Genetic patterns, sublineages and dynamics of tuberculosis transmission in Cuba, a low burden country
Keywords:
Mycobacterium tuberculosis, molecular typing, Cuba, tuberculosis, molecular biology, Mycobacterium tuberculosis/transmission, molecular epidemiology, Molecular characterizationAbstract
Introduction: In Cuba, a country with a low incidence of tuberculosis (TB), there is no information about of the dynamics of transmission of the disease for two decades.
Objective: Determine the genetic patterns and sublineages of Mycobacterium tuberculosis complex (MTBC) isolates circulating in 2009 and their relationship with the epidemiological data of the patients.
Methods: A retrospective descriptive study was carried out in Cuba with 178 MTBC isolates. Spoligotyping and mycobacterial interspersed repetitive-unit–variable-number tandem-repeat (MIRU-VNTR) typing with 24 loci were performed. For statistical analysis, non-parametric methods, analysis of variance and homogeneity test, were used.
Results: Spoligotyping produced 39 spoligotypes. The S, Beijing, LAM and Haarlem sublineages prevailed. The clustering rate was 75.84 % and the Hunter-Gaston discriminatory index (HGDI): 0.8734. MIRU-VNTR typing with 24-loci defined 154 genetic patterns: six grouped 30 isolates and 148 showed unique patterns. The clustering rate was 14.60 % and the HGDI: 0.9926. There was a predominance of sublineages by region: S, Beijing and LAM in the West, Center and East, respectively.
Conclusions: The dynamics of TB transmission in Cuba in 2009 is reported, inferring that this occurs in a limited manner and belonging to risk groups does not favor transmission. It serves to evaluate a megaproject of the Global Fund to reduce the transmission of TB in this country. The population genetic structure of MTBC resembles that of an Ibero-American country, with the exception of the high frequency of the Beijing and S sublineages.
Downloads
References
World Health Organization. Global tuberculosis control: WHO report 2011. Geneva: WHO; 2022. [Acceso: 16 Agosto, 2023]. Disponible en: https://www.who.int/publications/i/item/9789240037021
Varma-Basil M, Nair D- Molecular epidemiology of tuberculosis: Opportunities & challenges in disease control. Indian J Med Res. 2017;146:11-4.
https://doi.org/10.4103/ijmr.IJMR_941_17
Udwadia ZF, Patel JM. New treatments for Drug Resistant TB: Past imperfect, future bright. Lung India. 2023;40(1):1-3. https://doi.org/10.4103/lungindia.lungindia_556_22
Organización Panamericana de la Salud. Tuberculosis en las Américas. Informe regional 2021. Washington, D.C.: Organización Panamericana de la Salud; 2022. ISBN 978-92-75-32649-7 (PDF). https://doi.org/10.37774/9789275126493
World Health Organization. Tuberculosis Profile: Cuba. 2022. [Acceso: 10 Diciembre, 2023]. Disponible en: https://worldhealthorg.shinyapps.io/tb_profiles/?_inputs_&entity_type=%22country%22&lan=%22ES%22&iso2=%22CU%22
Dirección de Registros Médicos y Estadísticas de Salud. Ministerio de Salud Pública. Anuario Estadístico de Salud. 2022. 2023 [Acceso: 10 Diciembre, 2023]. Disponible en: https://files.sld.cu/dne/files/2023/10/Anuario-Estadistico-de-Salud-2022-Ed-20231.pdf
Díaz R, de Haas P, Gómez RI, Marrero A, Cabanas M, Valdivia JA et al. Molecular epidemiology of tuberculosis in Cuba outside of Havana, July 1994-Jun 1995: utility of spoligotyping versus IS6110 restriction fragment length polymorphism. Int J Tuberc Lung Dis.1998;2(9):743-50. https://www.ingentaconnect.com/content/iuatld/ijtld/1998/00000002/00000009/art00009
Diaz R, Gómez RI, Restrepo E, Rumbaut R, Valdivia JA, Soolingen D. Transmission of tuberculosis in Havana, Cuba; a molecular epidemiological study by IS6110 restriction fragment length polymorphism typing. Mem Inst Oswaldo Cruz 2001;96(4):437-43. https://doi.org/10.1590/S0074-02762001000400001
Gonzalez Dıaz A, Battaglioli T, Dıaz Rodrıguez R, Goza Valdes R, Gonzalez Ochoa E, Van der Stuyft P. Molecular epidemiology of tuberculosis in Havana, Cuba, 2009. Trop Med Int Hlth. 2015;20:1534-42. https://doi.org/10.1111/tmi.12569
Kamerbeek J, Schouls L, Kolk A, van Agterveld M, van Soolingen D, Kuijper S et al. Simultaneous detection and strain differentiation of Mycobacterium tuberculosis for diagnosis and epidemiology. J Clin Microbiol. 1997;35:907-14. https://doi.org/10.1128/jcm.35.4.907-914.1997
Supply P, Allix C, Lesjean S, Cardoso-Oelemann M, Rusgh-Gerdes S, Willery E, et al. Proposal for standardization of optimized mycobacterial interspersed repetitive unitvariable-number tandem repeat typing of Mycobacterium tuberculosis. J Clin Microbiol. 2006;44:4498-510. https://doi.org/10.1128/jcm.01392-06
Allix-Béguec 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
Couvin D, David A, Zozio T, Rastogi N. Macro-geographical specificities of the prevailing tuberculosis epidemic as seen through SITVIT2, an updated version of the Mycobacterium tuberculosis genotyping database. Infect. Genet. Evol. 2019;72:31-43. https://doi.org/10.1016/j.meegid.2018.12.030
Cave MD, Yang ZH, Stefanova R, Fomukong N, Ijaz K, Bates J et al. Epidemiologic import of tuberculosis cases whose isolates have similar but not identical IS6110 restriction fragment length polymorphism patterns. J. Clin. Microbiol. 2005;43:1228-33. https://doi.org/10.1128/jcm.43.3.1228-1233.2005
Small PM, Hopewell PC, Singh SP, Paz A, Parsonnet J, Ruston DC. et al. The epidemiology of tuberculosis in San Francisco. A population-based study using conventional and molecular methods. N Engl J Med. 1994;330:1703-9. https://doi.org/10.1056/NEJM199406163302402
Sola C, Filliol I, Legrand E, Lesjean S, Locht C, Supply P. et al. Genotyping of the Mycobacterium tuberculosis complex using MIRUs: association with VNTR and spoligotyping for molecular epidemiology and evolutionary genetics. Infect Genet Evol. 2003;3:125-33. https://doi.org/10.1016/S1567-1348(03)00011-X
Hunter PR, Gaston MA. Numerical index of the discriminatory ability of typing systems: an application of Simpson's index of diversity. J Clin Microbiol. 1988;26:2465-6. https://doi.org/10.1128/jcm.26.11.2465-2466.1988
van Belkum A, Tassios PT, Dijkshoorn L, Haeggman S, Cookson B, Fry NK. et al. Guidelines for the validation and application of typing methods for use in bacterial epidemiology. Clin Microb and Infect Dis. 2007;13:1-46. https://doi.org/10.1111/j.1469-0691.2007.01786.x
Gozá-Valdés R, Díaz-Rodríguez R. Análisis genotípico de aislamientos de Mycobacterium tuberculosis en La Habana en 2009. Rev Cubana Med Trop. 2014;66(2):263-72. http://scielo.sld.cu/scielo.php?pid=S0375-07602014000200011&script=sci_arttext&tlng=pt
Pedersen MK, Lillebaek T, Andersen AB, Soini H, Haanperä M, Groenheit R. et al. Trends and differences in tuberculosis incidences and clustering among natives in Denmark, Sweden and Finland: comparison of native incidences and molecular epidemiology among three low-incidence countries. Clin Microbiol Infect. 2018;24:717-23. https://doi.org/10.1016/j.cmi.2017.10.005
Sanchini A, Andrés M, Fiebig L, Albrecht S, Hauer B, Haas W. Assessment of the use and need for an integrated molecular surveillance of tuberculosis: an online survey in Germany. BMC Public Health. 2019;19:321. https://bmcpublichealth.biomedcentral.com/articles/10.1186/s12889-019-6631-6
Räisänen PE, Haanperä M, Soini H, Ruutu P, Nuorti JP, Lyytikäinen O. Transmission of tuberculosis between foreign-born and Finnish-born populations in Finland, 2014-2017. PLoS One. 2021;16:e0250674. https://doi.org/10.1371/journal.pone.0250674
Roof I, Jajou R, Kamst M, Mulder A, de Neeling A, van Hunen R, et al. Prevalence and characterization of heterogeneous Variable-Number Tandem-Repeat clusters comprising drug-susceptible and/or variable resistant Mycobacterium tuberculosis complex isolates in the Netherlands from 2004 to 2016. J Clin Microbiol. 2018;56(2):e00887-18. https://doi.org/10.1128/jcm.00887-18
Ghavidel M, Tadayon K, Mosavari N, Nourian K, Bahrami, Taghanaki HR, et al. Introducing the best six loci in Mycobacterial Interspersed Repetitive Unit-VariableNumber Tandem Repeat (MIRU-VNTR) typing for Mycobacterium tuberculosis genotyping. Rep Biochem Mol Biol. 2019; 8:335-46. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7103078/
Hadifar S, Kargarpour Kamakoli M, Eybpoosh S, Nakhaeizadeh M, Kargarpour Kamakoli MA, Ebrahimifard N, et al. The shortcut of mycobacterial interspersed repetitive unit-variable number tandem repeat typing for Mycobacterium tuberculosis differentiation. Front Microbiol. 2022; 13: 978355. https://doi.org/10.3389/fmicb.2022.978355
Pichat C, Couvin D, Carret G, Frédénucci I, Jacomo V, Carricajo A, et al. Combined Genotypic, phylogenetic, and epidemiologic aof Mycobacterium tuberculosis genetic diversity in the Rhône Alpes region, France. PLoS ONE 2016; 11: e0153580. https://doi.org/10.1371/journal. pone.0153580
Garzelli C, Lari N, Cuccu B, Tortoli E, Rindi L. Impact of immigration on tuberculosis in a low-incidence area of Italy: a molecular epidemiological approach. Clin Microbiol Infect. 2010; (11):1691-7. https://doi.org/10.1111/j.1469-0691.2010.03149.x
Herrera Avila YM, Fonseca Gómez CM, Gozá Valdés R, Martínez Rodríguez IM, Lemus Molina D, Llanes Cordero MJ et al. Tipificación con oligonucleótidos espaciadores de Mycobacterium tuberculosis en Cuba. Rev Cubana Med Trop. 2015; 67:85-96.
http://scielo.sld.cu/scielo.php?pid=S037507602015000100009&script=sci_arttext&tlng=pt
MI Cerezo-Cortés, JG Rodríguez-Castillo, R Hernández-Pando, MI Murcia. Circulation of M. tuberculosis Beijing genotype in Latin America and the Caribbean, Pathogens Global Health. 2019:113:336-351. https://doi.org/10.1080/20477724.2019.1710066
Mora Pinoargote C, Garzon Chavez D, Franco Sotomayor G, Leon Benitez M, Granda Pardo JC, Trueba G et al. Countrywide rapid screening for the Mycobacterium tuberculosis Beijing sublineage in Ecuador using a single nucleotide polymorphism polymerase chain reaction method. Int J Mycobacteriol. 2019:366-70. https://doi.org/10.4103/ijmy.ijmy_132_19
Almaraz-Velasco R, Munro-Rojas D, Fuentes-Domínguez J, Muñiz-Salazar R, Ibarra-Estela MA, Guevara-Méndez AD, et al. A first insight into the genetic diversity of Mycobacterium tuberculosis in Veracruz, Mexico. Int J Mycobacteriol 2017;6:14-20. https://journals.lww.com/ijmy/fulltext/2017/06010/a_first_insight_into_the_genetic_diversity_of.3.aspx
Tatara MB, Perdigão J, Viveiros M, Kritski A, Silva KED, Sacchi FPC, et al. Genetic diversity and molecular epidemiology of Mycobacterium tuberculosis in Roraima State, Brazil. Am J Trop Med Hyg. 2019;101:774-9. https://doi.org/10.4269/ajtmh.19-0324
Izumi K, Murase Y, Uchimura K, Kaebeta A, Ishihara K, Kaguraoka S, et al. Transmission of tuberculosis and predictors of large clusters within three years in an urban setting in Tokyo, Japan: a population-based molecular epidemiological study. BMJ Open. 2019;9:e029295. https://bmjopen.bmj.com/content/9/5/e029295
Tadokera R, Bekker LG, Kreiswirth BN, Mathema B, Middelkoop K. TB transmission is associated with prolonged stay in a low socio-economic, high burdened TB and HIV community in Cape Town, South Africa. BMC Infect Dis. 2020;20:120. https://link.springer.com/article/10.1186/s12879-020-4828-z
Houben RM, Crampin AC, Mallard K, Mwaungulu JN, Yates MD, Mwaungulu FDet al. HIV and the risk of tuberculosis due to recent transmission over 12 years in Karonga District, Malawi. Trans R Soc Trop Med Hyg. 2009;103:1187-9. https://doi.org/10.1016/j.trstmh.2009.03.013
Easterbrook PJ, Gibson A, Murad S, Lamprecht D, Ives N, Ferguson A, et al. High rates of clustering of strains causing tuberculosis in Harare, Zimbabwe: a molecular epidemiological study. J Clin Microbiol. 2004;42:4536-44. https://doi.org/10.1128/jcm.42.10.4536-4544.2004.
Malhotra B, Dashora D, Kumar V, Goyal S, Sharma B; Kumar M ; et al. Genetic diversity and drug sensitivity profiles of Mycobacterium tuberculosis isolates from two slums of Jaipur city, Rajasthan, India. Indian J Med Res. 2017;145:74-83. | https://doi.org/10.4103/ijmr.IJMR_336_14
Togo AC, Kodio O, Diarra B, Sanogo M, Coulibaly G, Bane S, et al. The most frequent Mycobacterium tuberculosis complex families in Mali (2006–2016) based on spoligotyping. Int J Mycobacteriol. 2017;6:379-86.
Downloads
Published
How to Cite
Issue
Section
License
La Revista Cubana de Higiene y Epidemiologia protege los derechos de autor, y opera con una Licencia Creative Commons 4.0.(Licencia Creative Commons Atribución-No Comercial 4.0 Internacional (CC BY-NC 4.0).Al publicar en ella los autores permiten copiar y redistribuir el material en cualquier medio o formato; remezclar, transformar y crear a partir del material. Debe reconocer adecuadamente la autoría, proporcionar un enlace a la licencia http://creativecommons.org/licenses/by-nc/4.0/ e indicar si se han realizado cambios. No puede utilizar el material para una finalidad comercial. No hay restricciones adicionales.
Los autores autorizan la publicación de sus escritos conservando los derechos de autoría, y cediendo y transfiriendo a la revista todos los derechos protegidos por las leyes de propiedad intelectual que rigen en Cuba, que implican la edición para difundir la obra.
Los autores podrán establecer acuerdos adicionales para la distribución no exclusiva de la versión de la obra publicada en la revista (por ejemplo, situarla en un repositorio institucional o publicarla en un libro), con el reconocimiento de haber sido publicada primero en esta revista.
