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Chapter 26 : Molecular Detection and Characterization of

Author: Betty A. Forbes1
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Affiliations: 1: Department of Pathology, Virginia Commonwealth University Medical Center, Medical College of Virginia Campus, Richmond, VA 23298
Content Type: Reference
Publication Year: 2011

Category: Clinical Microbiology; Bacterial Pathogenesis

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Abstract:

This chapter focuses on nucleic acid amplification based (NAA) assays that detect directly in clinical specimens; specifics regarding the laboratory diagnosis of infections caused by the nontuberculous mycobacteria are not included. The chapter talks about on NAA assays that detect directly in clinical specimens. The salient features of commercially available NAA assays are first briefly described, followed by an overview of in-house-developed assays. Second, similar to commercially available NAA assays, evaluation of in-house NAA assays has used primarily respiratory specimens, but testing has also been performed on nonrespiratory specimens such as pleural fluids, gastric aspirates, formalin-fixed and paraffin-embedded tissues, fresh tissues, cerebrospinal fluids (CSF), and other sterile body fluids. Third, in-house assays have also been developed to detect both complex and drug resistance. Finally, other miscellaneous aspects of NAA assays including their use in monitoring response to therapy, cost and cost-effectiveness, and newer approaches and modifications are addressed. Identifications obtained by use of the specific deletion profiles correlated 100% with the original identifications for all complex members except ; further characterization resulted in profiles specific for all members. Subsequent studies using genomic deletions revealed that by testing an isolate for signature deletions, members of the complex can be identified.

Citation: Forbes B. 2011. Molecular Detection and Characterization of , p 415-436. In Persing D, Tenover F, Tang Y, Nolte F, Hayden R, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555816834.ch26
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Molecular Detection and Characterization of Mycobacterium tuberculosis
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Citation: Forbes B. 2011. Molecular Detection and Characterization of , p 415-436. In Persing D, Tenover F, Tang Y, Nolte F, Hayden R, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555816834.ch26
/content/10.1128/9781555816834.ch26.ch26fig01
FIGURE 1
Examples of GenoType MTDBRplus strips (Hain Lifescience, Nehren, Germany). Lanes: 1, susceptible to INH and rifampin (RIF); 2, INH monoresistant S315T1 mutation); 3, MDR S531L mutation and S315T2 mutation; 4, MDR S531L mutation and S315T1 and C15T mutations; 5, RIF monoresistant (mutation in 530-533 region); 6, MDR TB, D516V and S315T1 mutations; 7, MDR S531L, and S315T2 mutations; 8, MDR TB, D516V, S315T1 mutation, and mutation at –15/–16; 9, uninterpretable result, no complex band; 10, negative control. (Reprinted from the [ ] with permission of the publisher.)
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10.1128/9781555816834/f0418-01.gif
Image of FIGURE 1
FIGURE 1

Examples of GenoType MTDBRplus strips (Hain Lifescience, Nehren, Germany). Lanes: 1, susceptible to INH and rifampin (RIF); 2, INH monoresistant S315T1 mutation); 3, MDR S531L mutation and S315T2 mutation; 4, MDR S531L mutation and S315T1 and C15T mutations; 5, RIF monoresistant (mutation in 530-533 region); 6, MDR TB, D516V and S315T1 mutations; 7, MDR S531L, and S315T2 mutations; 8, MDR TB, D516V, S315T1 mutation, and mutation at –15/–16; 9, uninterpretable result, no complex band; 10, negative control. (Reprinted from the [ ] with permission of the publisher.)

Citation: Forbes B. 2011. Molecular Detection and Characterization of , p 415-436. In Persing D, Tenover F, Tang Y, Nolte F, Hayden R, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555816834.ch26
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FIGURE 2
Detection of amplified target DNA using the LAMP method can be visually achieved through the byproduct of amplification, magnesium pyrophosphate. (A) White turbidity can be observed because of the production of large amounts of amplified product. (B) Amplified product can also be detected by fluorescence that is clearly distinguished by the naked eye under UV light. Calcein, a chaotropic agent that is fluorescent unless combined with manganese ion, is added to the reaction mix; manganese binds to pyrophosphate produced during amplification, thereby releasing the calcein, resulting in fluorescence. (Reprinted with permission of Eiken Chemical Co. Ltd.)
10.1128/9781555816834/f0428-01_thmb.gif
10.1128/9781555816834/f0428-01.gif
Image of FIGURE 2
FIGURE 2

Detection of amplified target DNA using the LAMP method can be visually achieved through the byproduct of amplification, magnesium pyrophosphate. (A) White turbidity can be observed because of the production of large amounts of amplified product. (B) Amplified product can also be detected by fluorescence that is clearly distinguished by the naked eye under UV light. Calcein, a chaotropic agent that is fluorescent unless combined with manganese ion, is added to the reaction mix; manganese binds to pyrophosphate produced during amplification, thereby releasing the calcein, resulting in fluorescence. (Reprinted with permission of Eiken Chemical Co. Ltd.)

Citation: Forbes B. 2011. Molecular Detection and Characterization of , p 415-436. In Persing D, Tenover F, Tang Y, Nolte F, Hayden R, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555816834.ch26
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FIGURE 3
Primers included in initial versions of the LAMP method. Shown are two sets of specially designed inner and outer primers; inner primers are called the forward inner primer (FIP) and the backward inner primer (BIP), and each contains two distinct sequences corresponding to the sense and antisense sequences of the target DNA, one for priming in the first stage and the other for self-priming in later stages ( ). The sequences inside both ends of the target region for amplification are designated F2c and B2, respectively. Two inner sequences that are 40 nucleotides in length from the ends of F2c and B2 are designated F1c and B1, and two sequences outside the ends of F2c and B2 are designated F3c and B3. In the initial steps of the LAMP reaction, all four primers are used, but later during the cycling reaction only the inner primers are used for strand displacement DNA synthesis. (Reprinted with permission of Eiken Chemical Co. Ltd.)
10.1128/9781555816834/f0428-02_thmb.gif
10.1128/9781555816834/f0428-02.gif
Image of FIGURE 3
FIGURE 3

Primers included in initial versions of the LAMP method. Shown are two sets of specially designed inner and outer primers; inner primers are called the forward inner primer (FIP) and the backward inner primer (BIP), and each contains two distinct sequences corresponding to the sense and antisense sequences of the target DNA, one for priming in the first stage and the other for self-priming in later stages ( ). The sequences inside both ends of the target region for amplification are designated F2c and B2, respectively. Two inner sequences that are 40 nucleotides in length from the ends of F2c and B2 are designated F1c and B1, and two sequences outside the ends of F2c and B2 are designated F3c and B3. In the initial steps of the LAMP reaction, all four primers are used, but later during the cycling reaction only the inner primers are used for strand displacement DNA synthesis. (Reprinted with permission of Eiken Chemical Co. Ltd.)

Citation: Forbes B. 2011. Molecular Detection and Characterization of , p 415-436. In Persing D, Tenover F, Tang Y, Nolte F, Hayden R, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555816834.ch26
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FIGURE 4
Representative IS6110-based RFLP image. Isolates represented by lanes 3, 5, 6, 9, and 10 have the same pattern and were epidemiologically linked. Lane S shows the CDC molecular weight standard. (From U.S. Department of Health, Education, and Welfare, Public Health Service, CDC, Atlanta, GA.)
10.1128/9781555816834/f0429-01_thmb.gif
10.1128/9781555816834/f0429-01.gif
Image of FIGURE 4
FIGURE 4

Representative IS6110-based RFLP image. Isolates represented by lanes 3, 5, 6, 9, and 10 have the same pattern and were epidemiologically linked. Lane S shows the CDC molecular weight standard. (From U.S. Department of Health, Education, and Welfare, Public Health Service, CDC, Atlanta, GA.)

Citation: Forbes B. 2011. Molecular Detection and Characterization of , p 415-436. In Persing D, Tenover F, Tang Y, Nolte F, Hayden R, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555816834.ch26
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FIGURE 5
Two examples of spoligotype results showing the original banding patterns as well as the steps involved in converting the banding pattern results to the final octal code designation. The original banding pattern is converted to a series of 1 ’s and 0’s (1 means the band is present, and 0 means it is absent) that is 43 digits long (i.e., binary code). The binary code is further simplified by converting to a 15-digit octal code designation in a two-step process. The binary code is divided into 14 sets of three digits plus one additional digit (spacer 43). Then, each three-digit binary set is converted to its octal equivalent, with the final additional digit remaining as 1 or 0. The octal designation is the form of the result that is reported by the genotyping laboratories to tuberculosis programs. (From U.S. Department of Health and Human Services, CDC, Atlanta, GA.)
10.1128/9781555816834/f0430-01_thmb.gif
10.1128/9781555816834/f0430-01.gif
Image of FIGURE 5
FIGURE 5

Two examples of spoligotype results showing the original banding patterns as well as the steps involved in converting the banding pattern results to the final octal code designation. The original banding pattern is converted to a series of 1 ’s and 0’s (1 means the band is present, and 0 means it is absent) that is 43 digits long (i.e., binary code). The binary code is further simplified by converting to a 15-digit octal code designation in a two-step process. The binary code is divided into 14 sets of three digits plus one additional digit (spacer 43). Then, each three-digit binary set is converted to its octal equivalent, with the final additional digit remaining as 1 or 0. The octal designation is the form of the result that is reported by the genotyping laboratories to tuberculosis programs. (From U.S. Department of Health and Human Services, CDC, Atlanta, GA.)

Citation: Forbes B. 2011. Molecular Detection and Characterization of , p 415-436. In Persing D, Tenover F, Tang Y, Nolte F, Hayden R, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555816834.ch26
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FIGURE 6
Examples of MIRU results. MIRU results are reported as a 12-digit designation, with each digit representing the number of repeats detected at the respective 12 MIRU loci. For loci with more than nine repeats, letters are used (e.g., “a” for 10 repeats, “b” for 11, etc.). (From U.S. Department of Health and Human Services, Public Health Service, CDC, Atlanta, GA.)
10.1128/9781555816834/f0431-01_thmb.gif
10.1128/9781555816834/f0431-01.gif
Image of FIGURE 6
FIGURE 6

Examples of MIRU results. MIRU results are reported as a 12-digit designation, with each digit representing the number of repeats detected at the respective 12 MIRU loci. For loci with more than nine repeats, letters are used (e.g., “a” for 10 repeats, “b” for 11, etc.). (From U.S. Department of Health and Human Services, Public Health Service, CDC, Atlanta, GA.)

Citation: Forbes B. 2011. Molecular Detection and Characterization of , p 415-436. In Persing D, Tenover F, Tang Y, Nolte F, Hayden R, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555816834.ch26
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References

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1. Acuna-Villaorduna, C.,, A. Vassall,, G. Henostroza,, C. Seas,, H. Guerra,, L. Vasquez,, N. Morcillo,, J. Saravia,, R. O’Brien,, M. D. Perkins,, J. Cunningham,, L. Llanos-Zavalaga, and, E. Gotuzzo. 2008. Cost-effectiveness analysis of introduction of rapid, alternative methods to identify multidrug-resistant tuberculosis in middle-income countries. Clin. Infect. Dis. 47: 487– 495.
2. American Thoracic Society. 1997. Rapid diagnostic tests for tuberculosis. What is the appropriate use? American Thoracic Society Workshop. Am. J. Respir. Crit. Care Med. 155: 804– 814.
3. American Thoracic Society. 2000. Diagnostic standards and classification of tuberculosis in adults and children. Am. J. Respir. Crit. Care Med. 161: 1376– 1395.
4. American Thoracic Society. 2000. Multi-drug resistant and extensively drug-resistant tuberculosis: the National Institute of Allergy and Infectious Diseases research agenda and recommendations for priority research. J. Infect. Dis. 197: 1493– 1498.
5. Baltussen, R.,, K. Floyd, and, C. Dye. 2005. Cost effectiveness analysis of strategies for tuberculosis control in developing countries. BMJ 331: 1364.
6. Baptista, P. V.,, M. Koziol-Montewka,, J. Paluch-Oles,, G. Doria, and, R. Franco. 2006. Gold-nanoparticle-probe-based assay for rapid and direct detection of Mycobacterium tuberculosis DNA in clinical samples. Clin. Chem. 52: 1433– 1434.
7. Barnard, M.,, H. Albert,, G. Coetzee,, R. O’Brien, and, M. E. Bosman. 2008. Rapid molecular screening for multidrug-resistant tuberculosis in a high-volume public health laboratory in South Africa. Am. J. Respir. Crit. Care Med. 177: 787– 792.
8. Barnes, P. F.,, and M. D. Cave. 2003. Molecular epidemiology of tuberculosis. N. Engl. J. Med. 349: 1149– 1156.
9. Bauer, J.,, A. B. Andersen,, K. Kremer, and, H. Miorner. 1999. Usefulness of spoligotyping to discriminate IS6110 low-copy-number Mycobacterium tuberculosis complex strains cultured in Denmark. J. Clin. Microbiol. 37: 2602– 2606.
10. 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.
11. Bifani, P. J.,, B. Mathema,, N. E. Kurepina, and, B. N. Kreiswirth. 2002. Global dissemination of the Mycobacterium tuberculosis W-Beijing family strains. Trends Microbiol. 10: 45– 52.
12. Boehme, C.,, P. Nabeta,, G. Henostroza,, R. Raqib,, Z. Rahim,, M. Gerhardt,, E. Sanga,, M. Hoelscher,, T. Notomi,, T. Hase, and, M. D. Perkins. 2007. Operational feasibility of using loop-mediated isothermal amplification for diagnosis of pulmonary tuberculosis in microscopy centers for developing countries. J. Clin. Microbiol. 45: 1936– 1940.
13. Brodie, D.,, and N. W. Schluger. 2005. The diagnosis of tuberculosis. Clin. Chest Med. 26: 247– 271.
14. 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.
15. 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,, H. M. Ly,, C. Martin,, I. Mokrousov,, O. Narvskaia,, Y. F. Ngeow,, L. Naumann,, S. Niemann,, I. Parwati,, M. 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.
16. Burggraf, S.,, U. Reischl,, N. Malik,, M. Bollwein,, L. Naumann, and, B. Olgemöller. 2005. Comparison of an internally controlled, large-volume LightCycler assay for detection of Mycobacterium tuberculosis in clinical samples with the COBAS AMPLICOR assay. J. Clin. Microbiol. 43: 1564– 1569.
17. Catanzaro, A.,, S. Perry,, J. Clarridge,, S. Dunbar,, S. Goodnight-White,, P. A. LoBoe,, C. Peter,, G. E. Pfyffer,, M. F. Sierra,, R. Weber,, G. Woods,, G. Mathews,, V. Jonas,, 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.
18. Cavusoglu, C.,, A. Turhan,, P. Akinci, and, I. Soyler. 2006. Evaluation of the Genotype MTBDR assay for rapid detection of rifampin and isoniazid resistance in Mycobacterium tuberculosis isolates. J. Clin. Microbiol. 44: 2338– 2342.
19. Centers for Disease Control and Prevention. 2000. Update: nucleic acid amplification tests for tuberculosis. Morb. Mortal. Wkly. Rep. 49: 593– 594.
20. Chakravorty, S.,, M. K. Sen, and, J. S. Tyagi. 2005. Diagnosis of extrapulmonary tuberculosis by smear, culture, and PCR using universal sample processing technology. J. Clin. Microbiol. 43: 4357– 4362.
21. Chakravorty, S.,, and J. S. Tyagi. 2001. Novel use of guanidinium isothiocyanate in the isolation of Mycobacterium tuberculosis DNA from clinical material. FEMS Microbiol. Lett. 205: 113– 117.
22. Chakravorty, S.,, M. Dudeja,, M. Hanif, and, J. S. Tyagi. 2005. Utility of universal sample processing methodology, combining smear microscopy, culture, and PCR, for diagnosis of pulmonary tuberculosis. J. Clin. Microbiol. 43: 2703– 2708.
23. Colebunders, R.,, and I. Bastian. 2000. A review of the diagnosis and treatment of smear-negative pulmonary tuberculosis. Int. J. Tuberc. Lung Dis. 4: 97– 107.
24. Conaty, S. J.,, A. P. Claxton,, D. A. Enoch,, A. C. Hayward, and, S. H. Gillespie. 2005. The interpretation of nucleic acid amplification tests for tuberculosis: do rapid tests change treatment decisions? J. Infect. 50: 187– 192.
25. Cooksey, R. C.,, G. P. Morlock,, S. Glickman, and, J. T. Crawford. 1997. Evaluation of a line probe assay kit for characterization of rpoB mutations in rifampin-resistant Mycobacterium tuberculosis isolates from New York City. J. Clin. Microbiol. 35: 1281– 1283.
26. Cousins, D. V.,, S. D. Wilton,, B. R. Francis, and, B. L. Gow. 1992. Use of polymerase chain reaction for rapid diagnosis of tuberculosis. J. Clin. Microbiol. 30: 255– 258.
27. Daley, P.,, S. Thomas, and, M. Pai. 2007. Nucleic acid amplification tests for the diagnosis of tuberculous lymphadenitis: a systematic review. Int. J. Tuberc. Lung Dis. 11: 1166– 1176.
28. DesJardin, L. E.,, M. D. Perkins,, L. Teixeira,, M. D. Cave, and, K. D. Eisenach. 1996. Alkaline decontamination of sputum specimens adversely affects stability of mycobacterial mRNA. J. Clin. Microbiol. 34: 2435– 2439.
29. Desjardin, L. E.,, Y. Chen,, M. D. Perkins,, L. Teixeira,, M. D. Cave, and, K. D. Eisenach. 1998. Comparison of the ABI 7700 system (TaqMan) and competitive PCR for quantification of IS6110 DNA in sputum during treatment of tuberculosis. J. Clin. Microbiol. 36: 1964– 1968.
30. Diaz, R.,, K. Kremer,, P. E. de Haas,, R. I. Gomez,, A. Marrero,, J. A. Valdivia,, J. D. van Embden, and, D. van Soolingen. 1998. Molecular epidemiology of tuberculosis in Cuba outside of Havana, July 1994-June 1995: utility of spoligotyping versus IS6110 restriction fragment length polymorphism. Int. J. Tuberc. Lung Dis. 2: 743– 750.
31. Dinnes, J.,, J. Deeks,, H. Kunst,, A. Gibson,, E. Cummins,, N. Waugh,, F. Drobniewski, and, A. Lalvani. 2007. A systematic review of rapid diagnostic tests for the detection of tuberculosis infection. Health Technol. Assess. 11: 1– 311.
32. 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.
33. Dye, C.,, S. Scheele,, P. Dolin,, V. Pathania, and, M. C. Raviglione. 1999. Consensus statement. Global burden of tuberculosis: estimated incidence, prevalence, and mortality by country. WHO Global Surveillance and Monitoring Project. JAMA 282: 677– 686.
34. Eisenach, K. D.,, M. D. Cave,, J. H. Bates, and, J. T. Crawford. 1990. Polymerase chain reaction amplification of a repetitive DNA sequence specific for Mycobacterium tuberculosis. J. Infect. Dis. 161: 977– 981.
35. 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.
36. Fauci, A. S., and the NIAID Tuberculosis Working Group. 2008. Multidrug-resistant and extensively drug resistant tuberculosis: the National Institute of Allergy and Infectious Diseases research agenda and recommendations for priority research. J. Infect. Dis. 197: 1493– 1498.
37. Feng, Z.,, M. H. Levy, and, W. Sumin. 1997. Sputum microscopy results at two and three months predict outcome of TB treatment. Int. J. Tuberc. Lung Dis. 1: 570– 572.
38. Flores, L. L.,, M. Pai,, J. M. Colford, Jr., and, L. W. Riley. 2005. In-house nucleic acid amplification tests for the detection of Mycobacterium tuberculosis in sputum specimens: meta-analysis and meta-regression. BMC Microbiol. 5: 55. doi:10.1186/1471-2180-5– 55.
39. Fomukong, N. G.,, T. H. Tang,, S. al Maamary,, W. A. Ibrahim,, S. Ramayah,, M. Yates,, Z. F. Zainuddin, and, J. W. Dale. 1994. Insertion sequence typing of Mycobacterium tuberculosis: characterization of a widespread subtype with a single copy of IS6110. Tuber. Lung Dis. 75: 435– 440.
40. Forbes, B. A. 2003. Introducing a molecular test into the clinical microbiology laboratory: development, evaluation, and validation. Arch. Pathol. Lab. Med. 127: 1106– 1111.
41. Forbes, B. A.,, G. E. Pfyffer, and, K. E. Eisenach. 2005. Molecular diagnosis of infection, p. 85-98. In S. T. Cole,, K. D. Eisenach,, D. N. McMurray, and, W. R. Jacobs, Jr. (ed.), Tuberculosis and the Tubercle Bacillus. ASM Press, Washington, DC.
42. Foulds, J.,, and R. O’Brien. 1998. New tools for the diagnosis of tuberculosis: the perspective of developing countries. Int. J. Tuberc. Lung Dis. 2: 778– 783.
43. Franco-Alvarez de Luna, F.,, P. Ruiz,, J. Gutierrez, and, M. Casal. 2006. Evaluation of the GenoType Mycobacteria Direct Assay for detection of Mycobacterium tuberculosis complex and four atypical mycobacterial species in clinical samples. J. Clin. Microbiol. 44: 3025– 3027.
44. 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.
45. 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.
46. Goessens, W. H.,, P. de Man,, J. G. Koeleman,, A. Luijendijk,, R. te Witt,, H. P. Endtz, and, A. van Belkum. 2005. Comparison of the COBAS AMPLICOR M. tuberculosis and BDProbeTec ET assays for detection of Mycobacterium tuberculosis in respiratory specimens. J. Clin. Microbiol. 43: 2563– 2566.
47. Gordin, F. M.,, G. Slutkin,, G. Schecter,, P. C. Goodman, and, P. C. Hopewell. 1989. Presumptive diagnosis and treatment of pulmonary tuberculosis based on radiographic findings. Am. Rev. Respir. Dis. 139: 1090– 1093.
48. Goyal, M.,, N. A. Saunders,, J. D. van Embden,, D. B. Young, and, R. J. Shaw. 1997. Differentiation of Mycobacterium tuberculosis isolates by spoligotyping and IS6110 restriction fragment length polymorphism. J. Clin. Microbiol. 35: 647– 651.
49. Greco, S.,, E. Girardi,, A. Navarra, and, C. Saltini. 2006. Current evidence on diagnostic accuracy of commercially based nucleic acid amplification tests for the diagnosis of pulmonary tuberculosis. Thorax 61: 783– 790.
50. Guerra, R. L.,, J. F. Baker,, R. Alborz,, D. T. Armstrong,, J. A. Kiehlbauch,, M. B. Conde,, S. E. Dorman, and, N. M. Hooper. 2008. Specimen dilution improves sensitivity of the amplified Mycobacterium tuberculosis direct test for smear microscopy-positive respiratory specimens. J. Clin. Microbiol. 46: 314– 316.
51. Guio, H.,, Y. Okayama,, Y. Ashino,, H. Saitoh,, P. Xiao,, M. Miki,, N. Yoshihara, and, S. Nakanowatari. 2006. Method for efficient storage and transportation of sputum specimens for molecular testing of tuberculosis. Int. J. Tuberc. Lung Dis. 10: 906– 910.
52. Haldar, S.,, S. Chakravorty,, M. Bhalla,, S. De Majumdar, and, J. S. Tyagi. 2007. Simplified detection of Mycobacterium tuberculosis in sputum using smear microscopy and PCR with molecular beacons. J. Med. Microbiol. 56: 1356– 1362.
53. 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.
54. Hellyer, T. J.,, L. E. Des Jardin,, G. L. Hehman,, M. D. Cave, and, K. D. Eisenach. 1999. Quantitative analysis of mRNA as a marker for viability of Mycobacterium tuberculosis. J. Clin. Microbiol. 37: 290– 295.
55. 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. The insertion element IS 987 for Mycobacterium bovis BCG is located in a hot spot integration region for insertion elements in M. tuberculosis strains. Infect. Immun. 59: 2695– 2705.
56. Herrara, E. A.,, and M. Segovia. 1996. Evaluation of mtp40 genomic fragment amplification for specific detection of Mycobacterium tuberculosis in clinical specimens. J. Clin. Microbiol. 34: 1108– 1113.
57. Hillemann, D.,, M. Weizenegger,, T. Kubica,, E. Richter, and, S. Nieman. 2005. Use of the Genotype MTBDR assay for the rapid detection of rifampin and isoniazid resistance in Mycobacterium tuberculosis complex isolates. J. Clin. Microbiol. 43: 3699– 3703.
58. Hillemann, D.,, S. RüschGerdes, and, E. Richter. 2007. Evaluation of the GenoType MTBDRplus assay for rifampin and isoniazid susceptibility testing of Mycobacterium tuberculosis strains and clinical specimens. J. Clin. Microbiol. 45: 2635– 2640.
59. Iinuma Y.,, S. Ichiyama,, S. Yamori,, S. Yamori,, J. Oohama,, N. Takagi,, Y. Hasegawa,, K. Shimokata, and, N. Nakashima. 1998. Diagnostic value of the Amplicor PCR assay for initial diagnosis and assessment of treatment response for pulmonary tuberculosis. Microbiol. Immunol. 42: 281– 287.
60. Iwamoto, T.,, T. Sonobe, and, K. Hayashi. 2003. Loop-mediated isothermal amplification of direct detection of Mycobacterium tuberculosis complex, M. avium, and M. intracellulare in sputum samples. J. Clin. Microbiol. 41: 2616– 2622.
61. Johansen, I. S.,, B. Lundgren,, A. Sosnovskaja, and, V. O. Thomsen. 2003. Direct detection of multidrug-resistant Mycobacterium tuberculosis in clinical specimens in low-and high-incidence countries by line probe assay. J. Clin. Microbiol. 41: 4454– 4456.
62. Jureen, P.,, J. Werngren, and, S. E. Hoffner. 2004. Evaluation of the line probe assay (LiPA) for rapid detection of rifampicin resistance in Mycobacterium tuberculosis. Tuberculosis (Edinburgh) 84: 311– 316.
63. 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.
64. Lebrun, L.,, N. Gönüllü,, N. Boutros,, A. Davoust,, M. Guibert,, D. Ingrand,, J. C. Ghnassia,, V. Vincent, and, F. Doucet-Populaire. 2003. Use of the INNO-LiPA assay for rapid identification of mycobacteria. Diagn. Microbiol. Infect. Dis. 46: 151– 153.
65. Lim, T. K.,, J. Cherian,, K. L. Poh, and, T. Y. Leong. 2000. The rapid diagnosis of smear-negative pulmonary tuberculosis: a cost-effectiveness analysis. Respirology 5: 403– 409.
66. Lim, T. K.,, A. Mukhopadhyay,, A. Gough,, K.-L. Khoo,, S.-M. Khoo,, K.-H. Lee, and, G. Kumararasinghe. 2003. Role of clinical judgment in the application of a nucleic acid amplification test for the rapid diagnosis of pulmonary tuberculosis. Chest 124: 902– 908.
67. Lin, S. Y.,, W. Probert,, M. Lo, and, E. Desmond. 2004. Rapid detection of isoniazid and rifampin resistance mutations in Mycobacterium tuberculosis complex from cultures or smear-positive sputa by use of molecular beacons. J. Clin. Microbiol. 42: 4204– 4208.
68. Ling, D. I.,, A. A. Zwerling, and, M. Pai. 2008. GenoType MTBDR assays for the diagnosis of multidrug-resistant tuberculosis: a meta-analysis. Eur. Respir. J. 32: 1165– 1174.
69. Ling, D. I.,, L. L. Flores,, L. W. Riley, and, M. Pai. 2008. Commercial nucleic-acid amplification tests for diagnosis of pulmonary tuberculosis in respiratory specimens: meta-analysis and meta-regression. PLoS ONE 3: el536.
70. Mäkinen, J.,, H. J. Marttila,, M. Marjamaki,, M. K. Viljanen, and, H. Soini. 2006. Comparison of two commercially available DNA line probe assays for detection of multidrug-resistant Mycobacterium tuberculosis. J. Clin. Microbiol. 44: 350– 352.
71. Marttila, H. J.,, H. Soini,, E. Vyshnevskaya,, B. I. Vyshnevsky,, T. F. Otten,, A. V. Vasilyef, and, M. K. Viljanen. 1999. Line probe assay in the rapid detection of rifampin-resistant Mycobacterium tuberculosis directly from clinical specimens. Scand. J. Infect. Dis. 31: 269– 273.
72. Mazars, E.,, S. Lesjean,, A. L. Banuls,, M. Gilbert,, V. Vincent,, B. Giquel,, M. Tibayrenc,, C. Locht, and, P. Supply. 2001. High-resolution minisatellite-based typing as a portable approach to global analysis of Mycobacterium tuberculosis molecular epidemiology. Proc. Natl. Acad. Sci. USA 98: 1901– 1906.
73. McHugh, T. D.,, C. F. Pope,, C. L. Ling,, S. Patel,, O. J. Billington,, R. D. Gosling,, M. C. Lipman, and, S. H. Gillespie. 2004. Prospective evaluation of BDProbeTec strand displacement amplification (SDA) system for diagnosis of tuberculosis in non-respiratory and respiratory samples. J. Med. Microbiol. 53: 1215– 1219.
74. Mijs, W.,, K. De Vreese,, A. Devos,, H. Pottel,, A. Valgaeren,, C. Evans,, J. Norton,, D. Parker,, L. Rigouts,, F. Portaels,, U. Reischl,, S. Watterson,, G. Pfyffer, and, R. Rossau. 2002. Evaluation of a commercial line probe assay for identification of Mycobacterium species from liquid and solid culture. Eur. J. Microbiol. Infect. Dis. 21: 794– 802.
75. 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 fluorogenic probes and real-time PCR. J. Clin. Microbiol. 40: 4143– 4147.
76. Moore, D. F.,, J. I. Curry,, C. A. Knott, and, V. Jonas. 1996. Amplification of rRNA for assessment of treatment response of pulmonary tuberculosis patients during antimicrobial therapy. J. Clin. Microbiol. 34: 1745– 1749.
77. Morgan, M.,, S. Kalantri,, L. Flores, and, M. Pai. 2005. A commercial line probe assay for the rapid detection of rifampicin resistance in Mycobacterium tuberculosis: a systematic review and meta-analysis. BMC Infect. Dis. 5: 62. doi: 10.1186/1471-2334-5– 62.
78. Mori, Y.,, K. Nagamine,, N. Tomita, and, T. Notomi. 2001. Detection of loop-mediated isothermal amplification reaction by turbidity derived from magnesium pyrophosphate formation. Biochem. Biophys. Res. Commun. 289: 150– 154.
79. Mostowy, S.,, D. Cousins,, J. Brinkman,, A. Aranaz, and, M. A. Behr. 2002. Genomic deletions suggest a phylogeny for the Mycobacterium tuberculosis complex. J. Infect. Dis. 186: 74– 80.
80. Nagamine, K.,, K. Watanabe,, K. Ohtsuka,, T. Hase, and, T. Notomi. 2001. Loop-mediated isothermal amplification reaction using a non-denatured template. Clin. Chem. 9: 1742– 1743.
81. Nagamine, K.,, T. Hase, and, T. Notomi. 2002. Accelerated reaction by loop-mediated isothermal amplification using loop primers. Mol. Cell. Probes 16: 223– 229.
82. Nahid, P.,, M. Pai, and, P. C. Hopewell. 2006. Advances in the diagnosis and treatment of tuberculosis. Proc. Am. Thorac. Soc. 3: 103– 110.
83. Noordhoek, G. T.,, S. Mulder,, P. Wallace, and, A. M. van Loon. 2004. Multicentre quality control study for detection of Mycobacterium tuberculosis in clinical samples by nucleic amplification methods. Clin. Microbiol. 10: 295– 301.
84. Notomi, T.,, H. Okayama,, H. Masubuchi,, T. Yonekawa,, K. Watanabe,, N. Amino, and, T. Hase. 2000. Loop-mediated isothermal amplification. Nucleic Acids Res. 28: E63.
85. Novais, R. C.,, S. Borsuk,, O. A. Dellagostin, and, Y. R. Thorstenson. 2008. Molecular inversion probes for sensitive detection of Mycobacterium tuberculosis. J. Microbiol. Methods 72: 60– 66.
86. Pai, M.,, L. L. Flores,, N. Pai,, A. Hubbard,, L. W. Riley, and, J. M. Colford, Jr. 2003. Diagnostic accuracy of nucleic acid amplification tests for tuberculous meningitis: a systematic review and meta-analysis. Lancet Infect. Dis. 3: 633– 643.
87. Pai, M.,, L. L. Flores,, A. Hubbard,, L. W. Riley, and, J. M. Colford, Jr. 2004. Nucleic acid amplification tests in the diagnosis of tuberculous pleuritis: a systematic review and meta-analysis. BMC Infect. Dis. 4: 6. www.biomedicalcentral.com/1471-2334/4/6.
88. Pai, M.,, M. McCulloch,, W. Enanoria, and, J. M. Colford. 2004. Systematic reviews of diagnostic test evaluations: what’s behind the scenes? ACP J. Club 141: A11– A13.
89. Pai, M.,, and R. O’Brien. 2006. Tuberculosis diagnostics trials: do they lack methodological rigor? Exp. Rev. Mol. Diagn. 6: 509– 514.
90. 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.
91. Patnaik, M.,, K. Liegmann, and, J. B. Peter. 2001. Rapid detection of smear-negative Mycobacterium tuberculosis by PCR and sequencing for rifampin resistance with DNA extracted directly from slides. J. Clin. Microbiol. 39: 51– 52.
92. Pfyffer, G. E.,, P. Kissling,, E. M. Jahn,, H. M. Welscher,, M. Salfinger, and, R. Weber. 1996. Diagnostic performance of amplified Mycobacterium tuberculosis direct test with cerebrospinal fluid, other nonrespiratory, and respiratory specimens. J. Clin. Microbiol. 34: 834– 841.
93. Pfyffer, G. E.,, P. Funke-Kissling,, E. Rundler, and, R. Weber. 1999. Performance characteristic of the BDProbeTec System for direct detection of Mycobacterium tuberculosis complex in respiratory specimens. J. Clin. Microbiol. 37: 137– 140.
94. Piersimoni, C.,, and C. Scarparo. 2003. Relevance of commercial amplification methods for direct detection of Mycobacterium tuberculosis complex in clinical samples. J. Clin. Microbiol. 41: 5355– 5365.
95. Piersimoni, C.,, D. Nista,, D. Zallocco,, M. Galassi,, M. E. Cimarelli, and, A. Tubaldi. 2005. Clinical suspicion as a primary guidance to use commercial amplification tests for rapid diagnosis of pulmonary tuberculosis. Diagn. Microbiol. Infect. Dis. 53: 195– 200.
96. Piersimoni, C.,, A. Telenti,, M. R. Murray,, H. El-Hajj, and, W. R. Jacobs. 2006. Current perspectives on drug susceptibility testing of Mycobacterium tuberculosis complex: the automated nonradiometric systems. J. Clin. Microbiol. 44: 20– 28.
97. Pollock, N.,, J. Westerling, and, A. Sloutsky. 2006. Specimen dilution increases the diagnostic utility of the Gen-Probe Mycobacterium tuberculosis Direct Test. Am. J. Clin. Pathol. 126: 142– 147.
98. Pontus, J.,, J. Werngren, and, S. E. Hoffner. 2004. Evaluation of the line probe assay (LiPA) for rapid detection of rifampicin resistance in Mycobacterium tuberculosis. Tuberculosis 84: 311– 316.
99. Quezada, C. M.,, E. Kamanzi,, J. Mukamutara,, P. De Rijk,, L. Rigouts,, F. Portaels, and, Y. Ben Amor. 2007. Implementation validation performed in Rwanda to determine whether the INNO-LiPA Rif.TB line probe assay can be used for detection of multidrug-resistant Mycobacterium tuberculosis in low-resource countries. J. Clin. Microbiol. 45: 3111– 3114.
100. Rajalahti, I.,, P. Vuorinen,, L. Liippo,, M. M. Nieminen, and, A. Miettinen. 2001. Evaluation of commercial DNA and rRNA amplification assays for assessment of treatment outcome in pulmonary tuberculosis patients. Eur. J. Microbiol. Infect. Dis. 20: 746– 750.
101. Ramarokoto, H.,, A. Randriamiharisoa,, T. Rakotoarisaonina,, T. Rasolovavalona,, V. Rasolofo, and, S. Chanteau. 2002. Bacteriological follow-up of tuberculosis treatment: a comparative study of smear microscopy and culture results at the second month of treatment. Int. J. Tubercle Lung Dis. 10: 909– 912.
102. Rattan, A.,, A. Kalia, and, N. Ahmad. 1998. Multidrug-resistant Mycobacterium tuberculosis: molecular perspectives. Emerg. Infect. Dis. 4: 195– 209.
103. Reider, H. L. 1996. Sputum smears conversion during directly observed treatment for tuberculosis. Tubercle Lung Dis. 77: 124– 129.
104. Roos, B. R.,, M. R. A. van Cleeff,, W. A. Githui,, L. Kivihya-Ndugga,, J. A. Odhiambo,, D. K. Kibuga, and, P. R. Klatser. 1998. Cost-effectiveness of the polymerase chain reaction versus smear examination for the diagnosis of tuberculosis in Kenya: a theoretical model. Int. J. Tuberc. Lung Dis. 2: 235– 241.
105. Roring, S.,, D. Brittain,, A. E. Bunschoten,, M. S. Hughes,, R. A. Skuce,, J. D. van Embden, and, S. D. Neill. 1998. Spacer oligotyping of Mycobacterium bovis isolates compared to typing by restriction fragment length polymorphism using PGRS, DR and IS6110 probes. Vet. Microbiol. 61: 111– 120.
106. 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 resistance to rifampin. Antimicrob. Agents Chemother. 41: 2093– 2098.
107. Sahadevan, R.,, S. Narayanan,, C. N. Paramasivan,, R. Prabhakar, and, P. R. Narayanan. 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.
108. Sarmiento, O. L.,, K. A. Weigle,, J. Alexander,, D. J. Weber, and, W. C. Miller. 2003. Assessment by meta-analysis of PCR for diagnosis of smear-negative pulmonary tuberculosis. J. Clin. Microbiol. 41: 3233– 3240.
109. Savine, E.,, R. M. Warren,, G. D. van der Spuy,, N. Beyers,, P. D. van Helden,, C. Locht, and, P. Supply. 2002. Stability of variable-number tandem repeats of mycobacterial interspersed repetitive units from 12 loci in serial isolates of Mycobacterium tuberculosis. J. Clin. Microbiol. 40: 4561– 4566.
110. Seagar, A.-L.,, C. Prendergast,, F. X. Emmanuel,, A. Rayner,, S. Thomson, and, I. F. Laurenson. 2008. Evaluation of the GenoType Mycobacteria Direct assay for the simultaneous detection of the Mycobacterium tuberculosis complex and four atypical mycobacterial species in smear-positive respiratory specimens. J. Med. Microbiol. 57: 605– 611.
111. Small, P. M.,, and M. D. Perkins. 2000. More rigour needed in trials of new diagnostic agents for tuberculosis. Lancet 354: 1048– 1049.
112. Somerville, W.,, L. Thiebert,, K. Schwartzman, and, M. A. Behr. 2005. Extraction of Mycobacterium tuberculosis DNA: a question of containment. J. Clin. Microbiol. 43: 2996– 2997.
113. 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.
114. Somoskovi, A.,, J. Dormandy,, D. Mitsani,, J. Rivenburg, and, M. Salfinger. 2006. Use of smear-positive samples to assess the PCR-based Genotype MTBDR assay for rapid, direct detection of the Mycobacterium tuberculosis complex as well as its resistance to isoniazid and rifampin. J. Clin. Microbiol. 44: 4459– 4463.
115. Suffys, P. N.,, A. da Silva Rocha,, M. de Oliveira,, C. E. Dias Campos,, A. M. Werneck Barreto,, F. Portaels,, L. Rigouts,, G. Wouters,, G. Jannes,, G. van Reybroeck,, W. Mijs, and, B. Vanderborght. 2001. Rapid identification of mycobacteria to the species level using INNO-LiPA mycobacteria, a reverse hybridization assay. J. Clin. Microbiol. 39: 4477– 4482.
116. Taegtmeyer, M.,, N. J. Beeching,, J. Scott,, K. Seddon,, S. Jamieson,, S. B. Squire,, H. C. Mwandumba,, A. R. O. Miller,, P. D. O. Davies, and, C. M. Perry. 2008. The clinical impact of nucleic acid amplification tests on the diagnosis and management of tuberculosis in a British hospital. Thorax 63: 317– 321.
117. Telenti, A.,, N. Honoré,, C. Bernasconi,, J. March,, A. Ortega,, H. E. Takiff, and, S. T. Cole. 1997. Genotyping assessment of isoniazid and rifampin resistance in Mycobacterium tuberculosis: a blind study at reference laboratory level. J. Clin. Microbiol. 35: 719– 723.
118. Thomsen, V. Ø.,, A. K. Jensen,, M. Buser,, S. P. Schulz, and, H. J. Burkardt. 1999. Monitoring treatment of patients with pulmonary tuberculosis; can PCR be applied? J. Clin. Microbiol. 37: 3601– 3607.
119. Tortoli, E.,, and F. Marcelli. 2007. Use of the INNO LiPA Rif.TB for detection of Mycobacterium tuberculosis DNA directly in clinical specimens and for simultaneous determination of rifampin susceptibility. Eur. J. Microbiol. Dis. 26: 51– 55.
120. Traore, H.,, A. van Deun,, I. C. Shamputa,, L. Rigouts, and, F. Portaels. 2006. Direct detection of Mycobacterium tuberculosis complex DNA and rifampin resistance in clinical specimens from tuberculosis patients by line probe assay. J. Clin. Microbiol. 44: 4384– 4388.
121. van der Vliet, G. M. E.,, P. Schepers,, R. A. F. Schukkink,, B. van Gemen, and, P. R. Klatser. 1994. Assessment of mycobacterial viability by RNA amplification. Antimicrob. Agents Chemother. 38: 1959– 1965.
122. 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, and, P. M. Small. 1993. Strain identification of Mycobacterium tuberculosis by DNA fingerprinting: recommendations for a standardized methodology. J. Clin. Microbiol. 31: 406– 409.
123. 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.
124. van Soolingen, D.,, P. E. de Haas,, J. Haagsma,, T. Eger,, P. W. Hermans,, V. Ritacco,, A. Alito, and, J. D. van Embden. 1994. Use of various genetic markers in differentiation of Mycobacterium bovis strains from animals and humans and for studying epidemiology of bovine tuberculosis. J. Clin. Microbiol. 32: 2425– 2433.
125. van Soolingen, D. 2001. Molecular epidemiology of tuberculosis and other mycobacterial infections: main methodologies and achievements. J. Intern. Med. 249: 1– 26.
126. Vidal, R.,, N. Martin-Casabona, and, A. Juan. 1996. Incidence and significance of acid-fast bacilli in sputum smears at the end of anti tuberculosis treatment. Chest 109: 1562– 1565.
127. Walsh, A.,, and R. McNerney. 2004. Guidelines for establishing trials of new tests to diagnose tuberculosis in endemic countries. Int. J. Tuberc. Lung Dis. 8: 609– 613.
128. Walter, S. D.,, L. Irwig, and, P. P. Glasziou. 1999. Meta-analysis of diagnostic tests with imperfect reference standards. J. Clin. Epidemiol. 52: 943– 951.
129. Wang, J.-Y.,, L. Lee,, C. Chou,, C.-Y. Huang,, S.-K. Wang,, H.-C. Lai,, P.-R. Hsueh, and, K.-T. Luh. 2004. Performance assessment of a nested-PCR assay (the RAPID BAP-M. tuberculosis) and the BD ProbeTec ET system for detection of Mycobacterium tuberculosis in clinical specimens. J. Clin. Microbiol. 42: 4599– 4603.
130. Wisnivesky, J. P.,, D. Serebrisky,, C. Moore,, H. S. Sacks,, M. C. Iannuzzi, and, T. McGinn. 2005. Validity of clinical prediction rules for isolating inpatients with suspected tuberculosis: a systematic review. J. Gen. Intern. Med. 20: 947– 952.
131. World Health Organization/International Union Against Tuberculosis and Lung Disease. 2004. WHO/IUATLD Global Project on Anti-Tuberculosis Drug Resistance Surveillance. Report No. 3. World Health Organization, Geneva, Switzerland.
132. Yuen, K. Y.,, K. S. Chan,, C. M. Chan,, B. S. Ho,, L. K. Dai,, P. Y. Chau, and, M. H. Ng. 1993. Use of PCR in routine diagnosis of treated and untreated pulmonary specimens. J. Clin. Microbiol. 46: 318– 322.

Tables

Molecular Detection and Characterization of Mycobacterium tuberculosis
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Citation: Forbes B. 2011. Molecular Detection and Characterization of , p 415-436. In Persing D, Tenover F, Tang Y, Nolte F, Hayden R, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555816834.ch26
/content/10.1128/9781555816834.ch26.ch26tab01
TABLE 1
Commercially available molecular assays for the direct detection of drug-resistant MTB complex and/or MTB complex in clinical specimens
Generic image for table
TABLE 1

Commercially available molecular assays for the direct detection of drug-resistant MTB complex and/or MTB complex in clinical specimens

Citation: Forbes B. 2011. Molecular Detection and Characterization of , p 415-436. In Persing D, Tenover F, Tang Y, Nolte F, Hayden R, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555816834.ch26
/content/10.1128/9781555816834.ch26.ch26tab02
TABLE 2
Results of recent meta-analyses and systematic reviews regarding the accuracy of NAA assays for direct detection of complex in clinical specimens
Generic image for table
TABLE 2

Results of recent meta-analyses and systematic reviews regarding the accuracy of NAA assays for direct detection of complex in clinical specimens

Citation: Forbes B. 2011. Molecular Detection and Characterization of , p 415-436. In Persing D, Tenover F, Tang Y, Nolte F, Hayden R, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555816834.ch26
/content/10.1128/9781555816834.ch26.ch26tab03
TABLE 3
Results of recent meta-analyses and systematic reviews regarding the accuracy of line probe assays for direct detection of M. tuberculosis complex
Generic image for table
TABLE 3

Results of recent meta-analyses and systematic reviews regarding the accuracy of line probe assays for direct detection of M. tuberculosis complex

Citation: Forbes B. 2011. Molecular Detection and Characterization of , p 415-436. In Persing D, Tenover F, Tang Y, Nolte F, Hayden R, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555816834.ch26

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