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Cruz-Saavedra L, Ospina C, Patiño LH, Villar JC, Sáenz Pérez LD, Cantillo-Barraza O, Jaimes-Dueñez J, Ballesteros N, Cáceres T, Vallejo G, Ramírez JD. Enhancing Trypanosomatid Identification and Genotyping with Oxford Nanopore Sequencing: Development and Validation of an 18S rRNA Amplicon-Based Method. J Mol Diagn 2024; 26:323-336. [PMID: 38360211 DOI: 10.1016/j.jmoldx.2024.01.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/22/2023] [Accepted: 01/19/2024] [Indexed: 02/17/2024] Open
Abstract
Trypanosomatids, including Trypanosoma and Leishmania species, present significant medical and veterinary challenges, causing substantial economic losses, health complications, and even fatalities. Diagnosing and genotyping these species and their genotypes is often complex, involving multiple steps. This study aimed to develop an amplicon-based sequencing (ABS) method using Oxford Nanopore long-read sequencing to enhance Trypanosomatid detection and genotyping. The 18S rDNA gene was targeted for its inter-species conservation. The Trypanosomatid-ABS method effectively distinguished between 11 Trypanosoma species (including Trypanosoma evansi, Trypanosoma theileri, Trypanosoma vivax, and Trypanosoma rangeli) and 6 Trypanosoma cruzi discrete typing units (TcI to TcVI and TcBat), showing strong concordance with conventional methods (κ index of 0.729, P < 0.001). It detected co-infections between Trypanosomatid genera and T. cruzi, with a limit of detection of one parasite per mL. The method was successfully applied to human, animal, and triatomine samples. Notably, TcI predominated in chronic Chagas samples, whereas TcII and TcIV were found in the acute stage. Triatomine vectors exhibited diverse Trypanosomatid infections, with Triatoma dimidiata mainly infected with TcI and occasional TcBat co-infections, and Rhodnius prolixus showing TcI and TcII infections, along with T. rangeli co-infections and mixed TcII infections. Animals were infected with T. vivax, T. theileri, and T. evansi. The ABS method's high resolution, sensitivity, and accuracy make it a valuable tool for understanding Trypanosomatid dynamics, enhancing disease control strategies, and enabling targeted interventions.
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Affiliation(s)
- Lissa Cruz-Saavedra
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Carlos Ospina
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Luz H Patiño
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Juan C Villar
- Fundación Cardioinfantil-Instituto de Cardiología, Bogotá, Colombia
| | | | | | - Jeiczon Jaimes-Dueñez
- Research Group in Animal Sciences-GRICA, Faculty of Veterinary Medicine and Zootechnics, Universidad Cooperativa de Colombia (UCC), Bucaramanga, Colombia
| | - Nathalia Ballesteros
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Tatiana Cáceres
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Gustavo Vallejo
- Tropical Parasitology Research Laboratory, Faculty of Sciences, Universidad del Tolima, Ibagué, Colombia
| | - Juan D Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia; Molecular Microbiology Laboratory, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York.
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Becker I, Miranda-Ortiz H, Fernández-Figueroa EA, Sánchez-Montes S, Colunga-Salas P, Grostieta E, Juárez-Gabriel J, Lozano-Sardaneta YN, Arce-Fonseca M, Rodríguez-Morales O, Meneses-Ruíz G, Pastén-Sánchez S, López Martínez I, González-Guzmán S, Paredes-Cervantes V, Moreira OC, Finamore-Araujo P, Canseco-Méndez JC, Coquis-Navarrete U, Rengifo-Correa L, González-Salazar C, Alfaro-Cortés MM, Falcón-Lezama JA, Tapia-Conyer R, Stephens CR. The Low Variability of Tc24 in Trypanosoma cruzi TcI as an Advantage for Chagas Disease Prophylaxis and Diagnosis in Mexico. Pathogens 2023; 12:pathogens12030368. [PMID: 36986290 PMCID: PMC10057631 DOI: 10.3390/pathogens12030368] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/28/2023] [Accepted: 02/03/2023] [Indexed: 02/25/2023] Open
Abstract
(1) Background: Chagas disease is the main neglected tropical disease in America. It is estimated that around 6 million people are currently infected with the parasite in Latin America, and 25 million live in endemic areas with active transmission. The disease causes an estimated economic loss of USD 24 billion dollars annually, with a loss of 75,200 working years per year of life; it is responsible for around ~12,000 deaths annually. Although Mexico is an endemic country that recorded 10,186 new cases of Chagas disease during the period of 1990–2017, few studies have evaluated the genetic diversity of genes that could be involved in the prophylaxis and/or diagnosis of the parasite. One of the possible candidates proposed as a vaccine target is the 24 kDa trypomastigote excretory–secretory protein, Tc24, whose protection is linked to the stimulation of T. cruzi-specific CD8+ immune responses. (2) Methods: The aim of the present study was to evaluate the fine-scale genetic diversity and structure of Tc24 in T. cruzi isolates from Mexico, and to compare them with other populations reported in the Americas with the aim to reconsider the potential role of Tc24 as a key candidate for the prophylaxis and improvement of the diagnosis of Chagas disease in Mexico. (3) Results: Of the 25 Mexican isolates analysed, 48% (12) were recovered from humans and 24% (6) recovered from Triatoma barberi and Triatoma dimidiata. Phylogenetic inferences revealed a polytomy in the T. cruzi clade with two defined subgroups, one formed by all sequences of the DTU I and the other formed by DTU II–VI; both subgroups had high branch support. Genetic population analysis detected a single (monomorphic) haplotype of TcI throughout the entire distribution across both Mexico and South America. This information was supported by Nei’s pairwise distances, where the sequences of TcI showed no genetic differences. (4) Conclusions: Given that both previous studies and the findings of the present work confirmed that TcI is the only genotype detected from human isolates obtained from various states of Mexico, and that there is no significant genetic variability in any of them, it is possible to propose the development of in silico strategies for the production of antigens that optimise the diagnosis of Chagas disease, such as quantitative ELISA methods that use this region of Tc24.
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Affiliation(s)
- Ingeborg Becker
- Centro de Medicina Tropical, Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
- Correspondence: (I.B.); (C.R.S.)
| | - Haydee Miranda-Ortiz
- Unidad de Secuenciación, Instituto Nacional de Medicina Genómica, Mexico City 14610, Mexico
| | | | - Sokani Sánchez-Montes
- Centro de Medicina Tropical, Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
- Laboratorio de Diagnóstico, Facultad de Ciencias Biológicas y Agropecuarias Región Poza Rica-Tuxpan, Universidad Veracruzana, Tuxpan de Rodríguez Cano 92870, Mexico
| | - Pablo Colunga-Salas
- Centro de Medicina Tropical, Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
- Instituto de Biotecnología y Ecología Aplicada, Universidad Veracruzana, Xalapa de Enríquez 91090, Mexico
| | - Estefanía Grostieta
- Centro de Medicina Tropical, Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Javier Juárez-Gabriel
- Centro de Medicina Tropical, Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
- Laboratorio de Diagnóstico, Facultad de Ciencias Biológicas y Agropecuarias Región Poza Rica-Tuxpan, Universidad Veracruzana, Tuxpan de Rodríguez Cano 92870, Mexico
| | - Yokomi N. Lozano-Sardaneta
- Centro de Medicina Tropical, Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Minerva Arce-Fonseca
- Department of Molecular Biology, National Institute of Cardiology “Ignacio Chávez”, Mexico City 14080, Mexico
| | - Olivia Rodríguez-Morales
- Department of Molecular Biology, National Institute of Cardiology “Ignacio Chávez”, Mexico City 14080, Mexico
| | - Gabriela Meneses-Ruíz
- Departamento de Parasitología, Instituto de Diagnóstico y Referencia Epidemiológicos, Secretaría de Salud, Mexico City 01480, Mexico
| | - Sergio Pastén-Sánchez
- Departamento de Parasitología, Instituto de Diagnóstico y Referencia Epidemiológicos, Secretaría de Salud, Mexico City 01480, Mexico
| | - Irma López Martínez
- Departamento de Parasitología, Instituto de Diagnóstico y Referencia Epidemiológicos, Secretaría de Salud, Mexico City 01480, Mexico
| | - Saúl González-Guzmán
- Laboratorio del Banco Central de Sangre del Centro Médico Nacional “La Raza”, Instituto Mexicano del Seguro Social, Mexico City 02990, Mexico
- Departamento de Investigación, Hospital Regional de Alta Especialidad de Zumpango, Zumpango 55600, Mexico
| | - Vladimir Paredes-Cervantes
- Unidad de Investigación Médica en Inmunología e Infectología, Hospital de Infectología, Centro Médico Nacional “La Raza”, Instituto Mexicano del Seguro Social, Mexico City 02990, Mexico
| | - Otacilio C. Moreira
- Laboratorio de Biología Molecular e Doencas Endêmicas, Instituto Oswaldo Cruz, Fiocruz 21040900, RJ, Brazil
| | - Paula Finamore-Araujo
- Laboratorio de Biología Molecular e Doencas Endêmicas, Instituto Oswaldo Cruz, Fiocruz 21040900, RJ, Brazil
| | | | - Uriel Coquis-Navarrete
- Departamento de Genómica Poblacional, Instituto Nacional de Medicina Genómica, Mexico City 14610, Mexico
| | - Laura Rengifo-Correa
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | | | | | - Jorge A. Falcón-Lezama
- División Académica de Ciencias de la Salud, Universidad Juárez Autónoma de Tabasco, Villahermosa 86100, Mexico
| | - Roberto Tapia-Conyer
- Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Christopher R. Stephens
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
- Correspondence: (I.B.); (C.R.S.)
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Jaime LD, Aracely LM, Paulina OM, Dumonteil E, Barnabé C, Waleckx E, Hernández-Giles RG, Ramos-Ligonio A. Molecular Characterization of Four Mexican Isolates of Trypanosoma cruzi and Their Profile Susceptibility to Nifurtimox. Acta Parasitol 2022; 67:1584-1593. [PMID: 36029434 DOI: 10.1007/s11686-022-00608-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 08/10/2022] [Indexed: 11/30/2022]
Abstract
PURPOSE The objective of this study was to molecularly characterize Mexican isolates of T. cruzi obtained from infected triatomine bugs (the vectors of T. cruzi) and to evaluate their susceptibility to Nifurtimox (NFX). METHODS Three isolates obtained from Triatoma dimidiata (collected in the State of Veracruz) and one isolate obtained from Triatoma bassolsae (collected in the State of Puebla) were molecularly characterized and the expression of genes associated with natural resistance to NFX was analyzed by qPCR. RESULTS Molecular characterization by PCR showed that isolates Zn3, Zn5, and SRB1 belong to the DTU TcI, while isolate Sum3 belongs to TcIV. The latter was also confirmed by sequencing of mitochondrial genes. Isolate Zn5 was the most sensitive to treatment with NFX (IC50, 6.8 μM), isolates SRB1 and Zn3 were partially resistant (IC50, 12.8 μM and 12.7 μM) and isolate Sum3 showed a high degree of resistance to NFX (IC50, 21.4 µM). We also found an association between decreased NTR1 or OYE gene expression with NFX resistance. CONCLUSION Our results also evidenced a high variability in the susceptibility to NFX of these T. cruzi isolates Central and Southeastern Mexico, suggesting the presence of naturally resistant isolates circulating in the country. These results have important implications for defining treatment policies for patients with Chagas disease.
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Affiliation(s)
- López-Domínguez Jaime
- LADISER de Inmunología y Biología Molecular, Facultad de Ciencias Químicas, Universidad Veracruzana, Edificio D, Prolongación de Oriente 6 #1009, Colonia Rafael Alvarado, C.P. 94340, 86039, Orizaba, Veracruz, Mexico.,Doctorado en Ciencias Biomédicas, Universidad Veracruzana, Xalapa, Veracruz, Mexico
| | - López-Monteon Aracely
- LADISER de Inmunología y Biología Molecular, Facultad de Ciencias Químicas, Universidad Veracruzana, Edificio D, Prolongación de Oriente 6 #1009, Colonia Rafael Alvarado, C.P. 94340, 86039, Orizaba, Veracruz, Mexico.,Asociacion Chagas con Ciencia y Conocimiento A.C., Orizaba, Veracruz, Mexico
| | - Ochoa-Martínez Paulina
- LADISER de Inmunología y Biología Molecular, Facultad de Ciencias Químicas, Universidad Veracruzana, Edificio D, Prolongación de Oriente 6 #1009, Colonia Rafael Alvarado, C.P. 94340, 86039, Orizaba, Veracruz, Mexico.,Doctorado en Ciencias Biomédicas, Universidad Veracruzana, Xalapa, Veracruz, Mexico
| | - Eric Dumonteil
- Department of Tropical Medicine, Tulane University, School of Public Health and Tropical Medicine, New Orleans, LA, USA
| | - Christian Barnabé
- Institut de Recherche pour le Développement, UMR INTERTRYP IRD, CIRAD, Université de Montpellier, Montpellier, France
| | - Etienne Waleckx
- Asociacion Chagas con Ciencia y Conocimiento A.C., Orizaba, Veracruz, Mexico.,Institut de Recherche pour le Développement, UMR INTERTRYP IRD, CIRAD, Université de Montpellier, Montpellier, France.,Laboratorio de Parasitología, Centro de Investigaciones Regionales "Dr. Hideyo Noguchi", Universidad Autónoma de Yucatán, Mérida, Yucatán, Mexico
| | - Rubén Gustavo Hernández-Giles
- LADISER de Inmunología y Biología Molecular, Facultad de Ciencias Químicas, Universidad Veracruzana, Edificio D, Prolongación de Oriente 6 #1009, Colonia Rafael Alvarado, C.P. 94340, 86039, Orizaba, Veracruz, Mexico.,Maestría en Ciencias en Procesos Biológicos, Facultad de Ciencias Químicas, Universidad Veracruzana, Orizaba, Veracruz, Mexico
| | - Angel Ramos-Ligonio
- LADISER de Inmunología y Biología Molecular, Facultad de Ciencias Químicas, Universidad Veracruzana, Edificio D, Prolongación de Oriente 6 #1009, Colonia Rafael Alvarado, C.P. 94340, 86039, Orizaba, Veracruz, Mexico. .,Asociacion Chagas con Ciencia y Conocimiento A.C., Orizaba, Veracruz, Mexico.
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4
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Dehesa-Rodríguez G, Martínez I, Bastida-Jaime C, Espinoza B. Trypanosoma cruzi blood trypomastigotes induce intense skeletal and cardiac muscle damage and Th1/ Th2 immune response in the acute phase of mice infected by the oral route. Acta Trop 2022; 234:106605. [PMID: 35820470 DOI: 10.1016/j.actatropica.2022.106605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 07/06/2022] [Accepted: 07/08/2022] [Indexed: 11/15/2022]
Abstract
Oral acquisition of Trypanosoma cruzi is a foodborne transmission by juices and fruits contaminated with metacyclic trypomastigotes (MT) or by the ingestion of wild reservoirs infected with blood trypomastigotes (BT). In Mexico, hunting and food consumption of wild animals are current practices, which could represent a risk factor for oral infection in the rural population. In this work, Balb/c mice were inoculated by oral route with BT of a highly virulent T. cruzi Mexican strain (DTU I) to evaluate the establishment of the infection, and the humoral and cellular immune response in the acute phase of the infection. We show that BT induces blood and tissue parasitism producing an inflammatory process in the heart and skeletal muscle and low parasitism and inflammation in the digestive tract of orally infected mice. Besides, in the acute phase, the BT promotes splenomegaly, intense damage in skeletal and cardiac muscles, a humoral response dominated by the IgG isotype, and the expression of pro-inflammatory cytokines.
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Affiliation(s)
- Génesis Dehesa-Rodríguez
- Laboratorio de Estudios sobre Tripanosomiasis Americana, Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico (Ciudad de México) C.P. 04510, Mexico
| | - Ignacio Martínez
- Laboratorio de Estudios sobre Tripanosomiasis Americana, Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico (Ciudad de México) C.P. 04510, Mexico
| | - Cristina Bastida-Jaime
- Laboratorio de Estudios sobre Tripanosomiasis Americana, Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico (Ciudad de México) C.P. 04510, Mexico
| | - Bertha Espinoza
- Laboratorio de Estudios sobre Tripanosomiasis Americana, Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico (Ciudad de México) C.P. 04510, Mexico.
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