MIRU-VNTR analysis of Mycobacterium tuberculosis from Tehran, Sistan-Baluchestan, Kermanshah and Hormozgan during 2014 and 2015

Mahroo Baghbanian; Hengameh Zandi; Samin Zamani; Sedigheh Javadpour; Gholam Reza Hamzehloo; Mohammad Mahdi Feizabadi

doi:10.14715/10.14715/cmb/2017.63.12.5

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Vol. 63 No. 12: Issue 12

Issue Published : December 19, 2017

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MIRU-VNTR analysis of Mycobacterium tuberculosis from Tehran, Sistan-Baluchestan, Kermanshah and Hormozgan during 2014 and 2015

https://doi.org/10.14715/10.14715/cmb/2017.63.12.5

Mahroo Baghbanian

Department of Microbiology, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran

Hengameh Zandi

Department of Microbiology, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran

Samin Zamani

Department of Microbiology, School of Medicine, Golestan University of Medical Sciences, Gorgan, Iran

Sedigheh Javadpour

Department of Microbiology, School of Medicine, Hormozgan University of Medical Sciences, Hormozgan, Iran

Gholam Reza Hamzehloo

Regional TB Refrence Laboratory, Tehran, Iran

Mohammad Mahdi Feizabadi

Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran

Corresponding Author(s) : Mahroo Baghbanian

Mah.baghbanian@yahoo.com

Cellular and Molecular Biology, Vol. 63 No. 12: Issue 12
Article Published : December 30, 2017

Abstract

Standard 15-locus Mycobacterial Interspersed Repetitive Unit Variable Number Tandem Repeat (MIRU-VNTR) typing of Mycobacterium tuberculosis (MTB) is a valuable instrumentation for TB control. Our knowledge about the genetic diversity of MTB and population structure of MTB circulating in Iran is limited. During 2014–2015, 98 MTB isolates were collected from the TB centers of four provinces of Iran. Isolates were genetically characterized using 15-locus based MIRU-VNTR typing. Ninety-five distinct mycobacterial interspersed repetitive unit MIRU-VNTR patterns were found among 98 isolates. 5 (5.1%) isolates grouped into 2 clusters and 93 (94.89%) isolates had a unique pattern. The HGDI was as high as 0.99 and 10 of loci were designated as highly discriminative. Clusters belonged to Tehran only. This indicates these patterns are rotating in Tehran. Unique patterns suggest that distribution of samples in each province and population differs. HGDI is higher than previous studies for MIRU-VNTR typing in Iran. We suggest MIRU-15 because it is a valid epidemiological background for clustering defined. Limited data is available on the genetic diversity and transmission dynamics of MTB in Iran. To examine the genetic diversity and transmission dynamics of MTB strains we genotyped a collection of isolates from four different parts of Iran. The method of 15-loci MIRU-VNTR demonstrated high discriminatory power and may be applied as a first-line genotyping instrumentation in investigating the molecular epidemiology of M. tuberculosis in Iran.

Keywords

Genotyping Mycobacterium tuberculosis MIRU-VNTR Iran Transmission.

Baghbanian, M., Zandi, H., Zamani, S., Javadpour, S., Hamzehloo, G. R., & Feizabadi, M. M. (2017). MIRU-VNTR analysis of Mycobacterium tuberculosis from Tehran, Sistan-Baluchestan, Kermanshah and Hormozgan during 2014 and 2015. Cellular and Molecular Biology, 63(12), 14–21. https://doi.org/10.14715/10.14715/cmb/2017.63.12.5

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References

Zamani S, Aflaki M, Fooladi A A I, Darban-Sarokhalil D, Bameri Z, Khazaee S, et al., MIRU-VNTR analysis of the Mycobacterium tuberculosis isolates from three provinces of Iran. Scand J Infect Dis, 2013. 45(2): p. 124-130.
Sun Y-J, Bellamy R, Lee A S, Ng S T, Ravindran S, Wong S-Y, et al., Use of mycobacterial interspersed repetitive unit-variable-number tandem repeat typing to examine genetic diversity of Mycobacterium tuberculosis in Singapore. J Clin Microbiol, 2004. 42(5): p. 1986-1993.
Asgharzadeh M, Samadi K H, Pourostadi M, Asadi F N, Rashedi J, and Mahdavipour B, Strain differentiation of Mycobacterium tuberculosis for epidemiology in northwest of Iran. Cell Mol Biol (Noisy-le-grand), 2016. 62(8): p. 15.
Asante-Poku A, Nyaho M S, Borrell S, Comas I, Gagneux S, and Yeboah-Manu D, Evaluation of customised lineage-specific sets of MIRU-VNTR Loci for genotyping Mycobacterium tuberculosis complex isolates in Ghana. PLoS One, 2014. 9(3).
Zhang J, Mi L, Wang Y, Liu P, Liang H, Huang Y, et al., Genotypes and drug susceptibility of Mycobacterium tuberculosis isolates in Shihezi, Xinjiang Province, China. BMC Res Notes, 2012. 5(1): p. 309.
Nasiri M J, Rezaei F, Zamani S, Darban-Sarokhalil D, Fooladi A A I, Shojaei H, et al., Drug resistance pattern of Mycobacterium tuberculosis isolates from patients of five provinces of Iran. Asian Pac J Trop Med, 2014. 7(3): p. 193-196.
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Ali A, Hasan Z, Tanveer M, Siddiqui A R, Ghebremichael S, Kallenius G, et al., Characterization of Mycobacterium tuberculosis Central Asian Strain1 using mycobacterial interspersed repetitive unit genotyping. BMC Microbiol, 2007. 7(1): p. 1.
Zamani S, Nasiri M, Haeili M, Kazemian H, Darban-Sarokhalil D, Fooladi A, et al., Determination of circulating Mycobacterium tuberculosis strains and transmission patterns among TB patients in Iran, using 15 loci MIRU-VNTR. Int J Mycobacteriol, 2015. 4: p. 119.
Allix C, Supply P, and Fauville-Dufaux M, Utility of Fast Mycobacterial Interspersed Repetitive Unit”Variable Number Tandem Repeat Genotyping in Clinical Mycobacteriological Analysis. Clin Infect Dis, 2004. 39(6): p. 783-789.
Å»aczek A, Brzostek A, Wojtasik A, Dziadek J, and Sajduda A, Genotyping of clinical Mycobacterium tuberculosis isolates based on IS6110 and MIRU-VNTR polymorphisms. Biomed Res Int, 2013. 2013: p. 865197.
Liu R, Li Q, Xing L, Peng Z, Zhu C, and Yang Z, Genotyping of clinical Mycobacterium tuberculosis isolates based on eight loci of MIRU-VNTR [Notes from the field]. Int J Tuberc Lung Dis, 2013. 17(2): p. 243-245.
Li M, Gong J, Cottrill M, Yu H, de Lange C, Burton J, et al., Evaluation of QIAamp® DNA Stool Mini Kit for ecological studies of gut microbiota. J Microbiol Methods, 2003. 54(1): p. 13-20.
Wang R-F, Cao W-W, and Cerniglia C E, PCR detection and quantitation of predominant anaerobic bacteria in human and animal fecal samples. Appl Environ Microbiol, 1996. 62(4): p. 1242-1247.
Supply P, Allix C, Lesjean S, Cardoso-Oelemann M, Rüsch-Gerdes S, Willery E, et al., Proposal for standardization of optimized mycobacterial interspersed repetitive unit-variable-number tandem repeat typing of Mycobacterium tuberculosis. J Clin Microbiol, 2006. 44(12): p. 4498-4510.
Velayati A A, Farnia P, Mozafari M, Sheikholeslami M F, Karahrudi M A, Tabarsi P, et al., High prevelance of rifampin-monoresistant tuberculosis: a retrospective analysis among Iranian pulmonary tuberculosis patients. Am J Trop Med Hyg, 2014. 90(1): p. 99-105.
Dong H, Shi L, Zhao X, Sang B, Lv B, Liu Z, et al., Genetic diversity of Mycobacterium tuberculosis isolates from Tibetans in Tibet, China. PLoS One, 2012. 7(3): p. e33904.
Guo J-h, Xiang W-l, Zhang G, Luo T, Xie N, Yang Z-r, et al., Mycobacterial Interspersed Repetitive Unit typing in Mycobacterium tuberculosis isolates from Sichuan Province in China. Indian J Med Res, 2011. 134: p. 362-368.
Luiz R d S S, Suffys P, Barroso E C, Kerr L R F S, Duarte C R, Freitas M V C, et al., Genotyping and drug resistance patterns of Mycobacterium tuberculosis strains observed in a tuberculosis high-burden municipality in Northeast, Brazil. Braz J Infect Dis, 2013. 17(3): p. 338-345.
Han H, Wang F, Xiao Y, Ren Y, Chao Y, Guo A, et al., Utility of mycobacterial interspersed repetitive unit typing for differentiating Mycobacterium tuberculosis isolates in Wuhan, China. J Med Microbiol, 2007. 56(9): p. 1219-1223.
Hanekom M, Van Der Spuy G, van Pittius N G, McEvoy C, Hoek K, Ndabambi S, et al., Discordance between mycobacterial interspersed repetitive-unit-variable-number tandem-repeat typing and IS6110 restriction fragment length polymorphism genotyping for analysis of Mycobacterium tuberculosis Beijing strains in a setting of high incidence of tuberculosis. J Clin Microbiol, 2008. 46(10): p. 3338-3345.
Yun K W, Song E J, Choi G E, Hwang I K, Lee E Y, and Chang C L, Mycobacterial Interspersed Repetitive Units-Variable Number of Tandem Repeats ë¥¼ ì”´ìš©í•œ êµë‚´ ê²°í•µê· ì”˜ ê· ì£¼ ê°ë³„.
Korean J Lab Med, 2009. 29(4).
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. 46(2): p. 98-106.
Alonso-Rodríguez N, Martínez-Lirola M, Herránz M, Sanchez-Benitez M, Barroso P, Bouza E, et al., Evaluation of the new advanced 15-loci MIRU-VNTR genotyping tool in Mycobacterium tuberculosis molecular epidemiology studies. BMC Microbiol, 2008. 8(1): p. 34.
Shamputa I C, Lee J, Allix-Béguec C, Cho E-J, Rajan V, Lee E G, et al., Genetic diversity of Mycobacterium tuberculosis isolates from a tertiary care tuberculosis hospital in South Korea. J Clin Microbiol, 2010. 48(2): p. 387-394.
Murase Y, Mitarai S, Sugawara I, Kato S, and Maeda S, Promising loci of variable numbers of tandem repeats for typing Beijing family Mycobacterium tuberculosis. J Med Microbiol, 2008. 57(7): p. 873-880.
Zhou A, Nawaz M, Xue X, Karakousis P, Yao Y, and Xu J, Molecular genotyping of Mycobacterium tuberculosis in Xi'an, China, using MIRU-VNTR typing. Int J Tuberc Lung Dis, 2011. 15(4): p. 517-522.
Liu Q, Yang D, Xu W, Wang J, Bing L, Shao Y, et al., Molecular typing of Mycobacterium tuberculosis isolates circulating in Jiangsu province, China. BMC Infect Dis, 2011. 11(1): p. 1.

References

Zamani S, Aflaki M, Fooladi A A I, Darban-Sarokhalil D, Bameri Z, Khazaee S, et al., MIRU-VNTR analysis of the Mycobacterium tuberculosis isolates from three provinces of Iran. Scand J Infect Dis, 2013. 45(2): p. 124-130.

Sun Y-J, Bellamy R, Lee A S, Ng S T, Ravindran S, Wong S-Y, et al., Use of mycobacterial interspersed repetitive unit-variable-number tandem repeat typing to examine genetic diversity of Mycobacterium tuberculosis in Singapore. J Clin Microbiol, 2004. 42(5): p. 1986-1993.

Asgharzadeh M, Samadi K H, Pourostadi M, Asadi F N, Rashedi J, and Mahdavipour B, Strain differentiation of Mycobacterium tuberculosis for epidemiology in northwest of Iran. Cell Mol Biol (Noisy-le-grand), 2016. 62(8): p. 15.

Asante-Poku A, Nyaho M S, Borrell S, Comas I, Gagneux S, and Yeboah-Manu D, Evaluation of customised lineage-specific sets of MIRU-VNTR Loci for genotyping Mycobacterium tuberculosis complex isolates in Ghana. PLoS One, 2014. 9(3).

Zhang J, Mi L, Wang Y, Liu P, Liang H, Huang Y, et al., Genotypes and drug susceptibility of Mycobacterium tuberculosis isolates in Shihezi, Xinjiang Province, China. BMC Res Notes, 2012. 5(1): p. 309.

Nasiri M J, Rezaei F, Zamani S, Darban-Sarokhalil D, Fooladi A A I, Shojaei H, et al., Drug resistance pattern of Mycobacterium tuberculosis isolates from patients of five provinces of Iran. Asian Pac J Trop Med, 2014. 7(3): p. 193-196.

Torkaman M R A, Nasiri M J, Farnia P, Shahhosseiny M H, Mozafari M, and Velayati A A, Estimation of Recent Transmission of Mycobacterium Tuberculosis Strains among Iranian and Afghan Immigrants: A Cluster-Based Study. J Clin Diagn Res, 2014. 8(9): p. DC05.

Ali A, Hasan Z, Tanveer M, Siddiqui A R, Ghebremichael S, Kallenius G, et al., Characterization of Mycobacterium tuberculosis Central Asian Strain1 using mycobacterial interspersed repetitive unit genotyping. BMC Microbiol, 2007. 7(1): p. 1.

Zamani S, Nasiri M, Haeili M, Kazemian H, Darban-Sarokhalil D, Fooladi A, et al., Determination of circulating Mycobacterium tuberculosis strains and transmission patterns among TB patients in Iran, using 15 loci MIRU-VNTR. Int J Mycobacteriol, 2015. 4: p. 119.

Allix C, Supply P, and Fauville-Dufaux M, Utility of Fast Mycobacterial Interspersed Repetitive Unit”Variable Number Tandem Repeat Genotyping in Clinical Mycobacteriological Analysis. Clin Infect Dis, 2004. 39(6): p. 783-789.

Å»aczek A, Brzostek A, Wojtasik A, Dziadek J, and Sajduda A, Genotyping of clinical Mycobacterium tuberculosis isolates based on IS6110 and MIRU-VNTR polymorphisms. Biomed Res Int, 2013. 2013: p. 865197.

Liu R, Li Q, Xing L, Peng Z, Zhu C, and Yang Z, Genotyping of clinical Mycobacterium tuberculosis isolates based on eight loci of MIRU-VNTR [Notes from the field]. Int J Tuberc Lung Dis, 2013. 17(2): p. 243-245.

Li M, Gong J, Cottrill M, Yu H, de Lange C, Burton J, et al., Evaluation of QIAamp® DNA Stool Mini Kit for ecological studies of gut microbiota. J Microbiol Methods, 2003. 54(1): p. 13-20.

Wang R-F, Cao W-W, and Cerniglia C E, PCR detection and quantitation of predominant anaerobic bacteria in human and animal fecal samples. Appl Environ Microbiol, 1996. 62(4): p. 1242-1247.

Supply P, Allix C, Lesjean S, Cardoso-Oelemann M, Rüsch-Gerdes S, Willery E, et al., Proposal for standardization of optimized mycobacterial interspersed repetitive unit-variable-number tandem repeat typing of Mycobacterium tuberculosis. J Clin Microbiol, 2006. 44(12): p. 4498-4510.

Velayati A A, Farnia P, Mozafari M, Sheikholeslami M F, Karahrudi M A, Tabarsi P, et al., High prevelance of rifampin-monoresistant tuberculosis: a retrospective analysis among Iranian pulmonary tuberculosis patients. Am J Trop Med Hyg, 2014. 90(1): p. 99-105.

Dong H, Shi L, Zhao X, Sang B, Lv B, Liu Z, et al., Genetic diversity of Mycobacterium tuberculosis isolates from Tibetans in Tibet, China. PLoS One, 2012. 7(3): p. e33904.

Guo J-h, Xiang W-l, Zhang G, Luo T, Xie N, Yang Z-r, et al., Mycobacterial Interspersed Repetitive Unit typing in Mycobacterium tuberculosis isolates from Sichuan Province in China. Indian J Med Res, 2011. 134: p. 362-368.

Luiz R d S S, Suffys P, Barroso E C, Kerr L R F S, Duarte C R, Freitas M V C, et al., Genotyping and drug resistance patterns of Mycobacterium tuberculosis strains observed in a tuberculosis high-burden municipality in Northeast, Brazil. Braz J Infect Dis, 2013. 17(3): p. 338-345.

Han H, Wang F, Xiao Y, Ren Y, Chao Y, Guo A, et al., Utility of mycobacterial interspersed repetitive unit typing for differentiating Mycobacterium tuberculosis isolates in Wuhan, China. J Med Microbiol, 2007. 56(9): p. 1219-1223.

Hanekom M, Van Der Spuy G, van Pittius N G, McEvoy C, Hoek K, Ndabambi S, et al., Discordance between mycobacterial interspersed repetitive-unit-variable-number tandem-repeat typing and IS6110 restriction fragment length polymorphism genotyping for analysis of Mycobacterium tuberculosis Beijing strains in a setting of high incidence of tuberculosis. J Clin Microbiol, 2008. 46(10): p. 3338-3345.

Yun K W, Song E J, Choi G E, Hwang I K, Lee E Y, and Chang C L, Mycobacterial Interspersed Repetitive Units-Variable Number of Tandem Repeats ë¥¼ ì”´ìš©í•œ êµë‚´ ê²°í•µê· ì”˜ ê· ì£¼ ê°ë³„.

Korean J Lab Med, 2009. 29(4).

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. 46(2): p. 98-106.

Alonso-Rodríguez N, Martínez-Lirola M, Herránz M, Sanchez-Benitez M, Barroso P, Bouza E, et al., Evaluation of the new advanced 15-loci MIRU-VNTR genotyping tool in Mycobacterium tuberculosis molecular epidemiology studies. BMC Microbiol, 2008. 8(1): p. 34.

Shamputa I C, Lee J, Allix-Béguec C, Cho E-J, Rajan V, Lee E G, et al., Genetic diversity of Mycobacterium tuberculosis isolates from a tertiary care tuberculosis hospital in South Korea. J Clin Microbiol, 2010. 48(2): p. 387-394.

Murase Y, Mitarai S, Sugawara I, Kato S, and Maeda S, Promising loci of variable numbers of tandem repeats for typing Beijing family Mycobacterium tuberculosis. J Med Microbiol, 2008. 57(7): p. 873-880.

Zhou A, Nawaz M, Xue X, Karakousis P, Yao Y, and Xu J, Molecular genotyping of Mycobacterium tuberculosis in Xi'an, China, using MIRU-VNTR typing. Int J Tuberc Lung Dis, 2011. 15(4): p. 517-522.

Liu Q, Yang D, Xu W, Wang J, Bing L, Shao Y, et al., Molecular typing of Mycobacterium tuberculosis isolates circulating in Jiangsu province, China. BMC Infect Dis, 2011. 11(1): p. 1.

Author biographies is not available.