PCR-Based Genotyping of Mycobacterium tuberculosis with New GC-Rich Repeated Sequences and IS6110 Inverted Repeats Used as Primers

Journal of Clinical Microbiology

Volumn 42, Issue 1, 2004, Pages 372-377

  Kotłowski, Roman ^a,b   Shamputa, Isdore Chola ^a   El Aila, Nabil Abdullah ^a   Sajduda, Anna ^a   Rigouts, Leen ^a   Van Deun, Armand ^a   Portaels, Françoise ^a  

^a INSTITUTE OF TROPICAL MEDICINE   (Belgium)

^b GDANSK UNIVERSITY OF TECHNOLOGY   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA;

ARTICLE; BACTERIUM ISOLATION; BINDING SITE; CELL DIFFERENTIATION; DIAGNOSTIC VALUE; DNA FINGERPRINTING; DNA FLANKING REGION; GC RICH SEQUENCE; GENE SEQUENCE; GENE TARGETING; GENOTYPE; INVERTED REPEAT; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL;

DNA FINGERPRINTING; DNA PRIMERS; DNA TRANSPOSABLE ELEMENTS; GENOTYPE; MYCOBACTERIUM TUBERCULOSIS; POLYMERASE CHAIN REACTION; REPETITIVE SEQUENCES, NUCLEIC ACID;

BACTERIA (MICROORGANISMS); MYCOBACTERIUM; MYCOBACTERIUM TUBERCULOSIS;

EID: 0345832014     PISSN: 00951137     EISSN: None     Source Type: Journal    
DOI: 10.1128/JCM.42.1.372-377.2004     Document Type: Article

References (16)

1. Athwal, R. S., S. S. Deo, and T. Imaeda. 1984. Deoxyribonucleic acid relatedness among Mycobacterium leprae, Mycobacterium lepraemurium and selected bacteria by dot blot and spectrophotometric deoxyribonucleic acid hybridization assays. Int. J. Syst. Bacteriol. 34:371-375.
2. Cole, S. T., R. Brosch, J. Parkhill, T. Garnier, C. Churcher, D. Harris, S. V. Gordon, K. Eiglmeier, S. Gas, C. E. Barry III, 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, B. G. Barrell, et al. 1998. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 11:537-544.
3. Cole, S. T., K. Eiglmeier, J. Parkhill, K. D. James, N. R. Thomson, P. R. Wheeler, N. Honore, T. Garnier, C. Churcher, D. Harris, K. Mungall, D. Basham, D. Brown, T. Chillingworth, R. Connor, R. M. Davies, K. Devlin, S. Duthoy, T. Feltwell, A. Fraser, N. Hamlin, S. Holroyd, T. Hornsby, K. Jagels, C. Lacroix, J. Maclean, S. Moule, L. Murphy, K. Oliver, M. A. Quail, M. A. Rajandream, K. M. Rutherford, S. Rutter, K. Seeger, S. Simon, M. Simmonds, J. Skelton, R. Squares, S. Squares, K. Stevens, K. Taylor, S. Whitehead, J. R. Woodward, and B. G. Barrell. 2001. Massive gene decay in the leprosy bacillus. Nature 409:1007-1011.
4. du Plessis, D. G., R. Warren, M. Richardson, J. J. Joubert, and P. D. van Helden. 2001. Demonstration of reinfection and reactivation in HIV-negative autopsied cases of secondary tuberculosis: multilesional genotyping of Mycobacterium tuberculosis utilizing IS6110 and other repetitive element-based DNA fingerprinting. Tuberculosis 81:211-220.
5. Fleischmann, R. D., D. Alland, J. A. Eisen, L. Carpenter, O. White, J. Peterson, R. DeBoy, R. Dodson, M. Gwinn, D. Haft, E. Hickey, J. F. Kolonay, W. C. Nelson, L. A. Umayam, M. Ermolaeva, S. L. Salzberg, A. Delcher, T. Utterhack, J. Weidman, H. Khouri, J. Gill, A. Mikula, W. Bishai, W. R. Jacobs, Jr., J. C. Venter, and C. M. Fraser. 2002. Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains. J. Bacteriol. 184:5479-5490.
6. 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. 33:1064-1069.
7. Garnier, T., K. Eiglmeier, J. C. Camus, N. Medina, H. Mansoor, M. Pryor, S. Duthoy, S. Grondin, C. Lacroix, C. Monsempe, S. Simon, B. Harris, R. Atkin, J. Doggett, R. Mayes, L. Keating, P. R. Wheeler, J. Parkhill, B. G. Barrell, S. T. Cole, S. V. Gordon, and R. G. Hewinson. 2003. The complete genome sequence of Mycobacterium bovis. Proc. Natl. Acad. Sci. USA 100: 7877-7882.
8. Kivi, M., X. Liu, S. Raychaudhuri, R. B. Altman, and P. M. Small. 2002. Determining the genomic locations of repetitive DNA sequences with a whole-genome microarray: IS6110 in Mycobacterium tuberculosis. J. Clin. Microbiol. 40:2192-2198.
9. Kotłowski, R., and R. Tylingo. 2003. Oligonucleotide repeats in genomes. Department of Food Chemistry and Technology, Gdansk University of Technology, Gdansk, Poland. [Online.] http://www.pg.gda.pl/chem/Katedry/Zywnosc/oligos.html.
10. Otal, I., S. Samper, M. P. Asensio, M. A. Vitoria, M. C. Rubio, R. Gomez-Lus, and C. Martin. 1997. Use of a PCR method based on IS6110 polymorphism for typing Mycobacterium tuberculosis strains from BACTEC cultures. J. Clin. Microbiol. 35:273-277.
11. Prod'hom, G., B. Lagier, V. Pelicic, A. J. Hance, B. Gicquel, and C. Guilhot. 1998. A reliable amplification technique for the characterization of genomic DNA sequences flanking insertion sequences. FEMS Microbiol. Lett. 158: 75-81.
12. Poulet, S., and S. T. Cole. 1995. Repeated DNA sequences in mycobacteria. Arch. Microbiol. 163:79-86.
13. van Embden, J. D., M. D. Cave, J. T. Crawford, J. W. Dale, K. D. Eisenach, B. Gicquel, P. Hermans, C. Martin, R. McAdam, T. M. Shinnick, et al. 1993. Strain identification of Mycobacterium tuberculosis by DNA fingerprinting: recommendations for a standardized methodology. J. Clin. Microbiol. 31:406-409.
14. van Rie, A., R. Warren, M. Richardson, T. C. Victor, R. P. Gie, D. A. Enarson, N. Beyers, and P. D. van Helden. 1999. Exogenous reinfection as a cause of recurrent tuberculosis after curative treatment. N. Engl. J. Med. 341:1174-1179.
15. van Soolingen, D., P. W. Hermans, P. E. de Haas, D. R. Soll, and J. D. van Embden. 1991. Occurrence and stability of insertion sequences in Mycobacterium tuberculosis complex strains: evaluation of an insertion sequence-dependent DNA polymorphism as a tool in the epidemiology of tuberculosis. J. Clin. Microbiol. 29:2578-2586.
16. World Health Organization. 2002. Tuberculosis. Fact sheet no. 104. World Health Organization, Geneva, Switzerland. [Online.] http://www.who.int/mediacentre/factsheets/who104/en/index.html.