Spoligotype signatures in the Mycobacterium tuberculosis complex

Journal of Clinical Microbiology

Volumn 45, Issue 1, 2007, Pages 237-240

  Streicher, E M ^a   Victor, T C ^a   Van Der Spuy, G ^a   Sola, C ^b   Rastogi, N ^b   Van Helden, P D ^a   Warren, R M ^a  

^a STELLENBOSCH UNIVERSITY   (South Africa)

^b Institut Pasteur de Guadeloupe   (Guadeloupe)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIBIOTIC RESISTANCE; ARTICLE; BACTERIAL STRAIN; DNA FINGERPRINTING; EVOLUTION; GENOTYPE; IMMUNITY; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; POPULATION STRUCTURE; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; SOUTH AFRICA; SPOLIGOTYPE;

BACTERIAL TYPING TECHNIQUES; DNA TRANSPOSABLE ELEMENTS; EVOLUTION, MOLECULAR; GENOTYPE; HUMANS; MYCOBACTERIUM TUBERCULOSIS; OLIGONUCLEOTIDES; REPETITIVE SEQUENCES, NUCLEIC ACID;

MYCOBACTERIUM TUBERCULOSIS; MYCOBACTERIUM TUBERCULOSIS COMPLEX;

EID: 33846241220     PISSN: 00951137     EISSN: None     Source Type: Journal    
DOI: 10.1128/JCM.01429-06     Document Type: Article

References (37)

1. Aga, R. S., E. Fair, N. F. Abernethy, K. DeRiemer, E. A. Paz, L. M. Kawamura, P. M. Small, and M. Kato-Maeda. 2006. Microevolution of the direct repeat locus of Mycobacterium tuberculosis in a strain prevalent in San Francisco. J. Clin. Microbiol. 44:1558-1560.
2. Bhanu, N. V., D. van Soolingen, J. D. van Embden, L. Dar, R. M. Pandey, and P. Seth. 2002. Predominance of a novel Mycobacterium tuberculosis genotype in the Delhi region of India. Tuberculosis (Edinburgh) 82:105-112.
3. Brosch, R., A. S. Pym, S. V. Gordon, and S. T. Cole. 2001. The evolution of mycobacterial pathogenicity: clues from comparative genomics. Trends Microbiol. 9:452-458.
4. Brudey, K., J. R. Driscoll, L. Rigouts, W. M. Prodinger, A. Gori, S. A. Al Hajoj, C. Allix, L. Aristimuno, J. Arora, V. Baumanis, L. Binder, P. Cafrune, A. Cataldi, S. Cheong, R. Diel, C. Ellermeier, J. T. Evans, M. Fauville-Dufaux, S. Ferdinand, D. Garcia de Viedma, C. Garzelli, L. Gazzola, H. M. Gomes, M. C. Gutierrez, P. M. Hawkey, P. D. van Helden, G. V. Kadival, B. N. Kreiswirth, K. Kremer, M. Kubin, S. P. Kulkarni, B. Liens, T. Lillebaek, M. L. Ho, C. Martin, C. Martin, I. Mokrousov, O. Narvskaia, Y. F. Ngeow, L. Naumann, S. Niemann, I. Parwati, Z. Rahim, V. Rasolofo-Razanamparany, T. Rasolonavalona, M. L. Rossetti, S. Rusch-Gerdes, A. Sajduda, S. Samper, I. Shemyakin, U. B. Singh, A. Somoskovi, R. Skuce, D. van Soolingen, E. M. Streicher, P. N. Suffys, E. Tortoli, T. Tracevska, V. Vincent, T. C. Victor, R. Warren, S. F. Yap, K. Zaman, F. Portaels, N. Rastogi, and C. Sola. 2006. Mycobacterium tuberculosis complex genetic diversity: mining the fourth international spoligotyping database (SpolDB4) for classification, population genetics and epidemiology. BMC Microbiol. 6:23.
5. Dale, J. W., G. H. Bothamley, F. Drobniewski, S. H. Gillespie, T. D. McHugh, and R. Pitman. 2005. Origins and properties of Mycobacterium tuberculosis isolates in London. J. Med. Microbiol. 54:575-582.
6. Douglas, J. T., L. Qian, J. C. Montoya, J. M. Musser, J. D. A. van Embden, D. van Soolingen, and K. Kremer. 2003. Characterization of the Manila family of Mycobacterium tuberculosis. J. Clin. Microbiol. 41:2723-2726.
7. Easterbrook, P. J., A. Gibson, S. Murad, D. Lamprecht, N. Ives, A. Ferguson, O. Lowe, P. Mason, A. Ndudzo, A. Taziwa, R. Makombe, L. Mbengeranwa, C. Sola, N. Rastogi, and F. Drobniewski. 2004. High rates of clustering of strains causing tuberculosis in Harare, Zimbabwe: a molecular epidemiological study. J. Clin. Microbiol. 42:4536-4544.
8. Filliol, I., J. R. Driscoll, D. van Soolingen, B. N. Kreiswirth, K. Kremer, G. Valetudie, D. D. Anh, R. Barlow, D. Banerjee, P. J. Bifani, K. Brudey, A. Cataldi, R. C. Cooksey, D. V. Cousins, J. W. Dale, O. A. Dellagostin, F. Drobniewski, G. Engelmann, S. Ferdinand, D. Gascoyne-Binzi, M. Gordon, M. C. Gutierrez, W. H. Haas, H. Heersma, G. Kallenius, E. Kassa-Kelembho, T. Koivula, H. M. Ly, A. Makristathis, C. Mammina, G. Martin, P. Mostrom, I. Mokrousov, V. Narbonne, O. Narvskaya, A. Nastasi, S. N. Niobe-Eyangoh, J. W. Pape, V. Rasolofo-Razanamparany, M. Ridell, M. L. Rossetti, F. Stauffer, P. N. Suffys, H. Takiff, J. Texier-Maugein, V. Vincent, J. H. De Waard, C. Sola, and N. Rastogi. 2002. Global distribution of Mycobacterium tuberculosis spoligotypes. Emerg. Infect. Dis. 8:1347-1349.
9. Filliol, I., A. S. Motiwala, M. Cavatore, W. Qi, M. H. Hazbón, M. Bobadilla del Valle, J. Fyfe, L. García-García, N. Rastogi, C. Sola, T. Zozio, M. I. Guerrero, C. I. León, J. Crabtree, S. Angiuoli, K. D. Eisenach, R. Durmaz, M. L. Joloba, A. Rendón, J. Sifuentes-Osornio, A. Ponce de León, M. D. Cave, R. Fleischmann, T. S. Whittam, and D. Alland. 2006. Global phylogeny of Mycobacterium tuberculosis based on single nucleotide polymorphism (SNP) analysis: insights into tuberculosis evolution, phylogenetic accuracy of other DNA fingerprinting systems, and recommendations for a minimal standard SNP set. J. Bacteriol. 188:759-772.
10. 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.
11. Garciá de Viedma, D., E. Bouza, N. Rastogi, and C. Sola. 2005. Analysis of Mycobacterium tuberculosis genotypes in Madrid and identification of two new families specific to Spain-related settings. J. Clin. Microbiol. 43:1797-1806.
12. 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.
13. 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.
14. Hermans, P. W., F. Messadi, H. Guebrexabher, D. van Soolingen, P. E. de Haas, H. Heersma, H. de Neeling, A. Ayoub, F. Portaels, and D. Frommel. 1995. Analysis of the population structure of Mycobacterium tuberculosis in Ethiopia, Tunisia, and The Netherlands: usefulness of DNA typing for global tuberculosis epidemiology. J. Infect. Dis. 171:1504-1513.
15. Hermans, P. W. M., D. van Soolingen, E. M. Bik, P. E. W. de Haas, J. W. Dale, and J. D. A. van Embden. 1991. Insertion element IS987 from Mycobacterium bovis BCG is located in a hot-spot integration region for insertion elements in Mycobacterium tuberculosis complex strains. Infect. Immun. 59:2695-2705.
16. Kamerbeek, J., L. Schouls, A. Kolk, M. van Agterveld, D. van Soolingen, S. Kuijper, A. Bunschoten, H. Molhuizen, R. Shaw, M. Goyal, and J. van Embden. 1997. Simultaneous detection and strain differentiation of Mycobacterium tuberculosis for diagnosis and epidemiology. J. Clin. Microbiol. 35:907-914.
17. Kremer, K., D. van Soolingen, R. Frothingham, W. H. Haas, P. W. M. Hermans, C. Martín, P. Palittapongarnpim, B. B. Plikaytis, L. W. Riley, M. A. Yakrus, J. M. Musser, and J. D. 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.
18. Molhuizen, H. O., A. E. Bunschoten, L. M. Schouls, and J. D. van Embden. 1998. Rapid detection and simultaneous strain differentiation of Mycobacterium tuberculosis complex bacteria by spoligotyping. Methods Mol. Biol. 101:381-394.
19. Nguyen, D., P. Brassard, J. Westley, L. Thibert, M. Proulx, K. Henry, K. Schwartzman, D. Menzies, and M. A. Behr. 2003. Widespread pyrazinamide-resistant Mycobacterium tuberculosis family in a low-incidence setting. J. Clin. Microbiol. 41:2878-2883.
20. Niobe-Eyangoh, S. N., C. Kuaban, P. Sorlin, P. Cunin, J. Thonnon, C. Sola, N. Rastogi, V. Vincent, and M. C. Gutierrez. 2003. Genetic biodiversity of Mycobacterium tuberculosis complex strains from patients with pulmonary tuberculosis in Cameroon. J. Clin. Microbiol. 41:2547-2553.
21. Niobe-Eyangoh, S. N., C. Kuaban, P. Sorlin, J. Thonnon, V. Vincent, and M. C. Gutierrez. 2004. Molecular characteristics of strains of the Cameroon family, the major group of Mycobacterium tuberculosis in a country with a high prevalence of tuberculosis. J. Clin. Microbiol. 42:5029-5035.
22. Richardson, M., S. W. van Lill, G. D. van der Spuy, Z. Munch, C. N. Booysen, N. Beyers, P. D. van Helden, and R. M. Warren. 2002. Historic and recent events contribute to the disease dynamics of Beijing-like Mycobacterium tuberculosis isolates in a high incidence region. Int. J. Tuberc. Lung Dis. 6:1001-1011.
23. Sebban, M., I. Mokrousov, N. Rastogi, and C. Sola. 2002. A data-mining approach to spacer oligonucleotide typing of Mycobacterium tuberculosis. Bioinformatics 18:235-243.
24. Singh, U. B., N. Suresh, N. V. Bhanu, J. Arora, H. Pant, S. Sinha, R. C. Aggarwal, S. Singh, J. N. Pande, C. Sola, and P. Seth. 2004. Predominant tuberculosis spoligotypes, Delhi, India. Emerg. Infect. Dis. 10:1138-1142.
25. Sreevatsan, S., X. Pan, K. E. Stockbauer, N. D. Connell, B. N. Kreiswirth, T. S. Whittam, and J. M. Musser. 1997. Restricted structural gene polymorphism in the Mycobacterium tuberculosis complex indicates evolutionarily recent global dissemination. Proc. Natl. Acad. Sci. USA 94:9869-9874.
26. Sun, Y.-J., A. S. G. Lee, S. T. Ng, S. Ravindran, K. Kremer, R. Bellamy, S.-Y. Wong, D. van Soolingen, P. Supply, and N. I. Paton. 2004. Characterization of ancestral Mycobacterium tuberculosis by multiple genetic markers and proposal of genotyping strategy. J. Clin. Microbiol. 42:5058-5064.
27. 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.
28. 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. Shinnick, and P. M. Small. 1993. Strain identification of Mycobacterium tuberculosis by DNA fingerprinting: recommendations for a standardized methodology. J. Clin. Microbiol. 31:406-409.
29. van Embden, J. D. A., T. van Gorkom, K. Kremer, R. Jansen, B. A. M. van der Zeijst, and L. M. Schouls. 2000. Genetic variation and evolutionary origin of the direct repeat locus of Mycobacterium tuberculosis complex bacteria. J. Bacteriol. 182:2393-2401.
30. van Soolingen, D., A. G. M. van der Zanden, P. E. W. de Haas, G. T. Noordhoek, A. Kiers, N. A. Foudraine, F. Portaels, A. H. J. Kolk, K. Kremer, and J. D. A. van Embden. 1998. Diagnosis of Mycobacterium microti infections among humans by using novel genetic markers. J. Clin. Microbiol. 36:1840-1845.
31. Victor, T. C., P. E. W. de Haas, A. M. Jordaan, G. D. van der Spuy, M. Richardson, D. van Soolingen, P. D. van Helden, and R. Warren. 2004. Molecular characteristics and global spread of Mycobacterium tuberculosis with a Western Cape F11 genotype. J. Clin. Microbiol. 42:769-772.
32. Vitol, I., J. Driscoll, B. Kreiswirth, N. Kurepina, and K. P. Bennett. 2006. Identifying Mycobacterium tuberculosis complex strain families using spoligotypes. Infect. Genet. Evol. 6:491-504.
33. Warren, R. M., S. L. Sampson, M. Richardson, G. D. van der Spuy, C. J. Lombard, T. C. Victor, and P. D. van Helden. 2000. Mapping of IS6110 flanking regions in clinical isolates of Mycobacterium tuberculosis demonstrates genome plasticity. Mol. Microbiol. 37:1405-1416.
34. Warren, R. M., E. M. Streicher, S. L. Sampson, G. D. van der Spuy, M. Richardson, D. Nguyen, M. A. Behr, T. C. Victor, and P. D. van Helden. 2002. Microevolution of the direct repeat region of Mycobacterium tuberculosis: implications for interpretation of spoligotyping data. J. Clin. Microbiol. 40:4457-4465.
35. Warren, R. M., T. C. Victor, E. M. Streicher, M. Richardson, G. D. van der Spuy, R. Johnson, V. N. Chihota, C. Locht, P. Supply, and P. D. van Helden. 2004. Clonal expansion of a globally disseminated lineage of Mycobacterium tuberculosis with low IS6110 copy numbers. J. Clin. Microbiol. 42:5774-5782.
36. 5 as a marker for Mycobacterium tuberculosis strain identification. J. Clin. Microbiol. 32:1318-1321.
37. Zozio, T., C. Allix, S. Gunal, Z. Saribas, A. Alp, R. Durmaz, M. Fauville-Dufaux, N. Rastogi, and C. Sola. 2005. Genotyping of Mycobacterium tuberculosis clinical isolates in two cities of Turkey: description of a new family of genotypes that is phylogeographically specific for Asia Minor. BMC Microbiol. 5:44.