Tuberc Respir Dis.  2014 Feb;76(2):59-65. 10.4046/trd.2014.76.2.59.

Optimal Combination of VNTR Typing for Discrimination of Isolated Mycobacterium tuberculosis in Korea

• Lee J
• Kang H
• Kim S
• Yoo H
• Kim HJ
• Park YK

• KMID: 1877342
• DOI: http://doi.org/10.4046/trd.2014.76.2.59

Abstract

BACKGROUND
Variable-number tandem repeat (VNTR) typing is a promising method to discriminate the Mycobacterium tuberculosis isolates in molecular epidemiology. The purpose of this study is to determine the optimal VNTR combinations for discriminating isolated M. tuberculosis strains in Korea.
METHODS
A total of 317 clinical isolates collected throughout Korea were genotyped by using the IS6110 restriction fragment length polymorphism (RFLP), and then analysed for the number of VNTR copies from 32 VNTR loci.
RESULTS
The results of discriminatory power according to diverse combinations were as follows: 25 clusters in 83 strains were yielded from the internationally standardized 15 VNTR loci (Hunter-Gaston discriminatory index [HGDI], 0.9958), 25 clusters in 65 strains by using IS6110 RFLP (HGDI, 0.9977), 14 clusters in 32 strains in 12 hyper-variable VNTR loci (HGDI, 0.9995), 6 clusters in 13 strains in 32 VNTR loci (HDGI, 0.9998), and 7 clusters in 14 strains of both the 12 hyper-variable VNTR and IS6110 RFLP (HDGI, 0.9999).
CONCLUSION
The combination of 12 hyper-variable VNTR typing can be an effective tool for genotyping Korean M. tuberculosis isolates where the Beijing strains are predominant.

Keyword

Mycobacterium tuberculosis; Molecular Epidemiology; Minisatellite Repeats

MeSH Terms

Discrimination (Psychology)*
Korea*
Methods
Minisatellite Repeats
Molecular Epidemiology
Mycobacterium tuberculosis*
Mycobacterium*
Polymorphism, Restriction Fragment Length
Tandem Repeat Sequences
Tuberculosis

Reference

1. van Embden JD, Cave MD, Crawford JT, Dale JW, Eisenach KD, Gicquel B, et al. Strain identification of Mycobacterium tuberculosis by DNA fingerprinting: recommendations for a standardized methodology. J Clin Microbiol. 1993; 31:406–409. PMID: 8381814.

2. Park YK, Bai GH, Kim SJ. Restriction fragment length polymorphism analysis of Mycobacterium tuberculosis isolated from countries in the western pacific region. J Clin Microbiol. 2000; 38:191–197. PMID: 10618086.

3. Park YK, Shin S, Ryu S, Cho SN, Koh WJ, Kwon OJ, et al. Comparison of drug resistance genotypes between Beijing and non-Beijing family strains of Mycobacterium tuberculosis in Korea. J Microbiol Methods. 2005; 63:165–172. PMID: 15893392.

4. Kang HY, Wada T, Iwamoto T, Maeda S, Murase Y, Kato S, et al. Phylogeographical particularity of the Mycobacterium tuberculosis Beijing family in South Korea based on international comparison with surrounding countries. J Med Microbiol. 2010; 59(Pt 10):1191–1197. PMID: 20576748.

5. Cowan LS, Diem L, Monson T, Wand P, Temporado D, Oemig TV, 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; 43:688–695. PMID: 15695665.

6. Smittipat N, Palittapongarnpim P. Identification of possible loci of variable number of tandem repeats in Mycobacterium tuberculosis. Tuber Lung Dis. 2000; 80:69–74. PMID: 10912281.

7. Supply P, Allix C, Lesjean S, Cardoso-Oelemann M, Rusch-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; 44:4498–4510. PMID: 17005759.

8. Jiao WW, Mokrousov I, Sun GZ, Guo YJ, Vyazovaya A, Narvskaya O, et al. Evaluation of new variable-number tandem-repeat systems for typing Mycobacterium tuberculosis with Beijing genotype isolates from Beijing, China. J Clin Microbiol. 2008; 46:1045–1049. PMID: 18199785.

9. Murase Y, Mitarai S, Sugawara I, Kato S, Maeda S. Promising loci of variable numbers of tandem repeats for typing Beijing family Mycobacterium tuberculosis. J Med Microbiol. 2008; 57(Pt 7):873–880. PMID: 18566146.

10. Mokrousov I, Narvskaya O, Vyazovaya A, Millet J, Otten T, Vishnevsky B, et al. Mycobacterium tuberculosis Beijing genotype in Russia: in search of informative variable-number tandem-repeat loci. J Clin Microbiol. 2008; 46:3576–3584. PMID: 18753356.

11. Mokrousov I, Vyazovaya A, Otten T, Zhuravlev V, Pavlova E, Tarashkevich L, et al. Mycobacterium tuberculosis population in northwestern Russia: an update from Russian-EU/Latvian border region. PLoS One. 2012; 7:e41318. PMID: 22844457.

12. Iwamoto T, Grandjean L, Arikawa K, Nakanishi N, Caviedes L, Coronel J, et al. Genetic diversity and transmission characteristics of Beijing family strains of Mycobacterium tuberculosis in Peru. PLoS One. 2012; 7:e49651. PMID: 23185395.

13. Kim SJ, Bai GH, Lee H, Kim HJ, Lew WJ, Park YK, et al. Transmission of Mycobacterium tuberculosis among high school students in Korea. Int J Tuberc Lung Dis. 2001; 5:824–830. PMID: 11573893.

14. Roring S, Scott A, Brittain D, Walker I, Hewinson G, Neill S, et al. Development of variable-number tandem repeat typing of Mycobacterium bovis: comparison of results with those obtained by using existing exact tandem repeats and spoligotyping. J Clin Microbiol. 2002; 40:2126–2133. PMID: 12037076.

15. Smittipat N, Billamas P, Palittapongarnpim M, Thong-On A, Temu MM, Thanakijcharoen P, et al. Polymorphism of variable-number tandem repeats at multiple loci in Mycobacterium tuberculosis. J Clin Microbiol. 2005; 43:5034–5043. PMID: 16207958.

16. Iwamoto T, Yoshida S, Suzuki K, Tomita M, Fujiyama R, Tanaka N, et al. Hypervariable loci that enhance the discriminatory ability of newly proposed 15-loci and 24-loci variable-number tandem repeat typing method on Mycobacterium tuberculosis strains predominated by the Beijing family. FEMS Microbiol Lett. 2007; 270:67–74. PMID: 17302938.

17. Sun YJ, Bellamy R, Lee AS, Ng ST, Ravindran S, Wong SY, 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; 42:1986–1993. PMID: 15131159.

18. 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. PMID: 3069867.

19. Shamputa IC, Lee J, Allix-Beguec C, Cho EJ, Lee JI, Rajan V, et al. Genetic diversity of Mycobacterium tuberculosis isolates from a tertiary care tuberculosis hospital in South Korea. J Clin Microbiol. 2010; 48:387–394. PMID: 20018816.

20. Chen YY, Chang JR, Huang WF, Kuo SC, Su IJ, Sun JR, et al. Genetic diversity of the Mycobacterium tuberculosis Beijing family based on SNP and VNTR typing profiles in Asian countries. PLoS One. 2012; 7:e39792. PMID: 22808061.