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Silvestrini MMA, Alessio GD, Frias BED, Sales Júnior PA, Araújo MSS, Silvestrini CMA, Brito Alvim de Melo GE, Martins-Filho OA, Teixeira-Carvalho A, Martins HR. New insights into Trypanosoma cruzi genetic diversity, and its influence on parasite biology and clinical outcomes. Front Immunol 2024; 15:1342431. [PMID: 38655255 PMCID: PMC11035809 DOI: 10.3389/fimmu.2024.1342431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 02/26/2024] [Indexed: 04/26/2024] Open
Abstract
Chagas disease, caused by Trypanosoma cruzi, remains a serious public health problem worldwide. The parasite was subdivided into six distinct genetic groups, called "discrete typing units" (DTUs), from TcI to TcVI. Several studies have indicated that the heterogeneity of T. cruzi species directly affects the diversity of clinical manifestations of Chagas disease, control, diagnosis performance, and susceptibility to treatment. Thus, this review aims to describe how T. cruzi genetic diversity influences the biology of the parasite and/or clinical parameters in humans. Regarding the geographic dispersion of T. cruzi, evident differences were observed in the distribution of DTUs in distinct areas. For example, TcII is the main DTU detected in Brazilian patients from the central and southeastern regions, where there are also registers of TcVI as a secondary T. cruzi DTU. An important aspect observed in previous studies is that the genetic variability of T. cruzi can impact parasite infectivity, reproduction, and differentiation in the vectors. It has been proposed that T. cruzi DTU influences the host immune response and affects disease progression. Genetic aspects of the parasite play an important role in determining which host tissues will be infected, thus heavily influencing Chagas disease's pathogenesis. Several teams have investigated the correlation between T. cruzi DTU and the reactivation of Chagas disease. In agreement with these data, it is reasonable to suppose that the immunological condition of the patient, whether or not associated with the reactivation of the T. cruzi infection and the parasite strain, may have an important role in the pathogenesis of Chagas disease. In this context, understanding the genetics of T. cruzi and its biological and clinical implications will provide new knowledge that may contribute to additional strategies in the diagnosis and clinical outcome follow-up of patients with Chagas disease, in addition to the reactivation of immunocompromised patients infected with T. cruzi.
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Affiliation(s)
| | - Glaucia Diniz Alessio
- Integrated Biomarker Research Group, René Rachou Institute, Fiocruz Minas, Oswaldo Cruz Foundation, Belo Horizonte, Minas Gerais, Brazil
| | - Bruna Estefânia Diniz Frias
- Integrated Biomarker Research Group, René Rachou Institute, Fiocruz Minas, Oswaldo Cruz Foundation, Belo Horizonte, Minas Gerais, Brazil
| | - Policarpo Ademar Sales Júnior
- Integrated Biomarker Research Group, René Rachou Institute, Fiocruz Minas, Oswaldo Cruz Foundation, Belo Horizonte, Minas Gerais, Brazil
| | - Márcio Sobreira Silva Araújo
- Integrated Biomarker Research Group, René Rachou Institute, Fiocruz Minas, Oswaldo Cruz Foundation, Belo Horizonte, Minas Gerais, Brazil
| | | | | | - Olindo Assis Martins-Filho
- Integrated Biomarker Research Group, René Rachou Institute, Fiocruz Minas, Oswaldo Cruz Foundation, Belo Horizonte, Minas Gerais, Brazil
| | - Andréa Teixeira-Carvalho
- Integrated Biomarker Research Group, René Rachou Institute, Fiocruz Minas, Oswaldo Cruz Foundation, Belo Horizonte, Minas Gerais, Brazil
| | - Helen Rodrigues Martins
- Department of Pharmacy, Federal University of the Jequitinhonha and Mucuri Valleys, Diamantina, Minas Gerais, Brazil
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Durães-Oliveira J, Palma-Marques J, Moreno C, Rodrigues A, Monteiro M, Alexandre-Pires G, da Fonseca IP, Santos-Gomes G. Chagas Disease: A Silent Threat for Dogs and Humans. Int J Mol Sci 2024; 25:3840. [PMID: 38612650 PMCID: PMC11011309 DOI: 10.3390/ijms25073840] [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: 02/06/2024] [Revised: 03/15/2024] [Accepted: 03/22/2024] [Indexed: 04/14/2024] Open
Abstract
Chagas disease (CD) is a vector-borne Neglected Zoonotic Disease (NZD) caused by a flagellate protozoan, Trypanosoma cruzi, that affects various mammalian species across America, including humans and domestic animals. However, due to an increase in population movements and new routes of transmission, T. cruzi infection is presently considered a worldwide health concern, no longer restricted to endemic countries. Dogs play a major role in the domestic cycle by acting very efficiently as reservoirs and allowing the perpetuation of parasite transmission in endemic areas. Despite the significant progress made in recent years, still there is no vaccine against human and animal disease, there are few drugs available for the treatment of human CD, and there is no standard protocol for the treatment of canine CD. In this review, we highlight human and canine Chagas Disease in its different dimensions and interconnections. Dogs, which are considered to be the most important peridomestic reservoir and sentinel for the transmission of T. cruzi infection in a community, develop CD that is clinically similar to human CD. Therefore, an integrative approach, based on the One Health concept, bringing together the advances in genomics, immunology, and epidemiology can lead to the effective development of vaccines, new treatments, and innovative control strategies to tackle CD.
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Affiliation(s)
- João Durães-Oliveira
- Global Health and Tropical Medicine, GHTM, Associate Laboratory in Translation and Innovation Towards Global Health, LA-REAL, Instituto de Higiene e Medicina Tropical, IHMT, Universidade NOVA de Lisboa, UNL, Rua da Junqueira 100, 1349-008 Lisbon, Portugal; (J.D.-O.); (G.S.-G.)
| | - Joana Palma-Marques
- Global Health and Tropical Medicine, GHTM, Associate Laboratory in Translation and Innovation Towards Global Health, LA-REAL, Instituto de Higiene e Medicina Tropical, IHMT, Universidade NOVA de Lisboa, UNL, Rua da Junqueira 100, 1349-008 Lisbon, Portugal; (J.D.-O.); (G.S.-G.)
| | - Cláudia Moreno
- Global Health and Tropical Medicine, GHTM, Associate Laboratory in Translation and Innovation Towards Global Health, LA-REAL, Instituto de Higiene e Medicina Tropical, IHMT, Universidade NOVA de Lisboa, UNL, Rua da Junqueira 100, 1349-008 Lisbon, Portugal; (J.D.-O.); (G.S.-G.)
| | - Armanda Rodrigues
- Global Health and Tropical Medicine, GHTM, Associate Laboratory in Translation and Innovation Towards Global Health, LA-REAL, Instituto de Higiene e Medicina Tropical, IHMT, Universidade NOVA de Lisboa, UNL, Rua da Junqueira 100, 1349-008 Lisbon, Portugal; (J.D.-O.); (G.S.-G.)
| | - Marta Monteiro
- Global Health and Tropical Medicine, GHTM, Associate Laboratory in Translation and Innovation Towards Global Health, LA-REAL, Instituto de Higiene e Medicina Tropical, IHMT, Universidade NOVA de Lisboa, UNL, Rua da Junqueira 100, 1349-008 Lisbon, Portugal; (J.D.-O.); (G.S.-G.)
- Centre for Interdisciplinary Research in Animal Health, CIISA, Faculty of Veterinary Medicine, FMV, University of Lisbon, ULisboa, 1649-004 Lisbon, Portugal; (G.A.-P.); (I.P.d.F.)
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 1300-477 Lisbon, Portugal
| | - Graça Alexandre-Pires
- Centre for Interdisciplinary Research in Animal Health, CIISA, Faculty of Veterinary Medicine, FMV, University of Lisbon, ULisboa, 1649-004 Lisbon, Portugal; (G.A.-P.); (I.P.d.F.)
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 1300-477 Lisbon, Portugal
| | - Isabel Pereira da Fonseca
- Centre for Interdisciplinary Research in Animal Health, CIISA, Faculty of Veterinary Medicine, FMV, University of Lisbon, ULisboa, 1649-004 Lisbon, Portugal; (G.A.-P.); (I.P.d.F.)
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 1300-477 Lisbon, Portugal
| | - Gabriela Santos-Gomes
- Global Health and Tropical Medicine, GHTM, Associate Laboratory in Translation and Innovation Towards Global Health, LA-REAL, Instituto de Higiene e Medicina Tropical, IHMT, Universidade NOVA de Lisboa, UNL, Rua da Junqueira 100, 1349-008 Lisbon, Portugal; (J.D.-O.); (G.S.-G.)
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Rusman F, Díaz AG, Ponce T, Floridia-Yapur N, Barnabé C, Diosque P, Tomasini N. Wide reference databases for typing Trypanosoma cruzi based on amplicon sequencing of the minicircle hypervariable region. PLoS Negl Trop Dis 2023; 17:e0011764. [PMID: 37956210 PMCID: PMC10681310 DOI: 10.1371/journal.pntd.0011764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 11/27/2023] [Accepted: 11/02/2023] [Indexed: 11/15/2023] Open
Abstract
BACKGROUND Trypanosoma cruzi, the etiological agent of Chagas Disease, exhibits remarkable genetic diversity and is classified into different Discrete Typing Units (DTUs). Strain typing techniques are crucial for studying T. cruzi, because their DTUs have significant biological differences from one another. However, there is currently no methodological strategy for the direct typing of biological materials that has sufficient sensitivity, specificity, and reproducibility. The high diversity and copy number of the minicircle hypervariable regions (mHVRs) makes it a viable target for typing. METHODOLOGY/PRINCIPAL FINDINGS Approximately 24 million reads obtained by amplicon sequencing of the mHVR were analyzed for 62 strains belonging to the six main T. cruzi DTUs. To build reference databases of mHVR diversity for each DTU and to evaluate this target as a typing tool. Strains of the same DTU shared more mHVR clusters than strains of different DTUs, and clustered together. Different identity thresholds were used to build the reference sets of the mHVR sequences (85% and 95%, respectively). The 95% set had a higher specificity and was more suited for detecting co-infections, whereas the 85% set was excellent for identifying the primary DTU of a sample. The workflow's capacity for typing samples obtained from cultures, a set of whole-genome data, under various simulated PCR settings, in the presence of co-infecting lineages and for blood samples was also assessed. CONCLUSIONS/SIGNIFICANCE We present reference databases of mHVR sequences and an optimized typing workflow for T. cruzi including a simple online tool for deep amplicon sequencing analysis (https://ntomasini.github.io/cruzityping/). The results show that the workflow displays an equivalent resolution to that of the other typing methods. Owing to its specificity, sensitivity, relatively low cost, and simplicity, the proposed workflow could be an alternative for screening different types of samples.
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Affiliation(s)
- Fanny Rusman
- Unidad de Epidemiología Molecular (UEM), Instituto de Patología Experimental Dr. Miguel Ángel Basombrío, Universidad Nacional de Salta-CONICET, Salta, Salta, Argentina
| | - Anahí G. Díaz
- Unidad de Epidemiología Molecular (UEM), Instituto de Patología Experimental Dr. Miguel Ángel Basombrío, Universidad Nacional de Salta-CONICET, Salta, Salta, Argentina
| | - Tatiana Ponce
- Unidad de Epidemiología Molecular (UEM), Instituto de Patología Experimental Dr. Miguel Ángel Basombrío, Universidad Nacional de Salta-CONICET, Salta, Salta, Argentina
| | - Noelia Floridia-Yapur
- Unidad de Epidemiología Molecular (UEM), Instituto de Patología Experimental Dr. Miguel Ángel Basombrío, Universidad Nacional de Salta-CONICET, Salta, Salta, Argentina
| | - Christian Barnabé
- Institut de Recherche pour le Développement (IRD), UMR INTERTRYP IRD-CIRAD, University of Montpellier, Montpellier, France
| | - Patricio Diosque
- Unidad de Epidemiología Molecular (UEM), Instituto de Patología Experimental Dr. Miguel Ángel Basombrío, Universidad Nacional de Salta-CONICET, Salta, Salta, Argentina
| | - Nicolás Tomasini
- Unidad de Epidemiología Molecular (UEM), Instituto de Patología Experimental Dr. Miguel Ángel Basombrío, Universidad Nacional de Salta-CONICET, Salta, Salta, Argentina
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Barnabé C, Brenière SF, Santillán-Guayasamín S, Douzery EJP, Waleckx E. Revisiting gene typing and phylogeny of Trypanosoma cruzi reference strains: Comparison of the relevance of mitochondrial DNA, single-copy nuclear DNA, and the intergenic region of mini-exon gene. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 115:105504. [PMID: 37739149 DOI: 10.1016/j.meegid.2023.105504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 09/12/2023] [Accepted: 09/19/2023] [Indexed: 09/24/2023]
Abstract
Chagas disease is a widespread neglected disease in Latin America. Trypanosoma cruzi, the causative agent of the disease, is currently subdivided into six DTUs (discrete typing units) named TcI-TcVI, and although no clear association has been found between parasite genetics and different clinical outcomes of the disease or different transmission cycles, genetic characterization of T. cruzi strains remains crucial for integrated epidemiological studies. Numerous markers have been used for this purpose, although without consensus. These include mitochondrial genes, single or multiple-copy nuclear genes, ribosomal RNA genes, and the intergenic region of the repeated mini-exon gene. To increase our knowledge of these gene sequences and their usefulness for strain typing, we sequenced fragments of three mitochondrial genes, nine single-copy nuclear genes, and the repeated intergenic part of the mini-exon gene by Next Generation Sequencing (NGS) on a sample constituted of 16 strains representative of T. cruzi genetic diversity, to which we added the corresponding genetic data of the 38 T. cruzi genomes fully sequenced until 2022. Our results show that single-copy nuclear genes remain the gold standard for characterizing T. cruzi strains; the phylogenetic tree from concatenated genes (3959 bp) confirms the six DTUs previously recognized and provides additional information about the alleles present in the hybrid strains. In the tree built from the three mitochondrial concatenated genes (1274 bp), three main clusters are identified, including one with TcIII, TcIV, TcV, and TcVI DTUs which are not separated. Nevertheless, mitochondrial markers remain necessary for detecting introgression and heteroplasmy. The phylogenetic tree built from the sequence alignment of the repeated mini-exon gene fragment (327 bp) displayed six clusters, but only TcI was associated with a single cluster. The sequences obtained from strains belonging to the other DTUs were scattered into different clusters. Therefore, while the mini-exon marker may bring, for some biological samples, some advantages in terms of sensibility due to its repeated nature, mini-exon sequences must be used with caution and, when possible, avoided for T. cruzi typing and phylogenetic studies.
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Affiliation(s)
- Christian Barnabé
- Institut de Recherche pour le Développement (IRD), UMR INTERTRYP IRD, CIRAD, University of Montpellier, Montpellier, France.
| | - Simone Frédérique Brenière
- Institut de Recherche pour le Développement (IRD), UMR INTERTRYP IRD, CIRAD, University of Montpellier, Montpellier, France
| | - Soledad Santillán-Guayasamín
- Institut de Recherche pour le Développement (IRD), UMR INTERTRYP IRD, CIRAD, University of Montpellier, Montpellier, France; Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.
| | - Emmanuel J P Douzery
- Institut des Sciences de l'Évolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France.
| | - Etienne Waleckx
- Institut de Recherche pour le Développement (IRD), UMR INTERTRYP IRD, CIRAD, University of Montpellier, Montpellier, France; Laboratorio de Parasitología, Centro de Investigaciones Regionales "Dr Hideyo Noguchi", Universidad Autónoma de Yucatán, Mérida, Mexico; ACCyC, Asociación Chagas con Ciencia y Conocimiento, A. C, Orizaba, Mexico.
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Depickère S, Villacís AG, Santillán-Guayasamín S, Callapa Rafael JE, Brenière SF, Revollo Zepita S. Rhodnius (Stål, 1859) (Hemiptera, Triatominae) genus in Bolivian Amazonia: a risk for human populations? PARASITES & VECTORS 2022; 15:307. [PMID: 36038947 PMCID: PMC9426019 DOI: 10.1186/s13071-022-05423-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 07/15/2022] [Indexed: 11/26/2022]
Abstract
Background Chagas disease, one of the most important neglected tropical diseases in the countries of Latin America, is considered to be a particularly important public health concern in the Amazon region due to increases in the number of outbreaks of acute Chagas disease and increased local transmission in the last 20 years. However, relative to other countries, in Bolivia there is little information available on its transmission in the Amazon region. The aim of this study was to investigate the infestation of palm trees, the main habitat of Triatominae in the region, in several localities, to evaluate the danger they represent to inhabitants. Methods Triatominae were collected using live bait traps left overnight in six localities in Pando and Beni Departments, Bolivia. DNA extraction and sequencing were used to establish the Triatominae species (Cytb, 16S and 28S-D2 gene fragments), and the blood meal sources (Cytb fragment). Trypanosoma sp. infection was analyzed by sequencing gene fragments (GPX, GPI, HMCOAR, LAP, PDH and COII) or by mini-exon multiplex PCR. Results A total of 325 Rhodnius were captured (97.3% of nymphs) from the 1200 traps placed in 238 palm trees and 32 burrows/ground holes. Sequence analyses on DNA extracted from 114 insects and phylogeny analysis identified two triatomine species: Rhodnius stali (17%) and Rhodnius montenegrensis (equated to Rhodnius robustus II, 83%). These were found in palm trees of the genera Attalea (69%), Astrocaryum (13%), Copernicia (12%), Euterpe (2%) and Acrocomia (1%). The infection rate was around 30% (165 analyzed insects), with 90% of analyzed insects infected by Trypanosoma cruzi (only the TcI discrete typing unit was detected), 3% infected by Trypanosoma rangeli (first time found in Bolivian Triatominae) and 7% infected by mixed T. cruzi (TcI)-T. rangeli. Rhodnius specimens fed on Didelphidae, rodents, gecko and humans. Conclusions The results of this study highlight the epidemiological importance of Rhodnius in the Bolivian Amazon region. The huge geographical distribution of Rhodnius and their proximity to the human dwellings, high infection rate and frequent meals on the human population highlight a risk of transmission of Chagas disease in the region. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13071-022-05423-3.
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Hickson J, Athayde LFA, Miranda TG, Junior PAS, Dos Santos AC, da Cunha Galvão LM, da Câmara ACJ, Bartholomeu DC, de Souza RDCM, Murta SMF, Nahum LA. Trypanosoma cruzi iron superoxide dismutases: insights from phylogenetics to chemotherapeutic target assessment. Parasit Vectors 2022; 15:194. [PMID: 35668508 PMCID: PMC9169349 DOI: 10.1186/s13071-022-05319-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 05/10/2022] [Indexed: 11/25/2022] Open
Abstract
Background Components of the antioxidant defense system in Trypanosoma cruzi are potential targets for new drug development. Superoxide dismutases (SODs) constitute key components of antioxidant defense systems, removing excess superoxide anions by converting them into oxygen and hydrogen peroxide. The main goal of the present study was to investigate the genes coding for iron superoxide dismutase (FeSOD) in T. cruzi strains from an evolutionary perspective. Methods In this study, molecular biology methods and phylogenetic studies were combined with drug assays. The FeSOD-A and FeSOD-B genes of 35 T. cruzi strains, belonging to six discrete typing units (Tcl–TcVI), from different hosts and geographical regions were amplified by PCR and sequenced using the Sanger method. Evolutionary trees were reconstructed based on Bayesian inference and maximum likelihood methods. Drugs that potentially interacted with T. cruzi FeSODs were identified and tested against the parasites. Results Our results suggest that T. cruzi FeSOD types are members of distinct families. Gene copies of FeSOD-A (n = 2), FeSOD-B (n = 4) and FeSOD-C (n = 4) were identified in the genome of the T. cruzi reference clone CL Brener. Phylogenetic inference supported the presence of two functional variants of each FeSOD type across the T. cruzi strains. Phylogenetic trees revealed a monophyletic group of FeSOD genes of T. cruzi TcIV strains in both distinct genes. Altogether, our results support the hypothesis that gene duplication followed by divergence shaped the evolution of T. cruzi FeSODs. Two drugs, mangafodipir and polaprezinc, that potentially interact with T. cruzi FeSODs were identified and tested in vitro against amastigotes and trypomastigotes: mangafodipir had a low trypanocidal effect and polaprezinc was inactive. Conclusions Our study contributes to a better understanding of the molecular biodiversity of T. cruzi FeSODs. Herein we provide a successful approach to the study of gene/protein families as potential drug targets. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13071-022-05319-2.
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Affiliation(s)
- Jéssica Hickson
- René Rachou Institute, Oswaldo Cruz Foundation (Functional genomics of parasites group; Biosystems informatics, bioengineering and genomic group), Belo Horizonte, Minas Gerais, Brazil
| | - Lucas Felipe Almeida Athayde
- René Rachou Institute, Oswaldo Cruz Foundation (Functional genomics of parasites group; Biosystems informatics, bioengineering and genomic group), Belo Horizonte, Minas Gerais, Brazil.,Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Thainá Godinho Miranda
- René Rachou Institute, Oswaldo Cruz Foundation (Functional genomics of parasites group; Biosystems informatics, bioengineering and genomic group), Belo Horizonte, Minas Gerais, Brazil.,Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Policarpo Ademar Sales Junior
- René Rachou Institute, Oswaldo Cruz Foundation (Functional genomics of parasites group; Biosystems informatics, bioengineering and genomic group), Belo Horizonte, Minas Gerais, Brazil
| | - Anderson Coqueiro Dos Santos
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Lúcia Maria da Cunha Galvão
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil.,Department of Clinical and Toxicological Analysis, Federal University of Rio Grande do Norte State, Natal, Rio Grande do Norte, Brazil
| | - Antônia Cláudia Jácome da Câmara
- Department of Clinical and Toxicological Analysis, Federal University of Rio Grande do Norte State, Natal, Rio Grande do Norte, Brazil
| | - Daniella Castanheira Bartholomeu
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Rita de Cássia Moreira de Souza
- René Rachou Institute, Oswaldo Cruz Foundation (Functional genomics of parasites group; Biosystems informatics, bioengineering and genomic group), Belo Horizonte, Minas Gerais, Brazil
| | - Silvane Maria Fonseca Murta
- René Rachou Institute, Oswaldo Cruz Foundation (Functional genomics of parasites group; Biosystems informatics, bioengineering and genomic group), Belo Horizonte, Minas Gerais, Brazil.
| | - Laila Alves Nahum
- René Rachou Institute, Oswaldo Cruz Foundation (Functional genomics of parasites group; Biosystems informatics, bioengineering and genomic group), Belo Horizonte, Minas Gerais, Brazil. .,Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil. .,Promove College of Technology, Belo Horizonte, Minas Gerais, Brazil.
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Muñoz-Calderón A, Wehrendt D, Cura C, Gómez-Bravo A, Abril M, Giammaria M, Lucero RH, Schijman AG. Real-time polymerase chain reaction based algorithm for differential diagnosis of Kinetoplastidean species of zoonotic relevance. INFECTION GENETICS AND EVOLUTION 2020; 83:104328. [DOI: 10.1016/j.meegid.2020.104328] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 04/12/2020] [Accepted: 04/18/2020] [Indexed: 02/07/2023]
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Rusman F, Floridia-Yapur N, Ragone PG, Diosque P, Tomasini N. Evidence of hybridization, mitochondrial introgression and biparental inheritance of the kDNA minicircles in Trypanosoma cruzi I. PLoS Negl Trop Dis 2020; 14:e0007770. [PMID: 32004318 PMCID: PMC7015434 DOI: 10.1371/journal.pntd.0007770] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 02/12/2020] [Accepted: 01/13/2020] [Indexed: 11/21/2022] Open
Abstract
Background Genetic exchange in Trypanosoma cruzi is controversial not only in relation to its frequency, but also to its mechanism. Parasexual genetic exchange has been proposed based on laboratory hybrids, but population genomics strongly suggests meiosis in T. cruzi. In addition, mitochondrial introgression has been reported several times in natural isolates although its mechanism is not fully understood yet. Moreover, hybrid T. cruzi DTUs (TcV and TcVI) have inherited at least part of the kinetoplastic DNA (kDNA = mitochondrial DNA) from both parents. Methodology/Principal findings In order to address such topics, we sequenced and analyzed fourteen nuclear DNA fragments and three kDNA maxicircle genes in three TcI stocks which are natural clones potentially involved in events of genetic exchange. We also deep-sequenced (a total of 6,146,686 paired-end reads) the minicircle hypervariable region (mHVR) of the kDNA in such three strains. In addition, we analyzed the DNA content by flow cytometry to address cell ploidy. We observed that most polymorphic sites in nuclear loci showed a hybrid pattern in one cloned strain and the other two cloned strains were compatible as parental strains (or nearly related to the true parents). The three clones had almost the same ploidy and the DNA content was similar to the reference strain Sylvio (a nearly diploid strain). Despite maxicircle genes evolve faster than nuclear housekeeping ones, we detected no polymorphisms in the sequence of three maxicircle genes showing mito-nuclear discordance. Lastly, the hybrid stock shared 66% of its mHVR clusters with one putative parent and 47% with the other one; in contrast, the putative parental stocks shared less than 30% of the mHVR clusters between them. Conclusions/significance The results suggest a reductive division, a natural hybridization, biparental inheritance of the minicircles in the hybrid and maxicircle introgression. The models including such phenomena and explaining the relationships between these three clones are discussed. Chagas disease, an important public health problem in Latin America, is caused by the parasite Trypanosoma cruzi. Despite being a widely studied parasite, several questions on the biology of genetic exchange remain unanswered. Population genomic studies have inferred meiosis in T. cruzi, but this cellular division mechanism has not been observed in laboratory yet. In addition, previous results suggest that mitochondrial DNA (called kDNA) may be inherited from both parents in hybrids. Here, we analyzed a hybrid strain and its potential parents to address the mechanisms of genetic exchange at nuclear and mitochondrial levels. We observed that the hybrid strain had heterozygous patterns and DNA content compatible with a meiosis event. Also, we observed that the evolutionary histories of nuclear DNA and kDNA maxicircles were discordant and that the three strains shared identical DNA sequences. Mitochondrial introgression of maxicircle DNA from one genotype to another may explain this observation. In addition, we demonstrated that the hybrid strain shared kDNA minicircles with both parental strains. Our results suggest that hybridization implied meiosis and biparental inheritance of the kDNA. Further research is required to address such phenomena in detail.
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Affiliation(s)
- Fanny Rusman
- Unidad de Epidemiología Molecular (UEM), Instituto de Patología Experimental, Universidad Nacional de Salta-CONICET, Salta, Salta, Argentina
| | - Noelia Floridia-Yapur
- Unidad de Epidemiología Molecular (UEM), Instituto de Patología Experimental, Universidad Nacional de Salta-CONICET, Salta, Salta, Argentina
| | - Paula G. Ragone
- Unidad de Epidemiología Molecular (UEM), Instituto de Patología Experimental, Universidad Nacional de Salta-CONICET, Salta, Salta, Argentina
| | - Patricio Diosque
- Unidad de Epidemiología Molecular (UEM), Instituto de Patología Experimental, Universidad Nacional de Salta-CONICET, Salta, Salta, Argentina
| | - Nicolás Tomasini
- Unidad de Epidemiología Molecular (UEM), Instituto de Patología Experimental, Universidad Nacional de Salta-CONICET, Salta, Salta, Argentina
- * E-mail:
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9
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Lauthier JJ, Ruybal P, Barroso PA, Hashiguchi Y, Marco JD, Korenaga M. Development of a Multilocus sequence typing (MLST) scheme for Pan-Leishmania. Acta Trop 2020; 201:105189. [PMID: 31580847 DOI: 10.1016/j.actatropica.2019.105189] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 09/06/2019] [Accepted: 09/19/2019] [Indexed: 12/14/2022]
Abstract
Since the description of the Leishmania genus, its identification and organization have been a challenge. A high number of molecular markers have been developed to resolve phylogenetic differences at the species level and for addressing key epidemiological and population genetics questions. Based on Multilocus enzyme electrophoresis (MLEE), Multilocus sequence typing (MLST) schemes have been developed using different gene candidates. From 38 original gene targets proposed by other authors, 27 of them were chosen. In silico selection was made by analyzing free access genomic sequence data of 33 Leishmania species, one Paraleishmania representative, and one outgroup, in order to select the best 15 loci. De novo amplifications and primers redesign of these 15 genes were analyzed over a panel of 20 reference strains and isolates. Phylogenetic analysis was made at every step. Two MLST schemes were selected. The first one was based on the analysis of three-gene fragments, and it is suitable for species assignment as well as basic phylogenetic studies. By the addition of seven-genes, an approach based on the analysis of ten-gene fragments was also proposed. This is the first work that two optimized MLST schemes have been suggested, validated against a phylogenetically diverse panel of Leishmania isolates. MLST is potentially a powerful phylogenetic approach, and most probably the new gold standard for Leishmania spp. characterization.
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Affiliation(s)
- Juan Jose Lauthier
- Parasitology Department, Kochi Medical School, Kochi University, Okocho Kohasu, Nankoku, Kochi Prefecture 783-8505, Japan.
| | - Paula Ruybal
- Universidad de Buenos Aires. Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM). Facultad de Medicina. Paraguay 2155 Piso: 12, CABA (1121). Argentina
| | - Paola Andrea Barroso
- Instituto de Patología Experimental, Facultad de Ciencias de la Salud, Universidad Nacional de Salta / CONICET, Salta, Argentina
| | - Yoshihisa Hashiguchi
- Parasitology Department, Kochi Medical School, Kochi University, Okocho Kohasu, Nankoku, Kochi Prefecture 783-8505, Japan; Departamento de Parasitología y Medicina Tropical, Carrera de Medicina, Facultad de Ciencias Médicas, Universidad Católica de Santiago de Guayaquil, Guayaquil, Ecuador
| | - Jorge Diego Marco
- Instituto de Patología Experimental, Facultad de Ciencias de la Salud, Universidad Nacional de Salta / CONICET, Salta, Argentina
| | - Masataka Korenaga
- Parasitology Department, Kochi Medical School, Kochi University, Okocho Kohasu, Nankoku, Kochi Prefecture 783-8505, Japan.
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Elucidating diversity in the class composition of the minicircle hypervariable region of Trypanosoma cruzi: New perspectives on typing and kDNA inheritance. PLoS Negl Trop Dis 2019; 13:e0007536. [PMID: 31247047 PMCID: PMC6619836 DOI: 10.1371/journal.pntd.0007536] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 07/10/2019] [Accepted: 06/10/2019] [Indexed: 12/18/2022] Open
Abstract
Background Trypanosoma cruzi, the protozoan causative of Chagas disease, is classified into six main Discrete Typing Units (DTUs): TcI-TcVI. This parasite has around 105 copies of the minicircle hypervariable region (mHVR) in their kinetoplastic DNA (kDNA). The genetic diversity of the mHVR is virtually unknown. However, cross-hybridization assays using mHVRs showed hybridization only between isolates belonging to the same genetic group. Nowadays there is no methodologic approach with a good sensibility, specificity and reproducibility for direct typing on biological samples. Due to its high copy number and apparently high diversity, mHVR becomes a good target for typing. Methodology/Principal findings Around 22 million reads, obtained by amplicon sequencing of the mHVR, were analyzed for nine strains belonging to six T. cruzi DTUs. The number and diversity of mHVR clusters was variable among DTUs and even within a DTU. However, strains of the same DTU shared more mHVR clusters than strains of different DTUs and clustered together. In addition, hybrid DTUs (TcV and TcVI) shared similar percentages (1.9–3.4%) of mHVR clusters with their parentals (TcII and TcIII). Conversely, just 0.2% of clusters were shared between TcII and TcIII suggesting biparental inheritance of the kDNA in hybrids. Sequencing at low depth (20,000–40,000 reads) also revealed 95% of the mHVR clusters for each of the analyzed strains. Finally, the method revealed good correlation in cluster identity and abundance between different replications of the experiment (r = 0.999). Conclusions/Significance Our work sheds light on the sequence diversity of mHVRs at intra and inter-DTU level. The mHVR amplicon sequencing workflow described here is a reproducible technique, that allows multiplexed analysis of hundreds of strains and results promissory for direct typing on biological samples in a future. In addition, such approach may help to gain knowledge on the mechanisms of the minicircle evolution and phylogenetic relationships among strains. Chagas disease is an important public health problem in Latin America showing a wide diversity of clinical manifestations and epidemiological patterns. It is caused by the parasite Trypanosoma cruzi. This parasite is genetically diverse and classified into six main lineages. However, the relationship between intra-specific genetic diversity and clinical or epidemiological features is not clear, mainly because low sensitivity for direct typing on biological samples. For this reason, genetic markers with high copy number are required to achieve sensitivity. Here, we deep sequenced and analyzed a DNA region present in the large mitochondria of the parasite (named as mHVR, 105 copies per parasite) from strains belonging to the six main lineages in order to analyze mHVR diversity and to evaluate its usefulness for typing. Despite the high sequence diversity, strains of the same lineage shared more sequences than strains of different lineages. Curiously, hybrid lineages shared mHVR sequences with both parents suggesting that mHVR (and DNA minicircles from the mitochondria) are inherited from both parentals. The mHVR amplicon sequencing workflow proposed here is reproducible and, potentially, it would be useful for typing hundreds of biological samples at time. It also provides a valuable approach to perform evolutionary and functional studies.
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Evaluation of the multispecies coalescent method to explore intra-Trypanosoma cruzi I relationships and genetic diversity. Parasitology 2019; 146:1063-1074. [PMID: 31046857 DOI: 10.1017/s0031182019000428] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Chagas Disease is a zoonosis caused by the parasite Trypanosoma cruzi. Several high-resolution markers have subdivided T. cruzi taxon into at least seven lineages or Discrete Typing Units (DTUs) (TcI-TcVI and TcBat). Trypanosoma cruzi I is the most diverse and geographically widespread DTU. Recently a TcI genotype related to domestic cycles was proposed and named as TcIDOM. Herein, we combined traditional markers and housekeeping genes and applied a Multispecies Coalescent method to explore intra-TcI relationships, lineage boundaries and genetic diversity in a random set of isolates and DNA sequences retrieved from Genbank from different countries in the Americas. We found further evidence supporting TcIDOM as an independent and emerging genotype of TcI at least in Colombia and Venezuela. We also found evidence of high phylogenetic incongruence between parasite's gene trees (including introgression) and embedded species trees, and a lack of genetic structure among geography and hosts, illustrating the complex dynamics and epidemiology of TcI across the Americas. These findings provide novel insights into T. cruzi systematics and epidemiology and support the need to assess parasite diversity and lineage boundaries through hypothesis testing using different approaches to those traditionally employed, including the Bayesian Multispecies coalescent method.
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A systematic review of the Trypanosoma cruzi genetic heterogeneity, host immune response and genetic factors as plausible drivers of chronic chagasic cardiomyopathy. Parasitology 2018; 146:269-283. [PMID: 30210012 DOI: 10.1017/s0031182018001506] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Chagas disease is a complex tropical pathology caused by the kinetoplastid Trypanosoma cruzi. This parasite displays massive genetic diversity and has been classified by international consensus in at least six Discrete Typing Units (DTUs) that are broadly distributed in the American continent. The main clinical manifestation of the disease is the chronic chagasic cardiomyopathy (CCC) that is lethal in the infected individuals. However, one intriguing feature is that only 30-40% of the infected individuals will develop CCC. Some authors have suggested that the immune response, host genetic factors, virulence factors and even the massive genetic heterogeneity of T. cruzi are responsible of this clinical pattern. To date, no conclusive data support the reason why a few percentages of the infected individuals will develop CCC. Therefore, we decided to conduct a systematic review analysing the host genetic factors, immune response, cytokine production, virulence factors and the plausible association of the parasite DTUs and CCC. The epidemiological and clinical implications are herein discussed.
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Roman F, das Chagas Xavier S, Messenger LA, Pavan MG, Miles MA, Jansen AM, Yeo M. Dissecting the phyloepidemiology of Trypanosoma cruzi I (TcI) in Brazil by the use of high resolution genetic markers. PLoS Negl Trop Dis 2018; 12:e0006466. [PMID: 29782493 PMCID: PMC5983858 DOI: 10.1371/journal.pntd.0006466] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 06/01/2018] [Accepted: 04/19/2018] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Trypanosoma cruzi, the causal agent of Chagas disease, is monophyletic but genetically heterogeneous. It is currently represented by six genetic lineages (Discrete Typing Units, DTUs) designated TcI-TcVI. TcI is the most geographically widespread and genetically heterogeneous lineage, this as is evidenced by a wide range of genetic markers applied to isolates spanning a vast geographic range in Latin America. METHODOLOGY/PRINCIPAL FINDINGS In total, 78 TcI isolated from hosts and vectors distributed in 5 different biomes of Brazil, were analyzed using 6 nuclear housekeeping genes, 25 microsatellite loci and one mitochondrial marker. Nuclear markers reveal substantial genetic diversity, significant gene flow between biomes, incongruence in phylogenies, and haplotypic analysis indicative of intra-DTU genetic exchange. Phylogenetic reconstructions based on mitochondrial and nuclear loci were incongruent, and consistent with introgression. Structure analysis of microsatellite data reveals that, amongst biomes, the Amazon is the most genetically diverse and experiences the lowest level of gene flow. Investigation of population structure based on the host species/genus, indicated that Didelphis marsupialis might play a role as the main disperser of TcI. CONCLUSIONS/SIGNIFICANCE The present work considers a large TcI sample from different hosts and vectors spanning multiple ecologically diverse biomes in Brazil. Importantly, we combine fast and slow evolving markers to contribute to the epizootiological understanding of TcI in five distinct Brazilian biomes. This constitutes the first instance in which MLST analysis was combined with the use of MLMT and maxicircle markers to evaluate the genetic diversity of TcI isolates in Brazil. Our results demonstrate the existence of substantial genetic diversity and the occurrence of introgression events. We provide evidence of genetic exchange in TcI isolates from Brazil and of the relative isolation of TcI in the Amazon biome. We observe the absence of strict associations with TcI genotypes to geographic areas and/or host species.
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Affiliation(s)
- Fabiola Roman
- Laboratório de Bleiologia de Tripanossomatídeos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brasil
| | - Samanta das Chagas Xavier
- Laboratório de Bleiologia de Tripanossomatídeos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brasil
| | - Louisa A. Messenger
- Faculty of Infectious and Tropical Diseases, Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Márcio G. Pavan
- Laboratório de Mosquitos Transmissores de Hematozoários, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Michael A. Miles
- Faculty of Infectious and Tropical Diseases, Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Ana María Jansen
- Laboratório de Bleiologia de Tripanossomatídeos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brasil
| | - Matthew Yeo
- Faculty of Infectious and Tropical Diseases, Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
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Roman F, Iñiguez AM, Yeo M, Jansen AM. Multilocus sequence typing: genetic diversity in Trypanosoma cruzi I (TcI) isolates from Brazilian didelphids. Parasit Vectors 2018; 11:107. [PMID: 29471851 PMCID: PMC5824584 DOI: 10.1186/s13071-018-2696-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 02/02/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Trypanosoma cruzi is a protozoan parasite characterized by extensive genetic heterogeneity. There are currently six recognised, genetically distinct, monophyletic clades designated discrete typing units (DTUs). TcI has the broadest geographical range and most genetic diversity evidenced by a wide range of genetic markers applied to isolates spanning a vast geographical range across Latin America. However, little is known of the diversity of TcI that exists within sylvatic mammals across the geographical expanse of Brazil. RESULTS Twenty-nine sylvatic TcI isolates spanning multiple ecologically diverse biomes across Brazil were analyzed by the application of multilocus sequence typing (MLST) using four nuclear housekeeping genes. Results revealed extensive genetic diversity and also incongruence among individual gene trees. There was no association of intralineage genotype with geography or with any particular biome, with the exception of isolates from Caatinga that formed a single cluster. However, haplotypic analyses of METIII and LYT1 constitutive markers provided evidence of recombination events in two isolates derived from Didelphis marsupialis and D. albiventris, respectively. For diversity studies all possible combinations of markers were assessed with the objective of selecting the combination of gene targets that are most resolutive using the minimum number of genes. A panel of just three gene fragments (DHFR-TS, LYT1 and METIII) discriminated 26 out of 35 genotypes. CONCLUSIONS These findings showed geographical association of genotypes clustering in Caatinga but more characteristically TcI genotypes widely distributed without specific association to geographical areas or biomes. Importantly, we detected the signature of recombination events at the nuclear level evidenced by haplotypic analysis and incongruence.
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Affiliation(s)
- Fabiola Roman
- Laboratório de Biologia de Tripanosomatídeos, Instituto Oswaldo Cruz, Fundacao Oswaldo Cruz, Rio de Janeiro, RJ, Brazil.
| | - Alena M Iñiguez
- Laboratório de Biologia de Tripanosomatídeos, Instituto Oswaldo Cruz, Fundacao Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
| | - Matthew Yeo
- Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Ana M Jansen
- Laboratório de Biologia de Tripanosomatídeos, Instituto Oswaldo Cruz, Fundacao Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
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Tomasini N. Introgression of the Kinetoplast DNA: An Unusual Evolutionary Journey in Trypanosoma cruzi. Curr Genomics 2018; 19:133-139. [PMID: 29491741 PMCID: PMC5814961 DOI: 10.2174/1389202918666170815124832] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 03/02/2017] [Accepted: 04/16/2017] [Indexed: 11/22/2022] Open
Abstract
INTRODUCTION Phylogenetic relationships between different lineages of Trypanosoma cruzi, the agent of Chagas disease, have been controversial for several years. However, recent phylogenetic and phylogenomic analyses clarified the nuclear relationships among such lineages. However, incongruence between nuclear and kinetoplast DNA phylogenies has emerged as a new challenge. This incongruence implies several events of mitochondrial introgression at evolutionary level. However, the mechanism that gave origin to introgressed lineages is unknown. Here, I will review and discuss how maxicircles of the kinetoplast were horizontally and vertically transferred between different lineages of T. cruzi. CONCLUSION Finally, I will discuss what we know - and what we don't - about the kDNA transference and inheritance in the context of sexual reproduction in this parasite.
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Affiliation(s)
- Nicolás Tomasini
- Instituto de Patología Experimental, Facultad de Ciencias de la Salud, Universidad Nacional de Salta, CONICET, Salta, Argentina
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16
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Rodrigues MS, Morelli KA, Jansen AM. Cytochrome c oxidase subunit 1 gene as a DNA barcode for discriminating Trypanosoma cruzi DTUs and closely related species. Parasit Vectors 2017; 10:488. [PMID: 29037251 PMCID: PMC5644147 DOI: 10.1186/s13071-017-2457-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Accepted: 10/05/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The DNA barcoding system using the cytochrome c oxidase subunit 1 mitochondrial gene (cox1 or COI) is highly efficient for discriminating vertebrate and invertebrate species. In the present study, we examined the suitability of cox1 as a marker for Trypanosoma cruzi identification from other closely related species. Additionally, we combined the sequences of cox1 and the nuclear gene glucose-6-phosphate isomerase (GPI) to evaluate the occurrence of mitochondrial introgression and the presence of hybrid genotypes. METHODS Sixty-two isolates of Trypanosoma spp. obtained from five of the six Brazilian biomes (Amazon Forest, Atlantic Forest, Caatinga, Cerrado and Pantanal) were sequenced for cox1 and GPI gene fragments. Phylogenetic trees were reconstructed using neighbor-joining, maximum likelihood, parsimony and Bayesian inference methods. Molecular species delimitation was evaluated through pairwise intraspecific and interspecific distances, Automatic Barcode Gap Discovery, single-rate Poisson Tree Processes and multi-rate Poisson Tree Processes. RESULTS Both cox1 and GPI genes recognized and differentiated T. cruzi, Trypanosoma cruzi marinkellei, Trypanosoma dionisii and Trypanosoma rangeli. Cox1 discriminated Tcbat, TcI, TcII, TcIII and TcIV. Additionally, TcV and TcVI were identified as a single group. Cox1 also demonstrated diversity in the discrete typing units (DTUs) TcI, TcII and TcIII and in T. c. marinkellei and T. rangeli. Cox1 and GPI demonstrated TcI and TcII as the most genetically distant branches, and the position of the other T. cruzi DTUs differed according to the molecular marker. The tree reconstructed with concatenated cox1 and GPI sequences confirmed the separation of the subgenus Trypanosoma (Schizotrypanum) sp. and the T. cruzi DTUs TcI, TcII, TcIII and TcIV. The evaluation of single nucleotide polymorphisms (SNPs) was informative for DTU differentiation using both genes. In the cox1 analysis, one SNP differentiated heterozygous hybrids from TcIV sequences. In the GPI analysis one SNP discriminated Tcbat from TcI, while another SNP distinguished TcI from TcIII. CONCLUSIONS DNA barcoding using the cox1 gene is a reliable tool to distinguish T. cruzi from T. c. marinkellei, T. dionisii and T. rangeli and identify the main T. cruzi genotypes.
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Affiliation(s)
- Marina Silva Rodrigues
- Laboratory of Trypanosomatid Biology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil
| | - Karina Alessandra Morelli
- Department of Ecology, Institute of Biology Roberto Alcantara Gomes, State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Ana Maria Jansen
- Laboratory of Trypanosomatid Biology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil
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Dorn PL, McClure AG, Gallaspy MD, Waleckx E, Woods AS, Monroy MC, Stevens L. The diversity of the Chagas parasite, Trypanosoma cruzi, infecting the main Central American vector, Triatoma dimidiata, from Mexico to Colombia. PLoS Negl Trop Dis 2017; 11:e0005878. [PMID: 28957315 PMCID: PMC5619707 DOI: 10.1371/journal.pntd.0005878] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Accepted: 08/17/2017] [Indexed: 01/02/2023] Open
Abstract
Little is known about the strains of Trypanosoma cruzi circulating in Central America and specifically in the most important vector in this region, Triatoma dimidiata. Approximately six million people are infected with T. cruzi, the causative agent of Chagas disease, which has the greatest negative economic impact and is responsible for ~12,000 deaths annually in Latin America. By international consensus, strains of T. cruzi are divided into six monophyletic clades called discrete typing units (DTUs TcI-VI) and a seventh DTU first identified in bats called TcBat. TcI shows the greatest geographic range and diversity. Identifying strains present and diversity within these strains is important as different strains and their genotypes may cause different pathologies and may circulate in different localities and transmission cycles, thus impacting control efforts, treatment and vaccine development. To determine parasite strains present in T. dimidiata across its geographic range from Mexico to Colombia, we isolated abdominal DNA from T. dimidiata and determined which specimens were infected with T. cruzi by PCR. Strains from infected insects were determined by comparing the sequence of the 18S rDNA and the spliced-leader intergenic region to typed strains in GenBank. Two DTUs were found: 94% of infected T. dimidiata contained TcI and 6% contained TcIV. TcI exhibited high genetic diversity. Geographic structure of TcI haplotypes was evident by Principal Component and Median-Joining Network analyses as well as a significant result in the Mantel test, indicating isolation by distance. There was little evidence of association with TcI haplotypes and host/vector or ecotope. This study provides new information about the strains circulating in the most important Chagas vector in Central America and reveals considerable variability within TcI as well as geographic structuring at this large geographic scale. The lack of association with particular vectors/hosts or ecotopes suggests the parasites are moving among vectors/hosts and ecotopes therefore a comprehensive approach, such as the Ecohealth approach that makes houses refractory to the vectors will be needed to successfully halt transmission of Chagas disease.
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Affiliation(s)
- Patricia L. Dorn
- Loyola University New Orleans, New Orleans, Louisiana, United States of America
| | - Annie G. McClure
- Loyola University New Orleans, New Orleans, Louisiana, United States of America
| | - Meghan D. Gallaspy
- Loyola University New Orleans, New Orleans, Louisiana, United States of America
| | | | - Adrienne S. Woods
- Loyola University New Orleans, New Orleans, Louisiana, United States of America
| | | | - Lori Stevens
- University of Vermont, Burlington, Vermont, United States of America
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ACOSTA NIDIA, LÓPEZ ELSA, LEWIS MICHAELD, LLEWELLYN MARTINS, GÓMEZ ANA, ROMÁN FABIOLA, MILES MICHAELA, YEO MATTHEW. Hosts and vectors of Trypanosoma cruzi discrete typing units in the Chagas disease endemic region of the Paraguayan Chaco. Parasitology 2017; 144:884-898. [PMID: 28179034 PMCID: PMC5471830 DOI: 10.1017/s0031182016002663] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Revised: 12/16/2016] [Accepted: 12/19/2016] [Indexed: 12/29/2022]
Abstract
Active Trypanosoma cruzi transmission persists in the Gran Chaco region, which is considered hyperendemic for Chagas disease. Understanding domestic and sylvatic transmission cycles and therefore the relationship between vectors and mammalian hosts is crucial to designing and implementing improved effective control strategies. Here we describe the species of triatomine vectors and the sylvatic mammal reservoirs of T. cruzi, in different localities of the Paraguayan and Bolivian Chaco. We identify the T. cruzi genotypes discrete typing units (DTUs) and provide a map of their geographical distribution. A total of 1044 triatomines and 138 sylvatic mammals were captured. Five per cent of the triatomines were microscopically positive for T. cruzi (55 Triatoma infestans from Paraguay and one sylvatic Triatoma guasayana from Bolivia) and 17 animals (12·3%) comprising eight of 28 (28·5%) Dasypus novemcinctus, four of 27 (14·8%) Euphractus sexcinctus, three of 64 (4·7%) Chaetophractus spp. and two of 14 (14·3%) Didelphis albiventris. The most common DTU infecting domestic triatomine bugs was TcV (64%), followed by TcVI (28%), TcII (6·5%) and TcIII (1·5%). TcIII was overwhelmingly associated with armadillo species. We confirm the primary role of T. infestans in domestic transmission, armadillo species as the principal sylvatic hosts of TcIII, and consider the potential risk of TcIII as an agent of Chagas disease in the Chaco.
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Affiliation(s)
- NIDIA ACOSTA
- Departamento de Medicina Tropical, Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción – UNA, San Lorenzo CP 2160, Paraguay
| | - ELSA LÓPEZ
- Departamento de Medicina Tropical, Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción – UNA, San Lorenzo CP 2160, Paraguay
| | - MICHAEL D. LEWIS
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - MARTIN S. LLEWELLYN
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - ANA GÓMEZ
- Centro para el Desarrollo de la Investigación Científica (CEDIC)/Díaz Gill Medicina Laboratorial/Fundación Moisés Bertoni, Asunción, Paraguay
| | - FABIOLA ROMÁN
- Centro para el Desarrollo de la Investigación Científica (CEDIC)/Díaz Gill Medicina Laboratorial/Fundación Moisés Bertoni, Asunción, Paraguay
| | - MICHAEL A. MILES
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - MATTHEW YEO
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
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Tomasini N, Ragone PG, Gourbière S, Aparicio JP, Diosque P. Epidemiological modeling of Trypanosoma cruzi: Low stercorarian transmission and failure of host adaptive immunity explain the frequency of mixed infections in humans. PLoS Comput Biol 2017; 13:e1005532. [PMID: 28481887 PMCID: PMC5440054 DOI: 10.1371/journal.pcbi.1005532] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 05/22/2017] [Accepted: 04/24/2017] [Indexed: 01/27/2023] Open
Abstract
People living in areas with active vector-borne transmission of Chagas disease have multiple contacts with its causative agent, Trypanosoma cruzi. Reinfections by T. cruzi are possible at least in animal models leading to lower or even hardly detectable parasitaemia. In humans, although reinfections are thought to have major public health implications by increasing the risk of chronic manifestations of the disease, there is little quantitative knowledge about their frequency and the timing of parasite re-inoculation in the course of the disease. Here, we implemented stochastic agent-based models i) to estimate the rate of re-inoculation in humans and ii) to assess how frequent are reinfections during the acute and chronic stages of the disease according to alternative hypotheses on the adaptive immune response following a primary infection. By using a hybrid genetic algorithm, the models were fitted to epidemiological data of Argentinean rural villages where mixed infections by different genotypes of T. cruzi reach 56% in humans. To explain this percentage, the best model predicted 0.032 (0.008-0.042) annual reinfections per individual with 98.4% of them occurring in the chronic phase. In addition, the parasite escapes to the adaptive immune response mounted after the primary infection in at least 20% of the events of re-inoculation. With these low annual rates, the risks of reinfection during the typically long chronic stage of the disease stand around 14% (4%-18%) and 60% (21%-70%) after 5 and 30 years, with most individuals being re-infected 1-3 times overall. These low rates are better explained by the weak efficiency of the stercorarian mode of transmission than a highly efficient adaptive immune response. Those estimates are of particular interest for vaccine development and for our understanding of the higher risk of chronic disease manifestations suffered by infected people living in endemic areas.
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Affiliation(s)
- Nicolás Tomasini
- Instituto de Patología Experimental, Facultad de Ciencias de la Salud, CONICET, Universidad Nacional de Salta, Salta, Argentina
| | - Paula Gabriela Ragone
- Instituto de Patología Experimental, Facultad de Ciencias de la Salud, CONICET, Universidad Nacional de Salta, Salta, Argentina
| | - Sébastien Gourbière
- UMR 228 ESPACE-DEV-IMAGES, ‘Institut de Modélisation et d'Analyses en Géo-Environnement et Santé’, Université de Perpignan Via Domitia, Perpignan, France
| | - Juan Pablo Aparicio
- Instituto de Investigaciones en Energía no Convencional, CONICET, Universidad Nacional de Salta, Salta, Argentina
| | - Patricio Diosque
- Instituto de Patología Experimental, Facultad de Ciencias de la Salud, CONICET, Universidad Nacional de Salta, Salta, Argentina
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Tibayrenc M, Ayala FJ. Relevant units of analysis for applied and basic research dealing with neglected transmissible diseases: The predominant clonal evolution model of pathogenic microorganisms. PLoS Negl Trop Dis 2017; 11:e0005293. [PMID: 28448491 PMCID: PMC5407763 DOI: 10.1371/journal.pntd.0005293] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The predominant clonal evolution (PCE) model seeks to formulate a common population genetics framework for all micropathogens (namely, parasitic protozoa, fungi and yeasts, bacteria, and viruses). It relies on a definition of clonality that is only based on population structure features (namely, strongly restrained genetic recombination). Its clear-cut properties make it of strong interest for applied and basic research, since it permits the definition of stable, clearly delimited units of analysis below the species level: clonal genotypes and discrete genetic subdivisions (“near-clades”). These units of analysis can be used for clinical and epidemiological studies, vaccine and drug design, species description, and evolutionary studies on natural and experimental populations. In this review, the evolutionary and population genetics background of the model will be only briefly mentioned, while considerable emphasis will be given to its practical significance for the study and control of neglected tropical diseases. The goal of the paper is to make this practical usefulness accessible to a broad audience of readers, including scientists who are not evolution specialists, such as epidemiologists, field scientists, and clinicians. For extensive developments about the evolutionary background of the model, see our previous papers [1–9]. Citations of these former articles lead to the many references quoted in them, which cannot be listed again here.
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Affiliation(s)
- Michel Tibayrenc
- Maladies Infectieuses et Vecteurs Ecologie, Génétique, Evolution et Contrôle MIVEGEC (IRD 224-CNRS 5290-UM1-UM2), Institut de Rercherche pour le Développement (IRD), Montpellier, France
- * E-mail:
| | - Francisco J. Ayala
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, United States of America
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Muñoz-San Martín C, Apt W, Zulantay I. Real-time PCR strategy for the identification of Trypanosoma cruzi discrete typing units directly in chronically infected human blood. INFECTION GENETICS AND EVOLUTION 2017; 49:300-308. [PMID: 28185987 DOI: 10.1016/j.meegid.2017.02.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 02/03/2017] [Accepted: 02/04/2017] [Indexed: 10/20/2022]
Abstract
The protozoan Trypanosoma cruzi is the causative agent of Chagas disease, a major public health problem in Latin America. This parasite has a complex population structure comprised by six or seven major evolutionary lineages (discrete typing units or DTUs) TcI-TcVI and TcBat, some of which have apparently resulted from ancient hybridization events. Because of the existence of significant biological differences between these lineages, strain characterization methods have been essential to study T. cruzi in its different vectors and hosts. However, available methods can be laborious and costly, limited in resolution or sensitivity. In this study, a new genotyping strategy by real-time PCR to identify each of the six DTUs in clinical blood samples have been developed and evaluated. Two nuclear (SL-IR and 18S rDNA) and two mitochondrial genes (COII and ND1) were selected to develop original primers. The method was evaluated with eight genomic DNA of T. cruzi populations belonging to the six DTUs, one genomic DNA of Trypanosoma rangeli, and 53 blood samples from individuals with chronic Chagas disease. The assays had an analytical sensitivity of 1-25fg of DNA per reaction tube depending on the DTU analyzed. The selectivity of trials with 20fg/μL of genomic DNA identified each DTU, excluding non-targets DTUs in every test. The method was able to characterize 67.9% of the chronically infected clinical samples with high detection of TcII followed by TcI. With the proposed original genotyping methodology, each DTU was established with high sensitivity after a single real-time PCR assay. This novel protocol reduces carryover contamination, enables detection of each DTU independently and in the future, the quantification of each DTU in clinical blood samples.
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Affiliation(s)
- Catalina Muñoz-San Martín
- Laboratorio de Parasitología Básico-Clínico, Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Werner Apt
- Laboratorio de Parasitología Básico-Clínico, Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Inés Zulantay
- Laboratorio de Parasitología Básico-Clínico, Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile.
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Izeta-Alberdi A, Ibarra-Cerdeña CN, Moo-Llanes DA, Ramsey JM. Geographical, landscape and host associations of Trypanosoma cruzi DTUs and lineages. Parasit Vectors 2016; 9:631. [PMID: 27923409 PMCID: PMC5142175 DOI: 10.1186/s13071-016-1918-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 11/28/2016] [Indexed: 01/04/2023] Open
Abstract
Background The evolutionary history and ecological associations of Trypanosoma cruzi, the need to identify genetic markers that can distinguish parasite subpopulations, and understanding the parasite’s evolutionary and selective processes have been the subject of a significant number of publications since 1998, the year when the first DNA sequence analysis for the species was published. Methods The current analysis systematizes and re-analyzes this original research, focusing on critical methodological and analytical variables and results that have given rise to interpretations of putative patterns of genetic diversity and diversification of T. cruzi lineages, discrete typing units (DTUs), and populations, and their associations with hosts, vectors, and geographical distribution that have been interpreted as evidence for parasite subpopulation specificities. Results Few studies use hypothesis-driven or quantitative analysis for T. cruzi phylogeny (16/58 studies) or phylogeography (10/13). Among these, only one phylogenetic and five phylogeographic studies analyzed molecular markers directly from tissues (i.e. not from isolates). Analysis of T. cruzi DTU or lineage niche and its geographical projection demonstrate extensive sympatry among all clades across the continent and no significant niche differences among DTUs. DTU beta-diversity was high, indicating diverse host assemblages across regions, while host dissimilarity was principally due to host species turnover and to a much lesser degree to nestedness. DTU-host order specificities appear related to trophic or microenvironmental interactions. Conclusions More rigorous study designs and analyses will be required to discern evolutionary processes and the impact of landscape modification on population dynamics and risk for T. cruzi transmission to humans. Electronic supplementary material The online version of this article (doi:10.1186/s13071-016-1918-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Carlos N Ibarra-Cerdeña
- Departamento de Ecología Humana, Centro de Investigación y de Estudios Avanzados del IPN (Cinvestav) Unidad Mérida, Mérida, Yucatán, Mexico
| | - David A Moo-Llanes
- Centro Regional de Investigación en Salud Pública (CRISP), Instituto Nacional de Salud Pública (INSP), Tapachula, Chiapas, Mexico
| | - Janine M Ramsey
- Centro Regional de Investigación en Salud Pública (CRISP), Instituto Nacional de Salud Pública (INSP), Tapachula, Chiapas, Mexico.
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Brenière SF, Waleckx E, Barnabé C. Over Six Thousand Trypanosoma cruzi Strains Classified into Discrete Typing Units (DTUs): Attempt at an Inventory. PLoS Negl Trop Dis 2016; 10:e0004792. [PMID: 27571035 PMCID: PMC5003387 DOI: 10.1371/journal.pntd.0004792] [Citation(s) in RCA: 144] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 05/31/2016] [Indexed: 01/06/2023] Open
Abstract
Trypanosoma cruzi, the causative agent of Chagas disease, presents wide genetic diversity. Currently, six discrete typing units (DTUs), named TcI to TcVI, and a seventh one called TcBat are used for strain typing. Beyond the debate concerning this classification, this systematic review has attempted to provide an inventory by compiling the results of 137 articles that have used it. A total of 6,343 DTU identifications were analyzed according to the geographical and host origins. Ninety-one percent of the data available is linked to South America. This sample, although not free of potential bias, nevertheless provides today's picture of T. cruzi genetic diversity that is closest to reality. DTUs were genotyped from 158 species, including 42 vector species. Remarkably, TcI predominated in the overall sample (around 60%), in both sylvatic and domestic cycles. This DTU known to present a high genetic diversity, is very widely distributed geographically, compatible with a long-term evolution. The marsupial is thought to be its most ancestral host and the Gran Chaco region the place of its putative origin. TcII was rarely sampled (9.6%), absent, or extremely rare in North and Central America, and more frequently identified in domestic cycles than in sylvatic cycles. It has a low genetic diversity and has probably found refuge in some mammal species. It is thought to originate in the south-Amazon area. TcIII and TcIV were also rarely sampled. They showed substantial genetic diversity and are thought to be composed of possible polyphyletic subgroups. Even if they are mostly associated with sylvatic transmission cycles, a total of 150 human infections with these DTUs have been reported. TcV and TcVI are clearly associated with domestic transmission cycles. Less than 10% of these DTUs were identified together in sylvatic hosts. They are thought to originate in the Gran Chaco region, where they are predominant and where putative parents exist (TcII and TcIII). Trends in host-DTU specificities exist, but generally it seems that the complexity of the cycles and the participation of numerous vectors and mammal hosts in a shared area, maintains DTU diversity.
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Affiliation(s)
- Simone Frédérique Brenière
- IRD-CIRAD, INTERTRYP (Interactions hôtes-vecteurs-parasites-environnement dans les maladies tropicales négligées dues aux Trypanosomatidés), IRD Center, Montpellier, France
- Pontificia Universidad Católica del Ecuador, Centro de Investigación para la Salud en América Latina (CISeAL), Quito, Ecuador
- * E-mail:
| | - Etienne Waleckx
- Centro de Investigaciones Regionales “Hideyo Noguchi”, Universidad Autónoma de Yucatán, Mérida, Yucatán, México
| | - Christian Barnabé
- IRD-CIRAD, INTERTRYP (Interactions hôtes-vecteurs-parasites-environnement dans les maladies tropicales négligées dues aux Trypanosomatidés), IRD Center, Montpellier, France
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Messenger LA, Ramirez JD, Llewellyn MS, Guhl F, Miles MA. Importation of Hybrid Human-Associated Trypanosoma cruzi Strains of Southern South American Origin, Colombia. Emerg Infect Dis 2016; 22:1452-5. [PMID: 27434772 PMCID: PMC4982185 DOI: 10.3201/eid2208.150786] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
We report the characterization of Trypanosoma cruzi of southern South American origin among humans, domestic vectors, and peridomestic hosts in Colombia using high-resolution nuclear and mitochondrial genotyping. Expanding our understanding of the geographic range of lineage TcVI, which is associated with severe Chagas disease, will help clarify risk of human infection for improved disease control.
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Barnabé C, Mobarec HI, Jurado MR, Cortez JA, Brenière SF. Reconsideration of the seven discrete typing units within the species Trypanosoma cruzi , a new proposal of three reliable mitochondrial clades. INFECTION GENETICS AND EVOLUTION 2016; 39:176-186. [DOI: 10.1016/j.meegid.2016.01.029] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 01/29/2016] [Accepted: 01/30/2016] [Indexed: 10/22/2022]
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26
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Molecular Approaches for Diagnosis of Chagas' Disease and Genotyping of Trypanosoma cruzi. Mol Microbiol 2016. [DOI: 10.1128/9781555819071.ch36] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Tibayrenc M, Ayala FJ. The population genetics of Trypanosoma cruzi revisited in the light of the predominant clonal evolution model. Acta Trop 2015; 151:156-65. [PMID: 26188332 PMCID: PMC7117470 DOI: 10.1016/j.actatropica.2015.05.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 05/02/2015] [Accepted: 05/06/2015] [Indexed: 01/18/2023]
Abstract
Comparing the population structure of Trypanosoma cruzi with that of other pathogens, including parasitic protozoa, fungi, bacteria and viruses, shows that the agent of Chagas disease shares typical traits with many other species, related to a predominant clonal evolution (PCE) pattern: statistically significant linkage disequilibrium, overrepresented multilocus genotypes, near-clades (genetic subdivisions somewhat blurred by occasional genetic exchange/hybridization) and "Russian doll" patterns (PCE is observed, not only at the level of the whole species, but also, within the near-clades). Moreover, T. cruzi population structure exhibits linkage with the diversity of several strongly selected genes, with gene expression profiles, and with some major phenotypic traits. We discuss the evolutionary significance of these results, and their implications in terms of applied research (molecular epidemiology/strain typing, analysis of genes of interest, vaccine and drug design, immunological diagnosis) and of experimental evolution. Lastly, we revisit the long-term debate of describing new species within the T. cruzi taxon.
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Lima L, Espinosa-Álvarez O, Ortiz PA, Trejo-Varón JA, Carranza JC, Pinto CM, Serrano MG, Buck GA, Camargo EP, Teixeira MM. Genetic diversity of Trypanosoma cruzi in bats, and multilocus phylogenetic and phylogeographical analyses supporting Tcbat as an independent DTU (discrete typing unit). Acta Trop 2015. [PMID: 26200788 DOI: 10.1016/j.actatropica.2015.07.015] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Trypanosoma cruzi is a complex of phenotypically and genetically diverse isolates distributed in six discrete typing units (DTUs) designated as TcI-TcVI. Five years ago, T. cruzi isolates from Brazilian bats showing unique patterns of traditional ribosomal and spliced leader PCRs not clustering into any of the six DTUs were designated as the Tcbat genotype. In the present study, phylogenies inferred using SSU rRNA (small subunit of ribosomal rRNA), gGAPDH (glycosomal glyceraldehyde 3-phosphate dehydrogenase) and Cytb (cytochrome b) genes strongly supported Tcbat as a monophyletic lineage prevalent in Brazil, Panama and Colombia. Providing strong support for Tcbat, sequences from 37 of 47 nuclear and 12 mitochondrial genes (retrieved from a draft genome of Tcbat) and reference strains of all DTUs available in databanks corroborated Tcbat as an independent DTU. Consistent with previous studies, multilocus analysis of most nuclear genes corroborated the evolution of T. cruzi from bat trypanosomes its divergence into two main phylogenetic lineages: the basal TcII; and the lineage clustering TcIV, the clade comprising TcIII and the sister groups TcI-Tcbat. Most likely, the common ancestor of Tcbat and TcI was a bat trypanosome. However, the results of the present analysis did not support Tcbat as the ancestor of all DTUs. Despite the insights provided by reports of TcIII, TcIV and TcII in bats, including Amazonian bats harbouring TcII, further studies are necessary to understand the roles played by bats in the diversification of all DTUs. We also demonstrated that in addition to value as molecular markers for DTU assignment, Cytb, ITS rDNA and the spliced leader (SL) polymorphic sequences suggest spatially structured populations of Tcbat. Phylogenetic and phylogeographical analyses, multiple molecular markers specific to Tcbat, and the degrees of sequence divergence between Tcbat and the accepted DTUs strongly support the definitive classification of Tcbat as a new DTU.
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de Oliveira MT, de Assis GFM, Oliveira e Silva JCV, Machado EMM, da Silva GN, Veloso VM, Macedo AM, Martins HR, de Lana M. Trypanosoma cruzi Discret Typing Units (TcII and TcVI) in samples of patients from two municipalities of the Jequitinhonha Valley, MG, Brazil, using two molecular typing strategies. Parasit Vectors 2015; 8:568. [PMID: 26520576 PMCID: PMC4628324 DOI: 10.1186/s13071-015-1161-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 10/09/2015] [Indexed: 02/04/2023] Open
Abstract
Background Trypanosoma cruzi is classified into six discrete taxonomic units (DTUs). For this classification, different biological markers and classification criteria have been used. The objective was to identify the genetic profile of T. cruzi samples isolated from patients of two municipalities of Jequitinhonha Valley, MG, Brazil. Methods Molecular characterization was performed using two different criteria for T. cruzi typing to characterize 63 T. cruzi samples isolated from chronic Chagas disease patients. The characterizations followed two distinct methodologies. Additionally, the RAPD technique was used to evaluate the existence of genetic intragroup variability. Results The first methodology identified 89 % of the samples as TcII, but it was not possible to define the genetic identity of seven isolates. The results obtained with the second methodology corroborated the classification as TcII of the same samples and defined the classification of the other seven as TcVI. RAPD analysis showed lower intra-group variability in TcII. Conclusions The results confirmed the preliminary data obtained in other municipalities of the Jequitinhonha Valley, showing a predominance of TcII, similar to that verified in northeast/south axis of Brazil and the first detection of TcVI in the study region. The second protocol was more simple and reliable to identify samples of hybrid character.
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Affiliation(s)
- Maykon Tavares de Oliveira
- Núcleo de Pesquisas em Ciências Biológicas (NUPEB), Universidade Federal de Ouro Preto (UFOP), Campus Universitário Morro do Cruzeiro, CEP: 35400-000, Ouro Preto, MG, Brazil.
| | - Girley Francisco Machado de Assis
- Departamento- Básico de Saúde, Universidade Federal de Juiz de Fora (UFJF), CEP: 35010-177, Campus Governador Valadares, Governador Valadares, MG, Brazil.
| | - Jaquelline Carla Valamiel Oliveira e Silva
- Núcleo de Pesquisas em Ciências Biológicas (NUPEB), Universidade Federal de Ouro Preto (UFOP), Campus Universitário Morro do Cruzeiro, CEP: 35400-000, Ouro Preto, MG, Brazil.
| | - Evandro Marques Menezes Machado
- Núcleo de Pesquisas em Ciências Biológicas (NUPEB), Universidade Federal de Ouro Preto (UFOP), Campus Universitário Morro do Cruzeiro, CEP: 35400-000, Ouro Preto, MG, Brazil.
| | - Glenda Nicioli da Silva
- Departamento de Análises Clínicas, Escola de Farmácia, UFOP, CEP: 35400-000 Campus Universitário Morro do Cruzeiro, CEP: 35400-000, Ouro Preto, MG, Brazil. .,Programa de Pós-Graduação em Ciências Farmacêuticas (CiPHARMA), Escola de Farmácia, UFOP, Campus Universitário Morro do Cruzeiro, 35400-000, Ouro Preto, MG, Brazil.
| | - Vanja Maria Veloso
- Departamento de Análises Clínicas, Escola de Farmácia, UFOP, CEP: 35400-000 Campus Universitário Morro do Cruzeiro, CEP: 35400-000, Ouro Preto, MG, Brazil. .,Programa de Pós-Graduação em Ciências Farmacêuticas (CiPHARMA), Escola de Farmácia, UFOP, Campus Universitário Morro do Cruzeiro, 35400-000, Ouro Preto, MG, Brazil.
| | - Andrea Mara Macedo
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas (ICB), Universidade Federal de Minas Gerais (UFMG), 6627, Belo Horizonte, 31270-901, MG, Brazil.
| | - Helen Rodrigues Martins
- Departamento de Farmácia, Faculdade de Ciências Biológicas e da Saúde, Universidade dos Vales do Jequitinhonha e Mucuri (UFVJM), 39100-000, Diamantina, MG, Brazil.
| | - Marta de Lana
- Núcleo de Pesquisas em Ciências Biológicas (NUPEB), Universidade Federal de Ouro Preto (UFOP), Campus Universitário Morro do Cruzeiro, CEP: 35400-000, Ouro Preto, MG, Brazil. .,Departamento de Análises Clínicas, Escola de Farmácia, UFOP, CEP: 35400-000 Campus Universitário Morro do Cruzeiro, CEP: 35400-000, Ouro Preto, MG, Brazil. .,Programa de Pós-Graduação em Ciências Farmacêuticas (CiPHARMA), Escola de Farmácia, UFOP, Campus Universitário Morro do Cruzeiro, 35400-000, Ouro Preto, MG, Brazil.
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Messenger LA, Miles MA, Bern C. Between a bug and a hard place: Trypanosoma cruzi genetic diversity and the clinical outcomes of Chagas disease. Expert Rev Anti Infect Ther 2015; 13:995-1029. [PMID: 26162928 PMCID: PMC4784490 DOI: 10.1586/14787210.2015.1056158] [Citation(s) in RCA: 134] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Over the last 30 years, concomitant with successful transnational disease control programs across Latin America, Chagas disease has expanded from a neglected, endemic parasitic infection of the rural poor to an urbanized chronic disease, and now a potentially emergent global health problem. Trypanosoma cruzi infection has a highly variable clinical course, ranging from complete absence of symptoms to severe and often fatal cardiovascular and/or gastrointestinal manifestations. To date, few correlates of clinical disease progression have been identified. Elucidating a putative role for T. cruzi strain diversity in Chagas disease pathogenesis is complicated by the scarcity of parasites in clinical specimens and the limitations of our contemporary genotyping techniques. This article systematically reviews the historical literature, given our current understanding of parasite genetic diversity, to evaluate the evidence for any association between T. cruzi genotype and chronic clinical outcome, risk of congenital transmission or reactivation and orally transmitted outbreaks.
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Affiliation(s)
- Louisa A Messenger
- Department of Pathogen Molecular Biology, Faculty of Infectious Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Michael A Miles
- Department of Pathogen Molecular Biology, Faculty of Infectious Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Caryn Bern
- Global Health Sciences, Department of Epidemiology and Biostatistics, School of Medicine, University of California San Francisco, San Francisco, CA, USA
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Cura CI, Duffy T, Lucero RH, Bisio M, Péneau J, Jimenez-Coello M, Calabuig E, Gimenez MJ, Valencia Ayala E, Kjos SA, Santalla J, Mahaney SM, Cayo NM, Nagel C, Barcán L, Málaga Machaca ES, Acosta Viana KY, Brutus L, Ocampo SB, Aznar C, Cuba Cuba CA, Gürtler RE, Ramsey JM, Ribeiro I, VandeBerg JL, Yadon ZE, Osuna A, Schijman AG. Multiplex Real-Time PCR Assay Using TaqMan Probes for the Identification of Trypanosoma cruzi DTUs in Biological and Clinical Samples. PLoS Negl Trop Dis 2015; 9:e0003765. [PMID: 25993316 PMCID: PMC4437652 DOI: 10.1371/journal.pntd.0003765] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 04/16/2015] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Trypanosoma cruzi has been classified into six Discrete Typing Units (DTUs), designated as TcI-TcVI. In order to effectively use this standardized nomenclature, a reproducible genotyping strategy is imperative. Several typing schemes have been developed with variable levels of complexity, selectivity and analytical sensitivity. Most of them can be only applied to cultured stocks. In this context, we aimed to develop a multiplex Real-Time PCR method to identify the six T. cruzi DTUs using TaqMan probes (MTq-PCR). METHODS/PRINCIPAL FINDINGS The MTq-PCR has been evaluated in 39 cultured stocks and 307 biological samples from vectors, reservoirs and patients from different geographical regions and transmission cycles in comparison with a multi-locus conventional PCR algorithm. The MTq-PCR was inclusive for laboratory stocks and natural isolates and sensitive for direct typing of different biological samples from vectors, reservoirs and patients with acute, congenital infection or Chagas reactivation. The first round SL-IR MTq-PCR detected 1 fg DNA/reaction tube of TcI, TcII and TcIII and 1 pg DNA/reaction tube of TcIV, TcV and TcVI reference strains. The MTq-PCR was able to characterize DTUs in 83% of triatomine and 96% of reservoir samples that had been typed by conventional PCR methods. Regarding clinical samples, 100% of those derived from acute infected patients, 62.5% from congenitally infected children and 50% from patients with clinical reactivation could be genotyped. Sensitivity for direct typing of blood samples from chronic Chagas disease patients (32.8% from asymptomatic and 22.2% from symptomatic patients) and mixed infections was lower than that of the conventional PCR algorithm. CONCLUSIONS/SIGNIFICANCE Typing is resolved after a single or a second round of Real-Time PCR, depending on the DTU. This format reduces carryover contamination and is amenable to quantification, automation and kit production.
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Affiliation(s)
- Carolina I. Cura
- Laboratorio de Biología Molecular de la Enfermedad de Chagas, Instituto de Investigaciones en Ingeniería Genética y Biología Molecular “Dr. Héctor N. Torres”—INGEBI-CONICET, Buenos Aires, Argentina
| | - Tomas Duffy
- Laboratorio de Biología Molecular de la Enfermedad de Chagas, Instituto de Investigaciones en Ingeniería Genética y Biología Molecular “Dr. Héctor N. Torres”—INGEBI-CONICET, Buenos Aires, Argentina
| | - Raúl H. Lucero
- Instituto de Medicina Regional, Universidad Nacional del Nordeste, Resistencia, Chaco, Argentina
| | - Margarita Bisio
- Laboratorio de Biología Molecular de la Enfermedad de Chagas, Instituto de Investigaciones en Ingeniería Genética y Biología Molecular “Dr. Héctor N. Torres”—INGEBI-CONICET, Buenos Aires, Argentina
| | - Julie Péneau
- Laboratoire Hospitalier et Universitaire-CH Andrée Rosemon, Cayenne, French Guiana, France
| | - Matilde Jimenez-Coello
- Laboratorio Biología Celular, Centro de Investigaciones Regionales “Dr. Hideyo Noguchi”, Universidad Autónoma de Yucatán, Mérida, Yucatán, Mexico
| | - Eva Calabuig
- Servicio de Medicina Interna, Hospital Politécnico LA FE, Valencia, Spain
| | - María J. Gimenez
- Servicio de Microbiología, Hospital Universitario y Politécnico LA FE, Valencia, Spain
| | - Edward Valencia Ayala
- Laboratorio de Investigación en Enfermedades Infecciosas, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Sonia A. Kjos
- Department of Biology, University of Minnesota Duluth, Duluth, Minnesota, United States of America
| | - José Santalla
- Laboratorio de Parasitología, Instituto Nacional de Laboratorios en Salud, Ministerio de Salud y Deportes de Bolivia, La Paz, Bolivia
| | - Susan M. Mahaney
- Southwest National Primate Research Center and Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas, United States of America
| | - Nelly M. Cayo
- Instituto de Biología de la Altura, Universidad Nacional de Jujuy, Jujuy, Argentina
| | - Claudia Nagel
- Epidemiología e Infectología Clínica, Hospital Universitario Fundación Favaloro, Buenos Aires, Argentina
| | - Laura Barcán
- Sección Infectología, Servicio de Clínica Médica, Hospital Italiano, Buenos Aires, Argentina
| | - Edith S. Málaga Machaca
- Laboratorio de Investigación en Enfermedades Infecciosas, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Karla Y. Acosta Viana
- Laboratorio Biología Celular, Centro de Investigaciones Regionales “Dr. Hideyo Noguchi”, Universidad Autónoma de Yucatán, Mérida, Yucatán, Mexico
| | - Laurent Brutus
- Institut de Recherche pour le Développement and University Paris Descartes, UMR 216, Mother and Child Facing Tropical Diseases, Paris, France
| | - Susana B. Ocampo
- Instituto de Biología de la Altura, Universidad Nacional de Jujuy, Jujuy, Argentina
| | - Christine Aznar
- Laboratoire Hospitalier et Universitaire-CH Andrée Rosemon, Cayenne, French Guiana, France
| | - Cesar A. Cuba Cuba
- Parasitologia Médica e Biologia de Vetores, Área de Patologia, Faculdade de Medicina, Universidade de Brasilia, Brasilia DF, Brazil
| | - Ricardo E. Gürtler
- Laboratorio de Eco-Epidemiología, Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Janine M. Ramsey
- Centro Regional de Investigación en Salud Pública, Instituto Nacional de Salud Pública, Tapachula, Chiapas, Mexico
| | - Isabela Ribeiro
- Drugs and Neglected Diseases Initiative, Genève, Switzerland
| | - John L. VandeBerg
- Southwest National Primate Research Center and Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas, United States of America
| | - Zaida E. Yadon
- Pan American Health Organization (PAHO), World Health Organization (WHO), Washington, D.C., United States of America
| | - Antonio Osuna
- Institute of Biotechnology, Molecular Parasitology Group, University of Granada, Granada, Spain
| | - Alejandro G. Schijman
- Laboratorio de Biología Molecular de la Enfermedad de Chagas, Instituto de Investigaciones en Ingeniería Genética y Biología Molecular “Dr. Héctor N. Torres”—INGEBI-CONICET, Buenos Aires, Argentina
- * E-mail:
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Ragone PG, Pérez Brandán C, Monje Rumi M, Tomasini N, Lauthier JJ, Cimino RO, Uncos A, Ramos F, Alberti D´Amato AM, Basombrío MA, Diosque P. Experimental evidence of biological interactions among different isolates of Trypanosoma cruzi from the Chaco Region. PLoS One 2015; 10:e0119866. [PMID: 25789617 PMCID: PMC4366099 DOI: 10.1371/journal.pone.0119866] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 01/16/2015] [Indexed: 01/06/2023] Open
Abstract
Many infectious diseases arise from co-infections or re-infections with more than one genotype of the same pathogen. These mixed infections could alter host fitness, the severity of symptoms, success in pathogen transmission and the epidemiology of the disease. Trypanosoma cruzi, the etiological agent of Chagas disease, exhibits a high biological variability often correlated with its genetic diversity. Here, we developed an experimental approach in order to evaluate biological interaction between three T. cruzi isolates belonging to different Discrete Typing Units (DTUs TcIII, TcV and TcVI). These isolates were obtained from a restricted geographical area in the Chaco Region. Different mixed infections involving combinations of two isolates (TcIII + TcV, TcIII + TcVI and TcV + TcVI) were studied in a mouse model. The parameters evaluated were number of parasites circulating in peripheral blood, histopathology and genetic characterization of each DTU in different tissues by DNA hybridization probes. We found a predominance of TcVI isolate in blood and tissues respect to TcIII and TcV; and a decrease of the inflammatory response in heart when the damage of mice infected with TcVI and TcIII + TcVI mixture were compared. In addition, simultaneous presence of two isolates in the same tissue was not detected. Our results show that biological interactions between isolates with different biological behaviors lead to changes in their biological properties. The occurrence of interactions among different genotypes of T. cruzi observed in our mouse model suggests that these phenomena could also occur in natural cycles in the Chaco Region.
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Affiliation(s)
- Paula G. Ragone
- Unidad de Epidemiología Molecular, Instituto de Patología Experimental, CONICET (Consejo Nacional de Investigaciones Científicas y Técnicas), Universidad Nacional de Salta, Salta-Capital, Argentina
- Instituto de Patología Experimental, CONICET (Consejo Nacional de Investigaciones Científicas y Técnicas), Universidad Nacional de Salta, Salta-Capital, Argentina
- * E-mail:
| | - Cecilia Pérez Brandán
- Unidad de Epidemiología Molecular, Instituto de Patología Experimental, CONICET (Consejo Nacional de Investigaciones Científicas y Técnicas), Universidad Nacional de Salta, Salta-Capital, Argentina
- Instituto de Patología Experimental, CONICET (Consejo Nacional de Investigaciones Científicas y Técnicas), Universidad Nacional de Salta, Salta-Capital, Argentina
| | - Mercedes Monje Rumi
- Unidad de Epidemiología Molecular, Instituto de Patología Experimental, CONICET (Consejo Nacional de Investigaciones Científicas y Técnicas), Universidad Nacional de Salta, Salta-Capital, Argentina
- Instituto de Patología Experimental, CONICET (Consejo Nacional de Investigaciones Científicas y Técnicas), Universidad Nacional de Salta, Salta-Capital, Argentina
| | - Nicolás Tomasini
- Unidad de Epidemiología Molecular, Instituto de Patología Experimental, CONICET (Consejo Nacional de Investigaciones Científicas y Técnicas), Universidad Nacional de Salta, Salta-Capital, Argentina
- Instituto de Patología Experimental, CONICET (Consejo Nacional de Investigaciones Científicas y Técnicas), Universidad Nacional de Salta, Salta-Capital, Argentina
| | - Juan J. Lauthier
- Unidad de Epidemiología Molecular, Instituto de Patología Experimental, CONICET (Consejo Nacional de Investigaciones Científicas y Técnicas), Universidad Nacional de Salta, Salta-Capital, Argentina
- Instituto de Patología Experimental, CONICET (Consejo Nacional de Investigaciones Científicas y Técnicas), Universidad Nacional de Salta, Salta-Capital, Argentina
| | - Rubén O. Cimino
- Cátedra de Química Biológica, Facultad de Ciencias Naturales, Universidad Nacional de Salta, Salta-Capital, Argentina
| | - Alejandro Uncos
- Instituto de Patología Experimental, CONICET (Consejo Nacional de Investigaciones Científicas y Técnicas), Universidad Nacional de Salta, Salta-Capital, Argentina
| | - Federico Ramos
- Instituto de Patología Experimental, CONICET (Consejo Nacional de Investigaciones Científicas y Técnicas), Universidad Nacional de Salta, Salta-Capital, Argentina
| | - Anahí M. Alberti D´Amato
- Unidad de Epidemiología Molecular, Instituto de Patología Experimental, CONICET (Consejo Nacional de Investigaciones Científicas y Técnicas), Universidad Nacional de Salta, Salta-Capital, Argentina
- Instituto de Patología Experimental, CONICET (Consejo Nacional de Investigaciones Científicas y Técnicas), Universidad Nacional de Salta, Salta-Capital, Argentina
| | - Miguel A. Basombrío
- Instituto de Patología Experimental, CONICET (Consejo Nacional de Investigaciones Científicas y Técnicas), Universidad Nacional de Salta, Salta-Capital, Argentina
| | - Patricio Diosque
- Unidad de Epidemiología Molecular, Instituto de Patología Experimental, CONICET (Consejo Nacional de Investigaciones Científicas y Técnicas), Universidad Nacional de Salta, Salta-Capital, Argentina
- Instituto de Patología Experimental, CONICET (Consejo Nacional de Investigaciones Científicas y Técnicas), Universidad Nacional de Salta, Salta-Capital, Argentina
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Messenger LA, Yeo M, Lewis MD, Llewellyn MS, Miles MA. Molecular genotyping of Trypanosoma cruzi for lineage assignment and population genetics. Methods Mol Biol 2015; 1201:297-337. [PMID: 25388123 DOI: 10.1007/978-1-4939-1438-8_19] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Trypanosoma cruzi, the etiological agent of Chagas disease, remains a major public health problem in Latin America. Infection with T. cruzi is lifelong and can lead to a spectrum of pathological sequelae ranging from subclinical to lethal cardiac and/or gastrointestinal complications. Isolates of T. cruzi can be assigned to six genetic lineages or discrete typing units (DTUs), which are broadly associated with disparate ecologies, transmission cycles, and geographical distributions. This extensive genetic diversity is also believed to contribute to the clinical variation observed among chagasic patients. Unravelling the population structure of T. cruzi is fundamental to understanding Chagas disease epidemiology, developing control strategies, and resolving the relationship between parasite genotype and clinical prognosis. To date, no single, widely validated, genetic target allows unequivocal resolution to DTU-level. In this chapter we present standardized methods for strain DTU assignment using PCR-restriction fragment length polymorphism analysis (PCR-RFLP) and nuclear multilocus sequence typing (MLST). PCR-RFLPs have the advantages of simplicity and reproducibility, requiring limited expertise and few laboratory consumables. MLST data are more laborious to generate but more informative; DNA sequences are readily transferable between research groups and amenable to recombination detection and intra-lineage analyses. We also recommend a mitochondrial (maxicircle) MLST scheme and a panel of 28 microsatellite loci for higher resolution population genetics studies. Due to the scarcity of T. cruzi in blood and tissue, all of these genotyping techniques have limited sensitivity when applied directly to clinical or biological specimens, particularly when targets are single (MLST) or low copy number (PCR-RFLPs). We therefore describe essential protocols to isolate parasites, derive biological clones, and extract T. cruzi genomic DNA from field and clinical samples.
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Affiliation(s)
- Louisa A Messenger
- London School of Hygiene and Tropical Medicine, Room 331A, Keppel Street, London, WC1E 7HT, UK
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Monje-Rumi MM, Brandán CP, Ragone PG, Tomasini N, Lauthier JJ, Alberti D'Amato AM, Cimino RO, Orellana V, Basombrío MA, Diosque P. Trypanosoma cruzi diversity in the Gran Chaco: mixed infections and differential host distribution of TcV and TcVI. INFECTION GENETICS AND EVOLUTION 2014; 29:53-9. [PMID: 25445658 DOI: 10.1016/j.meegid.2014.11.001] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 10/29/2014] [Accepted: 11/01/2014] [Indexed: 11/26/2022]
Abstract
The transmission cycles of Trypanosoma cruzi in the Gran Chaco are complex networks involving domestic and wild components, whose interrelationships are not well understood. Knowing the circuit of transmission of the different Discrete Typing Units (DTUs) of T. cruzi in the complex environment of the Chaco region is relevant to understanding how the different components (reservoirs, vectors, ecotopes) interact. In the present study we identified the DTUs infecting humans and dogs in two rural areas of the Gran Chaco in Argentina, using molecular methods which avoid parasite culture. Blood samples of humans and dogs were typified by PCR-DNA blotting and hybridization assays with five specific DNA probes (TcI, TcII, TcIII, TcV and TcVI). PCR analyses were performed on seropositive human and dog samples and showed the presence of T. cruzi DNA in 41.7% (98/235) and 53% (35/66) samples, respectively. The identification of infective DTUs was determined in 83.6% (82/98) and 91.4% (32/35) in human and dog samples, respectively. Single infections (36.7% - 36/98) and a previously not detected high proportion of mixed infections (47.9% - 47/98) were found. In a 15.3% (15/98) of samples the infecting DTU was not identified. Among the single infections TcV was the most prevalent DTU (30.6% - 30/98) in human samples; while TcVI (42.8% - 15/35) showed the highest prevalence in dog samples. TcV/TcVI was the most prevalent mixed infection in humans (32.6% - 32/98); and TcI/TcVI (14.3% - 5/35) in dogs. Significant associations between TcV with humans and TcVI with dogs were detected. For the first time, the presence of TcIII was detected in humans from this region. The occurrence of one human infected whit TcIII (a principally wild DTU) could be suggested the emergence of this, in domestic cycles in the Gran Chaco.
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Affiliation(s)
- María M Monje-Rumi
- Unidad de Epidemiología Molecular, Instituto de Patología Experimental, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Salta, Argentina; Instituto de Patología Experimental-CONICET, Universidad Nacional de Salta, Argentina.
| | - Cecilia Pérez Brandán
- Unidad de Epidemiología Molecular, Instituto de Patología Experimental, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Salta, Argentina; Instituto de Patología Experimental-CONICET, Universidad Nacional de Salta, Argentina
| | - Paula G Ragone
- Unidad de Epidemiología Molecular, Instituto de Patología Experimental, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Salta, Argentina; Instituto de Patología Experimental-CONICET, Universidad Nacional de Salta, Argentina
| | - Nicolás Tomasini
- Unidad de Epidemiología Molecular, Instituto de Patología Experimental, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Salta, Argentina; Instituto de Patología Experimental-CONICET, Universidad Nacional de Salta, Argentina
| | - Juan J Lauthier
- Unidad de Epidemiología Molecular, Instituto de Patología Experimental, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Salta, Argentina; Instituto de Patología Experimental-CONICET, Universidad Nacional de Salta, Argentina
| | - Anahí M Alberti D'Amato
- Unidad de Epidemiología Molecular, Instituto de Patología Experimental, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Salta, Argentina; Instituto de Patología Experimental-CONICET, Universidad Nacional de Salta, Argentina
| | - Rubén O Cimino
- Instituto de Investigaciones en Enfermedades Tropicales, Sede Regional Orán, Universidad Nacional de Salta, Argentina; Cátedra de Química Biológica, Facultad de Ciencias de Naturales, Universidad Nacional de Salta, Argentina
| | - Viviana Orellana
- Cátedra de Microbiología, Facultad de Ciencias de la Salud, Universidad Nacional de Salta, Argentina
| | - Miguel A Basombrío
- Instituto de Patología Experimental-CONICET, Universidad Nacional de Salta, Argentina
| | - Patricio Diosque
- Unidad de Epidemiología Molecular, Instituto de Patología Experimental, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Salta, Argentina; Instituto de Patología Experimental-CONICET, Universidad Nacional de Salta, Argentina
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Diosque P, Tomasini N, Lauthier JJ, Messenger LA, Monje Rumi MM, Ragone PG, Alberti-D'Amato AM, Pérez Brandán C, Barnabé C, Tibayrenc M, Lewis MD, Llewellyn MS, Miles MA, Yeo M. Optimized multilocus sequence typing (MLST) scheme for Trypanosoma cruzi. PLoS Negl Trop Dis 2014; 8:e3117. [PMID: 25167160 PMCID: PMC4148231 DOI: 10.1371/journal.pntd.0003117] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 07/15/2014] [Indexed: 11/30/2022] Open
Abstract
Trypanosoma cruzi, the aetiological agent of Chagas disease possess extensive genetic diversity. This has led to the development of a plethora of molecular typing methods for the identification of both the known major genetic lineages and for more fine scale characterization of different multilocus genotypes within these major lineages. Whole genome sequencing applied to large sample sizes is not currently viable and multilocus enzyme electrophoresis, the previous gold standard for T. cruzi typing, is laborious and time consuming. In the present work, we present an optimized Multilocus Sequence Typing (MLST) scheme, based on the combined analysis of two recently proposed MLST approaches. Here, thirteen concatenated gene fragments were applied to a panel of T. cruzi reference strains encompassing all known genetic lineages. Concatenation of 13 fragments allowed assignment of all strains to the predicted Discrete Typing Units (DTUs), or near-clades, with the exception of one strain that was an outlier for TcV, due to apparent loss of heterozygosity in one fragment. Monophyly for all DTUs, along with robust bootstrap support, was restored when this fragment was subsequently excluded from the analysis. All possible combinations of loci were assessed against predefined criteria with the objective of selecting the most appropriate combination of between two and twelve fragments, for an optimized MLST scheme. The optimum combination consisted of 7 loci and discriminated between all reference strains in the panel, with the majority supported by robust bootstrap values. Additionally, a reduced panel of just 4 gene fragments displayed high bootstrap values for DTU assignment and discriminated 21 out of 25 genotypes. We propose that the seven-fragment MLST scheme could be used as a gold standard for T. cruzi typing, against which other typing approaches, particularly single locus approaches or systematic PCR assays based on amplicon size, could be compared. The single-celled parasite Trypanosoma cruzi occurs in mammals and insect vectors in the Americas. When transmitted to humans it causes Chagas disease (American trypanosomiasis) a major public health problem. T. cruzi is genetically diverse and currently split into six groups, known as TcI to TcVI. Multilocus sequence typing (MLST) is a method used for studying the population structure and diversity of pathogens and involves sequencing DNA of several different genes and comparing the sequences between isolates. Here, we assess 13 T. cruzi genes and select the best combination for diversity studies. Outputs reveal that a combination of 7 genes can be used for both lineage assignment and high resolution studies of genetic diversity, and a reduced combination of four loci for lineage assignment. Application of MLST for assigning field isolates of T. cruzi to genetic groups and for detailed investigation of diversity provides a valuable approach to understanding the taxonomy, population structure, genetics, ecology and epidemiology of this important human pathogen.
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Affiliation(s)
- Patricio Diosque
- Unidad de Epidemiología Molecular (UEM), Instituto de Patología Experimental, CONICET- Universidad Nacional de Salta, Salta, Argentina
- * E-mail:
| | - Nicolás Tomasini
- Unidad de Epidemiología Molecular (UEM), Instituto de Patología Experimental, CONICET- Universidad Nacional de Salta, Salta, Argentina
| | - Juan José Lauthier
- Unidad de Epidemiología Molecular (UEM), Instituto de Patología Experimental, CONICET- Universidad Nacional de Salta, Salta, Argentina
| | - Louisa Alexandra Messenger
- Faculty of Infectious and Tropical Diseases, Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - María Mercedes Monje Rumi
- Unidad de Epidemiología Molecular (UEM), Instituto de Patología Experimental, CONICET- Universidad Nacional de Salta, Salta, Argentina
| | - Paula Gabriela Ragone
- Unidad de Epidemiología Molecular (UEM), Instituto de Patología Experimental, CONICET- Universidad Nacional de Salta, Salta, Argentina
| | - Anahí Maitén Alberti-D'Amato
- Unidad de Epidemiología Molecular (UEM), Instituto de Patología Experimental, CONICET- Universidad Nacional de Salta, Salta, Argentina
| | - Cecilia Pérez Brandán
- Unidad de Epidemiología Molecular (UEM), Instituto de Patología Experimental, CONICET- Universidad Nacional de Salta, Salta, Argentina
| | - Christian Barnabé
- Maladies Infectieuses et Vecteurs Ecologie, Génétique, Evolution et Contrôle, MIVEGEC (IRD 224-CNRS 5290-UM1-UM2), IRD Center, Montpellier, France
| | - Michel Tibayrenc
- Maladies Infectieuses et Vecteurs Ecologie, Génétique, Evolution et Contrôle, MIVEGEC (IRD 224-CNRS 5290-UM1-UM2), IRD Center, Montpellier, France
| | - Michael David Lewis
- Faculty of Infectious and Tropical Diseases, Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Martin Stephen Llewellyn
- Faculty of Infectious and Tropical Diseases, Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Michael Alexander Miles
- Faculty of Infectious and Tropical Diseases, Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Matthew Yeo
- Faculty of Infectious and Tropical Diseases, Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
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Arnaud-Haond S, Moalic Y, Barnabé C, Ayala FJ, Tibayrenc M. Discriminating micropathogen lineages and their reticulate evolution through graph theory-based network analysis: the case of Trypanosoma cruzi, the agent of Chagas disease. PLoS One 2014; 9:e103213. [PMID: 25148574 PMCID: PMC4141739 DOI: 10.1371/journal.pone.0103213] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 06/28/2014] [Indexed: 12/02/2022] Open
Abstract
Micropathogens (viruses, bacteria, fungi, parasitic protozoa) share a common trait, which is partial clonality, with wide variance in the respective influence of clonality and sexual recombination on the dynamics and evolution of taxa. The discrimination of distinct lineages and the reconstruction of their phylogenetic history are key information to infer their biomedical properties. However, the phylogenetic picture is often clouded by occasional events of recombination across divergent lineages, limiting the relevance of classical phylogenetic analysis and dichotomic trees. We have applied a network analysis based on graph theory to illustrate the relationships among genotypes of Trypanosoma cruzi, the parasitic protozoan responsible for Chagas disease, to identify major lineages and to unravel their past history of divergence and possible recombination events. At the scale of T. cruzi subspecific diversity, graph theory-based networks applied to 22 isoenzyme loci (262 distinct Multi-Locus-Enzyme-Electrophoresis -MLEE) and 19 microsatellite loci (66 Multi-Locus-Genotypes -MLG) fully confirms the high clustering of genotypes into major lineages or "near-clades". The release of the dichotomic constraint associated with phylogenetic reconstruction usually applied to Multilocus data allows identifying putative hybrids and their parental lineages. Reticulate topology suggests a slightly different history for some of the main "near-clades", and a possibly more complex origin for the putative hybrids than hitherto proposed. Finally the sub-network of the near-clade T. cruzi I (28 MLG) shows a clustering subdivision into three differentiated lesser near-clades ("Russian doll pattern"), which confirms the hypothesis recently proposed by other investigators. The present study broadens and clarifies the hypotheses previously obtained from classical markers on the same sets of data, which demonstrates the added value of this approach. This underlines the potential of graph theory-based network analysis for describing the nature and relationships of major pathogens, thereby opening stimulating prospects to unravel the organization, dynamics and history of major micropathogen lineages.
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Affiliation(s)
- Sophie Arnaud-Haond
- IFREMER (Institut Français de Recherche pour l'Exploitation de la Mer) - Département Ecosystèmes Marins Exploités, Sète, France
| | - Yann Moalic
- IFREMER (Institut Français de Recherche pour l'Exploitation de la Mer) - Département Ecosystèmes Marins Exploités, Sète, France
| | - Christian Barnabé
- Interactions hôte-vecteur-parasite dans les maladies dues aux Trypanosomatidés, INTERTRYP (IRD-CIRAD), Montpellier, France
| | - Francisco José Ayala
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California, United States of America
| | - Michel Tibayrenc
- Maladies Infectieuses et Vecteurs Ecologie, Génétique, Evolution et Contrôle, MIVEGEC (IRD 224-CNRS 5290-UM1-UM2), Montpellier, France
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Tomasini N, Lauthier JJ, Monje Rumi MM, Ragone PG, Alberti D'Amato AM, Brandán CP, Basombrío MA, Diosque P. Preponderant clonal evolution of Trypanosoma cruzi I from Argentinean Chaco revealed by Multilocus Sequence Typing (MLST). INFECTION GENETICS AND EVOLUTION 2014; 27:348-54. [PMID: 25111612 DOI: 10.1016/j.meegid.2014.08.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 08/01/2014] [Accepted: 08/02/2014] [Indexed: 10/24/2022]
Abstract
Trypanosoma cruzi has been historically classified as a species with preponderant clonal evolution (PCE). However, with the advent of highly polymorphic markers and studies at geographically reduced scales, the PCE in T. cruzi was challenged. In fact, some studies have suggested that recombination in T. cruzi lineage I (TcI) is much more frequent than previously believed. Further analyses of TcI populations from different geographical regions of Latin America are needed to examine this hypothesis. In the present study, we contribute to this topic by analyzing the population structure of TcI from a restricted geographical area in the Chaco region, Argentina. We analyzed TcI isolates from different hosts and vectors using a Multilocus Sequence Typing (MLST) approach. These isolates were previously characterized by sequencing the spliced leader intergenic region (SL-IR). Low levels of incongruence and well-supported clusters for MLST dataset were obtained from the analyses. Moreover, high linkage disequilibrium was found and five repeated and overrepresented genotypes were detected. In addition, a good correspondence between SL-IR and MLST was observed which is expected under PCE. However, recombination is not ruled out because five out of 28 pairs of loci were incompatible with strict clonality and one possible genetic exchange event was detected. Overall, our results represent evidence of PCE in TcI from the study area. Finally, considering our findings we discuss the scenario for the genetic structure of TcI.
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Affiliation(s)
- Nicolás Tomasini
- Unidad de Epidemiología Molecular (UEM), Instituto de Patología Experimental, Universidad Nacional de Salta-CONICET, Av. Bolivia 5150, CP4400 Salta, Argentina; Instituto de Patología Experimental, Universidad Nacional de Salta-CONICET, Av. Bolivia 5150, CP4400 Salta, Argentina.
| | - Juan J Lauthier
- Unidad de Epidemiología Molecular (UEM), Instituto de Patología Experimental, Universidad Nacional de Salta-CONICET, Av. Bolivia 5150, CP4400 Salta, Argentina; Instituto de Patología Experimental, Universidad Nacional de Salta-CONICET, Av. Bolivia 5150, CP4400 Salta, Argentina.
| | - María M Monje Rumi
- Unidad de Epidemiología Molecular (UEM), Instituto de Patología Experimental, Universidad Nacional de Salta-CONICET, Av. Bolivia 5150, CP4400 Salta, Argentina; Instituto de Patología Experimental, Universidad Nacional de Salta-CONICET, Av. Bolivia 5150, CP4400 Salta, Argentina
| | - Paula G Ragone
- Unidad de Epidemiología Molecular (UEM), Instituto de Patología Experimental, Universidad Nacional de Salta-CONICET, Av. Bolivia 5150, CP4400 Salta, Argentina; Instituto de Patología Experimental, Universidad Nacional de Salta-CONICET, Av. Bolivia 5150, CP4400 Salta, Argentina
| | - Anahí M Alberti D'Amato
- Unidad de Epidemiología Molecular (UEM), Instituto de Patología Experimental, Universidad Nacional de Salta-CONICET, Av. Bolivia 5150, CP4400 Salta, Argentina; Instituto de Patología Experimental, Universidad Nacional de Salta-CONICET, Av. Bolivia 5150, CP4400 Salta, Argentina
| | - Cecilia Pérez Brandán
- Unidad de Epidemiología Molecular (UEM), Instituto de Patología Experimental, Universidad Nacional de Salta-CONICET, Av. Bolivia 5150, CP4400 Salta, Argentina; Instituto de Patología Experimental, Universidad Nacional de Salta-CONICET, Av. Bolivia 5150, CP4400 Salta, Argentina
| | - Miguel A Basombrío
- Instituto de Patología Experimental, Universidad Nacional de Salta-CONICET, Av. Bolivia 5150, CP4400 Salta, Argentina
| | - Patricio Diosque
- Unidad de Epidemiología Molecular (UEM), Instituto de Patología Experimental, Universidad Nacional de Salta-CONICET, Av. Bolivia 5150, CP4400 Salta, Argentina; Instituto de Patología Experimental, Universidad Nacional de Salta-CONICET, Av. Bolivia 5150, CP4400 Salta, Argentina
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Tomasini N, Lauthier JJ, Ayala FJ, Tibayrenc M, Diosque P. How often do they have sex? A comparative analysis of the population structure of seven eukaryotic microbial pathogens. PLoS One 2014; 9:e103131. [PMID: 25054834 PMCID: PMC4108389 DOI: 10.1371/journal.pone.0103131] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 06/27/2014] [Indexed: 11/19/2022] Open
Abstract
The model of predominant clonal evolution (PCE) proposed for micropathogens does not state that genetic exchange is totally absent, but rather, that it is too rare to break the prevalent PCE pattern. However, the actual impact of this “residual” genetic exchange should be evaluated. Multilocus Sequence Typing (MLST) is an excellent tool to explore the problem. Here, we compared online available MLST datasets for seven eukaryotic microbial pathogens: Trypanosoma cruzi, the Fusarium solani complex, Aspergillus fumigatus, Blastocystis subtype 3, the Leishmania donovani complex, Candida albicans and Candida glabrata. We first analyzed phylogenetic relationships among genotypes within each dataset. Then, we examined different measures of branch support and incongruence among loci as signs of genetic structure and levels of past recombination. The analyses allow us to identify three types of genetic structure. The first was characterized by trees with well-supported branches and low levels of incongruence suggesting well-structured populations and PCE. This was the case for the T. cruzi and F. solani datasets. The second genetic structure, represented by Blastocystis spp., A. fumigatus and the L. donovani complex datasets, showed trees with weakly-supported branches but low levels of incongruence among loci, whereby genetic structuration was not clearly defined by MLST. Finally, trees showing weakly-supported branches and high levels of incongruence among loci were observed for Candida species, suggesting that genetic exchange has a higher evolutionary impact in these mainly clonal yeast species. Furthermore, simulations showed that MLST may fail to show right clustering in population datasets even in the absence of genetic exchange. In conclusion, these results make it possible to infer variable impacts of genetic exchange in populations of predominantly clonal micro-pathogens. Moreover, our results reveal different problems of MLST to determine the genetic structure in these organisms that should be considered.
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Affiliation(s)
- Nicolás Tomasini
- Unidad de Epidemiología Molecular (UEM), Instituto de Patología Experimental, Universidad Nacional de Salta-CONICET, Salta, Salta, Argentina
- * E-mail:
| | - Juan José Lauthier
- Unidad de Epidemiología Molecular (UEM), Instituto de Patología Experimental, Universidad Nacional de Salta-CONICET, Salta, Salta, Argentina
| | - Francisco José Ayala
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California, United States of America
| | - Michel Tibayrenc
- Maladies Infectieuses et Vecteurs Ecologie, Génétique, Evolution et Contrôle, MIVEGEC (IRD 224-CNRS 5290-UM1-UM2), IRD Center, Montpellier, France
| | - Patricio Diosque
- Unidad de Epidemiología Molecular (UEM), Instituto de Patología Experimental, Universidad Nacional de Salta-CONICET, Salta, Salta, Argentina
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Lima VS, Jansen AM, Messenger LA, Miles MA, Llewellyn MS. Wild Trypanosoma cruzi I genetic diversity in Brazil suggests admixture and disturbance in parasite populations from the Atlantic Forest region. Parasit Vectors 2014; 7:263. [PMID: 24903849 PMCID: PMC4062772 DOI: 10.1186/1756-3305-7-263] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 05/20/2014] [Indexed: 12/27/2022] Open
Abstract
Background Trypanosoma cruzi (Kinetoplastida, Trypanosomatidae) infection is an ancient and widespread zoonosis distributed throughout the Americas. Ecologically, Brazil comprises several distinct biomes: Amazonia, Cerrado, Caatinga, Pantanal and the Atlantic Forest. Sylvatic T. cruzi transmission is known to occur throughout these biomes, with multiple hosts and vectors involved. Parasite species-level genetic diversity can be a useful marker for ecosystem health. Our aims were to: investigate sylvatic T. cruzi genetic diversity across different biomes, detect instances of genetic exchange, and explore the possible impact of ecological disturbance on parasite diversity at an intra-species level. Methods We characterised 107 isolates of T. cruzi I (TcI; discrete typing unit, DTU I) from different major Brazilian biomes with twenty-seven nuclear microsatellite loci. A representative subset of biologically cloned isolates was further characterised using ten mitochondrial gene loci. We compared these data generated from Brazilian TcI isolates from around America. Results Genetic diversity was remarkably high, including one divergent cluster that branched outside the known genetic diversity of TcI in the Americas. We detected evidence for mitochondrial introgression and genetic exchange between the eastern Amazon and Caatinga. Finally, we found strong signatures of admixture among isolates from the Atlantic Forest region by comparison to parasites from other study sites. Conclusions Atlantic Forest sylvatic TcI populations are highly fragmented and admixed by comparison to others around Brazil. We speculate on: the possible causes of Atlantic Forest admixture; the role of T. cruzi as a sentinel for ecosystem health, and the impact disrupted sylvatic transmission cycles might have on accurate source attribution in oral outbreaks.
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Affiliation(s)
| | | | | | | | - Martin S Llewellyn
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.
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Genetic profiling of the isoprenoid and sterol biosynthesis pathway genes of Trypanosoma cruzi. PLoS One 2014; 9:e96762. [PMID: 24828104 PMCID: PMC4020770 DOI: 10.1371/journal.pone.0096762] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 04/04/2014] [Indexed: 12/02/2022] Open
Abstract
In Trypanosoma cruzi the isoprenoid and sterol biosynthesis pathways are validated targets for chemotherapeutic intervention. In this work we present a study of the genetic diversity observed in genes from these pathways. Using a number of bioinformatic strategies, we first identified genes that were missing and/or were truncated in the T. cruzi genome. Based on this analysis we obtained the complete sequence of the ortholog of the yeast ERG26 gene and identified a non-orthologous homolog of the yeast ERG25 gene (sterol methyl oxidase, SMO), and we propose that the orthologs of ERG25 have been lost in trypanosomes (but not in Leishmanias). Next, starting from a set of 16 T. cruzi strains representative of all extant evolutionary lineages, we amplified and sequenced ∼24 Kbp from 22 genes, identifying a total of 975 SNPs or fixed differences, of which 28% represent non-synonymous changes. We observed genes with a density of substitutions ranging from those close to the average (∼2.5/100 bp) to some showing a high number of changes (11.4/100 bp, for the putative lathosterol oxidase gene). All the genes of the pathway are under apparent purifying selection, but genes coding for the sterol C14-demethylase, the HMG-CoA synthase, and the HMG-CoA reductase have the lowest density of missense SNPs in the panel. Other genes (TcPMK, TcSMO-like) have a relatively high density of non-synonymous SNPs (2.5 and 1.9 every 100 bp, respectively). However, none of the non-synonymous changes identified affect a catalytic or ligand binding site residue. A comparative analysis of the corresponding genes from African trypanosomes and Leishmania shows similar levels of apparent selection for each gene. This information will be essential for future drug development studies focused on this pathway.
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Panunzi LG, Agüero F. A genome-wide analysis of genetic diversity in Trypanosoma cruzi intergenic regions. PLoS Negl Trop Dis 2014; 8:e2839. [PMID: 24784238 PMCID: PMC4006747 DOI: 10.1371/journal.pntd.0002839] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Accepted: 03/20/2014] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Trypanosoma cruzi is the causal agent of Chagas Disease. Recently, the genomes of representative strains from two major evolutionary lineages were sequenced, allowing the construction of a detailed genetic diversity map for this important parasite. However this map is focused on coding regions of the genome, leaving a vast space of regulatory regions uncharacterized in terms of their evolutionary conservation and/or divergence. METHODOLOGY Using data from the hybrid CL Brener and Sylvio X10 genomes (from the TcVI and TcI Discrete Typing Units, respectively), we identified intergenic regions that share a common evolutionary ancestry, and are present in both CL Brener haplotypes (TcII-like and TcIII-like) and in the TcI genome; as well as intergenic regions that were conserved in only two of the three genomes/haplotypes analyzed. The genetic diversity in these regions was characterized in terms of the accumulation of indels and nucleotide changes. PRINCIPAL FINDINGS Based on this analysis we have identified i) a core of highly conserved intergenic regions, which remained essentially unchanged in independently evolving lineages; ii) intergenic regions that show high diversity in spite of still retaining their corresponding upstream and downstream coding sequences; iii) a number of defined sequence motifs that are shared by a number of unrelated intergenic regions. A fraction of indels explains the diversification of some intergenic regions by the expansion/contraction of microsatellite-like repeats.
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Affiliation(s)
- Leonardo G. Panunzi
- Instituto de Investigaciones Biotecnológicas – Instituto Tecnológico de Chascomús, Universidad de San Martín – CONICET, Sede San Marítn, Buenos Aires, Argentina
| | - Fernán Agüero
- Instituto de Investigaciones Biotecnológicas – Instituto Tecnológico de Chascomús, Universidad de San Martín – CONICET, Sede San Marítn, Buenos Aires, Argentina
- * E-mail: ;
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Retrospective molecular integrated epidemiology of Chagas disease in Colombia. INFECTION GENETICS AND EVOLUTION 2013; 20:148-54. [DOI: 10.1016/j.meegid.2013.08.028] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Revised: 08/27/2013] [Accepted: 08/28/2013] [Indexed: 11/17/2022]
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Ramírez JD, Tapia-Calle G, Guhl F. Genetic structure of Trypanosoma cruzi in Colombia revealed by a High-throughput Nuclear Multilocus Sequence Typing (nMLST) approach. BMC Genet 2013; 14:96. [PMID: 24079755 PMCID: PMC3850472 DOI: 10.1186/1471-2156-14-96] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 09/25/2013] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Chagas disease is a systemic pathology caused by Trypanosoma cruzi. This parasite reveals remarkable genetic variability, evinced in six Discrete Typing Units (DTUs) named from T. cruzi I to T. cruzi VI (TcI to TcVI). Recently newly identified genotypes have emerged such as TcBat in Brazil, Colombia and Panama associated to anthropogenic bats. The genotype with the broadest geographical distribution is TcI, which has recently been associated to severe cardiomyopathies in Argentina and Colombia. Therefore, new studies unraveling the genetic structure and natural history of this DTU must be pursued. RESULTS We conducted a spatial and temporal analysis on 50 biological clones of T. cruzi I (TcI) isolated from humans with different clinical phenotypes, triatomine bugs and mammal reservoirs across three endemic regions for Chagas disease in Colombia. These clones were submitted to a nuclear Multilocus Sequence Typing (nMLST) analysis in order to elucidate its genetic diversity and clustering. After analyzing 13 nuclear housekeeping genes and obtaining a 5821 bp length alignment, we detected two robust genotypes within TcI henceforth named TcIDOM (associated to human infections) and a second cluster associated to peridomestic and sylvatic populations. Additionaly, we detected putative events of recombination and an intriguing lack of linkage disequilibrium. CONCLUSIONS These findings reinforce the emergence of an enigmatic domestic T. cruzi genotype (TcIDOM), and demonstrates the high frequency of recombination at nuclear level across natural populations of T. cruzi. Therefore, the need to pursue studies focused on the diferential virulence profiles of TcI strains. The biological and epidemiological implications of these findings are herein discussed.
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Affiliation(s)
- Juan David Ramírez
- Centro de Investigaciones en Microbiología y Parasitología Tropical (CIMPAT), Universidad de Los Andes, Bogotá, Colombia.
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MLSTest: novel software for multi-locus sequence data analysis in eukaryotic organisms. INFECTION GENETICS AND EVOLUTION 2013; 20:188-96. [PMID: 24025589 DOI: 10.1016/j.meegid.2013.08.029] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 08/29/2013] [Accepted: 08/31/2013] [Indexed: 11/22/2022]
Abstract
Multi-locus sequence typing (MLST) is a frequently used genotyping method whose goal is the unambiguous assignment of microorganisms to genetic clusters. MLST typically involves analysis of DNA sequence results generated from several house-keeping gene loci. MLST remains the gold standard for molecular typing of many bacterial pathogens. Eukaryotic pathogens have also been the subject of MLST, however, few tools are available to deal with diploid sequence data. Here we present novel software for MLST data analysis tailored towards diploid Eukaryotes: MLSTest. This software meets various methods used in MLST and introduces some novel methodologies for the evaluation of the data set. In addition to construction of allelic profiles and basic clustering analysis, the MLSTest looks for network structures that suggest genetic exchange in BURST graphs. Additionally, it uses several simple methods for tree construction with the advantage of managing heterozygous or three-state sites. Additionally, the software analyses whether concatenation of fragments from different genes is suitable for the data set using different tests (bionj-incongruence length difference test, Templeton test). It evaluates how the incongruence is distributed across the tree using a variation of the localized incongruence length difference test based on a modified neighbour joining algorithm. We tested the last method in simulated datasets. We showed that is conservative (adequate type I error rate) and moderately to highly powerful as well as useful to localize incongruences in two bacterial and two eukaryotic MLST datasets. MLSTest was also designed for developing MLST schemes. It thus has tools to optimize locus combinations and to reduce the number of targets required for typing. MLSTest also analyses whether the discriminatory power of the typing scheme is increased by including more loci. We evaluated the software over simulated and real datasets from bacterial and eukaryotic microorganisms. The software is freely available at http://www.ipe.unsa.edu.ar/software.
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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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Ramírez JD, Turriago B, Tapia-Calle G, Guhl F. Understanding the role of dogs (Canis lupus familiaris) in the transmission dynamics of Trypanosoma cruzi genotypes in Colombia. Vet Parasitol 2013; 196:216-9. [PMID: 23351975 DOI: 10.1016/j.vetpar.2012.12.054] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Revised: 12/19/2012] [Accepted: 12/24/2012] [Indexed: 11/16/2022]
Abstract
The dog (Canis lupus familiaris) is the most important domestic reservoir of Chagas disease, a zoonosis that affects more than 10 million people in Latin America. Trypanosoma cruzi, the etiologic agent of the disease, displays remarkable genetic variability, as indicated by its six genotypes (TcI-TcVI). A pilot study was conducted to establish the prevalence of T. cruzi among the canine population by analyzing 80 dogs. We report the identification of the TcI, TcII, TcIV and TcVI genotypes as single infections. TcI/TcII and TcI/TcIV presented as mixed infections and included the presence of Trypanosoma angel. The implications of this distribution are herein discussed. Based on the molecular epidemiology findings, this study suggests a plausible role for canine synanthropism in the transmission of T. cruzi.
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Affiliation(s)
- Juan David Ramírez
- Centro de Investigaciones en Microbiología y Parasitología Tropical-CIMPAT- Universidad de los Andes, Cra 1ª No. 18A-10, Bogotá, Colombia
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Ackermann AA, Panunzi LG, Cosentino RO, Sánchez DO, Agüero F. A genomic scale map of genetic diversity in Trypanosoma cruzi. BMC Genomics 2012; 13:736. [PMID: 23270511 PMCID: PMC3545726 DOI: 10.1186/1471-2164-13-736] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Accepted: 12/12/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Trypanosoma cruzi, the causal agent of Chagas Disease, affects more than 16 million people in Latin America. The clinical outcome of the disease results from a complex interplay between environmental factors and the genetic background of both the human host and the parasite. However, knowledge of the genetic diversity of the parasite, is currently limited to a number of highly studied loci. The availability of a number of genomes from different evolutionary lineages of T. cruzi provides an unprecedented opportunity to look at the genetic diversity of the parasite at a genomic scale. RESULTS Using a bioinformatic strategy, we have clustered T. cruzi sequence data available in the public domain and obtained multiple sequence alignments in which one or two alleles from the reference CL-Brener were included. These data covers 4 major evolutionary lineages (DTUs): TcI, TcII, TcIII, and the hybrid TcVI. Using these set of alignments we have identified 288,957 high quality single nucleotide polymorphisms and 1,480 indels. In a reduced re-sequencing study we were able to validate ~ 97% of high-quality SNPs identified in 47 loci. Analysis of how these changes affect encoded protein products showed a 0.77 ratio of synonymous to non-synonymous changes in the T. cruzi genome. We observed 113 changes that introduce or remove a stop codon, some causing significant functional changes, and a number of tri-allelic and tetra-allelic SNPs that could be exploited in strain typing assays. Based on an analysis of the observed nucleotide diversity we show that the T. cruzi genome contains a core set of genes that are under apparent purifying selection. Interestingly, orthologs of known druggable targets show statistically significant lower nucleotide diversity values. CONCLUSIONS This study provides the first look at the genetic diversity of T. cruzi at a genomic scale. The analysis covers an estimated ~ 60% of the genetic diversity present in the population, providing an essential resource for future studies on the development of new drugs and diagnostics, for Chagas Disease. These data is available through the TcSNP database (http://snps.tcruzi.org).
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Affiliation(s)
- Alejandro A Ackermann
- Instituto de Investigaciones Biotecnológicas - Instituto Tecnológico de Chascomús (IIB-INTECH), Universidad Nacional de San Martín - Consejo de Investigaciones Científicas y Técnicas (UNSAM-CONICET), Sede San Martín, B 1650 HMP, San Martín, Buenos Aires, Argentina
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Natural and emergent Trypanosoma cruzi I genotypes revealed by mitochondrial (Cytb) and nuclear (SSU rDNA) genetic markers. Exp Parasitol 2012; 132:487-94. [DOI: 10.1016/j.exppara.2012.09.017] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Revised: 09/20/2012] [Accepted: 09/24/2012] [Indexed: 11/18/2022]
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Boité MC, Mauricio IL, Miles MA, Cupolillo E. New insights on taxonomy, phylogeny and population genetics of Leishmania (Viannia) parasites based on multilocus sequence analysis. PLoS Negl Trop Dis 2012; 6:e1888. [PMID: 23133690 PMCID: PMC3486886 DOI: 10.1371/journal.pntd.0001888] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Accepted: 09/17/2012] [Indexed: 11/18/2022] Open
Abstract
The Leishmania genus comprises up to 35 species, some with status still under discussion. The multilocus sequence typing (MLST)--extensively used for bacteria--has been proposed for pathogenic trypanosomatids. For Leishmania, however, a detailed analysis and revision on the taxonomy is still required. We have partially sequenced four housekeeping genes--glucose-6-phosphate dehydrogenase (G6PD), 6-phosphogluconate dehydrogenase (6PGD), mannose phosphate isomerase (MPI) and isocitrate dehydrogenase (ICD)--from 96 Leishmania (Viannia) strains and assessed their discriminatory typing capacity. The fragments had different degrees of diversity, and are thus suitable to be used in combination for intra- and inter-specific inferences. Species-specific single nucleotide polymorphisms were detected, but not for all species; ambiguous sites indicating heterozygosis were observed, as well as the putative homozygous donor. A large number of haplotypes were detected for each marker; for 6PGD a possible ancestral allele for L. (Viannia) was found. Maximum parsimony-based haplotype networks were built. Strains of different species, as identified by multilocus enzyme electrophoresis (MLEE), formed separated clusters in each network, with exceptions. NeighborNet of concatenated sequences confirmed species-specific clusters, suggesting recombination occurring in L. braziliensis and L. guyanensis. Phylogenetic analysis indicates L. lainsoni and L. naiffi as the most divergent species and does not support L. shawi as a distinct species, placing it in the L. guyanensis cluster. BURST analysis resulted in six clonal complexes (CC), corresponding to distinct species. The L. braziliensis strains evaluated correspond to one widely geographically distributed CC and another restricted to one endemic area. This study demonstrates the value of systematic multilocus sequence analysis (MLSA) for determining intra- and inter-species relationships and presents an approach to validate the species status of some entities. Furthermore, it contributes to the phylogeny of L. (Viannia) and might be helpful for epidemiological and population genetics analysis based on haplotype/diplotype determinations and inferences.
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Affiliation(s)
- Mariana C. Boité
- Laboratório de Pesquisa em Leishmaniose, Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Isabel L. Mauricio
- Department of Pathogen Molecular Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Instituto de Higiene e Medicina Tropical/Unidade de Parasitologia e Microbiologia Médicas, Lisboa, Portugal
| | - Michael A. Miles
- Department of Pathogen Molecular Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Elisa Cupolillo
- Laboratório de Pesquisa em Leishmaniose, Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Rio de Janeiro, Brazil
- * E-mail:
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Zumaya-Estrada FA, Messenger LA, Lopez-Ordonez T, Lewis MD, Flores-Lopez CA, Martínez-Ibarra AJ, Pennington PM, Cordon-Rosales C, Carrasco HV, Segovia M, Miles MA, Llewellyn MS. North American import? Charting the origins of an enigmatic Trypanosoma cruzi domestic genotype. Parasit Vectors 2012; 5:226. [PMID: 23050833 PMCID: PMC3481457 DOI: 10.1186/1756-3305-5-226] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2012] [Accepted: 10/03/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Trypanosoma cruzi, the agent of Chagas disease, is currently recognized as a complex of six lineages or Discrete Typing Units (DTU): TcI-TcVI. Recent studies have identified a divergent group within TcI - TcI(DOM). TcI(DOM). is associated with a significant proportion of human TcI infections in South America, largely absent from local wild mammals and vectors, yet closely related to sylvatic strains in North/Central America. Our aim was to examine hypotheses describing the origin of the TcI(DOM) genotype. We propose two possible scenarios: an emergence of TcI(DOM) in northern South America as a sister group of North American strain progenitors and dispersal among domestic transmission cycles, or an origin in North America, prior to dispersal back into South American domestic cycles. To provide further insight we undertook high resolution nuclear and mitochondrial genotyping of multiple Central American strains (from areas of México and Guatemala) and included them in an analysis with other published data. FINDINGS Mitochondrial sequence and nuclear microsatellite data revealed a cline in genetic diversity across isolates grouped into three populations: South America, North/Central America and TcI(DOM). As such, greatest diversity was observed in South America (A(r) = 4.851, π = 0.00712) and lowest in TcI(DOM) (Ar = 1.813, π = 0.00071). Nuclear genetic clustering (genetic distance based) analyses suggest that TcI(DOM) is nested within the North/Central American clade. CONCLUSIONS Declining genetic diversity across the populations, and corresponding hierarchical clustering suggest that emergence of this important human genotype most likely occurred in North/Central America before moving southwards. These data are consistent with early patterns of human dispersal into South America.
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Affiliation(s)
- Federico A Zumaya-Estrada
- Centro Regional de Investigación en Salud Pública, Instituto Nacional de Salud Pública, Tapachula, Chiapas, México
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