1887

Chapter 6 : Molecular Diagnosis of Mycobacterial Infections

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Preview this chapter:
Zoom in
Zoomout

Molecular Diagnosis of Mycobacterial Infections, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555817657/9781555812959_Chap06-1.gif /docserver/preview/fulltext/10.1128/9781555817657/9781555812959_Chap06-2.gif

Abstract:

Clinical mycobacteriology laboratories play a key role in the control of the spread of tuberculosis (TB) through the timely detection, isolation, identification, and drug susceptibility testing of isolates. With the use of amplification systems, nucleic acid sequences can be detected directly in clinical specimens, offering better accuracy than acid-fast bacillus (AFB) smear and greater speed than culture. The LCx (ligase chain reaction) MTB assay detects the gene for the PAB protein, and is based on probe amplification and recommended for respiratory specimens. The ProbeTec Direct TB system is based on strand displacement amplification, which is an isothermal enzymatic process that amplifies DNA exponentially. TB assay can detect the presence of both and its resistance to rifampin and is discussed in the chapter. During the last two decades, mycobacteriology laboratories have realized important advances in mycobacterial identification through the application of molecular biology techniques. It may be useful to be able to identify the increasingly recognized subspecies and subspecies . Drugs administered in the therapy of TB mainly include compounds which inhibit cell wall synthesis (isoniazid [INH], ethambutol [EMB]), transcription (rifampin [RMP]), protein synthesis (streptomycin [SM] and other aminoglycosides), and nucleic acid synthesis (fluoroquinolones such as ofloxacin). The application of molecular testing methods in the mycobacteriology laboratory has the potential to significantly improve one’s ability to detect directly in clinical specimens or cultures as well as to differentiate mycobacterial species and drug-resistant strains.

Citation: Forbes B, Pfyffer G, Eisenach K. 2005. Molecular Diagnosis of Mycobacterial Infections, p 85-98. In Cole S, Eisenach K, McMurray D, Jacobs, Jr. W (ed), Tuberculosis and the Tubercle Bacillus. ASM Press, Washington, DC. doi: 10.1128/9781555817657.ch6

Key Concept Ranking

Clinical and Public Health
0.86410797
Mobile Genetic Elements
0.6764715
Ligase Chain Reaction
0.46490493
Enzyme-Linked Immunosorbent Assay
0.4331081
Single-Strand Conformation Polymorphism
0.42771253
16s rRNA Sequencing
0.4123189
0.86410797
Highlighted Text: Show | Hide
Loading full text...

Full text loading...

References

/content/book/10.1128/9781555817657.chap6
1. Alcaide, F.,, G. E. Pfyffer,, and A. Telenti. 1997. Role of embB in natural and acquired resistance to ethambutol in mycobacteria. Antimicrob. Agents Chemother. 41: 2270 2273.
2. American Thoracic Society Workshop. 1997. Rapid diagnostic tests for tuberculosis. What is the appropriate use? Am. J. Respir. Crit. Care Med. 155: 18041814.
3. Baker, C. A.,, C. P. Cartwright,, D. N. Williams,, S. M. Nelson,, and P. K. Peterson. 2002. Early detection of central nervous system tuberculosis with the Gen-Probe nucleic acid amplification assay: utility in an inner city hospital. Clin. Infect. Dis. 35: 339 342.
4. Bakonyte, D.,, A. Baranauskaite,, J. Cicenaite,, A. Sosnovskaja,, and P. Stakenas. 2003. Molecular characterization of isoniazid- resistant Mycobacterium tuberculosis clinical isolates in Lithuania. Antimicrob. Agents Chemother. 47: 2009 2011.
5. Barnes, P. F. 1997. Rapid diagnostic tests for tuberculosis: progress but no gold standard. Am. J. Respir. Crit. Care Med. 155: 1497 1498.
6. Bergmann, J. S., and G. L. Woods. 1999. Enhanced Amplified Mycobacterium tuberculosis Direct Test for detection of Mycobacterium tuberculosis complex in positive BACTEC 12B broth cultures of respiratory specimens. J. Clin. Microbiol. 37: 2099 2101.
7. Bergmann, J. S.,, G. Yuoh,, G. Fish,, and G. L. Woods. 1999. Clinical evaluation of the enhanced Gen-Probe Amplified Mycobacterium tuberculosis Direct Test for rapid diagnosis of tuberculosis in prison inmates. J. Clin. Microbiol. 37: 1419 1425.
8. Bishop, K. S.,, L. Blumberg,, P. Trollip,, A. N. Smith,, L. Roux,, D. F. York,, and P. Kiepela. 2001. Characterization of the pncA gene in Mycobacterium tuberculosis isolates from Gauteng, South Africa. Int. J. Tuberc. Lung Dis. 5: 952 957.
9. Bonington, A.,, J. I. G. Strang,, P. E. Klapper,, S. V. Hood,, W. Rubombora,, M. Penny,, R. Willers,, and E. G. L. Wilkins. 1998. Use of Roche AMPLICOR Mycobacterium tuberculosis PCR in early diagnosis of tuberculous meningitis. J. Clin. Microbiol. 36: 1251 1254.
10. Brown, T. J.,, E. G. Power,, and G. L. French. 1999. Evaluation of three commercial detection systems for Mycobacterium tuberculosis where clinical diagnosis is difficult. Clin. Pathol. 52: 193 197.
11. Brown-Elliott, B. A.,, D. E. Griffith,, and R. J. Wallace, Jr. 2002. Diagnosis of nontuberculous mycobacterial infections. Clin. Lab. Med. 22: 911 925.
12. Brunello, F.,, M. Ligozzi,, E. Cristell,, S. Bonora,, E. Tortoli,, and R. Fontana. 2001. Identification of 54 mycobacterial species by PCR-restriction fragment length polymorphism analysis of the hsp65 gene. J. Clin. Microbiol. 39: 2799 2806.
13. Catanzaro, A.,, S. Perry,, J. E. Clarridge,, S. Dunbar,, S. Goodnight- White,, P. A. LoBue,, C. Peter,, G. E. Pfyffer,, M. Sierra,, R. Weber,, G. Woods,, G. Mathews,, V. Jones,, K. Smith,, and P. Della- Latta. 2000. The role of clinical suspicion in evaluating a new diagnostic test for active tuberculosis. JAMA 283: 639 645.
14. Cavusoglu, C.,, S. Hilmioglu,, S. Guneri,, and A. Bilgic. 2002. Characterization of rpoB mutations in rifampin-resistant clinical isolates of Mycobacterium tuberculosis from Turkey by DNA sequencing and line probe assay. J. Clin. Microbiol. 40: 4435 4438.
15.Centers for Disease Control and Prevention. 2000. Update: nucleic acid amplification tests for tuberculosis. Morb. Mortal. Wkly. Rep. 49: 593594.
16. Cloud, J. L.,, H. Neal,, R. Rosenberry,, C. Y. Turenne,, M. Jama,, D. R. Hillyard,, and K. C. Carroll. 2002. Identification of Mycobacterium spp. by using a commercial 16S ribosomal DNA sequencing kit and additional sequencing libraries. J. Clin. Microbiol. 40: 400 406.
17. Cohen, R. A.,, S. Muzzafar,, D. Schwartz,, S. Bashir,, L. Luke,, L. P. McGartland,, and K. Kaul. 1998. Diagnosis of pulmonary tuberculosis using PCR assay on sputum collected within 24 hours of hospital admission. Am. J. Respir. Crit. Care Med. 156: 156 161.
18. Davies, A. P.,, O. J. Billington,, T. D. McHugh,, D. A. Mitchison,, and S. H. Gillespie. 2000. Comparison of phenotypic and genotypic methods for pyrazinamide susceptibility testing with Mycobacterium tuberculosis. J. Clin. Microbiol. 38: 3686 3688.
19. De Baere, T.,, R. de Mendonca,, G. Claeys,, G. Verschraegen,, W. Mijs,, R. Verhelst,, S. Rottiers,, L. Van Simaey,, C. De Ganck,, and M. Vaneechoutte. 2002. Evaluation of amplified rDNA restriction analysis (ARDRA) for the identification of cultured mycobacteria in a diagnostic laboratory. BMC Microbiol. 2: 4.
20. De Beenhouwer, H.,, Z. Lhiang,, G. Jannes,, W. Mijs,, L. Machtelinckx,, R. Rossau,, H. Traore,, and F. Portaels. 1995. Rapid detection of rifampicin resistance in sputum and biopsy specimens from tuberculosis patients by PCR and line probe assay. Tubercle Lung Dis. 76: 425 430.
21. Dowdy, D. W.,, A. Maters,, N. Parrish,, C. Beyrer,, and S. E. Dorman. 2003. Cost-effectiveness analysis of the Gen-Probe Amplified Mycobacterium tuberculosis Direct Test as used routinely on smear-positive respiratory specimens. J. Clin. Microbiol. 41: 948 953.
22. Edwards, K. J.,, L. A. Metherell,, M. Yates,, and N. A. Saunders. 2001. Detection of rpoB mutations in Mycobacterium tuberculosis by biprobe analysis. J. Clin. Microbiol. 39: 3350 3352.
23. Eisenach, K. D., 1999. Molecular diagnostics, p. 161 179. In C. Ratledge, and J. Dale (ed.), Mycobacteria: Molecular Biology and Virulence. Blackwell Science, Oxford, United Kingdom.
24. El-Hajj, H. H.,, S. A. Marras,, S. Tyagi,, F. R. Kramer,, and D. Alland. 2001. Detection of rifampin resistance in Mycobacterium tuberculosis in a single tube with molecular beacons. J. Clin. Microbiol. 39: 4131 4137.
25. Endoh, T.,, A. Yagihashi,, N. Uehara,, D. Kobayashi,, N. Tsuji,, M. Nakamura,, S. Hayashi,, N. Fujii,, and N. Watanabe. 2002. Pyrazinamide resistance associated with pncA gene mutations in Mycobacterium tuberculosis. Epidemiol. Infect. 128: 337 342.
26. Ergin, A.,, and G. Hascelik. 2004. Non tuberculous mycobacteria (NTM) in patients with underlying diseases: results obtained by using polymerase chain reaction-restriction enzyme analysis between 1997-2002. New Microbiol. 27: 49 53.
27. Gamboa, F.,, P. J. Cardona,, J. M. Manterola,, J. Lonca,, L. Matas,, E. Padilla,, J. R. Manzano,, and V. Ausina. 1998. Evaluation of a commercial probe assay for detection of rifampin resistance in Mycobacterium tuberculosis directly from respiratory and nonrespiratory clinical samples. Eur. J. Clin. Microbiol. Infect. Dis. 17: 189 192.
28. Garcia, L.,, M. Alonso-Sanz,, M. J. Rebollo,, J. C. Tercero,, and F. Chaves. 2001. Mutations in the rpoB gene of rifampinresistant Mycobacterium tuberculosis isolates in Spain and their rapid detection by PCR-enzyme-linked immunosorbent assay. J. Clin. Microbiol. 39: 1813 1818.
29. Garcia de Viedma, D.,, M. delSolDiazInfantes,, F. Lasala,, F. Chaves,, L. Alcala,, and E. Biouzal. 2002. New real-time PCR able to detect in a single tube multiple rifampin resistance mutations and high-level isoniazid resistance mutations in Mycobacterium tuberculosis. J. Clin. Microbiol. 40: 988 995.
30. Griffith, D. E.,, B. A. Brown-Elliott,, and R. J. Wallace. 2002. Diagnosing nontuberculous mycobacterial lung disease. Infect. Dis. Clin. North Am. 16: 235 249.
31. Hall, L.,, K. A. Doerr,, S. L. Wohlfiel,, and G. D. Roberts. 2003. Evaluation of the MicroSeq system for identification of mycobacteria by 16S ribosomal DNA sequencing and its integration into a routine clinical mycobacteriology laboratory. J. Clin. Microbiol. 41: 1447 1453.
32. Hannan, M. M.,, E. P. Desmond,, G. P. Morlock,, G. H. Mazurek,, and J. T. Crawford. 2001. Pyrazinamide-monoresistant Mycobacterium tuberculosis isolates in the United States. J. Clin. Microbiol. 39: 647 650.
33. Hellyer, T.,, T. W. Fletcher,, J. H. Bates,, W. W. Stead,, G. L. Templeton,, M. D. Cave,, and K. D. Eisenach. 1996. Strand displacement amplification and the polymerase chain reaction for monitoring response to treatment in patients with pulmonary tuberculosis. J. Infect. Dis. 173: 934 941.
34. Hou, L.,, D. Osei-Hyiaman,, Z. Zhang,, B. Wang,, A. Yang,, and K. Kano. 2000. Molecular characterization of pncA gene mutations in Mycobacterium tuberculosis clinical isolates from China. Epidemiol. Infect. 124: 227 232.
35. 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.
36. Johansen, I. S.,, V. O. Thomsen,, A. Johansen,, P. Andersen,, and B. Lundgren. 2002. Evaluation of a new commercial assay for diagnosis of pulmonary and nonpulmonary tuberculosis. Eur. J. Clin. Microbiol. Infect. Dis. 21: 455 460.
37. Katila, M. L.,, P. Katila,, and R. Erkinjuntti-Pekkanen. 2000. Accelerated detection of mycobacteria with MGIT 960 and COBAS AMPLICOR systems . J. Clin. Microbiol. 38: 960 964.
38. Kim, B. J.,, S. J. Kim,, B. H. Park,, M. A. Lyu,, I. M. Park,, G. H. Bai,, S. J. Kim,, C. Y. Cha,, and Y. H. Kook. 1997. Mutations in the rpoB gene of Mycobacterium tuberculosis that interfere with PCR-single-strand conformation polymorphism analysis for rifampin susceptibility testing. J. Clin. Microbiol. 35: 492 494.
39. Kim, B. J.,, K. H. Lee,, B. N. Park,, S. J. Kim,, E. M. Park,, Y. G. Park,, G. H. Bai,, S. J. Kim,, and Y. H. Kook. 2001. Detection of rifampin-resistant Mycobacterium tuberculosis in sputa by nested PCR-linked single-strand conformation polymorphism and DNA sequencing. J. Clin. Microbiol. 39: 2610 2617.
40. Lee, A. S.,, L. L. Tang,, I. H. Lim,, and S. Y. Wong. 2002. Characterization of pyrazinamide and ofloxacin resistance and drug resistant Mycobacterium tuberculosis isolates from Singapore. Int. J. Tuberc. Lung Dis. 6: 48 51.
41. Lim, T. K.,, A. Mukhopadhyay,, A. Gough,, K.-L. Khoo,, S.-M. Khoo,, K.-H. Lee,, and G. Kumarasinghe. 2003. Role of clinical judgment in the amplification of a nucleic acid amplification test for the rapid diagnosis of pulmonary tuberculosis. Chest 124: 902 908.
42. Liu, Y. P.,, M. A. Behr,, P. M. Small,, and N. Kurn. 2000. Genotypic determination of Mycobacterium tuberculosis antibiotic resistance using a novel mutation detection method, the branch migration inhibition M. tuberculosis antibiotic resistance test. J. Clin. Microbiol. 38: 3656 3662.
43. Mäkinen, J.,, A. Sarkola,, M. Marjamäki,, M. K. Viljanen,, and H. Soini. 2002. Evaluation of GenoType and LiPA MYCOBACTERIA assays for identification of Finnish mycobacterial isolates . J. Clin. Microbiol. 40: 3478 3481.
44. Maugein, J.,, J. Fourche,, S. Vacher,, C. Grimond,, and C. Bebear. Evaluation of the BDProbeTec ET DTB assay(1) for direct detection of Mycobacterium tuberculosis complex from clinical samples. Diagn. Microbiol. Infect. Dis. 44: 151 155.
45. Mikhailovich, V.,, S. Lapa,, D. Gryadunov,, A. Sobolev,, B. Strizhkov,, N. Chernyh,, O. Skotnikova,, O. Irtuganova,, A. Moroz,, V. Litvinov,, M. Vladimirskii,, M. Perelman,, L. Chernousova,, V. Erokhin,, A. Zasedat,, and A. Mirzabekov. 2001. Identification of rifampin-resistant Mycobacterium tuberculosis strains by hybridization, PCR, and ligase detection reaction on oligonucleotide microchips. J. Clin. Microbiol. 39: 2531 2540.
46. Mikhailovich, V. M.,, S. A. Lapa,, D. A. Gryadunov,, B. N. Strizhkov,, A. Y. Sobolev,, O. I. Skotnikova,, O. A. Irtuganova,, A. M. Moroz,, V. I. Litvinov,, L. K. Shipina,, M. A. Vladimirskii,, L. N. Chernousova,, V. V. Erokhin,, and A. D. Mirzabekov. 2001. Detection of rifampicin-resistant Mycobacterium tuberculosis strains by hybridization and polymerase chain reaction on specialized TB-microchip. Bull. Exp. Biol. Med. 131: 94 98.
47. Miller, N.,, S. Infante,, and T. Cleary. 2000. Evaluation of the LiPA MYCOBACTERIA assay for identification of mycobacterial species from BACTEC 12B bottles. J. Clin. Microbiol. 38: 1915 1919.
48. Miller, N.,, T. Cleary,, G. Kraus,, A. K. Young,, G. Spruill,, and H. J. Hnatyszyn. 2002. Rapid and specific detection of Mycobacterium tuberculosis from acid-fast bacillus smear-positive respiratory specimens and BacT/ALERT MP culture bottles by using fluorogenic probes and real-time PCR . J. Clin. Microbiol. 40: 4143 4147.
49. Mokrousov, I.,, I. Filliol,, E. Legrand,, C. Sola,, T. Otten,, E. Vyshnevskaya,, E. Limeschenko,, B. Vyshnevskiy,, O. Narvskaya,, and N. Rastogi. 2002. Molecular characterization of multiple-drug-resistant Mycobacterium tuberculosis isolates from northwestern Russia and analysis of rifampin resistance using RNA/RNA mismatch analysis as compared to the line probe assay and sequencing of the rpoB gene. Res. Microbiol. 153: 213 219.
50. Mokrousov, I.,, O. Narvskaya,, E. Limeschenko,, T. Otten,, and B. Vishnevskiy. 2002. Detection of ethambutol-resistant Mycobacterium tuberculosis strains by muliplex allele-specific PCR assay targeting embB306 mutations. J. Clin. Microbiol. 40: 1617 1620.
51. Mokrousov, I.,, T. Otten,, M. Filipenko,, A. Vyazovaya,, E. Chrapov,, E. Limeschenko,, L. Steklova,, B. Vishnevskiy,, and O. Narvskaya. 2002. Detection of isoniazid-resistant Mycobacterium tuberculosis strains by a multiplex allele-specific PCR assay targeting katG codon 315 variation. J. Clin. Microbiol. 40: 2509 2512.
52. Mokrousov, I.,, T. Otten,, B. Vyshnevskiy,, and O. Narvskaya. 2003. Allele-specific rpoB PCR assays for detection of rifampin- resistant Mycobacterium tuberculosis in sputum smears. Antimicrob. Agents Chemother. 47: 2231 2235.
53. Morcillo, N.,, M. Zumarraga,, A. Alito,, A. Dolmann,, L. Schouls,, A. Cataldi,, K. Kemer,, and D. van Soolingen. 2002. A low cost, home-made, reverse-line blot hybridization assay for rapid detection of rifampicin resistance in Mycobacterium tuberculosis. Int. J. Tuberc. Lung Dis. 6: 959 965.
54. Nachamkin, I.,, C. Kang,, and M. P. Weinstein. 1997. Detection of resistance to isoniazid, rifampin, and streptomycin of clinical isolates of Mycobacterium tuberculosis by molecular methods. Clin. Infect. Dis. 24: 894 900.
55. Noordhoek, G. T.,, J. D. A. van Embden,, and A. H. Kolk. 1996. Reliability of nucleic acid amplification for detection of Mycobacterium tuberculosis: an international collaborative quality control study among 30 laboratories. J. Clin. Microbiol. 34: 2522 2525.
56. O’Sullivan, C. E.,, D. R. Miller,, P. S. Schneider,, and G. D. Roberts. 2002. Evaluation of Gen-Probe Amplified Mycobacterium tuberculosis Direct Test by using respiratory and nonrespiratory specimens in a tertiary-care center laboratory. J. Clin. Microbiol. 40: 1723 1727.
57. Park do, Y.,, J. Y. Kim,, K. U. Choi,, J. S. Lee,, M. Y. Sol,, and K. S. Suh. 2003. Comparison of polymerase chain reaction with histopathologic features for diagnosis of tuberculosis in formalin-fixed, paraffin-embedded histologic specimens. Arch. Pathol. Lab. Med. 127: 326 330.
58. 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.
59. Pauls, R. J.,, C. Y. Turenne,, J. N. Wolfe,, and A. Kabani. 2003. A high proportion of novel mycobacteria species identified by 16S rDNA analysis among slowly growing AccuProbenegative strains in a clinical setting. Am. J. Clin. Pathol. 120: 560 566.
60. Piersimoni, C.,, C. Scarparo,, P. Piccoli,, A. Rigon,, G. Ruggiero,, D. Nista,, and S. Bornigia. 2002. Performance assessment of two commercial amplification assays for direct detection of Mycobacterium tuberculosis complex from respiratory and extrapulmonary specimens. J. Clin. Microbiol. 40: 4138 4142.
61. Piersimoni, C., and C. Scarparo. 2003. Relevance of commercial amplification methods for direct detection of Mycobacterium tuberculosis complex in clinical specimens. J. Clin. Microbiol. 41: 5355 5365.
62. Rajalahti, I.,, P. Vourinen,, M. M. Nieminen,, and A. Miettinen. 1998. Detection of Mycobacterium tuberculosis complex by the automated Roche Cobas Amplicor Mycobacterium tuberculosis test. J. Clin. Microbiol. 36: 975 978.
63. Ramaswamy, S. V.,, A. G. Amin,, S. Goksel,, C. E. Stager,, S. J. Dou,, H. El Sahly,, S. L. Moghazeh,, B. N. Kreiswirth,, and J. M. Musser. 2000. Molecular genetic analysis of nucleotide polymorphisms associated with ethambutol resistance in human isolates of Mycobacterium tuberculosis. Antimicrob. Agents Chemother. 44: 326 336.
64. Ramaswamy, S. V.,, R. Reich,, S.-J. Dou,, L. Jasperse,, X. Pan,, A. Wanger,, T. Quitugua,, and E. A. Graviss. 2003. Single nucleotide polymorphisms in genes associated with isoniazid resistance in Mycobacterium tuberculosis. Antimicrob. Agents Chemother. 47: 1241 1250.
65. Ramaswamy, S. V.,, S. J. Dou,, A. Rendon,, Z. Yang,, M. D. Cave,, and E. A. Graviss. 2004. Genotypic analysis of multidrugresistant Mycobacterium tuberculosis isolates from Monterrey, Mexico. J. Med. Microbiol. 53: 107 113.
66. Rimek, D.,, S. Tyagi,, and R. Kappe. 2002. Performance of an IS 6110-based PCR assay and the COBAS AMPLICOR MTB PCR system for detection of Mycobacterium tuberculosis complex DNA in human lymph node samples. J. Clin. Microbiol. 40: 3089 3092.
67. Rinder, H.,, K. T. Mieskes,, E. Tortoli,, E. Richter,, M. Casal,, M. Vaquero,, E. Cambau,, K. Feldmann,, and T. Loscher. 2001. Detection of embB codon 306 mutations in ethambutol resistant Mycobacterium tuberculosis directly from sputum samples: a low-cost, rapid approach. Mol. Cell. Probes 15: 37 42.
68. Riska, P. F.,, W. R. Jacobs, Jr.,, and D. Alland. 2000. Molecular determinants of drug resistance in tuberculosis. Int. J. Tuberc. Lung Dis. 4: S4 S10.
69. Rossau, R.,, H. Traore,, H. De Beenhouwer,, W. Mijs,, G. Jannes,, P. De Rijk,, and F. Portaels. 1997. Evaluation of the INNO-LiPA Rif. TB assay, a reverse hybridization assay for the simultaneous detection of Mycobacterium tuberculosis complex and its relevance to rifampin. Antimicrob. Agents Chemother. 41: 2093 2098.
70. Saribas, Z.,, T. Kocagöz,, A. Alp,, and A. Günalp. 2003. Rapid detection of rifampin resistance in Mycobacterium tuberculosis isolates by heteroduplex analysis and determination of rifamycin cross-resistance in rifampin-resistant isolates. J. Clin. Microbiol. 41: 816 818.
71. Scarparo, C.,, P. Piccoli,, A. Rigon,, G. Ruggiero,, M. Scagnelli,, and C. Piersimoni. 2000. Comparison of enhanced Mycobacterium tuberculosis amplified direct test with COBAS AMPLICOR Mycobacterium tuberculosis assay for direct detection of Mycobacterium tuberculosis complex in respiratory and extrapulmonary specimens. J. Clin. Microbiol. 38: 1559 1562.
72. Scarparo, C.,, P. Piccoli,, A. Rigon,, G. Ruggiero,, D. Nista,, and C. Piersimoni. 2001. Direct identification of mycobacteria from MB/BacT Alert 3D bottles: comparative evaluation of two commercial probe assays . J. Clin. Microbiol. 39: 3222 3227.
72.a. Scarpellini, P.,, S. Braglia,, P. Carrera,, M. Cedri,, P. Chichero,, A. Colombo,, R. Crucianelli,, A. Gori,, M. Ferrari,, and A. Lazzarin. 1999. Detection of rifampin resistance in Mycobacterium tuberculosis by double-gradient-denaturing gradient gel electrophoresis. Antimicrob. Agents Chemother. 43: 2550 2554.
73. Schluger, N. W. 2001. Changing approaches to the diagnosis of tuberculosis. Am. J. Respir. Crit. Care Med. 164: 2020 2024.
74. Schneegass, I., and Köhler, J. M. 2001. Flow-through polymerase chain reactions in chip thermocyclers. Rev. Mol. Biotechnol. 82: 101 121.
75. Shrestha, N. K.,, M. J. Tuohy,, G. S. Hall,, U. Reischl,, S. M. Gordon,, and G. W. Procop. 2003. Detection and differentiation of Mycobacterium tuberculosis and nontuberculous mycobacterial isolates by real-time PCR. J. Clin. Microbiol. 41: 5121 5126.
76. Somoskovi, A.,, J. Mester,, Y. M. Hale,, L.M. Parsons,, and M. Salfinger. 2002. Laboratory diagnosis of nontuberculous mycobacteria. Clin. Chest Med. 23: 585 597.
77. Somoskovi, A.,, Q. Song,, J. Mester,, C. Tanner,, Y. M. Hale,, L. M. Parsons,, and M. Salfinger. 2003. Use of molecular methods to identify the Mycobacterium tuberculosis complex (MTBC) and other mycobacterial species and to detect rifampin resistance in MTBC isolates following growth detection with the BACTEC MGIT 960 system. J. Clin. Microbiol. 41: 2822 2826.
78. Sougakoff, W.,, N. Lemaitre,, E. Cambau,, M. Szpytma,, V. Revel,, and V. Jarlier. 1997. Nonradioactive single-strand conformation polymorphism analysis for detection of fluoroquinolone resistance in mycobacteria. Eur. J. Clin. Microbiol. Infect. Dis. 16: 395 398.
79. Sougakoff, W.,, M. Rodrigue,, C. Truffot-Pernot,, M. Renard,, N. Durin,, M. Szpytma,, R. Vachon,, A. Troesch,, and V. Jarlier. 2004. Use of a high-density DNA probe array for detecting mutations involved in rifampicin resistance in Mycobacterium tuberculosis. Clin. Microbiol. Infect. 10: 289 294.
80. Sreevatsan, S.,, X. Pan,, K. E. Stockbauer,, D. L. Williams,, B. N. Kreiswirth,, and J. M. Musser. 1996. Characterization of rpsl and rrs mutations in streptomycin-resistant Mycobacterium tuberculosis isolates from diverse geographic regions. Antimicrob. Agents Chemother. 40: 1024 1026.
81. 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.
82. Sreevatsan S.,, K. E. Stockbauer,, X. Pan,, B. N. Kreiswirth,, S. L. Moghazeh,, W. R. Jacobs, Jr.,, A. Telenti,, and J. M. Musser. 1997. Ethambutol resistance in Mycobacterium tuberculosis: critical role for embB mutations . Antimicrob. Agents Chemother. 41: 1677 1681.
83. Stender, H.,, K. Lund,, K. H. Petersen,, O. F. Rasmussen,, P. Hongmanee,, H. Miörner,, and S. E. Godtfredsen. 1999. Fluorescence in situ hybridization assay using peptide nucleic acid probes for differentiation between tuberculous and nontuberculous Mycobacterium species in smears of Mycobacterium cultures . J. Clin. Microbiol. 37: 2760 2765.
84. Suzuki, Y.,, A. Suzuki,, A. Tamaru,, C. Katsukawa,, and H. Oda. 2002. Rapid detection of pyrazinamide-resistant Mycobacterium tuberculosis by a PCR-based in vitro system. J. Clin. Microbiol. 40: 501 507.
85. Takiff, H. E.,, L. Salazar,, C. Guerrero,, W. Philipp,, W. M. Huang,, B. Kreiswirth,, S. Cole,, W. R. Jacobs, Jr.,, and A. Telenti. 1994. Cloning and nucleotide sequence of Mycobacterium tuberculosis gyrA and gyrB genes and detection of quinolone resistance mutations. Antimicrob. Agents Chemother. 38: 773 780.
86. Telenti, A.,, P. Imboden,, F. Marchesi,, D. Lowrie,, S. Cole,, M. J. Colston,, L. Matter,, K. Schopfer,, and T. Bodmer. 1993. Detection of rifampin-resistant mutations in Mycobacterium tuberculosis. Lancet 341: 647 650.
87. Telenti, A.,, W. Philipp,, S. Sreevatsan,, C. Bernasconi,, K. E. Stockbauer,, B. Wieles,, J. M. Musser,, and W. R. Jacobs, Jr. 1997. The emb operon, a unique gene cluster of Mycobacterium tuberculosis involved in resistance to ethambutol. Nat. Med. 3: 567 570.
88. Torres, M. J.,, A. Craido,, J. C. Palomares,, and J. Aznar. 2000. Use of real-time PCR and fluorimetry for rapid detection of rifampin and isoniazid resistance-associated mutations in Mycobacterium tuberculosis. J. Clin. Microbiol. 38: 3194 3199.
89. Traore, H.,, K. Fissette,, I. Bastian,, M. Devleeschouwer,, and F. Portaels. 2000. Detection of rifampin resistance in Mycobacterium tuberculosis isolates from diverse countries by commercial line probe assay as an initial indicator of multidrug resistance. Int. J. Tuberc. Lung Dis. 4: 481 484.
90. Troesch, A.,, H. Nguyen,, C. G. Miyada,, S. Desvarenne,, T. R. Gingeras,, P. M. Kaplan,, P. Cros,, and C. Mabilat. 1999 . Mycobacterium species identification and rifampin resistance testing with high-density DNA probe arrays . J. Clin. Microbiol. 37: 49 55.
91. Turenne, C. Y.,, L. Tschetter,, J. Wolfe,, and A. Kabani. 2001. Necessity of quality-controlled 16S rRNA gene sequence databases: identifying nontuberculous Mycobacterium species. J. Clin. Microbiol. 39: 3637 3648.
92. Viader-Salvado, J. M.,, C. M. Luna-Aguirre,, J. M. Reyes-Ruiz,, R. Valdez-Leon,, L. del Bosque-Moncayo Mde,, R. Tijerina-Menchaca,, and M. Guerrero-Olazaran. 2003. Frequency of mutations in rpoB and codons 315 and 463 of katG in rifampinand/ or idoniazid-resistant Mycobacterium tuberculosis isolates from northeast Mexico. Microbiol. Drug Resist. 9: 33 38.
93. Whelen, A. C.,, T. A. Felmlee,, J. M. Hunt,, D. L. Williams,, G. D. Roberts,, L. Stockman,, and D. H. Persing. 1995. Direct genotypic detection of Mycobacterium tuberculosis rifampin resistance in clinical specimens by using single-tube, heminested PCR. J. Clin. Microbiol. 33: 556 561.
94. Williams, D. L.,, L. Spring,, T. P. Gillis,, M. Salfinger,, and D. H. Persing. 1998. Evaluation of a polymerase chain reactionbased universal heteroduplex generator assay for direct detection of rifampin susceptibility of Mycobacterium tuberculosis from sputum specimens. Clin. Infect. Dis. 26: 446 450.
95. Wolk, D.,, S. Mitchell,, and R. Patel. 2001. Principles of molecular biology testing methods. Infect. Dis. Clin. North Am. 15: 1157 1204.
96. Woods, G. L. 2001. Molecular techniques in mycobacterial detection . Arch. Pathol. Lab. Med. 125: 122 126.
97. Xu, C.,, B. N. Kreiswirth,, S. Sreevatsan,, J. M. Musser,, and K. Drlica. 1996. Fluoroquinolone resistance associated with specific gyrase mutations in clinical isolates of multidrug-resistant Mycobacterium tuberculosis. J. Infect. Dis. 174: 1127 1130.
98. Yue, J.,, W. Shi,, J. Xie,, Y. Li,, E. Zena,, and H. Wang. 2003. Mutations in the rpoB gene of multidrug-resistant Mycobacterium tuberculosis isolates from China. J. Clin. Microbiol. 41: 2209 2212.
99. Zhang, Y.,, and A. Telenti,. 2000. Genetics of drug resistance in Mycobacterium tuberculosis, p. 235 254. In G. Hatfull, and W. R. Jacobs (ed.), Molecular Genetics of Mycobacteria. ASM Press, Washington, D.C..

Tables

Generic image for table
Table 1

Molecular biology techniques commonly used to detect of mutations causing resistance to antimicrobial agents.

Citation: Forbes B, Pfyffer G, Eisenach K. 2005. Molecular Diagnosis of Mycobacterial Infections, p 85-98. In Cole S, Eisenach K, McMurray D, Jacobs, Jr. W (ed), Tuberculosis and the Tubercle Bacillus. ASM Press, Washington, DC. doi: 10.1128/9781555817657.ch6

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error