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Pessanha TS, Herrera HM, Jansen AM, Iñiguez AM. "Mi Casa, Tu Casa": the coati nest as a hub of Trypanosoma cruzi transmission in the southern Pantanal biome revealed by molecular blood meal source identification in triatomines. Parasit Vectors 2023; 16:26. [PMID: 36691054 PMCID: PMC9872340 DOI: 10.1186/s13071-022-05616-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 12/12/2022] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND The study of the ecology of Trypanosoma cruzi is challenging due to its extreme adaptive plasticity, resulting in the parasitism of hundreds of mammal species and dozens of triatomine species. The genetic analysis of blood meal sources (BMS) from the triatomine vector is an accurate and practical approach for gathering information on which wild mammal species participate in a local transmission network. South American coatis, Nasua nasua, act as important reservoir host species of T. cruzi in the Pantanal biome because of their high rate of infection and elevated parasitemia, with the main discrete typing unit (DTU) lineages (TcI and TcII). Moreover, the carnivore coati is the only mammal species to build high arboreal nests for breeding and resting that can be shared by various vertebrate and invertebrate species. Herein, we applied the sensitive and specific methodology of DNA barcoding and molecular cloning to study triatomines found in a coati nest to access the diversity of mammal species that explore this structure, and therefore, may be involved in the parasite transmission network. METHODS Twenty-three Triatoma sordida were collected in one coati's nest in the subregion of Nhecolândia, Pantanal. The DNA isolated from the gut of insects was subjected to BMS detection by PCR using universal primers that flank variable regions of the cytochrome b (cytb) and 12S rDNA mitochondrial genes from vertebrates. The Trypanosoma spp. diagnosis and DTU genotyping were based on an 18S rDNA molecular marker and also using new cytb gene primers designed in this study. Phylogenetic analyses and chord diagrams were constructed to visualize BMS haplotypes, DTU lineages detected on vectors, and their interconnections. RESULTS Twenty of 23 triatomines analyzed were PCR-positive (86.95%) showing lineages T. cruzi DTU TcI (n = 2), TcII (n = 6), and a predominance of TcI/TcII (n = 12) mixed infection. Intra-DTU diversity was observed mainly from different TcI haplotypes. Genetic analyses revealed that the southern anteater, Tamandua tetradactyla, was the unique species detected as the BMS of triatomines collected from the coati's nest. At least three different individuals of T. tetradactyla served as BMS of 21/23 bugs studied, as indicated by the cytb and 12S rDNA haplotypes identified. CONCLUSIONS The identification of multiple BMS, and importantly, different individuals of the same species, was achieved by the methodology applied. The study demonstrated that the southern anteaters can occupy the South American coati's nest, serving as the BMS of T. sordida specimens. Since anteaters have an individualist nonsocial behavior, the three individuals detected as BMS stayed at the coati's nest at different times, which added a temporal character to BMS detection. The TcI and TcII infection, and significantly, a predominance of TcI/TcII mixed infection profile with different TcI and TcII haplotypes was observed, due to the discriminatory capacity of the methodology applied. Tamandua tetradactyla, a host which has been little studied, may have an important role in the T. cruzi transmission in that Pantanal subregion. The data from the present study indicate the sharing of coatis' nests by other mammal species, expanding the possibilities for T. cruzi transmission in the canopy strata. We propose that coatis' nests can act as the true hubs of the T. cruzi transmission web in Pantanal, instead of the coatis themselves, as previously suggested.
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Affiliation(s)
- Thaíla Santos Pessanha
- grid.418068.30000 0001 0723 0931Laboratório de Biologia em Tripanosomatídeos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro Brasil
| | - Heitor Miraglia Herrera
- grid.442132.20000 0001 2111 5825Laboratório de Biologia Parasitária, Universidade Católica Dom Bosco, Campo Grande, Mato Grosso Do Sul Brasil
| | - Ana Maria Jansen
- grid.418068.30000 0001 0723 0931Laboratório de Biologia em Tripanosomatídeos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro Brasil
| | - Alena Mayo Iñiguez
- grid.418068.30000 0001 0723 0931Laboratório de Biologia em Tripanosomatídeos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro Brasil
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da Silva VS, Machado CR. Sex in protists: A new perspective on the reproduction mechanisms of trypanosomatids. Genet Mol Biol 2022; 45:e20220065. [PMID: 36218381 PMCID: PMC9552303 DOI: 10.1590/1678-4685-gmb-2022-0065] [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: 02/28/2022] [Accepted: 08/07/2022] [Indexed: 11/04/2022] Open
Abstract
The Protist kingdom individuals are the most ancestral representatives of eukaryotes. They have inhabited Earth since ancient times and are currently found in the most diverse environments presenting a great heterogeneity of life forms. The unicellular and multicellular algae, photosynthetic and heterotrophic organisms, as well as free-living and pathogenic protozoa represents the protist group. The evolution of sex is directly associated with the origin of eukaryotes being protists the earliest protagonists of sexual reproduction on earth. In eukaryotes, the recombination through genetic exchange is a ubiquitous mechanism that can be stimulated by DNA damage. Scientific evidences support the hypothesis that reactive oxygen species (ROS) induced DNA damage can promote sexual recombination in eukaryotes which might have been a decisive factor for the origin of sex. The fact that some recombination enzymes also participate in meiotic sex in modern eukaryotes reinforces the idea that sexual reproduction emerged as consequence of specific mechanisms to cope with mutations and alterations in genetic material. In this review we will discuss about origin of sex and different strategies of evolve sexual reproduction in some protists such that cause human diseases like malaria, toxoplasmosis, sleeping sickness, Chagas disease, and leishmaniasis.
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Affiliation(s)
- Verônica Santana da Silva
- Universidade Federal de Minas Gerais, Departamento de Genética,
Ecologia e Evolução, Belo Horizonte, MG, Brazil
| | - Carlos Renato Machado
- Universidade Federal de Minas Gerais, Departamento de Bioquímica e
Imunologia, Belo Horizonte, MG, Brazil
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Tibayrenc M, Ayala FJ. Microevolution and subspecific taxonomy of Trypanosoma cruzi. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 103:105344. [PMID: 35926722 DOI: 10.1016/j.meegid.2022.105344] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 07/25/2022] [Accepted: 07/26/2022] [Indexed: 06/15/2023]
Abstract
Trypanosoma cruzi, the agent of Chagas disease, is a highly polymorphic species, subdivided into 6 main evolutionary lineages or near-clades (formerly discrete typing units or DTUs). An additional near-clade (TC-bat) has recently been evidenced. This pattern is considered to be the result of predominant clonal evolution (PCE). PCE is compatible with occasional mating/hybridization, which do not break the prevalent pattern of clonal evolution, the main trait of it being the presence of Multigene Bifurcating Trees (MGBTs) at all evolutionary levels ("clonal frame"). The development of highly resolutive genetic (microsatellites*) and genomic (sequencing and multi-single nucleotide polymorphism {SNP}* typing) markers shows that PCE also operates at a microevolutionary* level within each of the near-clades ("Russian doll pattern"), in spite of occasional meiosis and hybridization events. Within each near-clade, one can evidence widespread clonal multilocus genotypes*, linkage disequilibrium*, Multigene Bifurcating Trees and lesser near-clades. The within near-clade population structure is like a miniature picture of that of the whole species, suggesting gradual rather than saltatory evolution. Additional data are required to evaluate the stability of these lesser near-clades in the long run and to evaluate the need for an adequate nomenclature for this microevolutionary level.
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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 Recherche Pour le Développement, BP 6450134394 Montpellier Cedex 5, France.
| | - Francisco J Ayala
- Catedra Francisco Jose Ayala of Science, Technology, and Religion, University of Comillas, 28015 Madrid, Spain. 2 Locke Court, Irvine, CA 92617, USA
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Martín-Escolano J, Marín C, Rosales MJ, Tsaousis AD, Medina-Carmona E, Martín-Escolano R. An Updated View of the Trypanosoma cruzi Life Cycle: Intervention Points for an Effective Treatment. ACS Infect Dis 2022; 8:1107-1115. [PMID: 35652513 PMCID: PMC9194904 DOI: 10.1021/acsinfecdis.2c00123] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Chagas disease (CD)
is a parasitic, systemic, chronic, and often
fatal illness caused by infection with the protozoan Trypanosoma
cruzi. The World Health Organization classifies CD as the
most prevalent of poverty-promoting neglected tropical diseases, the
most important parasitic one, and the third most infectious disease
in Latin America. Currently, CD is a global public health issue that
affects 6–8 million people. However, the current approved treatments
are limited to two nitroheterocyclic drugs developed more than 50
years ago. Many efforts have been made in recent decades to find new
therapies, but our limited understanding of the infection process,
pathology development, and long-term nature of this disease has made
it impossible to develop new drugs, effective treatment, or vaccines.
This Review aims to provide a comprehensive update on our understanding
of the current life cycle, new morphological forms, and genetic diversity
of T. cruzi, as well as identify intervention points
in the life cycle where new drugs and treatments could achieve a parasitic
cure.
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Affiliation(s)
- Javier Martín-Escolano
- Unit of Infectious Diseases, Microbiology and Preventive Medicine, Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/CSIC/University of Seville, E41013 Seville, Spain
| | - Clotilde Marín
- Department of Parasitology, University of Granada, Severo Ochoa s/n, 18071 Granada, Spain
| | - María J. Rosales
- Department of Parasitology, University of Granada, Severo Ochoa s/n, 18071 Granada, Spain
| | - Anastasios D. Tsaousis
- Laboratory of Molecular & Evolutionary Parasitology, RAPID group, School of Biosciences, University of Kent, Canterbury CT2 7NJ, U.K
| | - Encarnación Medina-Carmona
- Department of Physical Chemistry, University of Granada, 18071 Granada, Spain
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, U.K
| | - Rubén Martín-Escolano
- Laboratory of Molecular & Evolutionary Parasitology, RAPID group, School of Biosciences, University of Kent, Canterbury CT2 7NJ, U.K
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Flores-López CA, Mitchell EA, Reisenman CE, Sarkar S, Williamson PC, Machado CA. Phylogenetic diversity of two common Trypanosoma cruzi lineages in the Southwestern United States. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 99:105251. [PMID: 35183751 DOI: 10.1016/j.meegid.2022.105251] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 02/11/2022] [Accepted: 02/14/2022] [Indexed: 06/14/2023]
Abstract
Trypanosoma cruzi is the causative agent of Chagas disease, a devastating parasitic disease endemic to Central and South America, Mexico, and the USA. We characterized the genetic diversity of Trypanosoma cruzi circulating in five triatomine species (Triatoma gerstaeckeri, T. lecticularia, T.indictiva, T. sanguisuga and T. recurva) collected in Texas and Southern Arizona using multilocus sequence typing (MLST) with four single-copy loci (cytochrome oxidase subunit II- NADH dehydrogensase subunit 1 region (COII-ND1), mismatch-repair class 2 (MSH2), dihydrofolate reductase-thymidylate synthase (DHFR-TS) and a nuclear gene with ID TcCLB.506529.310). All T. cruzi variants fall in two main genetic lineages: 75% of the samples corresponded to T. cruzi Discrete Typing Unit (DTU) I (TcI), and 25% to a North American specific lineage previously labelled TcIV-USA. Phylogenetic and sequence divergence analyses of our new data plus all previously published sequence data from those four loci collected in the USA, show that TcIV-USA is significantly different from any other previously defined T. cruzi DTUs. The significant level of genetic divergence between TcIV-USA and other T. cruzi DTUs should lead to an increased focus on understanding the epidemiological importance of this DTU, as well as its geographical range and pathogenicity in humans and domestic animals. Our findings further corroborate the fact that there is a high genetic diversity of the parasite in North America and emphasize the need for appropriate surveillance and vector control programs for Chagas disease in southern USA and Mexico.
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Affiliation(s)
- Carlos A Flores-López
- Department of Biology, University of Maryland, College Park, MD, USA; Facultad de Ciencias, Universidad Autónoma de Baja California, Ensenada, Baja California, Mexico
| | - Elizabeth A Mitchell
- Tick-Borne Disease Research Laboratory, Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, TX, USA; Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Carolina E Reisenman
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
| | - Sahotra Sarkar
- Department of Philosophy and Department of Integrative Biology, University of Texas, Austin, TX, USA
| | - Philip C Williamson
- Tick-Borne Disease Research Laboratory, Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, TX, USA; Creative Testing Solutions, Tempe, AZ, USA
| | - Carlos A Machado
- Department of Biology, University of Maryland, College Park, MD, USA.
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Sato H, Mafie E. "Visiting old, learn new": taxonomical overview of chiropteran trypanosomes from the morphology to the genes. Parasitol Res 2022; 121:805-822. [PMID: 35106654 DOI: 10.1007/s00436-022-07423-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 01/02/2022] [Indexed: 11/25/2022]
Abstract
Bats (the order Chiroptera) account for more than 20% of all mammalian species in the world; remarkably, they are the only mammals capable of true and sustained flight using their wing-like forelimbs. Since the beginning of the twentieth century, various morphotypes (or genotypes in the last decade) of haemoflagellates in the genus Trypanosoma (Euglenozoa: Kinetoplastea: Trypanosomatidae) have been reported worldwide in the blood of bats. Of note, the latent nature of chiropteran trypanosome infection with low levels of parasitaemia, together with the apparent morphological variation of the bloodstream forms related to phenotypical plasticity and the morphological resemblance of different parasite species, has hampered the taxonomic classification of bat trypanosomes based on morphological criteria. This said, 50 years ago, Hoare (1972) provisionally divided bat trypanosomes into two major morphotypes: the megadermae group (corresponding to the subgenus Megatrypanum in the traditional taxonomic system; 8 species) and the vespertilionis group (similar to the subgenus Schizotrypanum; 5 species). Importantly, the biological and biochemical analyses of bat trypanosomes isolated by haemoculture, together with the molecular genetic characterisation using various gene markers, allowed the establishment of clear phylogenetic and taxonomic relationships of various isolates from different continents in the last two decades. Here, we review the historical taxonomic approaches used to define chiropteran trypanosomes, as well as the ones currently employed to shed light on the diversity and evolutional tracks of the globally distributed chiropteran trypanosomes.
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Affiliation(s)
- Hiroshi Sato
- Laboratory of Parasitology, Joint Faculty of Veterinary Medicine, Yamaguchi University, 1677-1 Yoshida, Yamaguchi, 753-8515, Japan.
- Division of Pathogenic Microorganisms, Research Center for Thermotolerant Microbial Resources, Yamaguchi University, 1677-1 Yoshida, Yamaguchi, 753-8515, Japan.
| | - Eliakunda Mafie
- Department of Microbiology, Parasitology and Biotechnology, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, Morogoro, Tanzania
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7
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Miles MA. Trypanosoma cruzi and Chagas disease: diversity, progress and challenges. Mem Inst Oswaldo Cruz 2022; 117:e210193chgsb. [PMID: 35544859 PMCID: PMC9088430 DOI: 10.1590/0074-02760210193chgsb] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 12/17/2021] [Indexed: 11/22/2022] Open
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Leishmania and the Model of Predominant Clonal Evolution. Microorganisms 2021; 9:microorganisms9112409. [PMID: 34835534 PMCID: PMC8620605 DOI: 10.3390/microorganisms9112409] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 11/18/2021] [Accepted: 11/20/2021] [Indexed: 01/23/2023] Open
Abstract
As it is the case for other pathogenic microorganisms, the respective impact of clonality and genetic exchange on Leishmania natural populations has been the object of lively debates since the early 1980s. The predominant clonal evolution (PCE) model states that genetic exchange in these parasites’ natural populations may have a high relevance on an evolutionary scale, but is not sufficient to erase a persistent phylogenetic signal and the existence of bifurcating trees. Recent data based on high-resolution markers and genomic polymorphisms fully confirm the PCE model down to a microevolutionary level.
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Tibayrenc M, Ayala FJ. Models in parasite and pathogen evolution: Genomic analysis reveals predominant clonality and progressive evolution at all evolutionary scales in parasitic protozoa, yeasts and bacteria. ADVANCES IN PARASITOLOGY 2021; 111:75-117. [PMID: 33482977 DOI: 10.1016/bs.apar.2020.12.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The predominant clonal evolution (PCE) model of pathogenic microorganisms postulates that the impact of genetic recombination in those pathogens' natural populations is not enough to erase a persistent phylogenetic signal at all evolutionary scales from microevolution till geological times in the whole ecogeographical range of the species considered. We have tested this model with a set of representative parasitic protozoa, yeasts and bacteria in the light of the most recent genomic data. All surveyed species, including those that were considered as highly recombining, exhibit similar PCE patterns above and under the species level, from macro- to micro-evolutionary scales (Russian doll pattern), suggesting gradual evolution. To our knowledge, it is the first time that such a strong common evolutionary feature among very diverse pathogens has been evidenced. The implications of this model for basic biology and applied research are exposed. These implications include our knowledge on the pathogens' reproductive mode, their population structure, the possibility to type strain and to follow up epidemics (molecular epidemiology) and to revisit pathogens' taxonomy through a flexible use of the phylogenetic species concept (Cracraft, 1983).
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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 recherche pour le développement, Montpellier Cedex 5, France.
| | - Francisco J Ayala
- Catedra Francisco Jose Ayala of Science, Technology, and Religion, University of Comillas, Madrid, Spain; 2 Locke Court, Irvine, CA, United States
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Añez N, Crisante G. The tissue specific tropism in Trypanosoma cruzi. Is it true? Acta Trop 2021; 213:105736. [PMID: 33159898 DOI: 10.1016/j.actatropica.2020.105736] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 09/15/2020] [Accepted: 10/14/2020] [Indexed: 10/23/2022]
Abstract
Systematic microscopical observations on tissues from mice, inoculated with different Trypanosoma cruzi isolates, were carried out in order to assess whether the parasite expresses tissue-specific tropism, or if it can invade tissues pervasively within the mammal host. A total of ninety mice were included in the study. Sixty, subcutaneously-inoculated with 15 × 104T. cruzi-blood trypomastigotes were dissected and examined daily for detecting and counting parasites during 12 days of acute infection. Additionally, two long-term experiments using mice inoculated with 5 × 103 metacyclic-forms were performed. A group of 10 mice inoculated intraperitoneally and another group of 20 mice inoculated intradermally. Results demonstrated that T. cruzi does not exhibit a tissue-specific tropism, revealing characteristics of a paninfective species able to invade tissues of ectodermal, mesodermal, and endodermal embryonic origin, irrespective of the parasite's lineage, infective form, route of entry, or size of the inoculum causing the host's infection. Details on T. cruzi-tissue invasion, tissue-parasite load during the course time, and the hypothetical potential pseudocyst/amastigote whole-body burden in the murine model is analyzed. The importance of the findings and its interpretation related to human Chagas disease and the tissue-parasite persistence is also discussed.
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Martín-Escolano J, Medina-Carmona E, Martín-Escolano R. Chagas Disease: Current View of an Ancient and Global Chemotherapy Challenge. ACS Infect Dis 2020; 6:2830-2843. [PMID: 33034192 DOI: 10.1021/acsinfecdis.0c00353] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Chagas disease is a neglected tropical disease and a global public health issue. In terms of treatment, no progress has been made since the 1960s, when benznidazole and nifurtimox, two obsolete drugs still prescribed, were used to treat this disease. Hence, currently, there are no effective treatments available to tackle Chagas disease. Over the past 20 years, there has been an increasing interest in the disease. However, parasite genetic diversity, drug resistance, tropism, and complex life cycle, along with the limited understanding of the disease and inadequate methodologies and strategies, have resulted in the absence of new insights in drugs development and disappointing outcomes in clinical trials so far. In summary, new drugs are urgently needed. This Review considers the relevant aspects related to the lack of drugs for Chagas disease, resumes the advances in tools for drug discovery, and discusses the main features to be taken into account to develop new effective drugs.
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Affiliation(s)
- Javier Martín-Escolano
- Department of Parasitology, Instituto de Investigación Biosanitaria (ibs.Granada), Hospitales Universitarios De Granada/University of Granada, Severo Ochoa s/n, 18071 Granada, Spain
| | | | - Rubén Martín-Escolano
- Department of Parasitology, Instituto de Investigación Biosanitaria (ibs.Granada), Hospitales Universitarios De Granada/University of Granada, Severo Ochoa s/n, 18071 Granada, Spain
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Genomic Organization and Generation of Genetic Variability in the RHS (Retrotransposon Hot Spot) Protein Multigene Family in Trypanosoma cruzi. Genes (Basel) 2020; 11:genes11091085. [PMID: 32957642 PMCID: PMC7563717 DOI: 10.3390/genes11091085] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 09/11/2020] [Accepted: 09/14/2020] [Indexed: 12/15/2022] Open
Abstract
Retrotransposon Hot Spot (RHS) is the most abundant gene family in Trypanosoma cruzi, with unknown function in this parasite. The aim of this work was to shed light on the organization and expression of RHS in T. cruzi. The diversity of the RHS protein family in T. cruzi was demonstrated by phylogenetic and recombination analyses. Transcribed sequences carrying the RHS domain were classified into ten distinct groups of monophyletic origin. We identified numerous recombination events among the RHS and traced the origins of the donors and target sequences. The transcribed RHS genes have a mosaic structure that may contain fragments of different RHS inserted in the target sequence. About 30% of RHS sequences are located in the subtelomere, a region very susceptible to recombination. The evolution of the RHS family has been marked by many events, including gene duplication by unequal mitotic crossing-over, homologous, as well as ectopic recombination, and gene conversion. The expression of RHS was analyzed by immunofluorescence and immunoblotting using anti-RHS antibodies. RHS proteins are evenly distributed in the nuclear region of T. cruzi replicative forms (amastigote and epimastigote), suggesting that they could be involved in the control of the chromatin structure and gene expression, as has been proposed for T. brucei.
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Genomics and High-Resolution Typing Confirm Predominant Clonal Evolution Down to a Microevolutionary Scale in Trypanosoma cruzi. Pathogens 2020; 9:pathogens9050356. [PMID: 32397142 PMCID: PMC7281314 DOI: 10.3390/pathogens9050356] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 05/07/2020] [Accepted: 05/07/2020] [Indexed: 12/27/2022] Open
Abstract
Trypanosoma cruzi, the agent of Chagas disease, is a paradigmatic case of the predominant clonal evolution (PCE) model, which states that the impact of genetic recombination in pathogens' natural populations is not sufficient to suppress a persistent phylogenetic signal at all evolutionary scales. In spite of indications for occasional recombination and meiosis, recent genomics and high-resolution typing data in T. cruzi reject the counterproposal that PCE does not operate at lower evolutionary scales, within the evolutionary units (=near-clades) that subdivide the species. Evolutionary patterns in the agent of Chagas disease at micro- and macroevolutionary scales are strikingly similar ("Russian doll pattern"), suggesting gradual, rather than saltatory evolution.
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Berry ASF, Salazar-Sánchez R, Castillo-Neyra R, Borrini-Mayorí K, Chipana-Ramos C, Vargas-Maquera M, Ancca-Juarez J, Náquira-Velarde C, Levy MZ, Brisson D. Sexual reproduction in a natural Trypanosoma cruzi population. PLoS Negl Trop Dis 2019; 13:e0007392. [PMID: 31107905 PMCID: PMC6544315 DOI: 10.1371/journal.pntd.0007392] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 05/31/2019] [Accepted: 04/15/2019] [Indexed: 12/21/2022] Open
Abstract
Background Sexual reproduction provides an evolutionary advantageous mechanism that combines favorable mutations that have arisen in separate lineages into the same individual. This advantage is especially pronounced in microparasites as allelic reassortment among individuals caused by sexual reproduction promotes allelic diversity at immune evasion genes within individuals which is often essential to evade host immune systems. Despite these advantages, many eukaryotic microparasites exhibit highly-clonal population structures suggesting that genetic exchange through sexual reproduction is rare. Evidence supporting clonality is particularly convincing in the causative agent of Chagas disease, Trypanosoma cruzi, despite equally convincing evidence of the capacity to engage in sexual reproduction. Methodology/ Principle Findings In the present study, we investigated two hypotheses that can reconcile the apparent contradiction between the observed clonal population structure and the capacity to engage in sexual reproduction by analyzing the genome sequences of 123 T. cruzi isolates from a natural population in Arequipa, Peru. The distribution of polymorphic markers within and among isolates provides clear evidence of the occurrence of sexual reproduction. Large genetic segments are rearranged among chromosomes due to crossing over during meiosis leading to a decay in the genetic linkage among polymorphic markers compared to the expectations from a purely asexually-reproducing population. Nevertheless, the population structure appears clonal due to a high level of inbreeding during sexual reproduction which increases homozygosity, and thus reduces diversity, within each inbreeding lineage. Conclusions/ Significance These results effectively reconcile the apparent contradiction by demonstrating that the clonal population structure is derived not from infrequent sex in natural populations but from high levels of inbreeding. We discuss epidemiological consequences of this reproductive strategy on genome evolution, population structure, and phenotypic diversity of this medically important parasite. The rearrangement of alleles among individuals in a population during sexual reproduction maintains high allelic diversity within individuals in a population at polymorphic genes. Allelic diversity within individuals can be particularly important for parasites as it enhances their ability to evade host immune systems. Despite the potential benefits of sexual reproduction for parasites, natural populations of the protozoan parasite—and causative agent of human Chagas disease—Trypanosoma cruzi, exhibit clonal population structures indicative of asexual reproduction. This is particularly surprising as T. cruzi has the capacity for sexual reproduction. Here, we resolve this apparent contradiction by sequencing whole genomes of 123 T. cruzi isolates from a natural population in Arequipa, Peru. Evidence of past sexual reproduction and allelic rearrangements are common in this T. cruzi population. However, the majority of sexual reproduction events occur between close relatives resulting in an apparent clonal population structure. Sexual reproduction with distant relatives in areas with greater strain diversity has the potential to affect public health by increasing diversity in immune evasion genes within individuals and enhancing within-host survival, rapidly diversifying antigens that could affect the sensitivity of serological diagnostics, and by generating diversity in pathogenicity or drug resistance.
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Affiliation(s)
- Alexander S. F. Berry
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Renzo Salazar-Sánchez
- Universidad Peruana Cayetano Heredia/University of Pennsylvania Chagas Disease Field Laboratory, Arequipa, Peru
| | - Ricardo Castillo-Neyra
- Universidad Peruana Cayetano Heredia/University of Pennsylvania Chagas Disease Field Laboratory, Arequipa, Peru
- Department of Biostatistics, Epidemiology and Informatics, The Perelman School of Medicine of the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Katty Borrini-Mayorí
- Universidad Peruana Cayetano Heredia/University of Pennsylvania Chagas Disease Field Laboratory, Arequipa, Peru
| | - Claudia Chipana-Ramos
- Universidad Peruana Cayetano Heredia/University of Pennsylvania Chagas Disease Field Laboratory, Arequipa, Peru
| | - Melina Vargas-Maquera
- Universidad Peruana Cayetano Heredia/University of Pennsylvania Chagas Disease Field Laboratory, Arequipa, Peru
| | - Jenny Ancca-Juarez
- Universidad Peruana Cayetano Heredia/University of Pennsylvania Chagas Disease Field Laboratory, Arequipa, Peru
| | - César Náquira-Velarde
- Universidad Peruana Cayetano Heredia/University of Pennsylvania Chagas Disease Field Laboratory, Arequipa, Peru
| | - Michael Z. Levy
- Universidad Peruana Cayetano Heredia/University of Pennsylvania Chagas Disease Field Laboratory, Arequipa, Peru
- Department of Biostatistics, Epidemiology and Informatics, The Perelman School of Medicine of the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Dustin Brisson
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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15
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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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16
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Bradwell KR, Koparde VN, Matveyev AV, Serrano MG, Alves JMP, Parikh H, Huang B, Lee V, Espinosa-Alvarez O, Ortiz PA, Costa-Martins AG, Teixeira MMG, Buck GA. Genomic comparison of Trypanosoma conorhini and Trypanosoma rangeli to Trypanosoma cruzi strains of high and low virulence. BMC Genomics 2018; 19:770. [PMID: 30355302 PMCID: PMC6201504 DOI: 10.1186/s12864-018-5112-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 09/25/2018] [Indexed: 01/09/2023] Open
Abstract
Background Trypanosoma conorhini and Trypanosoma rangeli, like Trypanosoma cruzi, are kinetoplastid protist parasites of mammals displaying divergent hosts, geographic ranges and lifestyles. Largely nonpathogenic T. rangeli and T. conorhini represent clades that are phylogenetically closely related to the T. cruzi and T. cruzi-like taxa and provide insights into the evolution of pathogenicity in those parasites. T. rangeli, like T. cruzi is endemic in many Latin American countries, whereas T. conorhini is tropicopolitan. T. rangeli and T. conorhini are exclusively extracellular, while T. cruzi has an intracellular stage in the mammalian host. Results Here we provide the first comprehensive sequence analysis of T. rangeli AM80 and T. conorhini 025E, and provide a comparison of their genomes to those of T. cruzi G and T. cruzi CL, respectively members of T. cruzi lineages TcI and TcVI. We report de novo assembled genome sequences of the low-virulent T. cruzi G, T. rangeli AM80, and T. conorhini 025E ranging from ~ 21–25 Mbp, with ~ 10,000 to 13,000 genes, and for the highly virulent and hybrid T. cruzi CL we present a ~ 65 Mbp in-house assembled haplotyped genome with ~ 12,500 genes per haplotype. Single copy orthologs of the two T. cruzi strains exhibited ~ 97% amino acid identity, and ~ 78% identity to proteins of T. rangeli or T. conorhini. Proteins of the latter two organisms exhibited ~ 84% identity. T. cruzi CL exhibited the highest heterozygosity. T. rangeli and T. conorhini displayed greater metabolic capabilities for utilization of complex carbohydrates, and contained fewer retrotransposons and multigene family copies, i.e. trans-sialidases, mucins, DGF-1, and MASP, compared to T. cruzi. Conclusions Our analyses of the T. rangeli and T. conorhini genomes closely reflected their phylogenetic proximity to the T. cruzi clade, and were largely consistent with their divergent life cycles. Our results provide a greater context for understanding the life cycles, host range expansion, immunity evasion, and pathogenesis of these trypanosomatids. Electronic supplementary material The online version of this article (10.1186/s12864-018-5112-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Katie R Bradwell
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, USA.,Present address: Institute for Genome Sciences, University of Maryland, Baltimore, MD, USA
| | - Vishal N Koparde
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, USA
| | - Andrey V Matveyev
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, USA.,Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA, USA
| | - Myrna G Serrano
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, USA.,Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA, USA
| | - João M P Alves
- Department of Parasitology, ICB, University of São Paulo, São Paulo, SP, Brazil
| | - Hardik Parikh
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, USA.,Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA, USA
| | - Bernice Huang
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, USA.,Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA, USA
| | - Vladimir Lee
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, USA
| | | | - Paola A Ortiz
- Department of Parasitology, ICB, University of São Paulo, São Paulo, SP, Brazil
| | | | - Marta M G Teixeira
- Department of Parasitology, ICB, University of São Paulo, São Paulo, SP, Brazil
| | - Gregory A Buck
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, USA. .,Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA, USA.
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17
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Alves CL, Repolês BM, da Silva MS, Mendes IC, Marin PA, Aguiar PHN, Santos SDS, Franco GR, Macedo AM, Pena SDJ, Andrade LDO, Guarneri AA, Tahara EB, Elias MC, Machado CR. The recombinase Rad51 plays a key role in events of genetic exchange in Trypanosoma cruzi. Sci Rep 2018; 8:13335. [PMID: 30190603 PMCID: PMC6127316 DOI: 10.1038/s41598-018-31541-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 08/16/2018] [Indexed: 12/11/2022] Open
Abstract
Detection of genetic exchange has been a limiting factor to deepen the knowledge on the mechanisms by which Trypanosoma cruzi is able to generate progeny and genetic diversity. Here we show that incorporation of halogenated thymidine analogues, followed by immunostaining, is a reliable method not only to detect T. cruzi fused-cell hybrids, but also to quantify their percentage in populations of this parasite. Through this approach, we were able to detect and quantify fused-cell hybrids of T. cruzi clones CL Brener and Y. Given the increased detection of fused-cell hybrids in naturally-occurring hybrid CL Brener strain, which displays increased levels of RAD51 and BRCA2 transcripts, we further investigated the role of Rad51 - a recombinase involved in homologous recombination - in the process of genetic exchange. We also verified that the detection of fused-cell hybrids in T. cruzi overexpressing RAD51 is increased when compared to wild-type cells, suggesting a key role for Rad51 either in the formation or in the stabilization of fused-cell hybrids in this organism.
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Affiliation(s)
- Ceres Luciana Alves
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Bruno Marçal Repolês
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Marcelo Santos da Silva
- Laboratório Especial de Ciclo Celular, Centro de Toxinas, Resposta Imune e Sinalização Celular, Instituto Butantan, São Paulo, SP, Brazil
| | - Isabela Cecília Mendes
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Paula Andrea Marin
- Laboratório Especial de Ciclo Celular, Centro de Toxinas, Resposta Imune e Sinalização Celular, Instituto Butantan, São Paulo, SP, Brazil
| | | | - Selma da Silva Santos
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Glória Regina Franco
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Andréa Mara Macedo
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Sérgio Danilo Junho Pena
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | | | | | - Erich Birelli Tahara
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Maria Carolina Elias
- Laboratório Especial de Ciclo Celular, Centro de Toxinas, Resposta Imune e Sinalização Celular, Instituto Butantan, São Paulo, SP, Brazil
| | - Carlos Renato Machado
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.
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18
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Zingales B. Trypanosoma cruzi genetic diversity: Something new for something known about Chagas disease manifestations, serodiagnosis and drug sensitivity. Acta Trop 2018; 184:38-52. [PMID: 28941731 DOI: 10.1016/j.actatropica.2017.09.017] [Citation(s) in RCA: 245] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 08/18/2017] [Accepted: 09/18/2017] [Indexed: 11/27/2022]
Abstract
The genetic diversity of Trypanosoma cruzi, the protozoan agent of Chagas disease, is widely recognized. At present, T. cruzi is partitioned into seven discrete typing units (DTUs), TcI-TcVI and Tcbat. This article reviews the present knowledge on the parasite population structure, the evolutionary relationships among DTUs and their distinct, but not exclusive ecological and epidemiological associations. Different models for the origin of hybrid DTUs are examined, which agree that genetic exchange among T. cruzi populations is frequent and has contributed to the present parasite population structure. The geographic distribution of the prevalent DTUs in humans from the southern United States to Argentina is here presented and the circumstantial evidence of a possible association between T. cruzi genotype and Chagas disease manifestations is discussed. The available information suggests that parasite strains detected in patients, regardless of the clinical presentation, reflect the principal DTU circulating in the domestic transmission cycles of a particular region. In contrast, in several orally transmitted outbreaks, sylvatic strains are implicated. As a consequence of the genotypic and phenotypic differences of T. cruzi strains and the differential geographic distribution of DTUs in humans, regional variations in the sensitivity of the serological tests are verified. The natural resistance to benznidazole and nifurtimox, verified in vivo and in vitro for some parasite stocks, is not associated with any particular DTU, and does not explain the marked difference in the anti-parasitic efficacy of both drugs in the acute and chronic phases of Chagas disease. Throughout this review, it is emphasized that the interplay between parasite and host genetics should have an important role in the definition of Chagas disease pathogenesis, anti-T. cruzi immune response and chemotherapy outcome and should be considered in future investigations.
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Affiliation(s)
- Bianca Zingales
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Avenida Professor Lineu Prestes 748, 05508-000 São Paulo, SP, Brazil.
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Recent advances in trypanosomatid research: genome organization, expression, metabolism, taxonomy and evolution. Parasitology 2018; 146:1-27. [PMID: 29898792 DOI: 10.1017/s0031182018000951] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Unicellular flagellates of the family Trypanosomatidae are obligatory parasites of invertebrates, vertebrates and plants. Dixenous species are aetiological agents of a number of diseases in humans, domestic animals and plants. Their monoxenous relatives are restricted to insects. Because of the high biological diversity, adaptability to dramatically different environmental conditions, and omnipresence, these protists have major impact on all biotic communities that still needs to be fully elucidated. In addition, as these organisms represent a highly divergent evolutionary lineage, they are strikingly different from the common 'model system' eukaryotes, such as some mammals, plants or fungi. A number of excellent reviews, published over the past decade, were dedicated to specialized topics from the areas of trypanosomatid molecular and cell biology, biochemistry, host-parasite relationships or other aspects of these fascinating organisms. However, there is a need for a more comprehensive review that summarizing recent advances in the studies of trypanosomatids in the last 30 years, a task, which we tried to accomplish with the current paper.
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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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21
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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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Abstract
Chagas disease is caused by infection with the insect-transmitted protozoan Trypanosoma cruzi, and is the most important parasitic infection in Latin America. The current drugs, benznidazole and nifurtimox, are characterized by limited efficacy and toxic side-effects, and treatment failures are frequently observed. The urgent need for new therapeutic approaches is being met by a combined effort from the academic and commercial sectors, together with major input from not-for-profit drug development consortia. With the disappointing outcomes of recent clinical trials against chronic Chagas disease, it has become clear that an incomplete understanding of parasite biology and disease pathogenesis is impacting negatively on the development of more effective drugs. In addition, technical issues, including difficulties in establishing parasitological cure in both human patients and animal models, have greatly complicated the assessment of drug efficacy. Here, we outline the major questions that need to be addressed and discuss technical innovations that can be exploited to accelerate the drug development pipeline.
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Tomasini N, Diosque P. Phylogenomics of Trypanosoma cruzi: Few evidence of TcI/TcII mosaicism in TcIII challenges the hypothesis of an ancient TcI/TcII hybridization. INFECTION GENETICS AND EVOLUTION 2017; 50:25-27. [PMID: 28192210 DOI: 10.1016/j.meegid.2017.02.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 02/08/2017] [Accepted: 02/09/2017] [Indexed: 12/20/2022]
Abstract
Phylogenetic relationships among major lineages of Trypanosoma cruzi are still debatable. Particularly, it is controversial the origin of two main lineages: TcIII and TcIV. Some authors proposed that these lineages have been the result of an ancient hybridization between TcI and TcII, and this was one of the most accepted evolutionary models in the scientific community for several years. In the present paper we analyse several genomes of T. cruzi in order to examine if there is evidence supporting that TcIII is an ancient TcI/TcII hybrid. Our results show that TcIII is mainly related to TcI and not to TcII and there is few evidence of mosaicism for TcIII. Our results challenge the hypothesis of the ancient TcI/TcII hybridization.
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Affiliation(s)
- Nicolás Tomasini
- Instituto de Patología Experimental, Facultad de Ciencias de la Salud, Universidad Nacional de Salta - CONICET, Av. Bolivia 5150, 4400, Salta, Salta, Argentina.
| | - Patricio Diosque
- Instituto de Patología Experimental, Facultad de Ciencias de la Salud, Universidad Nacional de Salta - CONICET, Av. Bolivia 5150, 4400, Salta, Salta, Argentina
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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: 146] [Impact Index Per Article: 18.3] [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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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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Gómez-Palacio A, Lopera J, Rojas W, Bedoya G, Cantillo-Barraza O, Marín-Suarez J, Triana-Chávez O, Mejía-Jaramillo A. Multilocus analysis indicates that Trypanosoma cruzi I genetic substructure associated with sylvatic and domestic cycles is not an attribute conserved throughout Colombia. INFECTION GENETICS AND EVOLUTION 2015; 38:35-43. [PMID: 26631812 DOI: 10.1016/j.meegid.2015.11.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 11/24/2015] [Accepted: 11/25/2015] [Indexed: 10/22/2022]
Abstract
Trypanosoma cruzi, the causative agent of Chagas disease, has been classified into six discrete typing units (DTUs) named TcI to TcVI. Furthermore, subcontinental scale studies based on analysis of the splice leader intergenic region (SL-IR) of the mini-exon gene have subdivided TcI in five genetic groups (Ia-Ie) related to the domestic and non-domestic cycles. However, a current review of this marker among all the sequences deposited in the GenBank demonstrates no correlation between the genetic structure and the eco-epidemiological features of parasite transmission. In this study, we performed a multilocus analysis of TcI isolates from a diverse array of hosts and vectors in a wide eco-geographical area of Colombia. Sequences from SL-IR and mitochondrial cyt b genes as well as PCR-RFLP profiles for four nuclear genes were analyzed. Multilocus analysis indicates that genetic structuration associated with sylvatic and domestic cycles in Colombia is not an attribute conserved across the entire eco-geography where TcI can be found.
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Affiliation(s)
- Andrés Gómez-Palacio
- Grupo de Biología y Control de Enfermedades Infecciosas, BCEI, Universidad de Antioquia, Medellín, Colombia
| | - Juan Lopera
- Grupo de Genética Molecular, GENMOL, Universidad de Antioquia, Medellín, Colombia
| | - Winston Rojas
- Grupo de Genética Molecular, GENMOL, Universidad de Antioquia, Medellín, Colombia
| | - Gabriel Bedoya
- Grupo de Genética Molecular, GENMOL, Universidad de Antioquia, Medellín, Colombia
| | - Omar Cantillo-Barraza
- Grupo de Biología y Control de Enfermedades Infecciosas, BCEI, Universidad de Antioquia, Medellín, Colombia
| | - Johana Marín-Suarez
- Grupo de Biología y Control de Enfermedades Infecciosas, BCEI, Universidad de Antioquia, Medellín, Colombia
| | - Omar Triana-Chávez
- Grupo de Biología y Control de Enfermedades Infecciosas, BCEI, Universidad de Antioquia, Medellín, Colombia
| | - Ana Mejía-Jaramillo
- Grupo de Biología y Control de Enfermedades Infecciosas, BCEI, Universidad de Antioquia, Medellín, Colombia.
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Díaz ML, Leal S, Mantilla JC, Molina-Berríos A, López-Muñoz R, Solari A, Escobar P, González Rugeles CI. Acute Chagas outbreaks: molecular and biological features of Trypanosoma cruzi isolates, and clinical aspects of acute cases in Santander, Colombia. Parasit Vectors 2015; 8:608. [PMID: 26612724 PMCID: PMC4661967 DOI: 10.1186/s13071-015-1218-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 11/19/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Outbreaks of acute Chagas disease associated with oral transmission are easily detected nowadays with trained health personnel in areas of low endemicity, or in which the vector transmission has been interrupted. Given the biological and genetic diversity of Trypanosoma cruzi, the high morbidity, mortality, and the observed therapeutic failure, new characteristics of these outbreaks need to be addressed at different levels, both in Trypanosoma cruzi as in patient response. The aim of this work was to evaluate the patient's features involved in six outbreaks of acute Chagas disease which occurred in Santander, Colombia, and the characteristics of Trypanosoma cruzi clones isolated from these patients, to establish the potential relationship between the etiologic agent features with host behavior. METHODS The clinical, pathological and epidemiological aspects of outbreaks were analyzed. In addition, Trypanosoma cruzi clones were biologically characterized both in vitro and in vivo, and the susceptibility to the classical trypanocidal drugs nifurtimox and benznidazole was evaluated. Trypanosoma cruzi clones were genotyped by means of mini-exon intergenic spacer and cytochrome b genes sequencing. RESULTS All clones were DTU I, and based on the mini-exon intergenic spacer, belong to two genotypes: G2 related with sub-urban, and G11 with rural outbreaks. Girón outbreak clones with higher susceptibility to drugs presented G2 genotype and C/T transition in Cyt b. The outbreaks affected mainly young population (±25.9 years), and the mortality rate was 10 %. The cardiac tissue showed intense inflammatory infiltrate, myocardial necrosis and abundant amastigote nests. However, although the gastrointestinal tissue was congestive, no inflammation or parasites were observed. CONCLUSIONS Although all clones belong to DTU I, two intra-DTU genotypes were found with the sequencing of the mini-exon intergenic spacer, however there is no strict correlation between genetic groups, the cycles of the parasite or the clinical forms of the disease. Trypanosoma cruzi clones from Girón with higher sensitivity to nifurtimox presented a particular G2 genotype and C/T transition in Cyt b. When the diagnosis was early, the patients responded well to antichagasic treatment, which highlights the importance of diagnosis and treatment early to prevent fatal outcomes associated with these acute episodes.
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Affiliation(s)
- Martha Lucía Díaz
- Grupo de Inmunología y Epidemiología Molecular (GIEM), Facultad de Salud, Universidad Industrial de Santander, Bucaramanga, Colombia.
| | - Sandra Leal
- Grupo de Investigación en Enfermedades Tropicales (CINTROP), Departamento de Ciencias Básicas, Escuela de Medicina, Universidad Industrial de Santander, Bucaramanga, Colombia.
| | - Julio César Mantilla
- Grupo de Inmunología y Epidemiología Molecular (GIEM), Facultad de Salud, Universidad Industrial de Santander, Bucaramanga, Colombia.
| | - Alfredo Molina-Berríos
- Programa de Farmacología Molecular y Clínica, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile. .,Present address: Laboratorio de Farmacología y Farmacogenética, Instituto de Investigación en Ciencias Odontológicas (ICOD), Facultad de Odontología, Universidad de Chile, Santiago, Chile.
| | - Rodrigo López-Muñoz
- Programa de Farmacología Molecular y Clínica, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile. .,Present address: Instituto de Farmacología y Morfofisiología, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Valdivia, Chile.
| | - Aldo Solari
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile.
| | - Patricia Escobar
- Grupo de Investigación en Enfermedades Tropicales (CINTROP), Departamento de Ciencias Básicas, Escuela de Medicina, Universidad Industrial de Santander, Bucaramanga, Colombia.
| | - Clara Isabel González Rugeles
- Grupo de Inmunología y Epidemiología Molecular (GIEM), Facultad de Salud, Universidad Industrial de Santander, Bucaramanga, Colombia. .,Escuela de Microbiología, Facultad de Salud, Carrera 32 #29-31, Oficina 419, Universidad Industrial de Santander, Bucaramanga, Colombia.
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Messenger LA, Miles MA. Evidence and importance of genetic exchange among field populations of Trypanosoma cruzi. Acta Trop 2015; 151:150-5. [PMID: 26188331 PMCID: PMC4644990 DOI: 10.1016/j.actatropica.2015.05.007] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 04/25/2015] [Accepted: 05/06/2015] [Indexed: 10/31/2022]
Abstract
Many eukaryotic pathogenic microorganisms that were previously assumed to propagate clonally have retained cryptic sexual cycles. The principal reproductive mode of Trypanosoma cruzi, the aetiological agent of Chagas disease, remains a controversial topic. Despite the existence of two recent natural hybrid lineages, a pervasive view is that recombination has been restrained at an evolutionary scale and is of little epidemiological relevance to contemporary parasite populations. This article reviews the growing number of field studies which indicate that natural hybridization in T. cruzi may be frequent, non-obligatory and idiosyncratic; potentially involving independent exchange of kinetoplast and nuclear genetic material as well as canonical meiotic mechanisms. Together these observations now challenge the traditional paradigm of preponderate clonal evolution in T. cruzi and highlight the need for additional, intensive and appropriately sampled field surveys, complemented by high resolution, combined nuclear and mitochondrial population genetics analyses.
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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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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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Reis-Cunha JL, Rodrigues-Luiz GF, Valdivia HO, Baptista RP, Mendes TAO, de Morais GL, Guedes R, Macedo AM, Bern C, Gilman RH, Lopez CT, Andersson B, Vasconcelos AT, Bartholomeu DC. Chromosomal copy number variation reveals differential levels of genomic plasticity in distinct Trypanosoma cruzi strains. BMC Genomics 2015; 16:499. [PMID: 26141959 PMCID: PMC4491234 DOI: 10.1186/s12864-015-1680-4] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 06/01/2015] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Trypanosoma cruzi, the etiologic agent of Chagas disease, is currently divided into six discrete typing units (DTUs), named TcI-TcVI. CL Brener, the reference strain of the T. cruzi genome project, is a hybrid with a genome assembled into 41 putative chromosomes. Gene copy number variation (CNV) is well documented as an important mechanism to enhance gene expression and variability in T. cruzi. Chromosomal CNV (CCNV) is another level of gene CNV in which whole blocks of genes are expanded simultaneously. Although the T. cruzi karyotype is not well defined, several studies have demonstrated a significant variation in the size and content of chromosomes between different T. cruzi strains. Despite these studies, the extent of diversity in CCNV among T. cruzi strains based on a read depth coverage analysis has not been determined. RESULTS We identify the CCNV in T. cruzi strains from the TcI, TcII and TcIII DTUs, by analyzing the depth coverage of short reads from these strains using the 41 CL Brener chromosomes as reference. This study led to the identification of a broader extent of CCNV in T. cruzi than was previously speculated. The TcI DTU strains have very few aneuploidies, while the strains from TcII and TcIII DTUs present a high degree of chromosomal expansions. Chromosome 31, which is the only chromosome that is supernumerary in all six T. cruzi samples evaluated in this study, is enriched with genes related to glycosylation pathways, highlighting the importance of glycosylation to parasite survival. CONCLUSIONS Increased gene copy number due to chromosome amplification may contribute to alterations in gene expression, which represents a strategy that may be crucial for parasites that mainly depend on post-transcriptional mechanisms to control gene expression.
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Affiliation(s)
- João Luís Reis-Cunha
- Laboratório de Imunologia e Genômica de Parasitos, Departamento deParasitologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
| | - Gabriela F Rodrigues-Luiz
- Laboratório de Imunologia e Genômica de Parasitos, Departamento deParasitologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
| | - Hugo O Valdivia
- Laboratório de Imunologia e Genômica de Parasitos, Departamento deParasitologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
| | - Rodrigo P Baptista
- Laboratório de Imunologia e Genômica de Parasitos, Departamento deParasitologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
| | - Tiago A O Mendes
- Laboratório de Imunologia e Genômica de Parasitos, Departamento deParasitologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
| | | | - Rafael Guedes
- Laboratório Nacional de Computação Científica, Petrópolis, Rio de Janeiro, Brazil.
| | - Andrea M Macedo
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
| | - Caryn Bern
- University of California San Francisco, San Francisco, CA, USA.
| | - Robert H Gilman
- Universidad Cayetano Heredia, Lima, MD, Peru.
- Johns Hopkins University, Baltimore, MD, USA.
| | - Carlos Talavera Lopez
- Department of Cell and Molecular Biology, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden.
| | - Björn Andersson
- Department of Cell and Molecular Biology, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden.
| | | | - Daniella C Bartholomeu
- Laboratório de Imunologia e Genômica de Parasitos, Departamento deParasitologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
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Flores-López CA, Machado CA. Differences in inferred genome-wide signals of positive selection during the evolution of Trypanosoma cruzi and Leishmania spp. lineages: A result of disparities in host and tissue infection ranges? INFECTION GENETICS AND EVOLUTION 2015; 33:37-46. [DOI: 10.1016/j.meegid.2015.04.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Revised: 03/19/2015] [Accepted: 04/09/2015] [Indexed: 01/21/2023]
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Tomasini N, Diosque P. Evolution of Trypanosoma cruzi: clarifying hybridisations, mitochondrial introgressions and phylogenetic relationships between major lineages. Mem Inst Oswaldo Cruz 2015; 110:403-13. [PMID: 25807469 PMCID: PMC4489478 DOI: 10.1590/0074-02760140401] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 02/12/2015] [Indexed: 11/21/2022] Open
Abstract
Several different models of Trypanosoma cruzi evolution have been proposed. These
models suggest that scarce events of genetic exchange occurred during the
evolutionary history of this parasite. In addition, the debate has focused on the
existence of one or two hybridisation events during the evolution of T. cruzi
lineages. Here, we reviewed the literature and analysed available sequence data to
clarify the phylogenetic relationships among these different lineages. We observed
that TcI, TcIII and TcIV form a monophyletic group and that TcIII and TcIV are not,
as previously suggested, TcI-TcII hybrids. Particularly, TcI and TcIII are sister
groups that diverged around the same time that a widely distributed TcIV split into
two clades (TcIVS and TcIVN). In addition, we collected
evidence that TcIII received TcIVS kDNA by introgression on several
occasions. Different demographic hypotheses (surfing and asymmetrical introgression)
may explain the origin and expansion of the TcIII group. Considering these
hypotheses, genetic exchange should have been relatively frequent between TcIII and
TcIVS in the geographic area in which their distributions overlapped.
In addition, our results support the hypothesis that two independent hybridisation
events gave rise to TcV and TcVI. Consequently, TcIVS kDNA was first
transferred to TcIII and later to TcV and TcVI in TcII/TcIII hybridisation
events.
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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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Dutra WO, Menezes CAS, Magalhães LMD, Gollob KJ. Immunoregulatory networks in human Chagas disease. Parasite Immunol 2014; 36:377-87. [PMID: 24611805 DOI: 10.1111/pim.12107] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Accepted: 02/19/2014] [Indexed: 01/11/2023]
Abstract
Chagas disease, caused by the infection with Trypanosoma cruzi, is endemic in all Latin America. Due to the increase in population migration, Chagas disease has spread worldwide and is now considered a health issue not only in endemic countries. While most chronically infected individuals remain asymptomatic, approximately 30% of the patients develop a potentially deadly cardiomyopathy. The exact mechanisms that underlie the establishment and maintenance of the cardiac pathology are not clear. However, there is consistent evidence that immunoregulatory cytokines are critical for orchestrating the immune response and thus influence disease development or control. While the asymptomatic (indeterminate) form represents a state of balance between the host and the parasite, the establishment of the cardiac form represents the loss of this balance. Analysis of data obtained from several studies has led to the hypothesis that the indeterminate form is associated with an anti-inflammatory cytokine profile, represented by high expression of IL-10, while cardiac form is associated with a high production of IFN-gamma and TNF-alpha in relation to IL-10, leading to an inflammatory profile. Here, we discuss the immunoregulatory events that might influence disease outcome, as well as the mechanisms that influence the establishment of these complex immunoregulatory networks.
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Affiliation(s)
- W O Dutra
- Laboratório de Biologia das Interações Celulares, Departamento de Morfologia, Instituto de Ciências Biológicas, Belo Horizonte, MG, Brazil; Instituto Nacional de Ciência e Tecnologia - Doenças Tropicais - INCT-DT, Belo Horizonte, MG, Brazil
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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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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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Baptista RDP, D'Ávila DA, Segatto M, do Valle ÍF, Franco GR, Valadares HMS, Gontijo ED, Galvão LMDC, Pena SDJ, Chiari E, Machado CR, Macedo AM. Evidence of substantial recombination among Trypanosoma cruzi II strains from Minas Gerais. INFECTION GENETICS AND EVOLUTION 2013; 22:183-91. [PMID: 24296011 DOI: 10.1016/j.meegid.2013.11.021] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Revised: 11/22/2013] [Accepted: 11/23/2013] [Indexed: 01/06/2023]
Abstract
Due to the scarcity of evidence of sexuality in Trypanosoma cruzi, the causative agent of Chagas disease, it has been general accepted that the parasite reproduction is essentially clonal with infrequent genetic recombination. This assumption is mainly supported by indirect evidence, such as Hardy-Weinberg imbalances, linkage disequilibrium and a strong correlation between independent sets of genetic markers of T. cruzi populations. However, because the analyzed populations are usually isolated from different geographic regions, the possibility of population substructuring as generating these genetic marker imbalances cannot be eliminated. To investigate this possibility, we firstly compared the allele frequencies and haplotype networks using seven different polymorphic loci (two from mitochondrial and five from different nuclear chromosomes) in two groups of TcII strains: one including isolates obtained from different regions in Latin America and the other including isolates obtained only from patients of the Minas Gerais State in Brazil. Our hypothesis was that if the population structure is essentially clonal, Hardy-Weinberg disequilibrium and a sharp association between the clusters generated by analyzing independent markers should be observed in both strain groups, independent of the geographic origin of the samples. The results demonstrated that the number of microsatellite loci in linkage disequilibrium decreased from 4 to 1 when only strains from Minas Gerais were analyzed. Moreover, we did not observed any correlation between the clusters when analyzing the nuclear and mitochondrial loci, suggesting independent inheritance of these markers among the Minas Gerais strains. Besides, using a second subset of five physically linked microsatellite loci and the Minas Gerais strains, we could also demonstrate evidence of homologous recombination roughly proportional to the relative distance among them. Taken together, our results do not support a clonal population structure for T. cruzi, particularly in TcII, which coexists in the same geographical area, suggesting that genetic exchanges among these strains may occur more frequently than initially expected.
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Affiliation(s)
- Rodrigo de Paula Baptista
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Daniella Alchaar D'Ávila
- Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Marcela Segatto
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Ítalo Faria do Valle
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Glória Regina Franco
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | | | - Eliane Dias Gontijo
- Departamento de Medicina Preventiva e Social, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Lúcia Maria da Cunha Galvão
- Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil; Centro de Ciências da Saúde, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - Sérgio Danilo Junho Pena
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Egler Chiari
- Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Carlos Renato Machado
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
| | - Andréa Mara Macedo
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
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Barnabe C, Buitrago R, Bremond P, Aliaga C, Salas R, Vidaurre P, Herrera C, Cerqueira F, Bosseno MF, Waleckx E, Breniere SF. Putative panmixia in restricted populations of Trypanosoma cruzi isolated from wild Triatoma infestans in Bolivia. PLoS One 2013; 8:e82269. [PMID: 24312410 PMCID: PMC3843716 DOI: 10.1371/journal.pone.0082269] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Accepted: 10/29/2013] [Indexed: 01/26/2023] Open
Abstract
Trypanosoma cruzi, the causative agent of Chagas disease, is subdivided into six discrete typing units (DTUs; TcI-TcVI) of which TcI is ubiquitous and genetically highly variable. While clonality is the dominant mode of propagation, recombinant events play a significant evolutive role. Recently, foci of wild Triatoma infestans have been described in Bolivia, mainly infected by TcI. Hence, for the first time, we evaluated the level of genetic exchange within TcI natural potentially panmictic populations (single DTU, host, area and sampling time). Seventy-nine TcI stocks from wild T. infestans, belonging to six populations were characterized at eight microsatellite loci. For each population, Hardy-Weinberg equilibrium (HWE), linkage disequilibrium (LD), and presence of repeated multilocus genotypes (MLG) were analyzed by using a total of seven statistics, to test the null hypothesis of panmixia (H0). For three populations, none of the seven statistics allowed to rejecting H0; for another one the low size did not allow us to conclude, and for the two others the tests have given contradictory results. Interestingly, apparent panmixia was only observed in very restricted areas, and was not observed when grouping populations distant of only two kilometers or more. Nevertheless it is worth stressing that for the statistic tests of "HWE", in order to minimize the type I error (i. e. incorrect rejection of a true H0), we used the Bonferroni correction (BC) known to considerably increase the type II error ( i. e. failure to reject a false H0). For the other tests (LD and MLG), we did not use BC and the risk of type II error in these cases was acceptable. Thus, these results should be considered as a good indicator of the existence of panmixia in wild environment but this must be confirmed on larger samples to reduce the risk of type II error.
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Affiliation(s)
- Christian Barnabe
- MIVEGEC (Université de Montpellier 1 et 2 - CNRS 5290 - IRD 224), Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle, Institut de recherche pour le développement (IRD), Representation in Bolivia, La Paz, Bolivia
- Instituto Nacional de Laboratorios de Salud (INLASA), Department of Entomology, La Paz, Bolivia
| | - Rosio Buitrago
- MIVEGEC (Université de Montpellier 1 et 2 - CNRS 5290 - IRD 224), Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle, Institut de recherche pour le développement (IRD), Representation in Bolivia, La Paz, Bolivia
- Instituto Nacional de Laboratorios de Salud (INLASA), Department of Entomology, La Paz, Bolivia
| | - Philippe Bremond
- MIVEGEC (Université de Montpellier 1 et 2 - CNRS 5290 - IRD 224), Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle, Institut de recherche pour le développement (IRD), Representation in Bolivia, La Paz, Bolivia
| | - Claudia Aliaga
- MIVEGEC (Université de Montpellier 1 et 2 - CNRS 5290 - IRD 224), Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle, Institut de recherche pour le développement (IRD), Representation in Bolivia, La Paz, Bolivia
- Instituto Nacional de Laboratorios de Salud (INLASA), Department of Entomology, La Paz, Bolivia
| | - Renata Salas
- MIVEGEC (Université de Montpellier 1 et 2 - CNRS 5290 - IRD 224), Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle, Institut de recherche pour le développement (IRD), Representation in Bolivia, La Paz, Bolivia
- Instituto Nacional de Laboratorios de Salud (INLASA), Department of Entomology, La Paz, Bolivia
| | - Pablo Vidaurre
- Servicio Departamental de Salud (SEDES) of La Paz, La Paz, Bolivia
| | - Claudia Herrera
- Department of Tropical Medicine, Tulane University, School of Public Health and Tropical Medicine, New Orleans, Louisiana, United States of America
| | - Frédérique Cerqueira
- Plateforme Génomique Environnementale du Labex Centre "Méditerranéen Environnement Biodiversité", Séquençage – Génotypage, Université Montpellier 2, Montpellier, France
| | - Marie-France Bosseno
- MIVEGEC (Université de Montpellier 1 et 2 - CNRS 5290 - IRD 224), Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle, Institut de recherche pour le développement (IRD), Representation in Bolivia, La Paz, Bolivia
- Instituto Nacional de Laboratorios de Salud (INLASA), Department of Entomology, La Paz, Bolivia
| | - Etienne Waleckx
- MIVEGEC (Université de Montpellier 1 et 2 - CNRS 5290 - IRD 224), Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle, Institut de recherche pour le développement (IRD), Representation in Bolivia, La Paz, Bolivia
- Instituto Nacional de Laboratorios de Salud (INLASA), Department of Entomology, La Paz, Bolivia
| | - Simone Frédérique Breniere
- MIVEGEC (Université de Montpellier 1 et 2 - CNRS 5290 - IRD 224), Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle, Institut de recherche pour le développement (IRD), Representation in Bolivia, La Paz, Bolivia
- Instituto Nacional de Laboratorios de Salud (INLASA), Department of Entomology, La Paz, Bolivia
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Roellig DM, Savage MY, Fujita AW, Barnabé C, Tibayrenc M, Steurer FJ, Yabsley MJ. Genetic variation and exchange in Trypanosoma cruzi isolates from the United States. PLoS One 2013; 8:e56198. [PMID: 23457528 PMCID: PMC3572986 DOI: 10.1371/journal.pone.0056198] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Accepted: 01/10/2013] [Indexed: 12/22/2022] Open
Abstract
Trypanosoma cruzi, the causative agent of Chagas disease, is a multiclonal parasite with high levels of genetic diversity and broad host and geographic ranges. Molecular characterization of South American isolates of T. cruzi has demonstrated homologous recombination and nuclear hybridization, as well as the presence of 6 main genetic clusters or "discrete typing units" (DTUs). Few studies have extensively investigated such exchange events and genetic diversity in North American isolates. In the current study, we genetically characterized over 50 US isolates from wildlife reservoirs (e.g., raccoons, opossums, armadillos, skunks), domestic dogs, humans, nonhuman primates, and reduviid vectors from nine states (TX, CA, OK, SC, FL, GA, MD, LA, TN) using a multilocus sequencing method. Single nucleotide polymorphisms were identified in sequences of the mismatch-repair class 2 (MSH2) and Tc52 genes. Typing based on the two genes often paralleled genotyping by classic methodologies using mini-exon and 18S and 24Sα rRNA genes. Evidence for genetic exchange was obtained by comparing sequence phylogenies of nuclear and mitochondrial gene targets, dihydrofolate reductase-thymidylate synthase (DHFR-TS) and the cytochrome oxidase subunit II- NADH dehydrogenase subunit I region (COII-ND1), respectively. We observed genetic exchange in several US isolates as demonstrated by incongruent mitochondrial and nuclear genes phylogenies, which confirms a previous finding of a single genetic exchange event in a Florida isolate. The presence of SNPs and evidence of genetic exchange illustrates that strains from the US are genetically diverse, even though only two phylogenetic lineages have been identified in this region.
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Affiliation(s)
- Dawn M Roellig
- Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America.
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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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Morocoima A, Carrasco HJ, Boadas J, Chique JD, Herrera L, Urdaneta-Morales S. Trypanosoma cruzi III from armadillos (Dasypus novemcinctus novemcinctus) from Northeastern Venezuela and its biological behavior in murine model. Risk of emergency of Chagas’ disease. Exp Parasitol 2012; 132:341-7. [DOI: 10.1016/j.exppara.2012.08.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Revised: 06/18/2012] [Accepted: 08/01/2012] [Indexed: 11/16/2022]
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Barnabé C, Brenière SF. Scarce events of mitochondrial introgression in Trypanosoma cruzi: new case with a Bolivian strain. INFECTION GENETICS AND EVOLUTION 2012; 12:1879-83. [PMID: 22982157 DOI: 10.1016/j.meegid.2012.08.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Revised: 08/28/2012] [Accepted: 08/29/2012] [Indexed: 11/29/2022]
Abstract
Trypanosoma cruzi, the agent of Chagas disease, presents a predominantly clonal structure that has been shaped by recombination events leading to six genetic groups (DTUs, discrete typing units, TcI-TcVI). Several conventional and unconventional genetic exchange events have been described, including hybridization and mitochondrial introgression, which is explored here among Bolivian and Peruvian strains belonging to TcI because recombination events have been previously suspected by means of the MLMT method (multilocus microsatellite typing). We analyzed the variation of one nuclear (Gpi) and one mitochondrial (Nd1) gene among 60 TcI strains and 15 reference strains belonging to the six DTUs. The results clearly showed that one strain isolated from Triatoma infestans in the Cochabamba department (Bolivia) presented a genotype TcI for Gpi and a mitochondrial Nd1 genotype common to the DTUs TcIII, IV, V, and VI; this can be interpreted as a mitochondrial introgression event between distant DTUs. These kinds of events, although probably scarce, may have played an important role in the adaptive evolution of the species.
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Affiliation(s)
- Christian Barnabé
- MIVEGEC, Université de Montpellier 1 et 2 - CNRS 5290 - IRD 224, Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle, Institut de Recherche pour le Développement, Representation in Bolivia, Av Hernando Siles 5290, CP 9214 La Paz, Bolivia.
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Monteiro WM, Magalhães LKC, de Sá ARN, Gomes ML, Toledo MJDO, Borges L, Pires I, de Oliveira Guerra JA, Silveira H, Barbosa MDGV. Trypanosoma cruzi IV causing outbreaks of acute Chagas disease and infections by different haplotypes in the Western Brazilian Amazonia. PLoS One 2012; 7:e41284. [PMID: 22848457 PMCID: PMC3405119 DOI: 10.1371/journal.pone.0041284] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Accepted: 06/19/2012] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Chagas disease is an emergent tropical disease in the Brazilian Amazon Region, with an increasing number of cases in recent decades. In this region, the sylvatic cycle of Trypanosoma cruzi transmission, which constitutes a reservoir of parasites that might be associated with specific molecular, epidemiological and clinical traits, has been little explored. The objective of this work is to genetically characterize stocks of T. cruzi from human cases, triatomines and reservoir mammals in the State of Amazonas, in the Western Brazilian Amazon. METHODOLOGY/PRINCIPAL FINDINGS We analyzed 96 T. cruzi samples from four municipalities in distant locations of the State of Amazonas. Molecular characterization of isolated parasites from cultures in LIT medium or directly from vectors or whole human blood was performed by PCR of the non-transcribed spacer of the mini-exon and of the 24 S alfa ribosomal RNA gene, RFLP and sequencing of the mitochondrial cytochrome c oxidase subunit II (COII) gene, and by sequencing of the glucose-phosphate isomerase gene. The T. cruzi parasites from two outbreaks of acute disease were all typed as TcIV. One of the outbreaks was triggered by several haplotypes of the same DTU. TcIV also occurred in isolated cases and in Rhodnius robustus. Incongruence between mitochondrial and nuclear phylogenies is likely to be indicative of historical genetic exchange events resulting in mitochondrial introgression between TcIII and TcIV DTUs from Western Brazilian Amazon. TcI predominated among triatomines and was the unique DTU infecting marsupials. CONCLUSION/SIGNIFICANCE DTU TcIV, rarely associated with human Chagas disease in other areas of the Amazon basin, is the major strain responsible for the human infections in the Western Brazilian Amazon, occurring in outbreaks as single or mixed infections by different haplotypes.
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Affiliation(s)
- Wuelton Marcelo Monteiro
- Tropical Medicine Foundation Dr. Heitor Vieira Dourado, Manaus, Amazonas, Brazil
- University of the State of Amazonas, Manaus, Amazonas, Brazil
- Federal University of Amazonas, Manaus, Amazonas, Brazil
| | - Laylah Kelre Costa Magalhães
- Tropical Medicine Foundation Dr. Heitor Vieira Dourado, Manaus, Amazonas, Brazil
- University of the State of Amazonas, Manaus, Amazonas, Brazil
| | | | | | | | - Lara Borges
- Instituto de Higiene e Medicina Tropical, Center for Malaria Studies, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Isa Pires
- Instituto de Higiene e Medicina Tropical, Center for Malaria Studies, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Jorge Augusto de Oliveira Guerra
- Tropical Medicine Foundation Dr. Heitor Vieira Dourado, Manaus, Amazonas, Brazil
- University of the State of Amazonas, Manaus, Amazonas, Brazil
| | - Henrique Silveira
- Tropical Medicine Foundation Dr. Heitor Vieira Dourado, Manaus, Amazonas, Brazil
- Instituto de Higiene e Medicina Tropical, Center for Malaria Studies, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Maria das Graças Vale Barbosa
- Tropical Medicine Foundation Dr. Heitor Vieira Dourado, Manaus, Amazonas, Brazil
- University of the State of Amazonas, Manaus, Amazonas, Brazil
- Nilton Lins University Center, Manaus, Amazonas, Brazil
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Phylogenetic evidence based on Trypanosoma cruzi nuclear gene sequences and information entropy suggest that inter-strain intragenic recombination is a basic mechanism underlying the allele diversity of hybrid strains. INFECTION GENETICS AND EVOLUTION 2012; 12:1064-71. [DOI: 10.1016/j.meegid.2012.03.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Revised: 03/12/2012] [Accepted: 03/13/2012] [Indexed: 11/27/2022]
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Phylogenetic analysis of Bolivian bat trypanosomes of the subgenus schizotrypanum based on cytochrome B sequence and minicircle analyses. PLoS One 2012; 7:e36578. [PMID: 22590570 PMCID: PMC3348886 DOI: 10.1371/journal.pone.0036578] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Accepted: 04/10/2012] [Indexed: 11/19/2022] Open
Abstract
The aim of this study was to establish the phylogenetic relationships of trypanosomes present in blood samples of Bolivian Carollia bats. Eighteen cloned stocks were isolated from 115 bats belonging to Carollia perspicillata (Phyllostomidae) from three Amazonian areas of the Chapare Province of Bolivia and studied by xenodiagnosis using the vectors Rhodnius robustus and Triatoma infestans (Trypanosoma cruzi marenkellei) or haemoculture (Trypanosoma dionisii). The PCR DNA amplified was analyzed by nucleotide sequences of maxicircles encoding cytochrome b and by means of the molecular size of hyper variable regions of minicircles. Ten samples were classified as Trypanosoma cruzi marinkellei and 8 samples as Trypanosoma dionisii. The two species have a different molecular size profile with respect to the amplified regions of minicircles and also with respect to Trypanosoma cruzi and Trypanosoma rangeli used for comparative purpose. We conclude the presence of two species of bat trypanosomes in these samples, which can clearly be identified by the methods used in this study. The presence of these trypanosomes in Amazonian bats is discussed.
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Candidate targets for Multilocus Sequence Typing of Trypanosoma cruzi: Validation using parasite stocks from the Chaco Region and a set of reference strains. INFECTION GENETICS AND EVOLUTION 2012; 12:350-8. [DOI: 10.1016/j.meegid.2011.12.008] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Revised: 12/13/2011] [Accepted: 12/14/2011] [Indexed: 01/08/2023]
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