Polymorphism of variable-number tandem repeats at multiple loci in Mycobacterium tuberculosis

Journal of Clinical Microbiology

Volumn 43, Issue 10, 2005, Pages 5034-5043

  Smittipat, Nat ^a   Billamas, Pamaree ^a   Palittapongarnpim, Manee ^b   Thong On, Arunee ^b   Temu, Mansuet M ^b,d   Thanakijcharoen, Prateep ^c   Karnkawinpong, Opart ^c   Palittapongarnpim, Prasit ^a,b  

^a NATIONAL SCIENCE AND TECHNOLOGY DEVELOPMENT AGENCY   (Thailand)

^b MAHIDOL UNIVERSITY   (Thailand)

^c Amnat Charoen Hospital   (Thailand)

^d NATIONAL INSTITUTE FOR MEDICAL RESEARCH   (Tanzania)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELISM; ANIMAL CELL; ARTICLE; BIODIVERSITY; CONTROLLED STUDY; GENE LOCUS; GENETIC POLYMORPHISM; GENOTYPE; HYBRIDIZATION; MOLECULAR BIOLOGY; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; VARIABLE NUMBER OF TANDEM REPEAT;

BACTERIAL TYPING TECHNIQUES; BASE SEQUENCE; DNA TRANSPOSABLE ELEMENTS; EPIDEMIOLOGY, MOLECULAR; HUMANS; MINISATELLITE REPEATS; MOLECULAR SEQUENCE DATA; MYCOBACTERIUM TUBERCULOSIS; POLYMORPHISM, GENETIC; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; THAILAND; TUBERCULOSIS, PULMONARY;

ANIMALIA; MYCOBACTERIUM TUBERCULOSIS;

EID: 26944439060     PISSN: 00951137     EISSN: None     Source Type: Journal    
DOI: 10.1128/JCM.43.10.5034-5043.2005     Document Type: Article

References (33)

1. Bauer, J., A. B. Andersen, K. Kremer, and H. Miorrier. 1999. Usefulness of spoligotyping to discriminate IS6110 low-copy-number Mycobacterium tuberculosis complex strains cultured in Denmark. J. Clin. Microbiol. 37:2602-2606.
2. Chanchaem, W., and P. Palittapongarnpim. 2002. A variable number of tandem repeats result in polymorphic α-isopropylmalate synthase in Mycobacterium tuberculosis. Tuberculosis 81:1-6.
3. Cole, S. T., R. Brosch, J. Parkhill, T. Gamier, C. Churcher, D. Harris, S. V. Gordon, K. Eiglmeier, S. Gas, C. E. Barry, F. Tekaia, K. Badcock, D. Basham, D. Brown, T. Chillingworth, R. Connor, R. Davies, K. Devlin, T. Feltwell, S. Gentles, N. Hamlin, S. Holroyd, T. Hornsby, K. Jagels, A. Krogh, J. McClean, S. Moule, L. Murphy, K. Oliver, J. Osborne, M. A. Quail, M. Al Rajandream, J. Rodgers, S. Rutter, K. Seeger, J. Skelton, R. Squares, S. Squares, J. E. Sulston, K. Taylor, S. Whitehead, and B. G. Barrell. 1998. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393:537-544.
4. Cowan, L. S., L. Mosher, L. Diem, J. P. Massey, and J. T. Crawford. 2002. Variable-number tandem repeat typing of Mycobacterium tuberculosis isolates with low copy numbers of IS6110 by using mycobacterial interspersed repetitive units. J. Clin. Microbiol. 40:1592-1602.
5. Friedman, C. R., M. Y. Stoeckle, W. D. Johnson, Jr., and L. W. Riley. 1995. Double-repetitive-element PCR method for subtyping Mycobacterium tuberculosis clinical isolates. J. Clin. Microbiol. 33:1383-1384.
6. Frothingham, R., and W. A. Meeker-O'Connell. 1998. Genetic diversity in the Mycobacterium tuberculosis complex based on variable number of tandem DNA repeats. Microbiology 144:1189-1196.
7. Frothingham, R. 1995. Differentiation of strains m Mycobacterium tuberculosis complex by DNA sequence polymorphisms, including rapid identification of M. bovis BCG. J. Clin. Microbiol. 33:840-844.
8. Gillespie, S. H., N. Kennedy, F. I. Ngowi, N. G. Fomukong, S. al-Maamary, and J. W. Dale. 1995. Restriction fragment length polymorphism analysis of Mycobacterium tuberculosis isolated from patients with pulmonary tuberculosis in northern Tanzania. Trans. R. Soc. Trop. Med. Hyg. 89:335-338.
9. Goyal, M., D. Young, Y. Zhang, P. A. Jenkins, and R. J. Shaw. 1994. PCR amplification of variable sequence upstream of katG gene to subdivide strains of Mycobacterium tuberculosis complex. J. Clin. Microbiol. 32:3070-3071.
10. Groenen, P. M., A. E. Bunschoten, D. van Soolingen, and J. D. van Embden. 1993. Nature of DNA polymorphism in the direct repeat cluster of Mycobacterium tuberculosis: application for strain differentiation by a novel typing method. Mol. Microbiol. 10:1057-1065.
11. Haas, W. H., W. R. Butler, C. L. Woodley, and J. Crawford. 1993. Mixed-linker polymerase chain reaction: a new method for rapid fingerprinting of isolates of the Mycobacterium tuberculosis complex. J. Clin. Microbiol. 31: 1293-1298.
12. Hermans, P. W. M., D. van Soolingen, and J. D. A. van Embden. 1992. Characterization of a major polymorphic tandem repeat in Mycobacterium tuberculosis and its potential use in the epidemiology of Mycobacterium kansasii and Mycobacterium gordonae. J. Bacteriol. 174:4157-4165.
13. Jeffreys, A. J., V. Wilson, and S. L. Thein. 1985. Hypervariable "minisatellite" regions in human DNA. Nature 314:67-73.
14. Kamerbeek, J., L. Schouls, A. Kolk, M. van Agterveld, D. van Sooligen, S. Kuijper, A. Bunschoten, H. Molhuizen, R. Shaw, M. Goyal, and J. D. A. van Embden. 1997. Simultaneous detection and strain differentiation of Mycobacterium tuberculosis for diagnosis and epidemiology. J. Clin. Microbiol. 35:907-914.
15. Keim, P., L. B. Price, A. M. Klevytska, K. L. Smith, J. M. Schupp, R. Okinaka, P. J. Jackson, and M. E. Hugh-Jones. 1997. Multiple-locus variable-number tandem repeat analysis reveals genetic relationships within Bacillus anthracis. J. Bacteriol. 182:2928-2936.
16. Kremer, K., D. van Soolingen, R. Frothingham, W. H. Haas, P. W. M. Hermans, C. Martin, P. Palittappongarnpim, B. B. Plikaytis, L. W. Riley, M. A. Yakrus, J. M. Musser, and J. D. A. van Embden. 1999. Comparison of methods based on different molecular epidemiological markers for typing of Mycobacterium tuberculosis complex strains: interlaboratory study of discriminatory power and reproducibility. J. Clin. Microbiol. 37:2607-2618.
17. Le Flèche, P., M. Fahre, F. Denoeud, J. L. Koeck, and G. Vergnaud. 2002. High resolution, on-line identification of strains from the Mycobacterium tuberculosis complex based on tandem repeat typing. BMC Microbiol. 2:37-48.
18. Mazars, E., S. Lesjean, A. U. Banuls, M. Gillbert, V. Vincent, B. Gicquel, M. Tibayrenc, C. Locht, and P. Supply. 2001. High-resolution minisatellite-based typing as a portable approach to global analysis of Mycobacterium tuberculosis molecular epidemiology. Proc. Natl. Acad. Sci. USA 98:1901-1906.
19. Moström, P., M. Gordon, C. Sola, M. Ridell, and N. Rastogi. 2002. Methods used in the molecular epidemiology of tuberculosis. Clin. Microbiol. Infect. 8:694-704.
20. Namwat, W., P. Luangsook, and P. Palittapongarnpim. 1998. The genetic diversity of Mycobacterium tuberculosis strains in Thailand studied by amplification of DNA segments containing direct repetitive sequences. Int. J. Tuberc. Lung Dis. 2:153-159.
21. Palittapongarnpim, P., S. Chomyc, A. Fanning, and D. Kunimoto. 1993. DNA fingerprinting of Mycobacterium tuberculosis isolates by ligation-mediated polymerase chain reaction. Nucleic Acids Res. 21:761-762.
22. Palittapongarnpim, P., P. Luangsook, S. Tansuphaswadikul, C. Chuchottaworn, R. Prachaktam, and B. Sathapatayavoogs. 1997. Restriction fragment length polymorphism study of Mycobacterium tuberculosis in Thailand using IS6110 as probe. Int. J. Tuberc. Lung Dis. 1:370-376.
23. Roring, S., A. Scott, D. Brittain, I. Walker, G. Hewinson, S. Neill, and R. Skuce. 2002. 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. 40:2126-2133.
24. Ross, B. C., K. Raios, K. Jackson, and B. Dwyer. 1992. Molecular cloning of a highly repeated DNA element from Mycobacterium tuberculosis and its use as an epidemiological tool. J. Clin. Microbiol. 30:942-946.
25. Savine, E., R. M. Warren, G. D. van der Spuy, N. Beyers, P. D. van Haden, C. Locht, and P. Supply. 2002. Stability of variable-number tandem repeats of mycobacterial interspersed repetitive units from 12 loci in serial isolates of Mycobacterium tuberculosis. J. Clin. Microbiol. 40:4561-4566.
26. Skuce, R. A., T. P. McCorry, J. F. McCarroll, S. M. M. Roring, A. N. Scott, D. Brittain, S. L. Hughes, R. G. Hewinson, and S. D. Neill. 2002. Discrimination of Mycobacterium tuberculosis complex bacteria using novel VNTR-PCR targets. Microbiology 148:519-528.
27. Smittipat, N., and P. Palittapongarnpim. 2000. Identification of possible loci of variable number of tandem repeats in Mycobacterium tuberculosis. Tuberc. Lung Dis. 80:69-74.
28. Spurgiesz, R. S., T. N. Quitugua, K. L. Smith, J. Schupp, E. G. Palmer, R. A. Cox, and P. Keim. 2003. Molecular typing of Mycobacterium tuberculosis by using nine novel variable-number tandem repeats across the Beijing family and low-copy-number IS6110 isolates. J. Clin. Microbiol. 41:4224-4230.
29. Supply, P., S. Lesjean, E. Savine, K. Kremer, D. van Soolingen, and C. Locht. 2001. Automated high-throughput genotyping for study of global epidemiology of Mycobacterium tuberculosis based on mycobacterial interspersed repetitive units. J. Clin. Microbiol. 39:3563-3571.
30. Supply, P., J. Magdalena, S. Himpens, and C. Locht. 1997. Identification of novel intergenic repetitive units in a mycobacterial two-component system operon. Mol. Microbiol. 26:991-1003.
31. Supply, P., E. Mazars, S. Lesjean, V. Vincent, B. Gicquel, and C. Locht. 2000. Variable human minisatellite-like regions in the Mycobacterium tuberculosis genome. Mol. Microbiol. 36:762-771.
32. Supply, P., R. M. Warren, A. L. Banuls, S. Lesjean, G. D. van der Spuy, L. A. Lewis, M. Tibayrenc, P. D. van Helden, and C. Locht. 2003. Linkage disequilibrium between minisatellite loci supports clonal evolution of Mycobacterium tuberculosis in a high tuberculosis incidence area. Mol. Microbiol. 47:529-538.
33. van Soolingen, D., P. E. W. de Haas, P. W. M. Hermans, P. M. A. Groenen, and J. D. A. van Embden. 1993. Comparison of various repetitive DNA elements as genetic markers for strain differentiation and epidemiology of Mycobacterium tuberculosis. J. Clin. Microbiol. 31:1987-1995.