1887

Abstract

The aim of this study was to improve the identification of species in the context of a UK teaching hospital. Real-time PCR assays were established to enable the rapid differentiation between (MTB) complex and species other than (MOTT), followed by 16S rRNA gene sequencing for the speciation of MOTT. Real-time PCR assays gave comparable results to those from the reference laboratory. The implementation of these PCR assays using an improved bead extraction method has enhanced the mycobacterial diagnostic service at the Royal Free Hospital by providing a rapid means of differentiating between MTB complex and MOTT, and would be simple to implement in similar laboratories. Sequence analysis successfully identified a range of spp. representative of those encountered in the clinical setting of the authors, including complex, group, group, and . It provides a useful tool for the identification of MOTT when clinically indicated.

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2007-05-01
2019-11-12
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References

  1. Adekambi, T., Colson, P. & Drancourt, M. ( 2003; ). rpoB-based identification of nonpigmented and late-pigmenting rapidly growing mycobacteria. J Clin Microbiol 41, 5699–5708.[CrossRef]
    [Google Scholar]
  2. Arnold, L. J., Hammond, P. W., Wiese, W. A. & Nelson, N. C. ( 1989; ). Assay formats involving acridinium-ester-labeled DNA probes. Clin Chem 35, 1588–1594.
    [Google Scholar]
  3. Blackwood, K. S., He, C., Gunton, J., Turenne, C. Y., Wolfe, J. & Kabani, A. M. ( 2000; ). Evaluation of recA sequences for identification of Mycobacterium species. J Clin Microbiol 38, 2846–2852.
    [Google Scholar]
  4. Bogard, M., Vincelette, J., Antinozzi, R., Alonso, R., Fenner, T., Schirm, J., Aubert, D., Gaudreau, C., Sala, E. & other authors ( 2001; ). Multicenter study of a commercial, automated polymerase chain reaction system for the rapid detection of Mycobacterium tuberculosis in respiratory specimens in routine clinical practice. Eur J Clin Microbiol Infect Dis 20, 724–731.[CrossRef]
    [Google Scholar]
  5. Broccolo, F., Scarpellini, P., Locatelli, G., Zingale, A., Brambilla, A. M., Cichero, P., Sechi, L. A., Lazzarin, A., Lusso, P. & Malnati, M. S. ( 2003; ). Rapid diagnosis of mycobacterial infections and quantitation of Mycobacterium tuberculosis load by two real-time calibrated PCR assays. J Clin Microbiol 41, 4565–4572.[CrossRef]
    [Google Scholar]
  6. Brown-Elliott, B. A. & Wallace, R. J. ( 2002; ). Clinical and taxonomic status of pathogenic nonpigmented or late-pigmenting rapidly growing mycobacteria. Clin Microbiol Rev 15, 716–746.[CrossRef]
    [Google Scholar]
  7. Collins, E. H., Grange, T. M. & Yates, M. D. ( 1997; ). Tuberculosis Bacteriology: Organisation and Practice, 2nd edn, London: Butterworth Heinemann.
  8. Conaty, S. J., Claxton, A. P., Enoch, D. A., Hayward, A. C., Lipman, M. C. I. & Gillespie, S. H. ( 2005; ). The interpretation of nucleic acid amplification tests for tuberculosis: do rapid tests change treatment decisions?. J Infect 50, 187–192.[CrossRef]
    [Google Scholar]
  9. Davies, A. P., Newport, L. E., Billington, O. J. & Gillespie, S. H. ( 1999; ). Length of time to laboratory diagnosis of Mycobacterium tuberculosis infection: comparison of in-house methods with reference laboratory results. J Infect 39, 205–208.[CrossRef]
    [Google Scholar]
  10. De Beenhouwer, H., Liang, Z., de Rizk, P., van Eekeren, C. & Portaels, F. ( 1995; ). Detection and identification of mycobacteria by DNA amplification and oligonucleotide specific capture plate hybridization. J Clin Microbiol 33, 2994–2998.
    [Google Scholar]
  11. Devulder, G., Perouse de Montclos, M. & Flandrois, J. P. ( 2005; ). A multigene approach to phylogenetic analysis using the genus Mycobacterium as a model. Int J Syst Evol Microbiol 55, 293–302.[CrossRef]
    [Google Scholar]
  12. Fiss, E. H., Chehab, F. F. & Brooks, G. F. ( 1992; ). DNA amplification and reverse dot blot hybridization for detection and identification of mycobacteria to the species level in the clinical laboratory. J Clin Microbiol 30, 1220–1224.
    [Google Scholar]
  13. Gillespie, S. H., Dickens, A. & McHugh, T. D. ( 2000; ). False molecular clusters due to non-random association of IS6110 with Mycobacterium tuberculosis. J Clin Microbiol 38, 2081–2086.
    [Google Scholar]
  14. Hall, L., Doerr, K. A., Wohlfiel, S. L. & Roberts, G. D. ( 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.[CrossRef]
    [Google Scholar]
  15. Han, X. Y., Pham, A. S., Tarrand, J. J., Sood, P. K. & Luthra, R. ( 2002; ). Rapid and accurate identification of mycobacteria by sequencing hypervariable regions of the 16S ribosomal RNA gene. Am J Clin Pathol 118, 796–801.[CrossRef]
    [Google Scholar]
  16. Hong, S. K., Kim, B. J., Yun, Y. J., Lee, K. H., Kim, E. C., Park, E. M., Park, Y. G., Bai, G. H. & Kook, Y. H. ( 2004; ). Identification of Mycobacterium tuberculosis by PCR-linked reverse hybridization using specific rpoB oligonucleotide probes. J Microbiol Methods 59, 71–79.[CrossRef]
    [Google Scholar]
  17. Kasai, H., Ezaki, T. & Harayama, S. ( 2000; ). Differentiation of phylogenetically related slowly growing mycobacteria by their gyrB sequences. J Clin Microbiol 38, 301–308.
    [Google Scholar]
  18. Katoch, V. M. ( 2004; ). Infections due to non-tuberculous mycobacteria (NTM). Indian J Med Res 120, 290–304.
    [Google Scholar]
  19. Kim, B. J., Lee, S. H., Lyu, M. A., Kim, S. J., Bai, G. H., Kim, S. J., Chae, G. T., Kim, E. C., Cha, C. Y. & Kook, Y. H. ( 1999; ). Identification of mycobacterial species by comparative sequence analysis of the RNA polymerase gene (rpoB). J Clin Microbiol 37, 1714–1720.
    [Google Scholar]
  20. Kim, B. J., Hong, S. K., Lee, K. H., Yun, Y. J., Kim, E. C., Park, Y. G., Bai, G. H. & Kook, Y. H. ( 2004; ). Differential identification of Mycobacterium tuberculosis complex and nontuberculous mycobacteria by duplex PCR assay using the RNA polymerase gene (rpoB). J Clin Microbiol 42, 1308–1312.[CrossRef]
    [Google Scholar]
  21. Kim, H., Kim, S.-H., Shim, T.-S., Kim, M.-N., Bai, G.-H., Park, Y.-G., Lee, S.-H., Cha, C.-Y., Kook, Y.-H. & Kim, B.-J. ( 2005; ). PCR restriction fragment length polymorphism analysis (PRA)-algorithm targeting 644 bp Heat Shock Protein 65 (hsp65) gene for differentiation of Mycobacterium spp. J Microbiol Methods 62, 199–209.[CrossRef]
    [Google Scholar]
  22. Kurabachew, M., Enger, O., Sandaa, R., Skuce, R. & Bjorvatn, B. ( 2004; ). A multiplex chain reaction assay for genus-, group- and species-specific detection of mycobacteria. Diagn Microbiol Infect Dis 49, 99–104.[CrossRef]
    [Google Scholar]
  23. Lee, H., Park, H.-J., Cho, S.-N., Bai, G.-H. & Kim, S.-J. ( 2000; ). Species identification of mycobacteria by PCR-restriction fragment length polymorphism of the rpoB gene. J Clin Microbiol 38, 2966–2971.
    [Google Scholar]
  24. Lindbrathen, A., Gaustad, P., Hovig, B. & Tonjum, T. ( 1997; ). Direct detection of Mycobacterium tuberculosis from patients in Norway by ligase chain reaction. J Clin Microbiol 35, 3248–3253.
    [Google Scholar]
  25. McHugh, T. D., Pope, C. F., Ling, C. L., Patel, S., Billington, O. J., Gosling, R. D., Lipman, M. C. & Gillespie, S. H. ( 2004; ). Prospective evaluation of BD ProbeTec strand displacement amplification (SDA) system for diagnosis of tuberculosis in non-respiratory and respiratory samples. J Med Microbiol 53, 1215–1219.[CrossRef]
    [Google Scholar]
  26. O'Sullivan, C. E., Miller, D. R., Schneider, P. S. & Roberts, G. D. ( 2002; ). Evaluation of Gen-Probe amplified Mycobacterium tuberculosis direct test by using respiratory and non-respiratory specimens in a tertiary care center laboratory. J Clin Microbiol 40, 1723–1727.[CrossRef]
    [Google Scholar]
  27. Padilla, E., Gonzalez, V., Manterola, J. M., Perez, A., Quesada, M. D., Gordillo, S., Vilaplana, C., Pallares, M. A., Molinos, S. & other authors ( 2004; ). Comparative evaluation of the new version of the INNO-LiPA Mycobacteria and GenoType mycobacterium assays for identification of Mycobacterium species from MB/BacT liquid cultures artificially inoculated with mycobacterial strains. J Clin Microbiol 42, 3083–3088.[CrossRef]
    [Google Scholar]
  28. Pauls, R. J., Turenne, C. Y., Wolfe, J. N. & Kabani, A. ( 2003; ). A high proportion of novel mycobacteria species identified by 16S rDNA analysis among slowly growing AccuProbe-negative strains in a clinical setting. Am J Clin Pathol 120, 560–566.[CrossRef]
    [Google Scholar]
  29. Portaels, F., Aguiar, J., Fissetle, K., Fonteyne, P. A., de Beenhouwer, H., de Rijk, P., Guedenon, A., Lemans, R., Steunou, C. & other authors ( 1997; ). Direct detection and identification of Mycobacterium ulcerans in clinical specimens by PCR and oligonucleotide specific capture plate hybridization. J Clin Microbiol 35, 1097–1100.
    [Google Scholar]
  30. Ringuet, H., Akoua-Koffi, C., Honore, S., Varnerot, A., Vincent, V., Berche, P., Gaillard, J. L. & Pierre-Audigier, C. ( 1999; ). hsp65 sequencing for identification of rapidly growing mycobacteria. J Clin Microbiol 37, 852–857.
    [Google Scholar]
  31. Roth, A., Reischl, U., Streubel, A., Naumann, L., Koppenstedt, R. M., Habicht, M., Fischer, M. & Mauch, H. ( 2000; ). Novel diagnostic algorithm for identification of mycobacteria using genus-specific amplification of the 16S–23S rRNA gene spacer and restriction endonucleases. J Clin Microbiol 38, 1094–1104.
    [Google Scholar]
  32. Sakai, T., Kobayashi, C. & Shinohara, M. ( 2005; ). Mycobacterium peregrinum infection in a patient with AIDS. Intern Med 44, 266–269.[CrossRef]
    [Google Scholar]
  33. Schinsky, M. F., McNeil, M. N., Whitney, A. M., Steigerwalt, A. G., Lasker, B. A., Floyd, M. M., Hogg, G. G., Brenner, D. J. & Brown, J. M. ( 2000; ). Mycobacterium septicum sp. nov., a new and rapidly growing species associated with catheter-related bacteraemia. Int J Syst Evol Microbiol 50, 575–581.[CrossRef]
    [Google Scholar]
  34. Shrestha, N. K., Tuohy, M. J., Hall, G. S., Reischl, U., Gordon, S. M. & Procop, G. W. ( 2003; ). Detection and differentiation of Mycobacterium tuberculosis and nontuberculous mycobacterial isolates by real time PCR. J Clin Microbiol 41, 5121–5126.[CrossRef]
    [Google Scholar]
  35. Soini, H., Bottger, E. C. & Viljanen, M. K. ( 1994; ). Identification of mycobacteria by PCR-based sequence determination of the 32-kioldalton protein gene. J Clin Microbiol 32, 2944–2947.
    [Google Scholar]
  36. Subcommittee of the Joint Tuberculosis Committee of the British Thoracic Society ( 2000; ). Management of opportunistic mycobacterial infections: Joint Tuberculosis Committee guidelines 1999. Thorax 55, 210–218.[CrossRef]
    [Google Scholar]
  37. Tanaka, I. I., Anno, I. S., Andrade Leite, S. R., Cooksey, R. C. & Leite, C. Q. F. ( 2003; ). Comparison of a multiplex-PCR assay with mycolic acids analysis and conventional methods for the identification of mycobacteria. Microbiol Immunol 47, 307–312.[CrossRef]
    [Google Scholar]
  38. Tortoli, E., Nanetti, A., Piersimoni, C., Chichero Farina, C., Mucignat, G., Scarparo, C., Bartolini, L., Valentini, R., Nista, D. & other authors ( 2001; ). Performance assessment of new multiplex probe assay for identification of mycobacteria. J Clin Microbiol 39, 1079–1084.[CrossRef]
    [Google Scholar]
  39. Turenne, C. Y., Tschetter, L., Wolfe, J. & Kabani, A. ( 2001; ). Necessity of quality controlled 16S rRNA gene sequence databases: identifying nontuberculous Mycobacterium species. J Clin Microbiol 39, 3637–3648.[CrossRef]
    [Google Scholar]
  40. Vaneechoutte, M., Beenhouwer, H. D., Claeys, G., Verschraegen, G., De Rouck, A., Paepe, N., Elaichouni, A. & Portaels, F. ( 1993; ). Identification of Mycobacterium species by using amplified ribosomal DNA restriction analysis. J Clin Microbiol 31, 2061–2065.
    [Google Scholar]
  41. Velayati, A. A., Boloorsaze, M. R., Farnia, P., Mohammadi, F., Karam, M. B., Soheyla-Zahirifard, M. D. & Masjedi, M. R. ( 2005; ). Mycobacterium gastri causing disseminated infection in children of same family. Pediatr Pulmonol 39, 284–287.[CrossRef]
    [Google Scholar]
  42. Yam, W.-C., Yuen, K.-Y., Kam, S.-Y., Yiu, L.-S., Chan, K.-S., Leung, C.-C., Tam, C.-M., Ho, P.-O., Yew, W.-W. & other authors ( 2006; ). Diagnostic application of genotypic identification of mycobacteria. J Med Microbiol 55, 529–536.[CrossRef]
    [Google Scholar]
  43. Zolg, J. W. & Philippi-Schulz, S. ( 1994; ). The superoxide dismutase gene, a target for detection and identification of Mycobacteria by PCR. J Clin Microbiol 32, 2801–2812.
    [Google Scholar]
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