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In Vitro Nucleic Acid Amplification: An Introduction

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Advanced Techniques in Diagnostic Microbiology

Abstract

Over the past decade, the development of a series of in vitro nucleic acid ampli- fication (NAA) technologies has opened new avenues for the detection, identifi- cation, and characterization of pathogenic organisms in diagnostic microbiology (Tang et al., 1997; Jungkind and Kessler, 2002; Yolken, 2002). The promise of these techniques is the replacement of traditional biological amplification of live pathogens by enzymatic amplification of specific nucleic acid sequences. These techniques have reduced the dependency of the clinical microbiology laboratory on culture-based methods and created new opportunities for the field to enhance patient care. According to the theoretical basis for each methods, in vitro nucleic acid amplification techniques can be placed into one of three broad categories, which all share certain advantages over traditional methods, particularly for the detection of fastidious, unculturable, and/or highly contagious organisms (Table 10.1). Application of NAA techniques enhances the speed, sensitivity, and sometimes the specificity of an etiologic diagnosis (Tang et al., 1999; Yolken, 2002; Hayden, 2004).

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References

  • Beggs, M. L., Cave, M. D., Marlowe, C., Cloney, L., Duck, P., & Eisenach, K. D. (1996). Characterization of Mycobacterium tuberculosis complex direct repeat sequence for use in cycling probe reaction. J Clin Microbiol, 34, 2985–9.

    PubMed  CAS  Google Scholar 

  • Birkenmeyer, L. G., & Mushahwar, I. K. (1991). DNA probe amplification methods. J Virol Methods, 35, 117–26.

    Article  PubMed  CAS  Google Scholar 

  • Brow, M. A., Oldenburg, M. C., Lyamichev, V., Heisler, L. M., Lyamicheva, N., Hall, J. G., Eagan, N. J., Olive, D. M., Smith, L. M., Fors, L., & Dahlberg, J. E. (1996). Differentiation of bacterial 16S rRNA genes and intergenic regions and Mycobacterium tuberculosis katG genes by structure-specific endonuclease cleavage. J Clin Microbiol, 34, 3129–37.

    PubMed  CAS  Google Scholar 

  • Brown, D. R., Bryan, J. T., Cramer, H., & Fife, K. H. (1993). Analysis of human papillomavirus types in exophytic condylomata acuminata by hybrid capture and Southern blot techniques. J Clin Microbiol, 31, 2667–73.

    PubMed  CAS  Google Scholar 

  • Carroll, K. C., Aldeen, W. E., Morrison, M., Anderson, R., Lee, D., & Mottice, S. (1998). Evaluation of the Abbott LCx ligase chain reaction assay for detection of Chlamydia trachomatis and Neisseria gonorrhoeae in urine and genital swab specimens from a sexually transmitted disease clinic population. J Clin Microbiol, 36, 1630–3.

    PubMed  CAS  Google Scholar 

  • Cecil, J. A., Howell, M. R., Tawes, J. J., Gaydos, J. C., McKee, Jr. K. T., Quinn, T. C., & Gaydos, C. A. (2001). Features of Chlamydia trachomatis and Neisseria gonorrhoeae infection in male Army recruits. J Infect Dis, 184, 1216–9.

    Article  PubMed  CAS  Google Scholar 

  • Cloney, L., Marlowe, C., Wong, A., Chow, R., & Bryan, R. (1999). Rapid detection of mecA in methicillin resistant Staphylococcus aureus using cycling probe technology. Mol Cell Probes, 13, 191–7.

    Article  PubMed  CAS  Google Scholar 

  • Compton, J. (1991). Nucleic acid sequence-based amplification. Nature, 350, 91–2.

    Article  PubMed  CAS  Google Scholar 

  • Cooksey, R. C., Holloway, B. P., Oldenburg, M. C., Listenbee, S., & Miller, C. W. (2000). Evaluation of the invader assay, a linear signal amplification method, for identification of mutations associated with resistance to rifampin and isoniazid in Mycobacterium tuberculosis. Antimicrob Agents Chemother, 44, 1296–301.

    Article  PubMed  CAS  Google Scholar 

  • Duck, P., Alvarado-Urbina, G., Burdick, B., & Collier, B. (1990). Probe amplifier system based on chimeric cycling oligonucleotides. Biotechniques, 9, 142–8.

    PubMed  CAS  Google Scholar 

  • Eisenstein, B. I. (1990). The polymerase chain reaction. A new method of using molecular genetics for medical diagnosis. N Engl J Med, 322, 178–83.

    Article  PubMed  CAS  Google Scholar 

  • Fong, W. K., Modrusan, Z.,McNevin, J. P., Marostenmaki, J., Zin, B., & Bekkaoui, F. (2000). Rapid solid-phase immunoassay for detection of methicillin-resistant Staphylococcus aureus using cycling probe technology. J Clin Microbiol, 38, 2525–9.

    PubMed  CAS  Google Scholar 

  • Gaydos, C. A., Quinn, T. C., Willis, D., Weissfeld, A., Hook, E. W., Martin, D. H., Ferrero, D. V., & Schachter, J. (2003). Performance of the APTIMA Combo 2 assay for detection of Chlamydia trachomatis and Neisseria gonorrhoeae in female urine and endocervical swab specimens. J Clin Microbiol, 41, 304–9.

    Article  PubMed  CAS  Google Scholar 

  • Harden, S. V., Thomas, D. C., Benoit, N., Minhas, K., Westra, W. H., Califano, J. A., Koch, W., & Sidransky, D. (2004). Real-time gap ligase chain reaction: a rapid semiquantitative assay for detecting p53 mutation at low levels in surgical margins and lymph nodes from resected lung and head and neck tumors. Clin Cancer Res, 10, 2379–85.

    Article  PubMed  CAS  Google Scholar 

  • Hayden, R. T. (2004). In vitro nucleic acid amplification techniques. In: Persing, D. H., Tenover, F. C., Versalovic, J., Tang, Y. W., Unger, E. R., Relman, D. A., & White, T. J., eds. Molecular Microbiology: Diagnostic Principles and Practice. American Society for Microbiology, Washington, DC, pp. 43–69.

    Google Scholar 

  • Hellyer, T. J., Fletcher, T. W., Bates, J. H., Stead, W. W., Templeton, G. L., Cave, M. D., & Eisenach, K. D. (1996). Strand displacement amplification and the polymerase chain reaction for monitoring response to treatment in patients with pulmonary tuberculosis. J Infect Dis, 173, 934–41.

    PubMed  CAS  Google Scholar 

  • Ho, S. K., Chan, T. M., Cheng, I. K., & Lai, K. N. (1999). Comparison of the secondgeneration digene hybrid capture assay with the branched-DNA assay for measurement of hepatitis B virus DNA in serum. J Clin Microbiol, 37, 2461–5.

    PubMed  CAS  Google Scholar 

  • Hollingsworth, R. C., Sillekens, P., van Deursen, P., Neal, K. R., & Irving, W. L. (1996). Serum HCV RNA levels assessed by quantitative NASBA: stability of viral load over time, and lack of correlation with liver disease. J Hepatol., 25, 301–6.

    Article  PubMed  CAS  Google Scholar 

  • Jungkind, D., & Kessler, H. H. (2002). Molecular methods for diagnosis of infectious diseases. In: Truant, A. L., ed. Manual of Commercial Methods in Clinical Microbiology. American Society for Microbiology, Washington, DC, pp. 306–23.

    Google Scholar 

  • Kwoh, D.Y., Davis, G. R., Whitfield, K. M., Chappelle, H. L., DiMichele, L. J., & Gingeras, T. R. (1989). Transcription-based amplification system and detection of amplified human immunodeficiency virus type 1 with a bead-based sandwich hybridization format. Proc Natl Acad Sci USA, 86, 1173–7.

    Article  PubMed  CAS  Google Scholar 

  • La Rocco, M. T., Wanger, A., Ocera, H., & Macias, E. (1994). Evaluation of a commercial rRNA amplification assay for direct detection of Mycobacterium tuberculosis in processed sputum. Eur J Clin Microbiol Infect Dis, 13, 726–31.

    Article  PubMed  CAS  Google Scholar 

  • Landry, M. L., Garner, R., & Ferguson, D. (2003). Comparison of the NucliSens Basic kit (Nucleic Acid Sequence-Based Amplification) and the Argene Biosoft Enterovirus Consensus Reverse Transcription-PCR assays for rapid detection of enterovirus RNA in clinical specimens. J Clin Microbiol, 41, 5006–10.

    Article  PubMed  CAS  Google Scholar 

  • Lau, J. Y., Davis, G. L., Kniffen, J., Qian, K. P., Urdea, M. S., Chan, C. S., Mizokami, M., Neuwald, P. D., & Wilber, J. C. (1993). Significance of serum hepatitis C virus RNA levels in chronic hepatitis C. Lancet, 341, 1501–4.

    Article  PubMed  CAS  Google Scholar 

  • Little, M. C., Andrews, J., Moore, R., Bustos, S., Jones, L., Embres, C., Durmowicz, G., Harris, J., Berger, D., Yanson, K., Rostkowski, C., Yursis, D., Price, J., Fort, T., Walters, A., Collis, M., Llorin, O., Wood, J., Failing, F., O’Keefe, C., Scrivens, B., Pope, B., Hansen, T., Marino, K., Williams, K., et al. (1999). Strand displacement amplification and homogeneous real-time detection incorporated in a second-generation DNA probe system, BDProbeTecET. Clin Chem, 45, 777–84.

    PubMed  CAS  Google Scholar 

  • Lyamichev, V., Mast, A. L., Hall, J. G., Prudent, J. R., Kaiser, M. W., Takova, T., Kwiatkowski, R. W., Sander, T. J., de Arruda, M., Arco, D. A., Neri, B. P., & Brow, M. A. (1999). Polymorphism identification and quantitative detection of genomic DNA by invasive cleavage of oligonucleotide probes. Nat. Biotechnol, 17, 292–6.

    Article  PubMed  CAS  Google Scholar 

  • Mazzulli, T., Drew, L. W., Yen-Lieberman, B., Jekic-McMullen, D., Kohn, D. J., Isada, C., Moussa, G., Chua, R., & Walmsley, S. (1999). Multicenter comparison of the digene hybrid capture CMV DNA assay (version 2.0), the pp65 antigenemia assay, and cell culture for detection of cytomegalovirus viremia. J Clin Microbiol, 37, 958–63.

    PubMed  CAS  Google Scholar 

  • Modrusan, Z., Marlowe, C., Wheeler, D., Pirseyedi, M., & Bryan, R. N. (2000). CPT-EIA assays for the detection of vancomycin resistant vanA and vanB genes in enterococci. Diagn Microbiol Infect Dis, 37, 45–50.

    Article  PubMed  CAS  Google Scholar 

  • Mullis, K. B. (1990). The unusual origin of the polymerase chain reaction. Sci Am, 262, 56–61, 64–5.

    Article  PubMed  Google Scholar 

  • Osiowy, C. (2002). Sensitive detection of HBsAg mutants by a gap ligase chain reaction assay. J Clin Microbiol, 40, 2566–71.

    Article  PubMed  CAS  Google Scholar 

  • Revets, H., Marissens, D., de Wit, S., Lacor, P., Clumeck, N., Lauwers, S., & Zissis, G. (1996). Comparative evaluation of NASBA HIV-1 RNA QT, AMPLICOR-HIV monitor, and QUANTIPLEX HIV RNA assay, three methods for quantification of human immunodeficiency virus type 1 RNA in plasma. J Clin Microbiol, 34, 1058–64.

    PubMed  CAS  Google Scholar 

  • Rossetti, S., Englisch, S., Bresin, E., Pignatti, P. F., & Turco, A. E. (1997). Detection of mutations in human genes by a new rapid method: cleavage fragment length polymorphism analysis (CFLPA). Mol Cell Probes, 11, 155–60.

    Article  PubMed  CAS  Google Scholar 

  • Saiki, R. K., Gelfand, D. H., Stoffel, S., Scharf, S. J., Higuchi, R., Horn, G. T., Mullis, K. B., & Erlich, H. A. (1988). Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science, 239, 487–91.

    Article  PubMed  CAS  Google Scholar 

  • Schachter, J., Hook, E. W., 3rd, McCormack, W. M., Quinn, T. C., Chernesky, M., Chong, S., Girdner, J. I., Dixon, P. B., DeMeo, L., Williams, E., Cullen, A., & Lorincz, A. (1999). Ability of the digene hybrid capture II test to identify Chlamydia trachomatis and Neisseria gonorrhoeae in cervical specimens. J Clin Microbiol, 37, 3668–71.

    PubMed  CAS  Google Scholar 

  • Schiffman, M. H., Kiviat, N. B., Burk, R. D., Shah, K. V., Daniel, R. W., Lewis, R.,Kuypers, J., Manos, M. M., Scott, D. R., & Sherman, M. E. (1995). Accuracy and interlaboratory reliability of human papillomavirus DNA testing by hybrid capture. J Clin Microbiol, 33, 545–50.

    PubMed  CAS  Google Scholar 

  • Spears, P. A., Linn, C. P., Woodard, D. L., & Walker, G. T. (1997). Simultaneous strand displacement amplification and fluorescence polarization detection of Chlamydia trachomatis DNA. Anal Biochem, 247, 130–7.

    Article  PubMed  CAS  Google Scholar 

  • Sreevatsan, S., Bookout, J. B., Ringpis, F. M., Pottathil, M. R., Marshall, D. J., De Arruda, M., Murvine, C., Fors, L., Pottathil, R. M., & Barathur, R. R. (1998). Algorithmic approach to high-throughput molecular screening for alpha interferon-resistant genotypes in hepatitis C patients. J Clin Microbiol, 36, 1895–901.

    PubMed  CAS  Google Scholar 

  • Tang, Y. W., & Persing, D. H. (1999). Molecular detection and identification of microorganisms. In: Murray, P. R., Jo Baron, E., Pfaller, M. A., Tenover, F. C., & Yolken, R. H. eds. Manual of Clinical Microbiology, 7th ed. American Society for Microbiology, Washington, DC, pp. 215–244.

    Google Scholar 

  • Tang, Y. W., Procop, G. W., & Persing, D. H. (1997). Molecular diagnostics of infectious diseases. Clin Chem, 43, 2021–38.

    PubMed  CAS  Google Scholar 

  • Urdea, M. S., Horn, T., Fultz, T. J., Anderson, M., Running, J. A., Hamren, S., Ahle, D., & Chang, C. A. (1991). Branched DNA amplification multimers for the sensitive, direct detection of human hepatitis viruses. Nuc Acids Symp Ser, 197–200.

    Google Scholar 

  • Walker, G. T., Fraiser, M. S., Schram, J. L., Little, M. C., Nadeau, J. G., & Malinowski, D. P. (1992). Strand displacement amplification-an isothermal, in vitro DNA amplification technique. Nucleic Acids Res, 20, 1691–6.

    Article  PubMed  CAS  Google Scholar 

  • Wu, D. Y., & Wallace, R. B. (1989). The ligation amplification reaction (LAR)- amplification of specific DNA sequences using sequential rounds of template-dependent ligation. Genomics, 4, 560–9.

    Article  PubMed  CAS  Google Scholar 

  • Yolken, R. H. (2002). Nucleic acid amplification assays for microbial diagnosis: challenges and opportunities. J Pediatr, 140, 290–2.

    Article  PubMed  Google Scholar 

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Li, H., Tang, YW. (2006). In Vitro Nucleic Acid Amplification: An Introduction. In: Advanced Techniques in Diagnostic Microbiology. Springer, Boston, MA. https://doi.org/10.1007/0-387-32892-0_10

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