1887

Abstract

Nucleic acid amplification technology is examined from the critical viewpoint of a clinical microbiologist working in a routine diagnostic bacteriology laboratory. Widely recognised limitations of amplification technology include those of false-positive and false-negative results, the difficulty of obtaining quantitative results, the problem of using this technology for susceptibility testing, and the difficulty of detecting routinely the wide range of possible pathogens contained in a clinical sample. On the positive side, amplification technology brings welcome new possibilities for rapid detection of specific pathogens in a sample, including viruses, slowly growing bacteria, fastidious or uncultivable bacteria, fungi and protozoa. Other possible applications include screening normally sterile clinical samples for non-specific bacterial contamination and the use of amplification-based DNA fingerprinting methods for identification and typing of microorganisms. Nevertheless, it is predicted that–in contrast to research and reference facilities–routine bacteriology laboratories will continue to rely on culture as the preferred ‘amplification method’ for most diagnostic applications.

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1997-03-01
2024-04-18
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References

  1. Saiki R. K., Scharf S., Faloona F. Enzymatic amplification of β-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. Science 1985; 230:1350–1354
    [Google Scholar]
  2. Mullis K. B., Faloona F. A. Specific synthesis of DNA in vitro via a polymerase-catalyzed chain reaction. Methods Enzymol 1987; 155:335–350
    [Google Scholar]
  3. Noordhoek G. T., Kolk A. H. J., Bjune G. Sensitivity and specificity of PCR for detection of Mycobacterium tuberculosis: a blind comparison study among seven laboratories. J Clin Microbiol 1994; 32:277–284
    [Google Scholar]
  4. Enns R. K., Bromley S. E., Day S. P. Molecular Diagnostic Methods for Infectious Diseases, Approved Guideline. NCCLS MM3-A. December 1995
  5. Kwok S., Higuchi R. Avoiding false positives with PCR. Nature 1989; 339:237–238
    [Google Scholar]
  6. Loewy Z. G., Mecca J., Diaco R. Enhancement of Borrelia burgdorferi PCR by uracil N-glycosylase. J Clin Microbiol 1994; 32:135–138
    [Google Scholar]
  7. Kocagöz T., Yilmaz E., Özkara S. Detection of Mycobacterium tuberculosis in sputum samples by polymerase chain reaction using a simplified procedure. J Clin Microbiol 1993; 31:1435–1438
    [Google Scholar]
  8. Böddinghaus B., Rogall T., Flohr Blöcker H., Böttger E. C. Detection and identification of Mycobacteria by amplification of rRNA. J Clin Microbiol 1990; 28:1751–1759
    [Google Scholar]
  9. Jonas V., Alden M. J., Curry J. I. Detection and identification of Mycobacterium tuberculosis directly from sputum sediments by amplification of rRNA. J Clin Microbiol 1993; 31:2410–2416
    [Google Scholar]
  10. van der Vliet G. M. E., Schukkink R. A. F., van Gemen B., Schepers P., Klatser P. R. Nucleic acid sequence-based amplification (NASBA) for the identification of mycobacteria. J Gen Microbiol 1993; 139:2423–2429
    [Google Scholar]
  11. Pierre C., Lecossier D., Boussougant Y. Use of a reamplification protocol improves sensitivity of detection of Mycobacterium tuberculosis in clinical samples by amplification of DNA. J Clin Microbiol 1991; 29:712–717
    [Google Scholar]
  12. Fiss E. H., Chehab F. F., Brooks G. F. DNA amplification and reverse dot blot hybridization for detection and identification of Mycobacteria to the species level in the clinical laboratory. J Clin Microbiol 1992; 30:1220–1224
    [Google Scholar]
  13. Wilson S. M., McNerney R., Nye P. M., Godfrey-Faussett P. D., Stoker N. G., Voller A. Progress toward a simplified polymerase chain reaction and its application to diagnosis of tuberculosis. J Clin Microbiol 1993; 31:776–782
    [Google Scholar]
  14. Zwadyk P., Down J. A., Myers N., Dey M. S. Rendering of mycobacteria safe for molecular diagnostic studies and development of a lysis method for strand displacement amplification and PCR. J Clin Microbiol 1994; 32:2140–2146
    [Google Scholar]
  15. Stuyver L., Rossau R., Wyseur A. Typing of hepatitis C virus isolates and characterization of new subtypes using a line probe assay. J Gen Virol 1993; 74:1093–1102
    [Google Scholar]
  16. Pallen M. J., Puckey L. H., Wren B. W. A rapid, simple method for detecting PCR failure. PCR Methods Appli 1992; 2:91–92
    [Google Scholar]
  17. Ursi J.-P., Ursi D., Ieven M., Pattyn S. R. Utility of an internal control for the polymerase chain reaction. Application to detection of Mycoplasma pneumoniae in clinical specimens. APMIS 1992; 100:635–639
    [Google Scholar]
  18. Boom R., Sol C. J. A., Salimans M. M. M., Jansen C. L., Wertheim-van Dillen P. M. E., van der Noordaa J. Rapid and simple method for purification of nucleic acids. J Clin Microbiol 1990; 28:495–503
    [Google Scholar]
  19. Cheung R. C., Matsui S. M., Greenberg H. B. Rapid and sensitive method for detection of hepatitis C virus RNA by using silica particles. J Clin Microbiol 1994; 32:2593–2597
    [Google Scholar]
  20. Mazurek G. H., Reddy V., Murphy D., Ansari T. Detection of Mycobacterium tuberculosis in cerebrospinal fluid following immunomagnetic enrichment. J Clin Microbiol 1996; 34:450–453
    [Google Scholar]
  21. Olsvik O., Popovic T., Skjerve E. Magnetic separation techniques in diagnostic microbiology. Clin Microbiol Rev 1994; 7:43–54
    [Google Scholar]
  22. Fluit A. C., Torensma R., Visser M. J. Detection of Listeria monocytogenes in cheese with the magnetic immuno-poly-merase chain reaction assay. Appl Environ Microbiol 1993; 59:1289–1293
    [Google Scholar]
  23. Mangiapan G., Vokurka M., Schouls L. Sequence capture-PCR improves detection of mycobacterial DNA in clinical specimens. J Clin Microbiol 1996; 34:1209–1215
    [Google Scholar]
  24. Niederhauser C., Luthy J., Candrian U. Direct detection of Listeria monocytogenes using paramagnetic bead DNA extraction and enzymatic DNA amplification. Mol Cell Probes 1994; 8:223–228
    [Google Scholar]
  25. Starbuck M. A., Hill P. J., Stewart G. S. Ultra sensitive detection of Listeria monocytogenes in milk by the polymerase chain reaction (PCR). Lett Appl Microbiol 1992; 15:248–252
    [Google Scholar]
  26. Ieven M., Goossens H. Molecular diagnostics in the clinical laboratory: a plea for prudence!. Acta Clin Belg 1995; 50:255–259
    [Google Scholar]
  27. Vuorinen P., Miettinen A., Vuento R., Hällström O. Direct detection of Mycobacterium tuberculosis complex in respiratory specimens by Gen-Probe Amplified Mycobacterium Tuberculosis Direct Test and Roche Amplicor Mycobacterium tuberculosis Test. J Clin Microbiol 1995; 33:1856–1859
    [Google Scholar]
  28. Reischl U., Kochanowski B. Quantitative PCR. A survey of the present technology. Mol Biotechnol 1995; 3:55–71
    [Google Scholar]
  29. Bassler H. A., Flood S. J., Livak K. J., Marmaro J., Knorr R., Batt C. A. Use of a fluorogenic probe in a PCR-based assay for the detection of Listeria monocytogenes . Appl Environ Microbiol 1995; 61:3724–3728
    [Google Scholar]
  30. Centers for Disease Control and Prevention Diagnosis of tuberculosis by nucleic acid amplification methods applied to clinical specimens. Morbid Mortal Weekly Rep 1993; 42:686
    [Google Scholar]
  31. Barry A. L., Thomsberry C. Susceptibility tests: diffusion test procedures. In Balows A., Hausler W. J., Herrmann K. L., Isenberg H. D., Shadomy H. J. (eds) Manual of clinical microbiology 5th edn Washington DC: American Society of Microbiology; 19911117–1125
    [Google Scholar]
  32. Wilton S., Cousins D. Detection and identification of multiple mycobacterial pathogens by DNA amplification in a single tube. PCR Methods Appl 1992; 1:269–273
    [Google Scholar]
  33. Jordan J. A. PCR identification of four medically important Candida species by using a single primer pair. J Clin Microbiol 1994; 32:2962–2967
    [Google Scholar]
  34. Reiman D. A., Falkow S. Identification of uncultured micro organisms: expanding the spectrum of characterized microbial pathogens. Infect Agents Dis 1992; 1:245–253
    [Google Scholar]
  35. Weiss J. B. DNA probes and PCR for diagnosis of parasitic infections. Clin Microbiol Rev 1995; 8:113–130
    [Google Scholar]
  36. Woese C. R. Bacterial evolution. Microbiol Rev 1987; 51:221–271
    [Google Scholar]
  37. Makimura K., Murayama S. Y., Yamaguchi H. Detection of a wide range of medically important fungi by the polymerase chain reaction. J Med Microbiol 1994; 40:358–364
    [Google Scholar]
  38. Telenti A., Imboden P., Marchesi F. Detection of rifampicin-resistance mutations in Mycobacterium tuberculosis . Lancet 1993; 341:647–650
    [Google Scholar]
  39. De Beenhouwer H., Lhiang Z., Jannes G. Rapid detection of rifampicin resistance in sputum and biopsy specimens from tuberculosis patients by PCR and line probe assay. Tuber Lung Dis 1995; 76:425–430
    [Google Scholar]
  40. Ünal S., Hoskins J., Flokowitsch J. E., Wu C. Y. E., Preston D. A., Skatrud P. L. Detection of methicillin-resistant Staphylococci by using the polymerase chain reaction. J Clin Microbiol 1992; 30:1685–1691
    [Google Scholar]
  41. Vilgalys R., Hester M. Rapid genetic identification and mapping of enzymatically amplified ribosomal DNA from several Cryptococcus species. J Bacteriol 1990; 172:4238–4246
    [Google Scholar]
  42. Vaneechoutte M., Dijkshoorn L., Tjernberg I. Identification of Acinetobacter genomic species by amplified ribosomal DNA restriction analysis. J Clin Microbiol 1995; 33:11–15
    [Google Scholar]
  43. Widjojoadmotjo M. N., Fluit A. C., Verhoef J. Rapid identification of bacteria by PCR-single-strand conformation polymorphism. J Clin Microbiol 1994; 32:3002–3007
    [Google Scholar]
  44. Welsh J., McClelland M. Genomic fingerprints produced by PCR with consensus tRNA gene primers. Nucleic Acids Res 1991; 19:861–866
    [Google Scholar]
  45. Jensen M. A., Webster J. A., Straus N. Rapid identification of bacteria on the basis of polymerase chain reaction-amplified ribosomal DNA spacer polymorphisms. Appl Environ Microbiol 1993; 59:945–952
    [Google Scholar]
  46. Kirschner P., Springer B., Vogel U. Genotypic identification of Mycobacteria by nucleic acid sequence determination: report of a 2-year experience in a clinical laboratory. J Clin Microbiol 1993; 31:2882–2889
    [Google Scholar]
  47. Martin F., Vairelles D., Henrion B. Automated ribosomal DNA fingerprinting by capillary electrophoresis of PCR products. Anal Biochem 1993; 214:182–189
    [Google Scholar]
  48. Wiedmann-Al-Ahmad M., Tichy H.-V., Schön G. Characterization of Acinetobacter type strains and isolates obtained from wastewater treatment plants by PCR fingerprinting. Appl Environ Microbiol 1994; 60:4066–4071
    [Google Scholar]
  49. Smith L. M. The future of DNA sequencing. Science 1993; 262:530–532
    [Google Scholar]
  50. Lipshutz R. J., Morris D., Chee M. Using oligonucleotide probe arrays to access genetic diversity. Biotechniques 1995; 19:442–447
    [Google Scholar]
  51. Eggers M., Ehrlich D. A review of microfabricated devices for gene-based diagnostics. Hematol Pathol 1995; 9:1–15
    [Google Scholar]
  52. Strachan N. J., Gray D. I. A rapid general method for the identification of PCR products using a fibre-optic biosensor and its application to the detection of Listeria . Lett Appl Microbiol 1995; 21:5–9
    [Google Scholar]
  53. Kopelman R., Tan W. Near-field optics: imaging single molecules. Science 1993; 262:1382–1384
    [Google Scholar]
  54. Welsh J., McClelland M. Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Res 1990; 18:7213–7218
    [Google Scholar]
  55. Williams J. G. K., Kubelik A. R., Livak K. J., Rafalski J. A., Tingey S. V. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res 1990; 18:6531–6535
    [Google Scholar]
  56. Gürtler V. Typing of Clostridium dijficile strains by PCR-amplification of variable length 16S-23S rDNA spacer regions. J Gen Microbiol 1993; 139:3089–3097
    [Google Scholar]
  57. Kostman J. R., Edlind T. D., LiPuma J. J., Stull T. L. Molecular epidemiology of Pseudomonas cepacia determined by polymerase chain reaction ribotyping. J Clin Microbiol 1992; 30:2084–2087
    [Google Scholar]
  58. Versalovic J., Koeuth T., Lupski J. R. Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes. Nucleic Acids Res 1991; 19:6823–6831
    [Google Scholar]
  59. Goh S.-H., Byrne S. K., Zhang J. L., Chow A. W. Molecular typing of Staphylococcus aureus on the basis of coagulase gene polymorphisms. J Clin Microbiol 1992; 30:1642–1645
    [Google Scholar]
  60. Frénay H. M. E., Theelen J. P. G., Schouls L. M. Discrimination of epidemic and nonepidemic methicillin-resistant Staphylococcus aureus strains on the basis of protein A gene polymorphism. J Clin Microbiol 1994; 32:846–847
    [Google Scholar]
  61. Gardiner D., Hartas J., Currie B., Mathews J. D., Kemp D. J., Sriprakash K. S. Vir typing: a long-PCR typing method for group A streptococci. PCR Methods Appl 1995; 4:288–293
    [Google Scholar]
  62. King V., Clayton C. L. Genomic investigation of phenotypic variation in Campylobacter jejuni flagellin. FEMS Microbiol Lett 1991; 84:107–111
    [Google Scholar]
  63. Vaneechoutte M. Review of DNA fingerprinting techniques for micro-organisms: a proposal for classification and nomenclature. Mol Biotechnol 1996; 6: (in press)
    [Google Scholar]
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