1887

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Volume 55, Issue 8

Identification of a repetitive sequence belonging to a PPE gene of and its use in diagnosis of tuberculosis Free

Abstract

A repetitive sequence specific to was isolated from a gt11 library of by DNA–DNA hybridization using genomic DNA of as probe followed by subtractive hybridization with a cocktail of other mycobacterial DNA. This led to identification of CD192, a 1291 bp fragment of containing repetitive sequences, which produced positive hybridization signals with DNA within 30 min. Nucleotide sequencing revealed the presence of several direct and inverted repeats within the 1291 bp fragment that belonged to a PPE family gene (Rv0355) of . The use of CD192 as a DNA probe for the identification of in culture and clinical samples was investigated. The 1291 bp sequence was present in , and BCG, but was not present in many of the other mycobacterial strains tested, including H37Ra. More than 300 clinical isolates of were probed with CD192, and the presence of the 1291 bp sequence was observed in all the clinical strains, including those lacking IS. The sequence displayed RFLP among the clinical isolates. A PCR assay was developed which detected with 100 % specificity from specimens of sputum, cerebrospinal fluid and pleural effusion from clinically diagnosed cases of tuberculosis.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): ATT, antitubercular treatment , CSF, cerebrospinal fluid , DR, direct repeat , IAC, internal amplification control , MPTR, major polymorphic tandem repeat , NPV, negative predictive value , PGRS, polymorphic GC-rich repetitive sequence , PPV, positive predictive value and TBM, tuberculous meningitis
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2006-08-01
2024-04-25
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References

  1. Biggins M. D., Gibson T. J., Hong G. F. 1983; Buffer gradient gels and 35S label as an aid to rapid DNA sequence determination. Proc Natl Acad Sci U S A 80:3963–3965 [CrossRef]
     [Google Scholar]
  2. Braden C. R., Templeton G. L., Cave M. D. & 7 other authors; 1997; Interpretation of restriction fragment length polymorhism. Analysis of Mycobacterium tuberculosis isolates from a state with a large rural population. J Infect Dis 175:1446–1452 [CrossRef]
     [Google Scholar]
  3. Chou P. Y., Fasman G. D. 1978; Prediction of the secondary structure of proteins from their amino acid sequence. Adv Enzymol 47:45–148
     [Google Scholar]
  4. Cole S. T., Brosch R., Parkhill J. & 39 other authors; 1998; Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393:537–544 [CrossRef]
     [Google Scholar]
  5. Connell N. D., Ollar R. A. 1999; The mycobacterial and nocardial genomes and their isolation and manipulation. In Molecular Mycobacteriology Techniques and Clinical Applications pp  87–107 Edited by Ollar R. A., Connell N. D. New York: Marcel Dekker;
     [Google Scholar]
  6. Eisenach K. D. 1999; Molecular diagnostics. In Mycobacteria, Molecular Biology and Virulence pp  161–179 Edited by Ratledge C., Dale J. Oxford, UK: Blackwell Science;
     [Google Scholar]
  7. Eisenach K. D., Cave M. D., Bates J. H., Crawford J. T. 1990; Polymerase chain reaction amplification of a repetitive DNA sequence specific for Mycobacterium tuberculosis . J Infect Dis 161:977–981 [CrossRef]
     [Google Scholar]
  8. Eisenach K. D., Cave M. D., Crawford J. T. 1993; PCR detection of Mycobacterium tuberculosis . In Diagnostic Molecular Microbiology Principles and Applications pp  191–196 Edited by Persing D. H., Smith T. F., Tenover F. C., White T. J. Washington, DC: American Society for Microbiology;
     [Google Scholar]
  9. Heifets L. B., Good R. C. 1994; Current laboratory methods for the diagnosis of tuberculosis. In Tuberculosis, Pathogenesis, Protection and Control pp  85–109 Edited by Bloom B. R. Washington DC: American Society for Microbiology;
     [Google Scholar]
  10. Hermans P. W. M., Van Soolingen D., Van Embden J. D. A. 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
     [Google Scholar]
  11. Hopp T. P., Woods K. P. 1981; Prediction of protein antigenic determinants from amino acid sequences. Proc Natl Acad Sci U S A 78:3824–3828 [CrossRef]
     [Google Scholar]
  12. Jonas V., Alden M. J., Curry J. I., Kamisango K., Knott C. A., Lankford R., Wolfe J. M., Moore D. F. 1993; Detection and identification of Mycobacterium tuberculosis directly from sputum sediments by amplification of rRNA. J Clin Microbiol 31:2410–2416
     [Google Scholar]
  13. Kent P. T., Kubica G. P. 1985 Public Health Mycobacteriology : a Guide for the Level III Laboratory Atlanta, GA: Centers for Disease Control;
     [Google Scholar]
  14. Kirschner P., Springer B., Vogel U., Meier A., Wrede A., Kiekenbeck M., Bange F. C., Bottger E. C. 1993; Genotypic identification of mycobacteria by nucleic acid sequence determination. Report of a 2-year experience in a clinical laboratory. J Clin Microbiol 31:2882–2889
     [Google Scholar]
  15. Kolk A. H. J., Schuitema A. R. J., Kuijper S., van Leeuwen J., Hermans P. W. M., van Embden J. D. A., Hartskeerl R. A. 1992; Detection of Mycobacterium tuberculosis in clinical samples by using polymerase chain reaction and the non radioactive detection system. J Clin Microbiol 30:2567–2575
     [Google Scholar]
  16. Koneman E. W., Allen S. D., Janda W. M., Schreckenberger P. C., Winn W. C. Jr 1997; Mycobacteria. In Color Atlas and Textbook of Diagnostic Microbiology , 5th edn. pp  893–952 Edited by Koneman E. W., Allen S. D., Janda W. M., Schreckenberger P. C, Winn W. C. Jr Philadelphia, PA: Lippincott-Raven;
     [Google Scholar]
  17. Marmur J. 1961; A procedure for the isolation of deoxyribonucleic acid from microorganisms. J Mol Biol 3:208–218 [CrossRef]
     [Google Scholar]
  18. Miyazaki Y., Koga H., Kohno S., Kaku M. 1993; Nested polymerase chain reaction for detection of Mycobacterium tuberculosis in clinical samples. J Clin Microbiol 31:2228–2232
     [Google Scholar]
  19. Pfyfer G. E., Kisling P., Jahn E. M. I., Martin H., Salfinger W. M., Weber R. 1996; Diagnostic performance of amplified Mycobacterium tuberculosis direct test with cerebrospinal fluid, other nonrespiratory and respiratory specimens. J Clin Microbiol 34:834–841
     [Google Scholar]
  20. Poulet S., Cole S. T. 1995; Repeated DNA sequences in mycobacteria. Arch Microbiol 163:79–86 [CrossRef]
     [Google Scholar]
  21. Prasad R., Lath S. K., Mukerji P. K., Agarwal S. K., Srivastava R. 2001; Clinical utility of polymerase chain reaction in patients of pulmonary tuberculosis. Indian J Tuberc 48:135–138
     [Google Scholar]
  22. Priyadarshi B. P. 1999; Evaluation of CSF by polymerase chain reaction analysis in diagnosis of tuberculous meningitis . MD thesis GSVM Medical College; Kanpur:
  23. Ross B. C., Raios K., Dwyer B. 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
     [Google Scholar]
  24. Sahadevan R., Narayanan S., Paramsivam C. N., Prabhakar R., Narayanan P. R. 1995; Restriction fragment length polymorphism typing of clinical isolates of Mycobacterium tuberculosis from patients with pulmonary tuberculosis in Madras, India, by use of direct-repeat probe. J Clin Microbiol 33:3037–3039
     [Google Scholar]
  25. Sambrook J., Fritsch E. F., Maniatis T. 1989 Molecular Cloning : a Laboratory Manual , 2nd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
     [Google Scholar]
  26. Scarparo C., Picoli P., Rigon A., Ruggiero G., Scagnelli M., Piersimoni C. 2000; Comparison of enhanced Mycobacterium tuberculosis amplified direct test with COBAS amplicor Mycobacterium tuberculosis complex in respiratory and extrapulmonary specimens. J Clin Microbiol 38:1559–1562
     [Google Scholar]
  27. Srivastava R., Kumar D., Srivastava B. S. 2000; A Mycobacterium tuberculosis specific DNA fragment . US Patent #6,114,514
     [Google Scholar]
  28. Van Soolingen D., Dehass P. E. W., Hermans P. W. M., Groenen P. M. A., Van Embden J. D. A. 1993; Comparison of various repetitive DNA elements as genetic markers for strain differentiation and epidemiology of Mycobacterium tuberculosis . J Clin Microbiol 31:1987–1995
     [Google Scholar]
  29. Veerottam P. 1999; Value of polymerase chain reaction in pleural fluid in the diagnosis of tuberculous pleural effusion . MD Thesis GSVM Medical College; Kanpur:
  30. Young R. A., Bloom B. R., Grossinsky C. M., Ivany J., Thomas D., Davis R. W. 1985; Dissection of Mycobacterium tuberculosis antigens using recombinant DNA. Proc Natl Acad Sci USA 82:2583–2587 [CrossRef]
     [Google Scholar]
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Identification of a repetitive sequence belonging to a PPE gene of Mycobacterium tuberculosis and its use in diagnosis of tuberculosis
J. Med. Microbiol. 55, 1071 (2006); https://doi.org/10.1099/jmm.0.46379-0
/content/journal/jmm/10.1099/jmm.0.46379-0
/content/journal/jmm/10.1099/jmm.0.46379-0
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