Mycobacterium africanum genotyping using novel spacer oligonucleotides in the direct repeat locus

Journal of Clinical Microbiology

Volumn 42, Issue 11, 2004, Pages 5053-5057

  Brudey, Karine ^a   Gutierrez, M Cristina ^b   Vincent, Véronique ^b   Parsons, Linda M ^c   Salfinger, Max ^c,d   Rastogi, Nalin ^a   Sola, Christophe ^a  

^a Institut Pasteur de Guadeloupe   (Guadeloupe)

^b INSTITUT PASTEUR   (France)

^c WADSWORTH CENTER   (United States)

^d ALBANY MEDICAL COLLEGE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

OLIGONUCLEOTIDE; SPACER DNA;

AFRICA; ARTICLE; BACTERIAL STRAIN; BACTERIUM ISOLATE; EVOLUTION; GENE DELETION; GENE LOCUS; GENETIC VARIABILITY; GENOTYPE; MYCOBACTERIUM AFRICANUM; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL;

AFRICA; BACTERIAL TYPING TECHNIQUES; GENOTYPE; HUMANS; MYCOBACTERIUM; OLIGONUCLEOTIDES; POLYMERASE CHAIN REACTION; REPETITIVE SEQUENCES, NUCLEIC ACID; SEQUENCE DELETION; TUBERCULOSIS;

ACTINOBACTERIA (CLASS); BACILLI; BACTERIA (MICROORGANISMS); INSERTION SEQUENCES; MYCOBACTERIUM; MYCOBACTERIUM AFRICANUM; MYCOBACTERIUM TUBERCULOSIS; PROKARYOTA; TRANSPOSONS; UNCULTURED ACTINOMYCETE;

EID: 8644291542     PISSN: 00951137     EISSN: None     Source Type: Journal    
DOI: 10.1128/JCM.42.11.5053-5057.2004     Document Type: Article

References (26)

1. Alland, D., T. S. Whittam, M. B. Murray, M. D. Cave, M. H. Hazbon, K. Dix, M. Kokoris, A. Duesterhoeft, J. A. Eisen, C. M. Fraser, and R. D. Fleischmann. 2003. Modeling bacterial evolution with comparative-genome-based marker systems: application to Mycobacterium tuberculosis evolution and pathogenesis. J. Bacteriol. 185:3392-3399.
2. Behr, M. A., M. A. Wilson, W. P. Gill, H. Salamon, G. K. Schoolnik, S. Rane, and P. M. Small. 1999. Comparative genomics of BCG vaccines by whole-genome DNA microarray. Science 284:1520-1523.
3. Brosch, R., S. V. Gordon, M. Marmiesse, P. Brodin, C. Buchrieser, K. Eiglmeier, T. Garnier, C. Gutierrez, G. Hewinson, K. Kremer, L. M. Parsons, A. S. Pym, S. Samper, D. van Soolingen, and S. T. Cole. 2002. A new evolutionary scenario for the Mycobacterium tuberculosis complex. Proc. Natl. Acad. Sci. USA 99:3684-3689.
4. Cousins, D. V., R. Bastida, A. Cataldi, V. Quse, S. Redrobe, S. Dow, P. Duignan, A. Murray, C. Dupont, N. Ahmed, D. M. Collins, W. R. Butler, D. Dawson, D. Rodriguez, J. Loureiro, M. I. Romano, A. Alito, M. Zumarraga, and A. Bernardelli. 2003. Tuberculosis in seals caused by a novel member of the Mycobacterium tuberculosis complex: Mycobacterium pinnipedii sp. nov. Int. J. Syst. Evol. Microbiol. 53:1305-1314.
5. David, H., V. Levy-Frebault, and M. F. Thorel. 1989. Méthodes de laboratoire pour Mycobactériologie clinique, p. 1-87. Institut Pasteur, Paris, France.
6. David, H. L., M. T. Jahan, A. Jumin, J. Grandry, and E. H. Lehmann. 1978. Numerical taxonomy of Mycobacterium africanum. Int. J. Syst. Bacteriol. 28:467-472.
7. Filliol, I., J. R. Driscoll, D. van Soolingen, B. N. Kreiswirth, K. Kremer, G. Valetudie, D. A. Dang, 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, E. Kassa-Kelembho, M. L. Ho, 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. Ride, M. L. Rossetti, F. Stauffer, P. N. Suffys, H. Takiff, J. Texier-Maugein, V. Vincent, J. H. de Waard, C. Sola, and N. Rastogi. 2003. Snapshot of moving and expanding clones of Mycobacterium tuberculosis and their global distribution assessed by spoligotyping in an international study. J. Clin. Microbiol. 41:1963-1970.
8. Gordon, S. V., R. Brosch, A. Billault, T. Garnier, K. Eiglmeier, and S. T. Cole. 1999. Identification of variable regions in the genomes of tubercle bacilli using bacterial artificial chromosome arrays. Mol. Microbiol. 32:643-655.
9. Gutacker, M. M., J. C. Smoot, C. A. Migliaccio, S. M. Ricklefs, S. Hua, D. V. Cousins, E. A. Graviss, E. Shashkina, B. N. Kreiswirth, and J. M. Musser. 2002. Genome-wide analysis of synonymous single nucleotide polymorphisms in Mycobacterium tuberculosis complex organisms. Resolution of genetic relationships among closely related microbial strains. Genetics 162:1533-1543.
10. Huard, R. C., L. C. de Oliveira Lazzarini, W. R. Butler, D. van Soolingen, and J. L. Ho. 2003. PCR-based method to differentiate the subspecies of the Mycobacterium tuberculosis complex on the basis of genomic deletions. J. Clin. Microbiol. 41:1637-1650.
11. Hunter, P. R., and M. A. Gaston. 1988. Numerical index of the discriminatory ability of typing systems: an application of Simpson's index of diversity. J. Clin. Microbiol. 26:2465-2466.
12. Källenius, G., T. Koivula, S. Ghebremichael, S. E. Hoffner, R. Norberg, E. Svensson, F. Dias, B. Marklund, and S. B. Svenson. 1999. Evolution and clonal traits of Mycobacterium tuberculosis in Guinea-Bissau. J. Clin. Microbiol. 37:3872-3878.
13. 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.
14. Kremer, K., D. van Soolingen, R. Frothingham, W. H. Haas, P. W. M. Hermans, C. Martin, P. Palittapongarnpim, 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 epidemiologial markers for typing of Mycobacterium tuberculosis strains: interlaboratory study of discriminatory power and reproducibility. J. Clin. Microbiol. 37:2607-2618.
15. Mostowy, S., and M. A. Behr. 2002. Comparative genomics in the fight against tuberculosis: diagnostics, epidemiology, and BCG vaccination. Am. J. Pharmacogenomics 2:189-196.
16. Niemann, S., S. Rusch-Gerdes, M. L. Joloba, C. C. Whalen, D. Guwatudde, J. J. Ellner, K. Eisenach, N. Fumokong, J. L. Johnson, T. Aisu, R. D. Mugerwa, A. Okwera, and S. K. Schwander. 2002. Mycobacterium africanum subtype II is associated with two distinct genotypes and is a major cause of human tuberculosis in Kampala, Uganda. J. Clin. Microbiol. 40:3398-3405
17. Parsons, L. M., R. Brosch, S. T. Cole, A. Somoskovi, A. Loder, G. Bretzel, D. Van Soolingen, Y. M. Hale, and M. Salfinger. 2002. Rapid and simple approach for identification of Mycobacterium tuberculosis complex isolates by PCR-based genomic deletion analysis. J. Clin. Microbiol. 40:2339-2345.
18. Rastogi, N., E. Legrand, and C. Sola. 2001. The mycobacteria: an introduction to nomenclature and pathogenesis. Rev. Sci. Tech. Off. Int. Epiz. 20:21-46.
19. Soini, H., X. Pan, A. Amin, E. A. Graviss, A. Siddiqui, and J. M. Musser. 2000. Characterization of Mycobacterium tuberculosis isolates from patients in Houston, Texas, by spoligotyping J. Clin. Microbiol. 38:669-676.
20. Sola, C., I. Filliol, E. Legrand, I. Mokrousov, and N. Rastogi. 2001. Mycobacterium tuberculosis phylogeny reconstruction based on combined numerical analysis with IS1081, IS6110, VNTR and DR-based spoligotyping suggests the existence of two new phylogeographical clades. J. Mol. Evol. 53:680-689.
21. Sola, C., N. Rastogi, M. C. Gutierrez, V. Vincent, R. Brosch, L. M. Parsons, S. Niemann, S. Rüsch-Gerdes, and S. K. Schwander. 2003. Is Mycobacterium africanum subtype II (Uganda I and Uganda II) a genetically well-defined subspecies of the Mycobacterium tuberculosis complex? J. Clin. Microbiol. 41:1345-1348.
22. 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.
23. van der Zanden, A. G., K. Kremer, L. M. Schouls, K. Caimi, A. Cataldi, A. Hulleman, N. J. Nagelkerke, and D. van Soolingen. 2002. Improvement of differentiation and interpretability of spoligotyping for Mycobacterium tuberculosis complex isolates by introduction of new spacer oligonucleotides. J. Clin. Microbiol. 40:4628-4639,
24. 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.
25. Viana-Niero, C., C. Gutierrez, C. Sola, I. Filliol, F. Boulahbal, V. Vincent, and N. Rastogi. 2001. Genetic diversity of Mycobacterium africanum clinical isolates based on IS6110-restriction fragment length polymorphism analysis, spoligotyping, and variable number of tandem DNA repeats. J. Clin. Microbiol. 39:57-65.
26. 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.