Insight into population structure of Mycobacterium tuberculosis isolates in the multiethnic province of Alborz, Iran
Abstract
Background and Objectives: Genetic diversity of Mycobacterium tuberculosis clinical isolates from tuberculosis patients in the multiethnic province of Alborz, Iran was assessed.
Materials and Methods: A total of 17 isolates in the period of 2012-2013 were collected and subjected to a Multiple-locus variable-number tandem repeat (VNTR) analysis (MLVA) consisted of 6 variable numbers of tandem repeats (VNTRs) including ETR-A, ETR-B, ETR-C, ElTR-D, ETR-E, ETR-F, 5 Mycobacterial Interspersed Repetitive Units including MIRU10, MIRU16, MIRU26, MIRU39, MIRU40, and 1 Queen University of Belfast locus, QUB11.
Results: This classified all isolates into 17 distinct MIRU-VNTR types, a reflection of a highly heterogenic population. Within the 12 used VNTR loci, ten proved highly or moderately discriminant according to the calculated HGDI scores. No cluster of isolates was identified in the study panel, giving a clustering rate of 0%, several events of SVL (N=5) and DVL (N=4) and TVL (N=3) were detected.
Conclusion: The greater heterogeneity observed here by MLVA-VNTR analysis is most likely due to limited background data in the study region rather than a genuine more heterogeneous population compared to other provinces of the country.
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13. 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;330:1703-1709.
14. Choisy M, Nguyen DH, Tran THT, Pham KLT, Dinh PTT, Philippe J, et al. High prevalence of Beijing and EAI4-VNM genotypes among M. tuberculosis isolates in northern Vietnam: sampling effect, rural and urban disparities. PLoS One 2012;7(9):e45553.
15. Somphavong S, Berland JL, Gauthier M, Vu TT, Nguyen QH, Iem V, et al. First insights into the genetic characteristics and drug resistance of Mycobacterium tuberculosis population collected during the first national tuberculosis prevalence survey of Lao PDR (2010-2011). BMC Infect Dis 2019;19:851.
16. Asgharzadeh M, Kafil HS, Roudsary AA, Hanifi GR. Tuberculosis transmission in Northwest of Iran: using MIRU-VNTR, ETR-VNTR and IS6110-RFLP methods. Infect Genet Evol 2011;11:124-131.
17. Asgharzadeh M, Samadi Kafil H, Pourostadi M, Asadi Faezi N, Rashedi J, Mahdavipour B. Strain differentiation of Mycobacterium tuberculosis for epidemiology in northwest of Iran. Cell Mol Biol (Noisy-le-grand) 2016;62:15-20.
18. Zamani S, Aflaki M, Fooladi AA, 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;45:124-130.
19. Farmanfarmaei G, Kargarpour Kamakoli M, Sadegh HR, Masoumi M, Abdolrahimi F, Fateh A, et al. Bias in detection of Mycobacterium tuberculosis polyclonal infection: Use clinical samples or cultures? Mol Cell Probes 2017;33:1-3.
20. Jafarian M, Aghali-Merza M, Farnia P, Ahmadi M, Masjedi MR, Velayati AA. Synchronous comparison of Mycobacterium tuberculosis epidemiology strains by "MIRU-VNTR" and "MIRU-VNTR and Spoligotyping" technique. Avicenna J Med Biotechnol 2010; 2: 145-152.
21. Wyllie DH, Davidson JA, Grace Smith E, Rathod P, Crook DW, Peto TEA, et al. A quantitative evaluation of MIRU-VNTR typing against whole-genome sequencing for identifying Mycobacterium tuberculosis transmission: A prospective observational cohort study. EBioMedicine 2018;34:122-130.
22. Rajwani R, Shehzad S, Siu GKH. MIRU-profiler: a rapid tool for determination of 24-loci MIRU-VNTR profiles from assembled genomes of Mycobacterium tuberculosis. PeerJ 2018;6:e5090.
2. Dos Vultos T, Mestre O, Rauzier J, Golec M, Rastogi N, Rasolofo V, et al. Evolution and diversity of clonal bacteria: the paradigm of Mycobacterium tuberculosis. PLoS One 2008;3(2):e1538.
3. Gagneux S. Ecology and evolution of Mycobacterium tuberculosis. Nat Rev Microbiol 2018;16:202-213.
4. Kargarpour Kamakoli M, Hadifar S, Khanipour S, Farmanfarmaei G, Fateh A, Siadat SD, et al. Comparison of MIRU-VNTR genotyping between old and fresh clinical samples in tuberculosis. Infect Dis (Lond) 2019;51:659-667.
5. Hadifar S, Shamkhali L, Kargarpour Kamakoli M, Mostafaei S, Khanipour S, Mansoori N, et al. Genetic diversity of Mycobacterium tuberculosis isolates causing pulmonary and extrapulmonary tuberculosis in the capital of Iran. Mol Phylogenet Evol 2019;132:46-52.
6. Mansoori N, Yaseri M, Vaziri F, Douraghi M. Genetic diversity of Mycobacterium tuberculosis complex isolates circulating in an area with high tuberculosis incidence: Using 24-locus MIRU-VNTR method. Tuberculosis (Edinb) 2018;112:89-97.
7. Riyahi Zaniani F, Moghim S, Mirhendi H, Ghasemian Safaei H, Fazeli H, Salehi M, et al. Genetic lineages of Mycobacterium tuberculosis i in Isfahan, Iran. Curr Microbiol 2017;74:14-21.
8. Huard RC, de Oliveira Lazzarini LC, Butler WR, van Soolingen D, Ho JL. PCR-based method to differentiate the subspecies of the Mycobacterium tuberculosis complex on the basis of genomic deletions. J Clin Microbiol 2003;41:1637-1650.
9. McHugh TD, Gillespie SH. Nonrandom association of IS6110 and Mycobacterium tuberculosis: implications for molecular epidemiological studies. J Clin Microbiol 1998;36:1410-1413.
10. Warren R, Gey van Pittius N, Barnard M, Hesseling A, Engelke E, De Kock M, et al. Differentiation of Mycobacterium tuberculosis complex by PCR amplification of genomic regions of difference. Int J Tuberc Lung Dis 2006;10:818-822.
11. 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;26:2465-2466.
12. Salvato RS, Schiefelbein S, Barcellos RB. Molecular characterisation of multidrug-resistant Mycobacterium tuberculosis isolates from a high-burden tuberculosis state in Brazil. Epidemiol Infect 2019;147: e216.
13. 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;330:1703-1709.
14. Choisy M, Nguyen DH, Tran THT, Pham KLT, Dinh PTT, Philippe J, et al. High prevalence of Beijing and EAI4-VNM genotypes among M. tuberculosis isolates in northern Vietnam: sampling effect, rural and urban disparities. PLoS One 2012;7(9):e45553.
15. Somphavong S, Berland JL, Gauthier M, Vu TT, Nguyen QH, Iem V, et al. First insights into the genetic characteristics and drug resistance of Mycobacterium tuberculosis population collected during the first national tuberculosis prevalence survey of Lao PDR (2010-2011). BMC Infect Dis 2019;19:851.
16. Asgharzadeh M, Kafil HS, Roudsary AA, Hanifi GR. Tuberculosis transmission in Northwest of Iran: using MIRU-VNTR, ETR-VNTR and IS6110-RFLP methods. Infect Genet Evol 2011;11:124-131.
17. Asgharzadeh M, Samadi Kafil H, Pourostadi M, Asadi Faezi N, Rashedi J, Mahdavipour B. Strain differentiation of Mycobacterium tuberculosis for epidemiology in northwest of Iran. Cell Mol Biol (Noisy-le-grand) 2016;62:15-20.
18. Zamani S, Aflaki M, Fooladi AA, 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;45:124-130.
19. Farmanfarmaei G, Kargarpour Kamakoli M, Sadegh HR, Masoumi M, Abdolrahimi F, Fateh A, et al. Bias in detection of Mycobacterium tuberculosis polyclonal infection: Use clinical samples or cultures? Mol Cell Probes 2017;33:1-3.
20. Jafarian M, Aghali-Merza M, Farnia P, Ahmadi M, Masjedi MR, Velayati AA. Synchronous comparison of Mycobacterium tuberculosis epidemiology strains by "MIRU-VNTR" and "MIRU-VNTR and Spoligotyping" technique. Avicenna J Med Biotechnol 2010; 2: 145-152.
21. Wyllie DH, Davidson JA, Grace Smith E, Rathod P, Crook DW, Peto TEA, et al. A quantitative evaluation of MIRU-VNTR typing against whole-genome sequencing for identifying Mycobacterium tuberculosis transmission: A prospective observational cohort study. EBioMedicine 2018;34:122-130.
22. Rajwani R, Shehzad S, Siu GKH. MIRU-profiler: a rapid tool for determination of 24-loci MIRU-VNTR profiles from assembled genomes of Mycobacterium tuberculosis. PeerJ 2018;6:e5090.
| Files | ||
| Issue | Vol 13 No 1 (2021) | |
| Section | Original Article(s) | |
| DOI | https://doi.org/10.18502/ijm.v13i1.5493 | |
| Keywords | ||
| Mycobacterium tuberculosis; Population; Genotype; Genetic heterogeneity; Polymorphism; Epidemiologic; Locus | ||
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This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License. |
How to Cite
1.
Sadat Farnad M, Momtaz H, Mosavari N, Khosravi Y, Tadayon K. Insight into population structure of Mycobacterium tuberculosis isolates in the multiethnic province of Alborz, Iran. Iran J Microbiol. 2021;13(1):58-64.
