MIRU-VNTR genotyping of Mycobacterium tuberculosis in a population of patients in Cali, Colombia, 2013-2015
Abstract
Introduction: Tuberculosis continues to be one of the main public health problems in the world. Together with the HIV infection, it is one of the main causes of death due to infections worldwide. In 2016, 6.3 million new cases of the disease were reported.
Objective: To describe the genetic patterns determined by genotyping using variable-number tandem repeats of mycobacterial interspersed repetitive units (MIRU-VNTR) in the study population and compare them with other studies carried out in Cali, Colombia, and the world.
Materials and methods: We genotyped a total of 105 DNA samples extracted from sputum or culture isolates of the Mycobacterium tuberculosis complex, which were obtained from pulmonary tuberculosis diagnosed patients over the period 2013-2015, in Cali. We performed PCR amplification of 24 loci by MIRU-VNTR on the DNA extracted from the samples. The amplicons were visualized in agarose gel electrophoresis (2%) with SYBR Safe™ staining. Then, the alleles were designated by graphical analysis using the GelAnalyzer 2010 software. These results were analyzed using the UPGMA logarithm and compared with the registers from the MIRU-VNTR plus and SITVITWEB databases.
Results: We genotyped 62 of the samples completely and we obtained 58 different MIRU-VNTR profiles. By comparing with the international databases, we determined the following distributions per lineage: LAM, 54.8%; Haarlem,25.8%; S, 14.5%; Beijing, 3.2%, and Cameroon, 1.6%. The MIRU-VNTR patterns corresponded to 17 different MITs; the most frequent were MIT 190 and MIT 110, with 22.6% and 6.5%, respectively.
Conclusions: These results demonstrated previous observations about the predominance of the LAM and Haarlem lineages in the city, and the presence of the MITs found in another city of Colombia.
Downloads
References
World Health Organization. Global tuberculosis control: WHO Report 2017. Geneva: World Health Organization; 2017. p. 224.
Organización Mundial de la Salud. Preguntas y respuestas: tuberculosis ultrarresistente (TB-XR). Fecha de consulta: 27 de mayo de 2018. Disponible en: http://www.who.int/features/qa/extensively-resistant-tuberculosis/es/
Pedraza L, García C, Muñoz A. Caracterización de pacientes con tuberculosis y tuberculosis resistente a múltiples medicamentos en instituciones de tercer nivel de Bogotá D.C. Enferm Glob. 2012;25:129-38 https://doi.org/10.4321/S1695-61412012000100008
Instituto Nacional de Salud. Informe del evento tuberculosis, Colombia, 2017. Fecha de consulta: 27 de mayo de 2018. Disponible en: http://www.ins.gov.co/buscador-eventos/Informesdeevento/TUBERCULOSIS%202017.pdf
Secretaría Departamental del Salud del Valle. Boletín epidemiológico semanal. Semana epidemiológica número 52 de 2015. Fecha de consulta: 10 de mayo de 2015. Disponible en: http://www.valledelcauca.gov.co/salud/descargar.php?id=17080
Secretaría Departamental del Salud del Valle. Informe anual, 2016: Vigilancia en salud pública. Fecha de consulta: 27 de mayo de 2017. Disponible en: http://www.valledelcauca.gov.co/salud/descargar.php?id=19934
Mathema B, Kurepina N, Bifani P, Kreiswirth B. Molecular epidemiology of tuberculosis: Current insights. Clin Microbiol Rev. 2006;19:658-85. https://doi.org/10.1128/CMR.00061-05
Kato-Maeda M, Small P. How molecular epidemiology has changed what we know about tuberculosis. West J Med. 2000;172:256-9.
van Soolingen D, De Haas W, Kremer K. Restriction fragment length polymorphism (RFLP) typing of micobacteria. Methods Mol Med. 2001;54:165-203. https://doi.org/10.1385/1-59259-147-7:165
Chaoui I, Zozio T, Lahlou O, Sabouni R, Abid M, El Aouad R, et al. Contribution of spoligotyping and MIRU-VNTRs to characterize prevalent Mycobacterium tuberculosis genotypes infecting tuberculosis patients in Morocco. Infect Genet Evol. 2014;21:463-71. https://doi.org/10.1016/j.meegid.2013.05.023
Cowan L, Mosher L, Diem L, Massey J, Crawford J. Variable-number tandem repeat typing of Mycobacterium tuberculosis isolates with low copy numbers of IS6110 by using mycobacterial interspersed repetitive units. J. Clin Microbiol. 2002;40:1592-602. https://doi.org/10.1128/JCM.40.5.1592-1602.2002
Pitondo-Silva A, Santos A, Jolley K, Leite C, Darini A. Comparison of three molecular typing methods to assess genetic diversity for Mycobacterium tuberculosis. J Microbiol Methods. 2013;93:42-8. https://doi.org/10.1016/j.mimet.2013.01.020
Barnes P, Cave M. Molecular epidemiology of tuberculosis. N Engl J Med. 2003;349:1149-56. https://doi.org/10.1056/NEJMra021964
van Embden J, Cave M, Crawford J, Dale J, Eisenach K, Gicquel B, et al. Strain identification of Mycobacterium tuberculosis by DNA fingerprinting: Recommendations for a standardized methodology. J Clin Microbiol. 1993;31:406-9.
Rozo J, Ribón W. Molecular tools for Mycobacterium tuberculosis genotyping. Rev Salud Pública (Bogotá). 2010;12:510-21.
Cowan L, Diem L, Monson T, Wand P, Temporado D, Oemig T, et al. Evaluation of a two-step approach for large-scale, prospective genotyping of Mycobacterium tuberculosis isolates in the United States. J Clin Microbiol. 2005;43:688-95. https://doi.org/10.1128/JCM.43.2.688-695.2005
Kamerbeek J, Schouls L, Kolk A, van Agterveld M, van Soolingen D. Simultaneous detection and strain differentiation of Mycobacterium tuberculosis for diagnosis and epidemiology. J Clin Microbiol. 1997;35:907-14.
Supply P, Allix C, Lesjean S, Cardoso-Oelemann M, Rüsch-Gerdes S, Willery E. Proposal for standardization of optimized mycobacterial interspersed repetitive unit-variable-number tandem repeat typing of Mycobacterium tuberculosis. J Clin Microbiol. 2006;44:4498-510. https://doi.org/10.1128/JCM.01392-06
Allix-Beguec C, Harmsen D, Weniger T, Supply P, Niemann S. Evaluation and strategy for use of MIRU-VNTRplus, a multifunctional database for online analysis of genotyping data and phylogenetic identification of Mycobacterium tuberculosis complex isolates. J Clin Microbiol. 2008;46:2692-9. https://doi.org/10.1128/JCM.00540-08
Demay C, Liens B, Burguière T, Hill V, Couvin D, Millet J, et al. SITVITWEB – A publicly available international multimarker database for studying Mycobacterium tuberculosis genetic diversity and molecular epidemiology. Infect Genet Evol. 2012;12:755-66. https://doi.org/10.1016/j.meegid.2012.02.004
Shabbeer A, Ozcaglar C, Yener B, Bennett K. Web tools for molecular epidemiology of tuberculosis. Infect Genet Evol. 2012;12:767-81. https://doi.org/ 10.1016/j.meegid.2011.08.019
García de Viedma D, Mokrousov I, Rastogi N. Innovations in the molecular epidemiology of tuberculosis. Enferm Infecc Microbiol Clin. 2011;29:8-13. https://doi.org/10.1016/S0213-005X(11)70012-X
Organización Panamericana de la Salud. Manual para el diagnóstico bacteriológico de la tuberculosis. Parte 2: Cultivo. Fecha de consulta: 10 de febrero de 2015. Disponible en: http://www1.paho.org/Spanish/AD/DPC/CD/tb-labs-cultivo.pdf
Sneath P, Sokal R. Numerical Taxonomy: The principles and practice of numerical classification. San Francisco, CA: Freeman and Company; 1973. p. 549.
Rodríguez N, Martínez M, Herranz M, Sánchez M, Barroso P, Bouza E, et al. Evaluation of the new advanced 15-loci MIRU-VNTR genotyping tool in Mycobacterium tuberculosis epidemiology studies. BMC Microbiol. 2008;8:34. https://doi.org/10.1186/1471-2180-8-34
Cerezo I, Jimenez Y, Hernández J, Zozio T, Murcia M, Rastogi N. First insight on the population structure of Mycobacterium tuberculosis complex as studied by spoligotyping and MIRU-VNTRs in Bogotá, Colombia. Infect Genet Evol. 2012;12:657-63. https://doi.org/10.1016/j.meegid.2011.07.006
Realpe T, Correa N, Rozo J, Ferro B, Gómez V, Zapata E, et al. Population structure among Mycobacterium tuberculosis isolates from pulmonary tuberculosis patients in Colombia. PLoS One. 2014;9:1-12. https://doi.org/10.1371/journal.pone.0093848
Beltrán MY. Genotipificación de Mycobacterium tuberculosis en aislados clínicos obtenidos de pacientes VIH positivos de los hospitales Simón Bolívar y Santa Clara de Bogotá (tesis). Bogotá: Universidad Nacional de Colombia; 2016. p. 106.
Castro C, Ricardo A, Zabaleta A, Llerena C, Puerto G. Caracterización de aislamientos clínicos de Mycobacterium tuberculosis obtenidos de individuos positivos para HIV en Colombia, 2012. Biomédica. 2017;37:86-95. https://doi.org/10.7705/biomedica.v37i1.3112
Nieto L, Ferro B, Villegas S, Mehaffy C, Forero L, Moreira C, et al. Characterization of extensively drug-resistant tuberculosis cases from Valle del Cauca, Colombia. J Clin Microbiol. 2012;50:4185-7. https://doi.org/10.1128/JCM.01946-12
Wirth T, Hildebrand F, Allix C, Wölbeling F, Kubica T, Kremer K, et al. Origin, spread and demography of the Mycobacterium tuberculosis complex. PLoS Pathog. 2008;4:1-10. https://doi.org/10.1371/journal.ppat.1000160
Barletta F, Otero L, Collante J, Asto B, de Jong B, Seas C, et al. Genetic variability of Mycobacterium tuberculosis complex in patients with no known risk factors for MDR-TB in the North-Eastern of Lima, Perú . BMC Infect Dis. 2013;13:397. https://doi.org/10.1186/1471-2334-13-397
Lu W, Lu B, Liu Q, Dong H, Shao Y, Jiang Y, et al. Genotypes of Mycobacterium tuberculosis isolates in rural China: Using MIRU-VNTR and spoligotyping methods. Scand J Infect Dis. 2014;26:98-106. https://doi.org/10.3109/00365548.2013.858182
Bidovec-Stojkovič U, Seme K, Žolnir-Dovč M, Supply P. Prospective genotyping of Mycobacterium tuberculosis from fresh clinical samples. PLoS One. 2014;9:e109547. https://doi.org/10.1371/journal.pone.0109547
Some similar items:
- María Lilia Díaz, Sulma Muñoz, Liz Betty Garcíad, Tuberculosis in the San José University Hospital in Popayán, Colombia, 1998-2000. , Biomedica: Vol. 24 (2004): Suplemento 1
- Juan Gabriel Bueno-Sánchez, Jairo René Martínez-Morales, Elena E. Stashenko, Wellman Ribón, Anti-tubercular activity of eleven aromatic and medicinal plants occurring in Colombia , Biomedica: Vol. 29 No. 1 (2009)
- María Consuelo Garzón, Dailyn Yorledy Angée, Claudia Llerena, Dora Leticia Orjuela, Jorge Ernesto Victoria, Surveillance of Mycobacterium tuberculosis resistance to antituberculosis drugs , Biomedica: Vol. 28 No. 3 (2008)
- Diego Chaves, Andrea Sandoval, Luis Rodríguez, Juan C. García, Silvia Restrepo, María Mercedes Zambrano, Comparative analysis of six Mycobacterium tuberculosis complex genomes , Biomedica: Vol. 30 No. 1 (2010)
- María Imaz, Sonia Allassia, Mónica Aranibar, Alba Gunia, Susana Poggi, Ana Togneri, Lidia Wolff, Group of Implementation of Fluorescence, Performance of LED fluorescence microscopy for the detection of acid-fast bacilli from respiratory samples in peripheral laboratories in Argentina , Biomedica: Vol. 37 No. 2 (2017)
- Diana Castaño, Mauricio Rojas, Alterations in recruitment and activation of Rab proteins during mycobacterial infection , Biomedica: Vol. 30 No. 2 (2010)
- Adriana Rojas-Villarraga, Carlos Andrés Agudelo, Ricardo Pineda-Tamayo, Alvaro Porras, Gustavo Matute, Juan Manuel Anaya, Tuberculosis in patientes treated with tumor necrosis factor alpha antagonists living in an endemic area. Is the risk worthwhile? , Biomedica: Vol. 27 No. 2 (2007)
- Carlos A. Torres-Duque, Claudia Díaz, Leslie Vargas, Elsa María Serpa, Walter Mosquera, María Consuelo Garzón, Graciela Mejía, Luz Mary García, Liliana Andrea González, Claudia Marcela Castro, Wellman Ribón, Disseminated mycobacteriosis affecting a prosthetic aortic valve: first case of Mycobacterium peregrinum type III reported , Biomedica: Vol. 30 No. 3 (2010)
- Francisco Cuervo, Luis F. Giraldo, Alirio Bastidas, Carlos Vélez, Maria R. Forero, Fibrinogen-thrombin as bridge therapy in massive hemoptysis , Biomedica: Vol. 33 No. 1 (2013)
- Alvaro Javier ldrovo, Notes on the onset of a pulmonary tuberculosis epidemic in Bogotá (1870-1920) , Biomedica: Vol. 21 No. 3 (2001)
| Article metrics | |
|---|---|
| Abstract views | |
| Galley vies | |
| PDF Views | |
| HTML views | |
| Other views | |
