie Tropicale, Université de la Guyane, Cayenne, French Guiana
| | - Ghislaine Prévot
- Equipe EA3593, Ecosystèmes Amazoniens et Pathologie Tropicale, Université de la Guyane, Cayenne, French Guiana
| | - Pierre Couppie
- Service de Dermatologie, Hôpital Andrée Rosemon, Cayenne, French Guiana
- Equipe EA3593, Ecosystèmes Amazoniens et Pathologie Tropicale, Université de la Guyane, Cayenne, French Guiana
- Centre National de Référence des Leishmanioses, laboratoire associé, Hôpital Andrée Rosemon, Cayenne, French Guiana
| | - Magalie Demar
- Equipe EA3593, Ecosystèmes Amazoniens et Pathologie Tropicale, Université de la Guyane, Cayenne, French Guiana
- Centre National de Référence des Leishmanioses, laboratoire associé, Hôpital Andrée Rosemon, Cayenne, French Guiana
- Laboratoire Hospitalo-Universitaire de Parasitologie-Mycologie, Hôpital Andrée Rosemon, Cayenne, French Guiana
| | - Romain Blaizot
- Service de Dermatologie, Hôpital Andrée Rosemon, Cayenne, French Guiana
- Equipe EA3593, Ecosystèmes Amazoniens et Pathologie Tropicale, Université de la Guyane, Cayenne, French Guiana
- Centre National de Référence des Leishmanioses, laboratoire associé, Hôpital Andrée Rosemon, Cayenne, French Guiana
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14
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Brilhante AF, Lima L, Zampieri RA, Nunes VLB, Dorval MEC, Malavazi PFNDS, Melchior LAK, Ishikawa EAY, Cardoso CDO, Floeter-Winter LM, Teixeira MMG, Galati EAB. Leishmania (Viannia) braziliensis type 2 as probable etiological agent of canine cutaneous leishmaniasis in Brazilian Amazon. PLoS One 2019; 14:e0216291. [PMID: 31039202 PMCID: PMC6490954 DOI: 10.1371/journal.pone.0216291] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 04/17/2019] [Indexed: 12/22/2022] Open
Abstract
Canine cutaneous leishmaniasis (CCL) is a zoonosis of public health interest, and in the Americas, Leishmania (Viannia) braziliensis has been identified as the main etiological agent. The present study sought to investigate Leishmania spp. infection in domestic dogs from a rural area of the Xapuri municipality, Acre state, Brazilian Amazonia. For this purpose, visits were carried out to domiciles where the human cases of American cutaneous leishmaniasis (ACL) occurred, followed by the clinical evaluation of the animals in search of clinical signs suggestive of CCL. Blood samples were collected from 40 dogs, 13 of which had lesions suggestive of CCL, and biopsies of these lesions were performed. The methods used were Neal, Novy, and Nicolle’s (NNN) medium cultures and direct parasitological examination. Further, to detect and characterize Leishmania DNA some molecular techniques were performed such as conventional polymerase chain reaction (PCR) and sequencing targeting SSU rDNA and ITS1, restriction fragment length polymorphism (RFLP) and high resolution melting (HRM) analysis targeting hsp70. The investigation revealed that the results obtained from the parasitological methods were negative. In PCR by ITS1 and network topology sequences, six strains from dogs, isolated from the Peruvian Andes, appeared identical to Leishmania (Viannia) braziliensis type 2 (99–100%). By other molecular methods these samples turned out to be positive to Leishmania (Viannia) sp.. The diagnosis of Leishmania in domestic dogs from Acre state showed a high proportion of infected animals, and the occurrence of L. braziliensis type 2 in Brazil for the first time. This new report suggests that L. braziliensis type 2 is both trans- and cis-Andean. However, more studies are needed regarding the clinical and diagnostic aspects of this species of Leishmania.
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Affiliation(s)
- Andreia Fernandes Brilhante
- Faculty of Public Health, University of São Paulo, São Paulo, Brazil
- Federal University of Acre, Rio Branco, Acre, Brazil
- * E-mail:
| | - Luciana Lima
- Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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15
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Abstract
Phylogenetics is an important component of the systems biology approach. Knowledge about evolution of the genus Leishmania is essential to understand various aspects of basic biology of these parasites, such as parasite-host or parasite-vector relationships, biogeography, or epidemiology. Here, we present a comprehensive guideline for performing phylogenetic studies based on DNA sequence data, but with principles that can be adapted to protein sequences or other molecular markers. It is presented as a compilation of the most commonly used genetic targets for phylogenetic studies of Leishmania, including their respective primers for amplification and references, as well as details of PCR assays. Guidelines are, then, presented to choose the best targets in relation to the types of samples under study. Finally, and importantly, instructions are given to obtain optimal sequences, alignments, and datasets for the subsequent data analysis and phylogenetic inference. Different bioinformatics methods and software for phylogenetic inference are presented and explained. This chapter aims to provide a compilation of methods and generic guidelines to conduct phylogenetics of Leishmania for nonspecialists.
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Affiliation(s)
- Katrin Kuhls
- Molekulare Biotechnologie und Funktionelle Genomik, Technische Hochschule Wildau, Wildau, Germany.
| | - Isabel Mauricio
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa (UNL), Lisbon, Portugal
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16
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Jaber HT, Hailu A, Pratlong F, Lami P, Bastien P, Jaffe CL. Analysis of genetic polymorphisms and tropism in East African Leishmania donovani by Amplified Fragment Length Polymorphism and kDNA minicircle sequencing. INFECTION GENETICS AND EVOLUTION 2018; 65:80-90. [PMID: 30016714 PMCID: PMC6218636 DOI: 10.1016/j.meegid.2018.07.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Revised: 07/06/2018] [Accepted: 07/13/2018] [Indexed: 01/01/2023]
Abstract
Visceral leishmaniasis (VL), the most severe form of leishmaniasis, is caused by Leishmania donovani. In addition to fatal VL, these parasites also cause skin diseases in immune-competent and -suppressed people, post-kala azar dermal leishmaniasis (PKDL) and HIV/VL co-infections, respectively. Genetic polymorphism in 36 Ethiopian and Sudanese L. donovani strains from VL, PKDL and HIV/VL patients was examined using Amplified Fragment Length Polymorphism (AFLP), kDNA minicircle sequencing and Southern blotting. Strains were isolated from different patient tissues: in VL from lymph node, spleen or bone marrow; and in HIV/VL from skin, spleen or bone marrow. When VL and PKDL strains from the same region in Sudan were examined by Southern blotting using a DNA probe to the L. donovani 28S rRNA gene only minor differences were observed. kDNA sequence analysis distributed the strains in no particular order among four clusters (A - D), while AFLP analysis grouped the strains according to geographical origin into two major clades, Southern Ethiopia (SE) and Sudan/Northern Ethiopia (SD/NE). Strains in the latter clade were further divided into subpopulations by zymodeme, geography and year of isolation, but not by clinical symptoms. However, skin isolates showed significantly (p < 0.0001) fewer polymorphic AFLP fragments (average 10 strains = 348.6 ± 8.1) than VL strains (average 26 strains = 383.5 ± 3.8).
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Affiliation(s)
- Hanan T Jaber
- Department of Microbiology and Molecular Genetics, Kuvin Centre for the Study of Infectious and Tropical Diseases, IMRIC, Hebrew University - Hadassah Medical School, Jerusalem, Israel
| | - Asrat Hailu
- School of Medicine, College of Health Sciences, Department of Microbiology, Immunology & Parasitology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Francine Pratlong
- Department of Parasitology-Mycology, National Reference Centre for Leishmanioses, Academic Hospital of Montpellier, France; University of Montpellier, CNRS 5290/IRD 224 "MiVEGEC", Montpellier, France
| | - Patrick Lami
- Department of Parasitology-Mycology, National Reference Centre for Leishmanioses, Academic Hospital of Montpellier, France; University of Montpellier, CNRS 5290/IRD 224 "MiVEGEC", Montpellier, France
| | - Patrick Bastien
- Department of Parasitology-Mycology, National Reference Centre for Leishmanioses, Academic Hospital of Montpellier, France; University of Montpellier, CNRS 5290/IRD 224 "MiVEGEC", Montpellier, France
| | - Charles L Jaffe
- Department of Microbiology and Molecular Genetics, Kuvin Centre for the Study of Infectious and Tropical Diseases, IMRIC, Hebrew University - Hadassah Medical School, Jerusalem, Israel.
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17
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Hashiguchi Y, Gomez EAL, Cáceres AG, Velez LN, Villegas NV, Hashiguchi K, Mimori T, Uezato H, Kato H. Andean cutaneous leishmaniasis (Andean-CL, uta) in Peru and Ecuador: the causative Leishmania parasites and clinico-epidemiological features. Acta Trop 2018; 177:135-145. [PMID: 29017878 DOI: 10.1016/j.actatropica.2017.09.028] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Revised: 09/18/2017] [Accepted: 09/30/2017] [Indexed: 11/28/2022]
Abstract
This study provides comprehensive information on the past and current status of the Andean cutaneous leishmaniasis (Andean-CL, uta) in Peru and Ecuador, mainly focusing on the causative Leishmania parasites and clinico-epidemiological features. Available information and data including our unpublished works were analyzed thoroughly. Endemic regions of the Andean-CL (uta) in Peru run from the north Piura/Cajamarca to the south Ayacucho at a wide range of the Pacific watersheds of the Andes through several departments, while in Ecuador those exist at limited and spotted areas in the country's mid-southwestern two provinces, Azuay and Chimborazo. The principal species of the genus Leishmania are completely different at subgenus level, L. (Viannia) peruviana in Peru, and L. (Leishmania) mexicana and L. (L.) major-like (infrequent occurrence) in Ecuador. The Peruvian uta is now prevalent in different age and sex groups, being not clearly defined as found in the past. The precise reasons are not known and should be elucidated further, though probable factors, such as emergence of other Leishmania parasites, non-immune peoples' migration into the areas, etc., were discussed briefly in the text. The Andean-CL cases in Ecuador are more rural than before, probably because of a rapid development of the Leishmania-positive communities and towns, and the change of life-styles of the inhabitants, including newly constructed houses and roads in the endemic areas. Such information is helpful for future management of the disease, not only for Leishmania-endemic areas in the Andes but also for other endemic areas.
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Affiliation(s)
- Yoshihisa Hashiguchi
- Departamento de Parasitologia y Medicina Tropical, Centro de Biomedicina, Carrera de Medicina, Facultad de Ciencias Medicas, Universidad Catolica de Santiago de Guayaquil, Guayaquil, Ecuador; Leishmaniasis Project, Facultad de Ciencias Medicas, Universidad Catolica de Santiago de Guayaquil, Guayaquil, Ecuador; Department of Parasitology, Kochi Medical School, Kochi University, Kochi, Japan.
| | - Eduardo A L Gomez
- Departamento de Parasitologia y Medicina Tropical, Centro de Biomedicina, Carrera de Medicina, Facultad de Ciencias Medicas, Universidad Catolica de Santiago de Guayaquil, Guayaquil, Ecuador; Leishmaniasis Project, Facultad de Ciencias Medicas, Universidad Catolica de Santiago de Guayaquil, Guayaquil, Ecuador
| | - Abraham G Cáceres
- Seccion de Entomologia, Instituto de Medicina Tropical "Daniel A. Carrion" y Departamento Academico de Microbiologia, Facultad de Medicina Humana, Universidad Nacional Mayor de San Marcos, Lima, Peru; Laboratorio de Entomologia, Instituto Nacional de Salud, Lima, Peru
| | - Lenin N Velez
- Departamento de Parasitologia y Medicina Tropical, Centro de Biomedicina, Carrera de Medicina, Facultad de Ciencias Medicas, Universidad Catolica de Santiago de Guayaquil, Guayaquil, Ecuador; Leishmaniasis Project, Facultad de Ciencias Medicas, Universidad Catolica de Santiago de Guayaquil, Guayaquil, Ecuador
| | - Nancy V Villegas
- Departamento de Parasitologia y Medicina Tropical, Centro de Biomedicina, Carrera de Medicina, Facultad de Ciencias Medicas, Universidad Catolica de Santiago de Guayaquil, Guayaquil, Ecuador; Leishmaniasis Project, Facultad de Ciencias Medicas, Universidad Catolica de Santiago de Guayaquil, Guayaquil, Ecuador
| | - Kazue Hashiguchi
- Leishmaniasis Project, Facultad de Ciencias Medicas, Universidad Catolica de Santiago de Guayaquil, Guayaquil, Ecuador
| | - Tatsuyuki Mimori
- Department of Microbiology, Faculty of Life Sciences, Graduate School of Health Sciences, Kumamoto University, Kumamoto, Japan
| | - Hiroshi Uezato
- Department of Dermatology, Faculty of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Hirotomo Kato
- Division of Medical Zoology, Department of Infection and Immunity, Jichi Medical University, Tochigi, Japan
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18
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Lachaud L, Fernández-Arévalo A, Normand AC, Lami P, Nabet C, Donnadieu JL, Piarroux M, Djenad F, Cassagne C, Ravel C, Tebar S, Llovet T, Blanchet D, Demar M, Harrat Z, Aoun K, Bastien P, Muñoz C, Gállego M, Piarroux R. Identification of Leishmania by Matrix-Assisted Laser Desorption Ionization-Time of Flight (MALDI-TOF) Mass Spectrometry Using a Free Web-Based Application and a Dedicated Mass-Spectral Library. J Clin Microbiol 2017; 55:2924-2933. [PMID: 28724559 PMCID: PMC5625378 DOI: 10.1128/jcm.00845-17] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 07/11/2017] [Indexed: 01/16/2023] Open
Abstract
Human leishmaniases are widespread diseases with different clinical forms caused by about 20 species within the Leishmania genus. Leishmania species identification is relevant for therapeutic management and prognosis, especially for cutaneous and mucocutaneous forms. Several methods are available to identify Leishmania species from culture, but they have not been standardized for the majority of the currently described species, with the exception of multilocus enzyme electrophoresis. Moreover, these techniques are expensive, time-consuming, and not available in all laboratories. Within the last decade, mass spectrometry (MS) has been adapted for the identification of microorganisms, including Leishmania However, no commercial reference mass-spectral database is available. In this study, a reference mass-spectral library (MSL) for Leishmania isolates, accessible through a free Web-based application (mass-spectral identification [MSI]), was constructed and tested. It includes mass-spectral data for 33 different Leishmania species, including species that infect humans, animals, and phlebotomine vectors. Four laboratories on two continents evaluated the performance of MSI using 268 samples, 231 of which were Leishmania strains. All Leishmania strains, but one, were correctly identified at least to the complex level. A risk of species misidentification within the Leishmania donovani, L. guyanensis, and L. braziliensis complexes was observed, as previously reported for other techniques. The tested application was reliable, with identification results being comparable to those obtained with reference methods but with a more favorable cost-efficiency ratio. This free online identification system relies on a scalable database and can be implemented directly in users' computers.
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Affiliation(s)
- Laurence Lachaud
- Département de Parasitologie-Mycologie, Centre National de Référence des Leishmanioses, Université de Montpellier, Centre Hospitalier Universitaire de Montpellier, Montpellier, France
| | - Anna Fernández-Arévalo
- Servei de Microbiologia, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
- Secció de Parasitologia, Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de Barcelona, Barcelona, Spain
- ISGlobal, Barcelona Center of International Health Research (CRESIB), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - Anne-Cécile Normand
- Laboratoire de Parasitologie-Mycologie, CHU Timone, Université d'Aix-Marseille, Marseille, France
| | - Patrick Lami
- Département de Parasitologie-Mycologie, Centre National de Référence des Leishmanioses, Université de Montpellier, Centre Hospitalier Universitaire de Montpellier, Montpellier, France
| | - Cécile Nabet
- Laboratoire Hospitalo-Universitaire de Parasito-Mycologie, EA 3593, EPaT Ecosystèmes Amazoniens et Pathologie Tropicale, Université de Guyane, Laboratoire Associé au CNR Leishmania, Cayenne, France
| | | | - Martine Piarroux
- Université Aix-Marseille, INSERM-IRD-AMU UMR 912, Marseille, France
| | - Farid Djenad
- Laboratoire de Parasitologie-Mycologie, CHU Timone, Université d'Aix-Marseille, Marseille, France
| | - Carole Cassagne
- Laboratoire de Parasitologie-Mycologie, CHU Timone, Université d'Aix-Marseille, Marseille, France
| | - Christophe Ravel
- Département de Parasitologie-Mycologie, Centre National de Référence des Leishmanioses, Université de Montpellier, Centre Hospitalier Universitaire de Montpellier, Montpellier, France
| | - Silvia Tebar
- Secció de Parasitologia, Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de Barcelona, Barcelona, Spain
| | - Teresa Llovet
- Servei de Microbiologia, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
- Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Denis Blanchet
- Laboratoire Hospitalo-Universitaire de Parasito-Mycologie, EA 3593, EPaT Ecosystèmes Amazoniens et Pathologie Tropicale, Université de Guyane, Laboratoire Associé au CNR Leishmania, Cayenne, France
| | - Magalie Demar
- Laboratoire Hospitalo-Universitaire de Parasito-Mycologie, EA 3593, EPaT Ecosystèmes Amazoniens et Pathologie Tropicale, Université de Guyane, Laboratoire Associé au CNR Leishmania, Cayenne, France
| | - Zoubir Harrat
- Laboratoire d'Eco-Épidemiologie Parasitaire et Génétique des Populations, Institut Pasteur d'Algerie, Algiers, Algeria
| | - Karim Aoun
- Laboratoire de Parasitologie Médicale, Biotechnologies et Biomolécules, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Patrick Bastien
- Département de Parasitologie-Mycologie, Centre National de Référence des Leishmanioses, Université de Montpellier, Centre Hospitalier Universitaire de Montpellier, Montpellier, France
| | - Carmen Muñoz
- Servei de Microbiologia, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
- Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Montserrat Gállego
- Secció de Parasitologia, Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de Barcelona, Barcelona, Spain
- ISGlobal, Barcelona Center of International Health Research (CRESIB), Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - Renaud Piarroux
- Laboratoire de Parasitologie-Mycologie, CHU Timone, Université d'Aix-Marseille, Marseille, France
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Restrepo CM, Llanes A, Lleonart R. Use of AFLP for the study of eukaryotic pathogens affecting humans. INFECTION GENETICS AND EVOLUTION 2017; 63:360-369. [PMID: 28935612 DOI: 10.1016/j.meegid.2017.09.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 09/13/2017] [Accepted: 09/15/2017] [Indexed: 12/29/2022]
Abstract
Amplified fragment length polymorphism (AFLP) is a genotyping technique based on PCR amplification of specific restriction fragments from a particular genome. The methodology has been extensively used in plant biology to solve a variety of scientific questions, including taxonomy, molecular epidemiology, systematics, population genetics, among many others. The AFLP share advantages and disadvantages with other types of molecular markers, being particularly useful in organisms with no previous DNA sequence knowledge. In eukaryotic pathogens, the technique has not been extensively used, although it has the potential to solve many important issues as it allows the simultaneous examination of hundreds or even thousands of polymorphic sites in the genome of the organism. Here we describe the main applications published on the use of AFLP in eukaryotic pathogens, with emphasis in species of the groups fungi, protozoa and helminths, and discuss the role of this methodology in the context of new techniques derived from the advances of the next generation sequencing.
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Affiliation(s)
- Carlos M Restrepo
- Center for Cellular and Molecular Biology of Diseases, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Edificio 219, Ciudad del Saber, Apartado 0843-01103, Ciudad de Panamá, Panama.; Department of Biotechnology, Acharya Nagarjuna University, Guntur, India..
| | - Alejandro Llanes
- Center for Cellular and Molecular Biology of Diseases, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Edificio 219, Ciudad del Saber, Apartado 0843-01103, Ciudad de Panamá, Panama.; Department of Biotechnology, Acharya Nagarjuna University, Guntur, India
| | - Ricardo Lleonart
- Center for Cellular and Molecular Biology of Diseases, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Edificio 219, Ciudad del Saber, Apartado 0843-01103, Ciudad de Panamá, Panama..
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20
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Van der Auwera G, Bart A, Chicharro C, Cortes S, Davidsson L, Di Muccio T, Dujardin JC, Felger I, Paglia MG, Grimm F, Harms G, Jaffe CL, Manser M, Ravel C, Robert-Gangneux F, Roelfsema J, Töz S, Verweij JJ, Chiodini PL. Comparison of Leishmania typing results obtained from 16 European clinical laboratories in 2014. ACTA ACUST UNITED AC 2017; 21:30418. [PMID: 27983510 PMCID: PMC5291127 DOI: 10.2807/1560-7917.es.2016.21.49.30418] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 07/13/2016] [Indexed: 11/20/2022]
Abstract
Leishmaniasis is endemic in southern Europe, and in other European countries cases are diagnosed in travellers who have visited affected areas both within the continent and beyond. Prompt and accurate diagnosis poses a challenge in clinical practice in Europe. Different methods exist for identification of the infecting Leishmania species. Sixteen clinical laboratories in 10 European countries, plus Israel and Turkey, conducted a study to assess their genotyping performance. DNA from 21 promastigote cultures of 13 species was analysed blindly by the routinely used typing method. Five different molecular targets were used, which were analysed with PCR-based methods. Different levels of identification were achieved, and either the Leishmania subgenus, species complex, or actual species were reported. The overall error rate of strains placed in the wrong complex or species was 8.5%. Various reasons for incorrect typing were identified. The study shows there is considerable room for improvement and standardisation of Leishmania typing. The use of well validated standard operating procedures is recommended, covering testing, interpretation, and reporting guidelines. Application of the internal transcribed spacer 1 of the rDNA array should be restricted to Old World samples, while the heat-shock protein 70 gene and the mini-exon can be applied globally.
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Affiliation(s)
| | - Aldert Bart
- Academic Medical Center, Amsterdam, The Netherlands
| | | | - Sofia Cortes
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, UNL, Lisbon, Portugal
| | | | | | - Jean-Claude Dujardin
- Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.,Biomedical Sciences, Antwerp University, Antwerp, Belgium
| | - Ingrid Felger
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Maria Grazia Paglia
- National Institute for Infectious Diseases (INMI) Lazzaro Spallanzani, Rome, Italy
| | - Felix Grimm
- Institute of Parasitology, University of Zürich, Zürich, Switzerland
| | - Gundel Harms
- Institute of Tropical Medicine and International Health, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Charles L Jaffe
- Hebrew University, Hadassah Medical Centre, Jerusalem, Israel
| | - Monika Manser
- United Kingdom National External Quality Assessment Service, London, United Kingdom
| | | | | | - Jeroen Roelfsema
- National Institute for Public Health and the Environment, RIVM, Bilthoven, The Netherlands
| | - Seray Töz
- Ege University, Faculty of Medicine, Department of Parasitology, Izmir, Turkey
| | | | - Peter L Chiodini
- Hospital for Tropical Diseases, London, United Kingdom.,London School of Hygiene and Tropical Medicine, London, United Kingdom
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21
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Tibayrenc M, Ayala FJ. Is Predominant Clonal Evolution a Common Evolutionary Adaptation to Parasitism in Pathogenic Parasitic Protozoa, Fungi, Bacteria, and Viruses? ADVANCES IN PARASITOLOGY 2016; 97:243-325. [PMID: 28325372 DOI: 10.1016/bs.apar.2016.08.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We propose that predominant clonal evolution (PCE) in microbial pathogens be defined as restrained recombination on an evolutionary scale, with genetic exchange scarce enough to not break the prevalent pattern of clonal population structure. The main features of PCE are (1) strong linkage disequilibrium, (2) the widespread occurrence of stable genetic clusters blurred by occasional bouts of genetic exchange ('near-clades'), (3) the existence of a "clonality threshold", beyond which recombination is efficiently countered by PCE, and near-clades irreversibly diverge. We hypothesize that the PCE features are not mainly due to natural selection but also chiefly originate from in-built genetic properties of pathogens. We show that the PCE model obtains even in microbes that have been considered as 'highly recombining', such as Neisseria meningitidis, and that some clonality features are observed even in Plasmodium, which has been long described as panmictic. Lastly, we provide evidence that PCE features are also observed in viruses, taking into account their extremely fast genetic turnover. The PCE model provides a convenient population genetic framework for any kind of micropathogen. It makes it possible to describe convenient units of analysis (clones and near-clades) for all applied studies. Due to PCE features, these units of analysis are stable in space and time, and clearly delimited. The PCE model opens up the possibility of revisiting the problem of species definition in these organisms. We hypothesize that PCE constitutes a major evolutionary strategy for protozoa, fungi, bacteria, and viruses to adapt to parasitism.
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Affiliation(s)
- M Tibayrenc
- Institut de Recherche pour le Développement, Montpellier, France
| | - F J Ayala
- University of California at Irvine, United States
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22
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Miranda A, Samudio F, González K, Saldaña A, Brandão A, Calzada JE. Calmodulin Polymerase Chain Reaction-Restriction Fragment Length Polymorphism for Leishmania Identification and Typing. Am J Trop Med Hyg 2016; 95:383-7. [PMID: 27352873 DOI: 10.4269/ajtmh.15-0709] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 05/15/2016] [Indexed: 11/07/2022] Open
Abstract
A precise identification of Leishmania species involved in human infections has epidemiological and clinical importance. Herein, we describe a preliminary validation of a restriction fragment length polymorphism assay, based on the calmodulin intergenic spacer region, as a tool for detecting and typing Leishmania species. After calmodulin amplification, the enzyme HaeIII yielded a clear distinction between reference strains of Leishmania mexicana, Leishmania amazonensis, Leishmania infantum, Leishmania lainsoni, and the rest of the Viannia reference species analyzed. The closely related Viannia species: Leishmania braziliensis, Leishmania panamensis, and Leishmania guyanensis, are separated in a subsequent digestion step with different restriction enzymes. We have developed a more accessible molecular protocol for Leishmania identification/typing based on the exploitation of part of the calmodulin gene. This methodology has the potential to become an additional tool for Leishmania species characterization and taxonomy.
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Affiliation(s)
- Aracelis Miranda
- Instituto Conmemorativo Gorgas de Estudios de la Salud, Panama City, Panama
| | - Franklyn Samudio
- Instituto Conmemorativo Gorgas de Estudios de la Salud, Panama City, Panama. Laboratorio Interdisciplinar de Pesquisas Médicas, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil
| | - Kadir González
- Instituto Conmemorativo Gorgas de Estudios de la Salud, Panama City, Panama
| | - Azael Saldaña
- Instituto Conmemorativo Gorgas de Estudios de la Salud, Panama City, Panama
| | - Adeilton Brandão
- Laboratorio Interdisciplinar de Pesquisas Médicas, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil
| | - Jose E Calzada
- Instituto Conmemorativo Gorgas de Estudios de la Salud, Panama City, Panama.
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23
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Molecular identification of Leishmania spp. clinical isolates from Colombia based on hsp70 gene. BIOMEDICA 2016; 36:37-44. [PMID: 27622623 DOI: 10.7705/biomedica.v36i2.2688] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 06/04/2015] [Indexed: 11/21/2022]
Abstract
INTRODUCTION Leishmaniasis is highly prevalent in Colombia, where at least six different species can cause disease of varying clinical presentations in humans. The identification of the infecting species is quite important for prognosis, therapeutics and epidemiology. Different techniques with variable discriminatory power have been used for the identification. OBJECTIVE To carry out the molecular identification of Leishmania species through the amplification of a fragment of the hsp70 gene. MATERIALS AND METHODS Molecular amplification of the hsp70 gene fragment (PCR-hsp70) followed by restriction fragment length polymorphism analysis (RFLP) was done for identification purposes using DNA from 81 clinical isolates of Leishmania. RESULTS A single amplicon was obtained for all samples analyzed. The enzymatic restrictions of the 81 PCR products identified 70 with a banding pattern corresponding to L. braziliensis with two different patterns (62 and eight isolates, respectively), nine isolates compatible with L. panamensis and two with L. guyanensis. The geographical origin of the isolates is consistent with previous reports about the distribution of the corresponding species in Colombia. CONCLUSIONS The PCR-hsp70/RFLP technique used is a valid tool for the identification of Leishmania species isolated from clinical samples of patients in Colombia, which may also be applicable to the study of strains obtained from vectors and reservoirs with epidemiological significance.
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24
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Valdivia HO, Reis-Cunha JL, Rodrigues-Luiz GF, Baptista RP, Baldeviano GC, Gerbasi RV, Dobson DE, Pratlong F, Bastien P, Lescano AG, Beverley SM, Bartholomeu DC. Comparative genomic analysis of Leishmania (Viannia) peruviana and Leishmania (Viannia) braziliensis. BMC Genomics 2015; 16:715. [PMID: 26384787 PMCID: PMC4575464 DOI: 10.1186/s12864-015-1928-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 09/09/2015] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND The Leishmania (Viannia) braziliensis complex is responsible for most cases of New World tegumentary leishmaniasis. This complex includes two closely related species but with different geographic distribution and disease phenotypes, L. (V.) peruviana and L. (V.) braziliensis. However, the genetic basis of these differences is not well understood and the status of L. (V.) peruviana as distinct species has been questioned by some. Here we sequenced the genomes of two L. (V.) peruviana isolates (LEM1537 and PAB-4377) using Illumina high throughput sequencing and performed comparative analyses against the L. (V.) braziliensis M2904 reference genome. Comparisons were focused on the detection of Single Nucleotide Polymorphisms (SNPs), insertions and deletions (INDELs), aneuploidy and gene copy number variations. RESULTS We found 94,070 variants shared by both L. (V.) peruviana isolates (144,079 in PAB-4377 and 136,946 in LEM1537) against the L. (V.) braziliensis M2904 reference genome while only 26,853 variants separated both L. (V.) peruviana genomes. Analysis in coding sequences detected 26,750 SNPs and 1,513 indels shared by both L. (V.) peruviana isolates against L. (V.) braziliensis M2904 and revealed two L. (V.) braziliensis pseudogenes that are likely to have coding potential in L. (V.) peruviana. Chromosomal read density and allele frequency profiling showed a heterogeneous pattern of aneuploidy with an overall disomic tendency in both L. (V.) peruviana isolates, in contrast with a trisomic pattern in the L. (V.) braziliensis M2904 reference. Read depth analysis allowed us to detect more than 368 gene expansions and 14 expanded gene arrays in L. (V.) peruviana, and the likely absence of expanded amastin gene arrays. CONCLUSIONS The greater numbers of interspecific SNP/indel differences between L. (V.) peruviana and L. (V.) braziliensis and the presence of different gene and chromosome copy number variations support the classification of both organisms as closely related but distinct species. The extensive nucleotide polymorphisms and differences in gene and chromosome copy numbers in L. (V.) peruviana suggests the possibility that these may contribute to some of the unique features of its biology, including a lower pathology and lack of mucosal development.
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Affiliation(s)
- Hugo O Valdivia
- Laboratório de Imunologia e Genômica de Parasitos, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil. .,Department of Parasitology, U.S. Naval Medical Research Unit No. 6, Lima, Peru.
| | - João L Reis-Cunha
- Laboratório de Imunologia e Genômica de Parasitos, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
| | - Gabriela F Rodrigues-Luiz
- Laboratório de Imunologia e Genômica de Parasitos, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
| | - Rodrigo P Baptista
- Laboratório de Imunologia e Genômica de Parasitos, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
| | | | - Robert V Gerbasi
- Department of Parasitology, U.S. Naval Medical Research Unit No. 6, Lima, Peru.
| | - Deborah E Dobson
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA.
| | - Francine Pratlong
- Centre Hospitalier Universitaire de Montpellier, Departement de Parasitologie-Mycologie, Centre National de Reference des Leishmanioses, Montpellier, France.
| | - Patrick Bastien
- Centre Hospitalier Universitaire de Montpellier, Departement de Parasitologie-Mycologie, Centre National de Reference des Leishmanioses, Montpellier, France.
| | - Andrés G Lescano
- Department of Parasitology, U.S. Naval Medical Research Unit No. 6, Lima, Peru. .,Universidad Peruana Cayetano Heredia, School of Public Health and Management, Lima, Peru.
| | - Stephen M Beverley
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA.
| | - Daniella C Bartholomeu
- Laboratório de Imunologia e Genômica de Parasitos, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
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25
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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] [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.
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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
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26
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Abstract
Leishmania is an infectious protozoan parasite related to African and American trypanosomes. All Leishmania species that are pathogenic to humans can cause dermal disease. When one is confronted with cutaneous leishmaniasis, identification of the causative species is relevant in both clinical and epidemiological studies, case management, and control. This review gives an overview of the currently existing and most used assays for species discrimination, with a critical appraisal of the limitations of each technique. The consensus taxonomy for the genus is outlined, including debatable species designations. Finally, a numerical literature analysis is presented that describes which methods are most used in various countries and regions in the world, and for which purposes.
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Affiliation(s)
- Gert Van der Auwera
- Institute of Tropical Medicine, Department of Biomedical Sciences, Antwerp, Belgium
| | - Jean-Claude Dujardin
- Institute of Tropical Medicine, Department of Biomedical Sciences, Antwerp, Belgium Antwerp University, Department of Biomedical Sciences, Antwerp, Belgium
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Rougeron V, De Meeûs T, Bañuls AL. A primer for Leishmania population genetic studies. Trends Parasitol 2015; 31:52-9. [PMID: 25592839 DOI: 10.1016/j.pt.2014.12.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 12/03/2014] [Accepted: 12/06/2014] [Indexed: 02/04/2023]
Abstract
Leishmaniases remain a major public health problem. Despite the development of elaborate experimental techniques and sophisticated statistical tools, how these parasites evolve, adapt themselves to new environmental compartments and hosts, and develop resistance to new drugs remains unclear. Leishmania parasites constitute a complex model from a biological, ecological, and epidemiological point of view but also with respect to their genetics and phylogenetics. With this in view, we seek to outline the criteria, caveats, and confounding factors to be considered for Leishmania population genetic studies. We examine how the taxonomic complexity, heterozygosity, intraspecific and interspecific recombination, aneuploidy, and ameiotic recombination of Leishmania intersect with population genetic studies of this parasite.
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Affiliation(s)
- V Rougeron
- MIVEGEC (Laboratoire Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle), Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 5290 - Institut de Recherche pour le Développement (IRD) 224 - Universités Montpellier 1 et 2, Montpellier, France; Centre International de Recherches Médicales de Franceville, Franceville, Gabon.
| | - T De Meeûs
- IRD/Centre International de Recherche-Développement sur l'Élevage en zone Subhumide (CIRDES), UMR 177, INTERTRYP IRD-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), CIRDES 01, BP 454 Bobo-Dioulasso 01, Burkina Faso
| | - A-L Bañuls
- MIVEGEC (Laboratoire Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle), Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 5290 - Institut de Recherche pour le Développement (IRD) 224 - Universités Montpellier 1 et 2, Montpellier, France
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Evaluation of four single-locus markers for Leishmania species discrimination by sequencing. J Clin Microbiol 2014; 52:1098-104. [PMID: 24452158 DOI: 10.1128/jcm.02936-13] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Several genetic markers have been described for discriminating Leishmania species. In most reported cases, one or a few polymorphisms are the basis of species identification, and the methods were validated on a limited number of strains from a particular geographical region. Therefore, most techniques may underestimate the global intraspecies variability and are applicable only in certain areas. In addition, interlaboratory standardization is mostly absent, complicating comparisons among different studies. Here, we compared species typing results from all sequence polymorphisms found in four popular markers that can be applied directly on clinical samples: the miniexon or spliced leader, the internal transcribed spacer of the ribosomal DNA array, the 7SL RNA gene, and the heat shock protein 70 gene. Clustering was evaluated among 74 Leishmania strains, selected to represent a wide geographic distribution and genetic variability of the medically relevant species of the genus. Results were compared with a multilocus sequence typing (MLST) approach using 7 single-copy household genes and with multilocus enzyme electrophoresis (MLEE), still considered the gold standard by some. We show that strain groupings are highly congruent across the four different single-locus markers, MLST, and MLEE. Overall, the heat shock protein 70 gene and the miniexon presented the best resolutions for separating medically relevant species. As gene sequence analysis is validated here on a global scale, it is advocated as the method of choice for use in genetic, clinical, and epidemiological studies and for managing patients with unknown origins of infection, especially in Western infectious disease clinics dealing with imported leishmaniasis.
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Miranda A, Samudio F, Saldaña A, Castillo J, Brandão A, Calzada JE. The calmodulin intergenic spacer as molecular target for characterization of Leishmania species. Parasit Vectors 2014; 7:35. [PMID: 24438764 PMCID: PMC4021611 DOI: 10.1186/1756-3305-7-35] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Accepted: 01/14/2014] [Indexed: 11/18/2022] Open
Abstract
Background Human leishmaniasis is a neglected disease caused by parasites of the genus Leishmania. Clinical aspects of this disease can vary significantly, reflecting the wide range of parasites in the genus Leishmania. Knowing accurately the Leishmania species infecting humans is important for clinical case management and evaluation of epidemiological risk. Calmodulin is an essential gene in trypanosomatids that modulates the calcium metabolism in various cellular activities. Despite its strong conservation in trypanosomatids, it has been recently observed that its untranslated regions (UTR) diverge among species. Methods In this study we analyzed the sequences and the absolute dinucleotide frequency of the intergenic spacer of the calmodulin gene (containing both, 3′ and 5′UTR) in nine reference Leishmania species and ten clinical isolates obtained from patients with cutaneous leishmaniasis. Results We show that the short calmodulin intergenic spacers exhibit features that make them interesting for applications in molecular characterization and phylogenetic studies of Leishmania. Dendrograms based on sequence alignments and on the dinucleotide frequency indicate that this particular region of calmodulin gene might be useful for species typing between the Leishmania and Viannia subgenera. Conclusions Mutations and composition of the calmodulin intergenic spacer from Leishmania species might have taxonomic value as parameters to define if an isolate is identical to a certain species or belongs to one of the two current subgenera.
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Affiliation(s)
| | | | | | | | | | - Jose E Calzada
- Instituto Conmemorativo Gorgas de Estudios de Salud, Ciudad de Panamá, Panamá.
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Kuhls K, Cupolillo E, Silva SO, Schweynoch C, Côrtes Boité M, Mello MN, Mauricio I, Miles M, Wirth T, Schönian G. Population structure and evidence for both clonality and recombination among Brazilian strains of the subgenus Leishmania (Viannia). PLoS Negl Trop Dis 2013; 7:e2490. [PMID: 24205418 PMCID: PMC3814519 DOI: 10.1371/journal.pntd.0002490] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Accepted: 09/08/2013] [Indexed: 12/03/2022] Open
Abstract
Background/Objectives: Parasites of the subgenus Leishmania (Viannia) cause varying clinical symptoms ranging from cutaneous leishmaniases (CL) with single or few lesions, disseminated CL (DL) with multiple lesions to disfiguring forms of mucocutaneous leishmaniasis (MCL). In this population genetics study, 37 strains of L. (V.) guyanensis, 63 of L. (V.) braziliensis, four of L. (V.) shawi, six of L. (V.) lainsoni, seven of L. (V.) naiffi, one each of L. (V.) utingensis and L. (V.) lindenbergi, and one L. (V.) lainsoni/L. naiffi hybrid from different endemic foci in Brazil were examined for variation at 15 hyper-variable microsatellite markers. Methodology/Principal findings: The multilocus microsatellite profiles obtained for the 120 strains were analysed using both model- and distance-based methods. Significant genetic diversity was observed for all L. (Viannia) strains studied. The two cluster analysis approaches identified two principal genetic groups or populations, one consisting of strains of L. (V.) guyanensis from the Amazon region and the other of strains of L. (V.) braziliensis isolated along the Atlantic coast of Brazil. A third group comprised a heterogeneous assembly of species, including other strains of L. braziliensis isolated from the north of Brazil, which were extremely polymorphic. The latter strains seemed to be more closely related to those of L. (V.) shawi, L. (V.) naiffi, and L. (V.) lainsoni, also isolated in northern Brazilian foci. The MLMT approach identified an epidemic clone consisting of 13 strains of L. braziliensis from Minas Gerais, but evidence for recombination was obtained for the populations of L. (V.) braziliensis from the Atlantic coast and for L. (V.) guyanensis. Conclusions/Significance: Different levels of recombination versus clonality seem to occur within the subgenus L. (Viannia). Though clearly departing from panmixia, sporadic, but long-term sustained recombination might explain the tremendous genetic diversity and limited population structure found for such L. (Viannia) strains. Cutaneous leishmaniasis (CL) constitutes a significant public health problem in all federal states of Brazil. Most cases are caused by parasites of the subgenus Leishmania (Viannia) which can cause a variety of clinical symptoms ranging from single or few lesions, disseminated CL with multiple lesions, to disfiguring forms of mucocutaneous leishmaniasis. This study has used a multilocus microsatellite typing approach for exploring the genetic diversity and population structure among 120 strains representing different subgenus L. (Viannia) species and different Brazilian CL foci. Genetic diversity within the subgenus was much higher than expected, especially within L. (V.) braziliensis, L. (V.) shawi, L. (V.) naiffi, and L. (V.) lainsoni which were all from the north of Brazil. These strains could not be assigned to well-defined populations, but presented a rather loosely associated group. Strains of L. (V.) braziliensis isolated along the Atlantic coast of Brazil and strains of L. (V.) guyanensis formed, however, two clearly separated populations exhibiting remarkable levels of sexual exchange. The latter finding is in contrast to previous studies suggesting clonal modes of propagation or inbreeding for natural populations of Leishmania parasites and might explain the genetic heterogeneity and limited population structure for Brazilian strains of subgenus L. (Viannia) observed in this study.
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Affiliation(s)
- Katrin Kuhls
- Institut für Mikrobiologie und Hygiene, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Elisa Cupolillo
- Laboratório de Pesquisa em Leishmaniose, Instituto Oswaldo Cruz - Fiocruz, Rio de Janeiro, Brazil
| | - Soraia O. Silva
- Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Carola Schweynoch
- Institut für Mikrobiologie und Hygiene, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Mariana Côrtes Boité
- Laboratório de Pesquisa em Leishmaniose, Instituto Oswaldo Cruz - Fiocruz, Rio de Janeiro, Brazil
| | - Maria N. Mello
- Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Isabel Mauricio
- Instituto de Higiene e Medicina Tropical, Lisboa, Portugal
- Department of Pathogen Molecular Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Michael Miles
- Department of Pathogen Molecular Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Thierry Wirth
- Ecole Pratique des Hautes Etudes, Muséum National d'Histoire Naturelle, Département de Systématique et Évolution, UMR-CNRS 7205, Paris, France
| | - Gabriele Schönian
- Institut für Mikrobiologie und Hygiene, Charité Universitätsmedizin Berlin, Berlin, Germany
- * E-mail:
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Fraga J, Montalvo AM, Maes L, Dujardin JC, Van der Auwera G. HindII and SduI digests of heat-shock protein 70 PCR for Leishmania typing. Diagn Microbiol Infect Dis 2013; 77:245-7. [PMID: 24050933 DOI: 10.1016/j.diagmicrobio.2013.07.023] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Revised: 07/30/2013] [Accepted: 07/31/2013] [Indexed: 10/26/2022]
Abstract
Restriction fragment length polymorphisms of the heat-shock protein 70 gene have been used for discriminating Leishmania species. Here, we validated HindII as a much cheaper alternative to EcoRII and SduI for discriminating Leishmania (Viannia) braziliensis from Leishmania (Viannia) naiffi and an atypical Leishmania (V.) braziliensis group, which was previously not possible.
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Affiliation(s)
- Jorge Fraga
- Departamento de Parasitología, Instituto de Medicina Tropical "Pedro Kourí", Havana, Cuba
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Restrepo CM, De La Guardia C, Sousa OE, Calzada JE, Fernández PL, Lleonart R. AFLP polymorphisms allow high resolution genetic analysis of American Tegumentary Leishmaniasis agents circulating in Panama and other members of the Leishmania genus. PLoS One 2013; 8:e73177. [PMID: 24039881 PMCID: PMC3767818 DOI: 10.1371/journal.pone.0073177] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 07/18/2013] [Indexed: 11/18/2022] Open
Abstract
American Tegumentary Leishmaniasis is caused by parasites of the genus Leishmania, and causes significant health problems throughout the Americas. In Panama, Leishmania parasites are endemic, causing thousands of new cases every year, mostly of the cutaneous form. In the last years, the burden of the disease has increased, coincident with increasing disturbances in its natural sylvatic environments. The study of genetic variation in parasites is important for a better understanding of the biology, population genetics, and ultimately the evolution and epidemiology of these organisms. Very few attempts have been made to characterize genetic polymorphisms of parasites isolated from Panamanian patients of cutaneous leishmaniasis. Here we present data on the genetic variability of local isolates of Leishmania, as well as specimens from several other species, by means of Amplified Fragment Length Polymorphisms (AFLP), a technique seldom used to study genetic makeup of parasites. We demonstrate that this technique allows detection of very high levels of genetic variability in local isolates of Leishmania panamensis in a highly reproducible manner. The analysis of AFLP fingerprints generated by unique selective primer combinations in L. panamensis suggests a predominant clonal mode of reproduction. Using fluorescently labeled primers, many taxon-specific fragments were identified which may show potential as species diagnostic fragments. The AFLP permitted a high resolution genetic analysis of the Leishmania genus, clearly separating certain groups among L. panamensis specimens and highly related species such as L. panamensis and L. guyanensis. The phylogenetic networks reconstructed from our AFLP data are congruent with established taxonomy for the genus Leishmania, even when using single selective primer combinations. Results of this study demonstrate that AFLP polymorphisms can be informative for genetic characterization in Leishmania parasites, at both intra and inter-specific levels.
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Affiliation(s)
- Carlos M Restrepo
- Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT-AIP), Ciudad de Panamá, Panamá ; Department of Biotechnology, Acharya Nagarjuna University, Guntur, India
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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] [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.
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Affiliation(s)
- G Van der Auwera
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.
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34
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How clonal are Trypanosoma and Leishmania? Trends Parasitol 2013; 29:264-9. [DOI: 10.1016/j.pt.2013.03.007] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Revised: 03/12/2013] [Accepted: 03/13/2013] [Indexed: 11/20/2022]
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Evolution and species discrimination according to the Leishmania heat-shock protein 20 gene. INFECTION GENETICS AND EVOLUTION 2013; 18:229-37. [PMID: 23722022 DOI: 10.1016/j.meegid.2013.05.020] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2013] [Revised: 05/11/2013] [Accepted: 05/20/2013] [Indexed: 01/09/2023]
Abstract
The Leishmania genus comprises up to 35 species, of which 20 are responsible for human disease. However, the taxonomic status for many of them is under discussion. The small Heat Shock Proteins (sHSPs) are physiologically relevant, protecting cellular proteins from aggregation and maintaining cellular viability under intensive stress conditions. In Leishmania, a protein of this class was previously described, the 20-kDa heat-shock protein (HSP20), which is encoded by a single gene. In the present study, we used this target, alone or in combination with hsp70 gene, to investigate the phylogenetic relationships among Leishmania species. Using a pair of degenerate primers it was possible amplifying a 370bp fragment of the hsp20 coding region in 39 strains of very different geographic origins, representing in total 16 Leishmania species (14 if L. chagasi and L. archibaldi are considered synonymous names of L. infantum and L. donovani, respectively). Nucleotide sequences were readily obtained by direct sequencing of the amplification products. Both phylogenetic trees and networks based on either hsp20 sequences or combined datasets of hsp20 and hsp70 sequences were constructed. These phylogenic analyses supported the division of the Leishmania genus into nine species: L. (L.) donovani, L. (L.) major, L. (L.) tropica, L. (L.) aethiopica, L. (L.) mexicana, L. (V.) lainsoni, L. (V.) naiffi, L. (V.) guyanensis and L. (V.) braziliensis. Additionally, by network analysis, the subspecies L. (L.) donovani infantum and L. (V.) braziliensis peruviana were recognized within the L. (L.) donovani and L. (V.) braziliensis species, respectively. Therefore, hsp20 gene was found to be a suitable molecular marker for Leishmania typing and classification purposes. In addition, this study represents a solid contribution to the objective of establishing a more reliable taxonomy for the genus Leishmania.
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Accurate and rapid species typing from cutaneous and mucocutaneous leishmaniasis lesions of the New World. Diagn Microbiol Infect Dis 2012; 74:142-50. [DOI: 10.1016/j.diagmicrobio.2012.06.010] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Revised: 05/29/2012] [Accepted: 06/08/2012] [Indexed: 11/21/2022]
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