Mycobacterium tuberculosis Beijing genotype in Russia: In search of informative variable-number tandem-repeat loci

Journal of Clinical Microbiology

Volumn 46, Issue 11, 2008, Pages 3576-3584

  Mokrousov, Igor ^a   Narvskaya, Olga ^a   Vyazovaya, Anna ^a   Millet, Julie ^b   Otten, Tatiana ^c   Vishnevsky, Boris ^c   Rastogi, Nalin ^b  

^a ST PETERSBURG PASTEUR INSTITUTE   (Russian Federation)

^b Unite de la Tuberculose et des Mycobacteries   (Guadeloupe)

^c ST PETERSBURG RESEARCH INSTITUTE OF PHTHISIOPULMONOLOGY   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA;

ARTICLE; BACTERIAL GENE; BACTERIAL STRAIN; DNA FINGERPRINTING; DNA POLYMORPHISM; GENE CLUSTER; GENE LOCUS; GENOTYPE; MARKER GENE; MEDICAL INFORMATION; MOLECULAR CLONING; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; PREVALENCE; PRIORITY JOURNAL; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; RUSSIAN FEDERATION; TANDEM REPEAT;

BACTERIAL TYPING TECHNIQUES; CLUSTER ANALYSIS; DNA FINGERPRINTING; DNA TRANSPOSABLE ELEMENTS; DNA, BACTERIAL; GENOTYPE; MINISATELLITE REPEATS; MYCOBACTERIUM TUBERCULOSIS; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; RUSSIA; TUBERCULOSIS;

MYCOBACTERIUM TUBERCULOSIS;

EID: 55849142529     PISSN: 00951137     EISSN: None     Source Type: Journal    
DOI: 10.1128/JCM.00414-08     Document Type: Article

References (41)

1. Bifani, P. J., B. Mathema, N. E. Kurepina, and B. N. Kreiswirth. 2002. Global dissemination of the Mycobacterium tuberculosis W-Beijing family strains. Trends Microbiol. 10:45-52.
2. Caminero, J. A., M. J. Pena, M. I. Campos-Herrero, J. C. Rodriguez, I. Garcia, P. Cabrera, C. Lafoz, S. Samper, H. Takiff, O. Afonso, J. M. Pavon, M. J. Torres, D. van Soolingen, D. A. Enarson, and C. Martin. 2001. Epidemiological evidence of the spread of a Mycobacterium tuberculosis strain of the Beijing genotype on Gran Canaria Island. Am. J. Respir. Crit. Care Med. 164:1165-1170.
3. Cox, H. S., T. Kubica, D. Doshetov, Y. Kebede, S. Rüsch-Gerdess, and S. Niemann. 2005. The Beijing genotype and drug resistant tuberculosis in the Aral Sea region of Central Asia. Respir. Res. 6:134.
4. Drobniewski, F., Y. Balabanova, V. Nikolayevsky, M. Ruddy, S. Kuznetzov, S. Zakharova, A. Melentyev, and I. Fedorin. 2005. Drug-resistant tuberculosis, clinical virulence, and the dominance of the Beijing strain family in Russia. JAMA 293:2726-2731.
5. Felsenstein, J. 2004. PHYLIP (Phylogeny Inference Package) version 3.6b. Department of Genome Sciences, University of Washington, Seattle.
6. Frothingham, R., and W. A. Meeker-O'Connell. 1998. Genetic diversity in the Mycobacterium tuberculosis complex based on variable numbers of tandem DNA repeats. Microbiology 144:1189-1196.
7. García de Viedma, D., F. Chaves, J. Inigo, et al. 2006. New route of importation of Mycobacterium tuberculosis Beijing genotype. Emerg. Infect. Dis. 12:169-170.
8. Glynn, J. R., A. C. Crampin, H. Traore, M. D. Yates, F. D. Mwaungulu, B. M. Ngwira, S. D. Chaguluka, D. T. Mwafulirwa, S. Floyd, C. Murphy, F. A. Drobniewski, and P. E. Fine. 2005. Mycobacterium tuberculosis Beijing genotype, northern Malawi. Emerg. Infect. Dis. 11:150-153.
9. Glynn, J. R., J. Whiteley, P. J. Bifani, K. Kremer, and D. van Soolingen. 2002. Worldwide occurrence of Beijing/W strains of Mycobacterium tuberculosis: a systematic review. Emerg. Infect. Dis. 8:843-849.
10. Hunter, P. R., and M. A. Gaston. 1988. Numerical index of the discriminatory ability of typing systems: an application of Simpsons's index of diversity. J. Clin. Microbiol. 26:2465-2466.
11. Iwamoto, T., S. Yoshida, K. Suzuki, M. Tomita, R. Fujiyama, N. Tanaka, Y. Kawakami, and M. Ito. 2007. 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. 272:282-283.
12. Jiao, W. W., I. Mokrousov, G. Z. Sun, Y. J. Guo, A. Vyazovaya, O. Narvskaya, and A. D. Shen. 2008. Evaluation of new variable-number tandem repeat typing systems of Mycobacterium tuberculosis with Beijing genotype isolates from Beijing, China. J. Clin. Microbiol. 46:1045-1049.
13. Kam, K. M., C. W. Yip, K. L. Leung, K. L. Wong, W. M. Ko, and W. S. Wong. 2006. Optimization of variable number tandem repeat typing set for differentiating Mycobacterium tuberculosis strains in the Beijing family. FEMS Microbiol. Lett. 256:258-265.
14. Kamerbeek, J., L. Schouls, A. Kolk, M. van Agterveld, D. van Soolingen, 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. Kovalev, S. Y., E. Y. Kamaev, M. A. Kravchenko, N. E. Kurepina, and S. N. Skorniakov. 2005. Genetic analysis of Mycobacterium tuberculosis strains isolated in Ural region, Russian Federation, by MIRU-VNTR genotyping. Int. J. Tuberc. Lung Dis. 9:746-752.
16. Kremer, K., B. K. Au, P. C. Yip, R. Skuce, P. Supply, K. M. Kam, and D. van Soolingen. 2005. Use of variable-number tandem-repeat typing to differentiate Mycobacterium tuberculosis Beijing family isolates from Hong Kong and comparison with IS6110 restriction fragment length polymorphism typing and spoligotyping. J. Clin. Microbiol. 43:314-320.
17. Kremer, K., J. R. Glynn, T. Lillebaek, S. Niemann, N. E. Kurepina, B. N. Kreiswirth, P. J. Bifani, and D. van Soolingen. 2004. Definition of the Beijing/W lineage of Mycobacterium tuberculosis on the basis of genetic markers. J. Clin. Microbiol. 42:4040-4049.
18. Krüüner, A., S. E. Hoffner, H. Sillastu, M. Danilovits, K. Levina, S. B. Svenson, S. Ghebremichael, T. Koivula, and G. Källenius. 2001. Spread of drug-resistant pulmonary tuberculosis in Estonia. J. Clin. Microbiol. 39: 3339-3345.
19. Kubica, T., R. Agzamova, A. Wright, M. A. Aziz, G. Rakishev, V. Bismilda, E. Richter, S. Rüsch-Gerdes, and S. Niemann. 2005. The Beijing genotype is a major cause of drug-resistant tuberculosis in Kazakhstan Int. J. Tuberc. Lung Dis. 9:646-653.
20. Kubica, T., S. Rüsch-Gerdes, and S. Niemann. 2004. The Beijing genotype is emerging among multidrug-resistant Mycobacterium tuberculosis strains from Germany. Int. J. Tuberc. Lung Dis. 8:1107-1113.
21. Lavender, C., M. Globan, A. Sievers, H. Billman-Jacobe, and J. Fyfe. 2005. Molecular characterization of isoniazid-resistant Mycobacterium tuberculosis isolates collected in Australia. Antimicrob. Agents Chemother. 49:4068-4074.
22. López, B., D. Aguilar, H. Orozco, M. Burger, C. Espitia, V. Ritacco, L. Barrera, K. Kremer, R. Hernandez-Pando, K. Huygen, and D. van Soolingen. 2003. A marked difference in pathogenesis and immune response induced by different Mycobacterium tuberculosis genotypes. Clin. Exp. Immunol. 133:30-37.
23. Medvedeva, T. V., O. B. Ogarkov, O. M. Nekipelov, I. V. Ushakov, E. S. Koziakova, and R. G. Skvortsova. 2004. MIRU-VNTR genotyping of Mycobacterium tuberculosis strains from East Siberian: Beijing family versus Kilimanjaro family. Mol. Gen. Mikrobiol. Virusol. 4:33-38. (In Russian.)
24. Millet, J., C. Miyagi-Shiohira, N. Yamane, C. Sola, and N. Rastogi. 2007. Assessment of mycobacterial interspersed repetitive unit-QUB markers to further discriminate the Beijing genotype in a population-based study of the genetic diversity of Mycobacterium tuberculosis clinical isolates from Okinawa, Ryukyu Islands, Japan. J. Clin. Microbiol. 45:3606-3615.
25. Mokrousov, I., H. M. Ly, T. Otten, N. N. Lan, B. Vyshnevskyi, S. Hoffner, and O. Narvskaya. 2005. Origin and primary dispersal of the Mycobacterium tuberculosis Beijing genotype: clues from human phylogeography. Genome Res. 15:1357-1364.
26. Mokrousov, I., O. Narvskaya, E. Limeschenko, A. Vyazovaya, T. Otten, and B. Vyshnevskyi. 2004. Analysis of the allelic diversity of the mycobacterial interspersed repetitive units in Mycobacterium tuberculosis strains of the Beijing family: practical implications and evolutionary considerations. J. Clin. Microbiol. 42:2438-2444.
27. Morcillo, N., B. Di Giulio, C. Chirico, A. Kuriger, A. Dolmann, A. Alito, M. Zumarraga, D. van Soolingen, K. Kremer, and A. Cataldi. 2005. First description of Mycobacterium tuberculosis Beijing genotype in Argentina. Rev. Argent. Microbiol. 37:92-95.
28. Narvskaya, O. 2003. Genome polymorphism of Mycobacterium tuberculosis and its significance in the epidemic process. D.Sc. dissertation, St. Petersburg, Russia.
29. Narvskaya, O., I. Mokrousov, T. Otten, and B. Vishnevsky. 2005. Molecular markers: application for studies of Mycobacterium tuberculosis population in Russia, p. 111-125. In M. M. Read (ed.), Trends in DNA fingerprinting research. Nova Science Publishers, New York, NY.
30. Narvskaya, O., T. Otten, E. Limeschenko, N. Sapozhnikova, O. Graschenkova, L. Steklova, A. Nikonova, M. L. Filipenko, I. Mokrousov, and B. Vyshnevskiy. 2002. Nosocomial outbreak of multidrug-resistant tuberculosis caused by a strain of Mycobacterium tuberculosis W-Beijing family in St. Petersburg, Russia. Eur. J. Clin. Microbiol. Infect. Dis. 21:596-602.
31. Nikolayevskyy, V., K. Gopaul, Y. Balabanova, T. Brown, I. Fedorin, and F. Drobniewski. 2006. Differentiation of tuberculosis strains in a population with mainly Beijing-family strains. Emerg. Infect. Dis. 12:1406-1413.
32. Sun, Y. J., R. Bellamy, A. S. Lee, S. T. Ng, S. Ravindran, S. Y. Wong, C. Locht, P. Supply, and N. I. Paton. 2004. Use of mycobacterial interspersed repetitive unit-variable-number tandem repeat typing to examine genetic diversity of Mycobacterium tuberculosis in Singapore. J. Clin. Microbiol. 42: 1986-1993.
33. Supply, P., C. Allix, S. Lesjean, M. Cardoso-Oelemann, S. Rusch-Gerdes, E. Willery, E. Savine, P. de Haas, H. van Deutekom, S. Roring, P. Bifani, N. Kurepina, B. Kreiswirth, C. Sola, N. Rastogi, V. Vatin, M. C. Gutierrez, M. Fauville, S. Niemann, R. Skuce, K. Kremer, C. Locht, and D. van Soolingen. 2006. Proposal for standardization of optimized mycobacterial interspersed repetitive unit-variable-number tandem repeat typing of Mycobacterium tuberculosis. J. Clin. Microbiol. 44:4498-4510.
34. 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.
35. Surikova, O. V., D. S. Voitech, G. Kuzmicheva, S. I. Tatkov, I. V. Mokrousov, O. V. Narvskaya, M. A. Rot, D. van Soolingen, and M. L. Filipenko. 2005. Efficient differentiation of Mycobacterium tuberculosis strains of the W-Beijing family from Russia using highly polymorphic VNTR loci. Eur. J. Epidemiol. 20:963-974.
36. Swofford, D. L. 2002. PAUP*: phylogenetic analysis using parsimony (and other methods) 4.0 beta. Sinauer Associates, Sunderland, MA.
37. Toungoussova, O. S., P. Sandven, A. O. Mariandyshev, N. I. Nizovtseva, G. Bjune, and D. A. Caugant. 2002. Spread of drug-resistant Mycobacterium tuberculosis strains of the Beijing genotype in the Archangel Oblast, Russia. J. Clin. Microbiol. 40:1930-1937.
38. van Embden, J. D. A., M. D. Cave, J. T. Crawford, J. W. Dale, K. D. Eisenach, B. Gicquel, P. Hermans, C. Martin, R. McAdam, T. M. Shinnik, and P. Small. 1993. Strain identification of Mycobacterium tuberculosis by DNA fingerprinting: recommendations for a standardized methodology. J. Clin. Microbiol. 31:406-409.
39. van Soolingen, D., L. Qian, P. E. W. de Haas, J. T. Douglas, H. Traore, F. Portaels, Z. Quing, D. Enkhasaikan, P. Nymadawa, and J. D. A. van Embden. 1995. Predominance of a single genotype of Mycobacterium tuberculosis in countries of East Asia. J. Clin. Microbiol. 33:3234-3238.
40. Vishnevskii, B. I., O. V. Narvskaia, S. N. Vasil'eva, N. V. Sapozhnikova, I. V. Mokrousov, and T. F. Otten. 2002. Virulence of Mycobacterium tuberculosis. Probl. Tuberk. 10:33-36. (In Russian.)
41. Yokoyama, E., K. Kishida, M. Uchimura, and S. Ichinohe. 2007. Improved differentiation of Mycobacterium tuberculosis strains, including many Beijing genotype strains, using a new combination of variable number of tandem repeats loci. Infect. Genet. Evol. 7:499-508.