Chapter 3 : In Vitro Nucleic Acid Amplification Techniques

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

Preview this chapter:
Zoom in

In Vitro Nucleic Acid Amplification Techniques, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555816834/9781555814977_Chap03-1.gif /docserver/preview/fulltext/10.1128/9781555816834/9781555814977_Chap03-2.gif


Nucleic acid amplification (NAA) techniques have come of age. The specific amplification and detection of an oligonucleotide sequence went from the fictional to the mundane in the span of two decades. By looking at the theoretical basis for each method, NAA techniques can be placed into one of two broad categories: (i) target amplification systems, including PCR, ligase chain reaction (LCR), self-sustaining sequence amplification (3SR), nucleic acid sequence-based amplification (NASBA), transcription-based amplification system (TAS), transcription-mediated amplification (TMA), strand displacement amplification (SDA), and loop-mediated isothermal amplification (LAMP); and (ii) signal amplification systems (including probe amplification methods), such as branched-DNA technologies (bDNA) and cleavage-based signal amplification (cycling probe technologies [CPT] and Invader assays). Proofreading may help maintain fidelity of replication, and its absence can result in a relatively high rate of nucleotide incorporation errors (misincorporation), most relevant when starting with low target numbers. Misincorporation can produce amplicon mismatched to detection probes and can also result in inefficient amplification (especially when longer genetic stretches are targeted), due to primer mismatch in subsequent amplification rounds. Successful ligation relies on contiguous positioning and correct base pairing of the 3' and 5' ends of oligonucleotide probes on a target DNA molecule. The reliability of sequence data has improved, and the taxonomic and cytogenetic characterization of microorganisms has advanced tremendously. These improvements give the tools to allow the rapid and increasingly routine development of molecular methods for the identification, quantification, and characterization of microorganisms.

Citation: Datta V, Hayden R. 2011. In Vitro Nucleic Acid Amplification Techniques, p 33-61. 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.ch3
Highlighted Text: Show | Hide
Loading full text...

Full text loading...


Image of FIGURE 1

Use of NAA in clinical microbiology.

Citation: Datta V, Hayden R. 2011. In Vitro Nucleic Acid Amplification Techniques, p 33-61. 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.ch3
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 2

Comparative material and kit costs of culture-based and NAA-based diagnostic assays for infectious disease.

Citation: Datta V, Hayden R. 2011. In Vitro Nucleic Acid Amplification Techniques, p 33-61. 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.ch3
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 3

Fact or fallacy? While at face value these assumptions seem to be self-evident facts, such is not always the case.

Citation: Datta V, Hayden R. 2011. In Vitro Nucleic Acid Amplification Techniques, p 33-61. 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.ch3
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 4

Scheme for PCR. Reprinted from reference with permission.

Citation: Datta V, Hayden R. 2011. In Vitro Nucleic Acid Amplification Techniques, p 33-61. 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.ch3
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 5

Scheme for LCR. Reprinted from reference with permission.

Citation: Datta V, Hayden R. 2011. In Vitro Nucleic Acid Amplification Techniques, p 33-61. 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.ch3
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 6

Scheme for SDA. Reprinted from reference with permission.

Citation: Datta V, Hayden R. 2011. In Vitro Nucleic Acid Amplification Techniques, p 33-61. 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.ch3
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 7

Scheme for transcription-based amplification. Reprinted from reference with permission.

Citation: Datta V, Hayden R. 2011. In Vitro Nucleic Acid Amplification Techniques, p 33-61. 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.ch3
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 8

Scheme for LAMP. Reprinted from reference with permission.

Citation: Datta V, Hayden R. 2011. In Vitro Nucleic Acid Amplification Techniques, p 33-61. 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.ch3
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 9

Scheme for bDNA signal amplification. Reprinted from reference with permission.

Citation: Datta V, Hayden R. 2011. In Vitro Nucleic Acid Amplification Techniques, p 33-61. 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.ch3
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 10

Scheme for the Invader assay. Reprinted from reference with permission.

Citation: Datta V, Hayden R. 2011. In Vitro Nucleic Acid Amplification Techniques, p 33-61. 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.ch3
Permissions and Reprints Request Permissions
Download as Powerpoint


1. Abu Al-Soud, W.,, and P. Radstrom. 1998. Capacity of nine thermostable DNA polymerases to mediate DNA amplification in the presence of PCR-inhibiting samples. Appl. Environ. Microbiol. 64: 37483753.
2. Albadalejo, J.,, R. Alonso,, R. Antinozzi,, M. Bogard,, A. M. Bourgault,, G. Colucci,, T. Fenner,, H. Petersen,, E. Sala,, J. Vincelette, and, C. Young. 1998. Multicenter evaluation of the COBAS AMPLICOR HCV assay, an integrated PCR system for rapid detection of hepatitis C virus RNA in the diagnostic laboratory. J. Clin. Microbiol. 36: 862865.
3. Amann, R. I.,, W. Ludwig, and, K. H. Schleifer. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59: 143169.
4. Anarbaev, R. O.,, I. B. Elepov, and, O. I. Lavrik. 1998. Klenow fragment and DNA polymerase alpha-primase fromserva calf thymus in water-in-oil microemulsions. Biochim. Biophys. Acta 1384: 315324.
5. Anderson, B. 1994. Broad-range polymerase chain reaction for detection and identification of bacteria. J. Fla. Med. Assoc. 81: 835837.
6. Arbeit, R. D. 1999. Laboratory procedures for the epidemiologic analysis of microorganisms, p. 116-137. In P. R. Murray,, E. J. Baron,, M. A. Pfaller,, F. C. Tenover, and, R. H. Yolken (ed.), Manual of Clinical Microbiology, 7th ed. ASM Press, Washington, DC.
7. Association for Molecular Pathology. 11 February 2010, posting date. FDA-cleared/approved molecular diagnostic tests. Association for Molecular Pathology, Bethesda, MD. http://www.amp.org/FDATable/FDATable.doc.
8. Baldanti, F.,, P. Grossi,, M. Furione,, L. Simoncini,, A. Sarasini,, P. Comoli,, R. Maccario,, R. Fiocchi, and, G. Gerna. 2000. High levels of Epstein-Barr virus DNA in blood of solid-organ transplant recipients and their value in predicting posttransplant lymphoproliferative disorders. J. Clin. Microbiol. 38: 613619.
9. Barany, F. 1991. Genetic disease detection and DNA amplification using cloned thermostable ligase. Proc. Natl. Acad. Sci. USA 88: 189193.
10. Barry, T.,, C. M. Glennon,, L. K. Dunican, and, F. Gannon. 1991. The 16s/23s ribosomal spacer region as a target for DNA probes to identify eubacteria. PCR Methods Appl. 1: 5156.
11. Baselski, V. S. 1996. The role of molecular diagnostics in the clinical microbiology laboratory. Clin. Lab. Med. 16: 4960.
12. Beggs, M. L.,, M. D. Cave,, C. Marlowe,, L. Cloney,, P. Duck, and, K. D. Eisenach. 1996. Characterization of Mycobacterium tuberculosis complex direct repeat sequence for use in cycling probe reaction. J. Clin. Microbiol. 34: 29852989.
13. Bej, A. K.,, M. H. Mahbubani,, R. Miller,, J. L. Dicesare,, L. Haff, and, R. M. Atlas. 1990. Multiplex PCR amplification and immobilized capture probes for detection of bacterial pathogens and indicators in water. Mol. Cell. Probes 4: 353365.
14. Berger, A.,, L. Scherzed,, M. Sturmer,, W. Preiser,, H. W. Doerr, and, H. F. Rabenau. 2005. Comparative evaluation of the Cobas Amplicor HIV-1 Monitor Ultrasensitive Test, the new Cobas AmpliPrep/Cobas Amplicor HIV-1 Monitor Ultrasensitive Test, and the Versant HIV RNA 3.0 assays for quantitation of HIV-1 RNA in plasma samples. J. Clin. Virol. 33: 4351.
15. Bickley, J.,, and D. Hopkins. 1999. Inhibitors and enhancers of PCR, p. 81-102. In H. Parkes and, V. Saunders (ed.), Analytical Molecular Biology Quality and Validation. The Royal Society of Chemistry, London, United Kingdom.
16. Birch, D. E. 1996. Simplified hot start PCR. Nature 381: 445446.
17. Blank, B. S.,, P. L. Meenhorst,, J. W. Mulder,, G. J. Weverling,, H. Putter,, W. Pauw,, W. C. van Dijk,, P. Smits,, A. L. Lie,, P. Reiss, and, J. M. Lange. 2000. Value of different assays for detection of human cytomegalovirus (HCMV) in predicting the development of HCMV disease in human immunodeficiency virus-infected patients. J. Clin. Microbiol. 38: 563569.
18. Boeckh, M.,, and G. Boivin. 1998. Quantitation of cytomegalovirus: methodologic aspects and clinical applications. Clin. Microbiol. Rev. 11: 533554.
19. Boivin, G.,, J. Handfield,, E. Toma,, G. Murray,, R. Lalonde, and, M. G. Bergeron. 1998. Comparative evaluation of the cytomegalovirus DNA load in polymorphonuclear leukocytes and plasma of human immunodeficiency virus-infected subjects. J. Infect. Dis. 177: 355360.
20. Boyer, N.,, and P. Marcellin. 2000. Pathogenesis, diagnosis and management of hepatitis C. J. Hepatol. 32: 98112.
21. Bretagne, S.,, J. M. Costa,, A. Marmorat-Khuong,, F. Poron,, C. Cordonnier,, M. Vidaud, and, J. Fleury-Feith. 1995. Detection of Aspergillus species DNA in bronchoalveolar lavage samples by competitive PCR. J. Clin. Microbiol. 33: 11641168.
22. Brow, M. A.,, M. C. Oldenburg,, V. Lyamichev,, L. M. Heisler,, N. Lyamicheva,, J. G. Hall,, N. J. Eagan,, D. M. Olive,, L. M. Smith,, L. Fors, and, J. E. Dahlberg. 1996. Differentiation of bacterial 16S rRNA genes and intergenic regions and Mycobacterium tuberculosis katG genes by structure-specific endonuclease cleavage. J. Clin. Microbiol. 34: 31293137.
23. Buhlmann, M.,, K. Bogli-Stuber,, S. Droz, and, K. Muhlemann. 2008. Rapid screening for carriage of methicillin-resistant Staphylococcus aureus by PCR and associated costs. J. Clin. Microbiol. 46: 21512154.
24. Carter, I. W.,, and M. J. Cloonan. 1995. Comparison between three PCR methods for detection of human cytomegalovirus DNA. Pathology 27: 161164.
25. Centers for Disease Control and Prevention. 1998. Recommendations for prevention and control of hepatitis C virus (HCV) infection and HCV-related chronic disease. MMWR Morb. Mortal. Wkly. Rep. 47: 139.
26. Centers for Disease Control and Prevention. 2001. Revised guidelines for HIV counseling, testing, and referral. MMWR Recommend. Rep. 50 (RR-19): 157.
27. Cha, R. S.,, and W. G. Thilly. 1993. Specificity, efficiency, and fidelity of PCR. PCR Methods Appl. 3: S18S29.
28. Chamberlain, J. S.,, R. A. Gibbs,, J. E. Ranier,, P. N. Nguyen, and, C. T. Caskey. 1988. Deletion screening of the Duchenne muscular dystrophy locus via multiplex DNA amplification. Nucleic Acids Res. 16: 1114111156.
29. Cimino, G. D.,, K. C. Metchette,, J. W. Tessman,, J. E. Hearst, and, S. T. Isaacs. 1991. Post-PCR sterilization: a method to control carryover contamination for the polymerase chain reaction. Nucleic Acids Res. 19: 99107.
30. Clarke, J. R.,, and M. O. McClure. 1999. HIV-1 viral load testing. J. Infect. 38: 141146.
31. Clayton, R. A.,, G. Sutton,, P. S. Hinkle, Jr.,, C. Bult, and, C. Fields. 1995. Intraspecific variation in small-subunit rRNA sequences in GenBank: why single sequences may not adequately represent prokaryotic taxa. Int. J. Syst. Bacteriol. 45: 595599.
32. Cline, J.,, J. C. Braman, and, H. H. Hogrefe. 1996. PCR fidelity of pfu DNA polymerase and other thermostable DNA polymerases. Nucleic Acids Res. 24: 35463551.
33. Cloney, L.,, C. Marlowe,, A. Wong,, R. Chow, and, R. Bryan. 1999. Rapid detection of mecA in methicillin resistant Staphylococcus aureus using cycling probe technology. Mol. Cell. Probes 13: 191197.
34. Cockerill, F. R., III. 1999. Genetic methods for assessing antimicrobial resistance. Antimicrob. Agents Chemother. 43: 199212.
35. Collins, M. L.,, B. Irvine,, D. Tyner,, E. Fine,, C. Zayati,, C. Chang,, T. Horn,, D. Ahle,, J. Detmer,, L. P. Shen,, J. Kolberg,, S. Bushnell,, M. S. Urdea, and, D. D. Ho. 1997. A branched DNA signal amplification assay for quantification of nucleic acid targets below 100 molecules/ml. Nucleic Acids Res. 25: 29792984.
36. Comanor, L.,, F. Anderson,, M. Ghany,, R. Perrillo,, E. J. Heathcote,, C. Sherlock,, I. Zitron,, D. Hendricks, and, S. C. Gordon. 2001. Transcription-mediated amplification is more sensitive than conventional PCR-based assays for detecting residual serum HCV RNA at end of treatment. Am. J. Gastroenterol. 96: 29682972.
37. Compton, J. 1991. Nucleic acid sequence-based amplification. Nature 350: 9192.
38. Cone, R. W.,, and M. R. Fairfax. 1993. Protocol for ultraviolet irradiation of surfaces to reduce PCR contamination. PCR Methods Appl. 3: S15S17.
39. Cooksey, R. C.,, B. P. Holloway,, M. C. Oldenburg,, S. Listenbee, and, C. W. Miller. 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: 12961301.
40. Dagan, R.,, O. Shriker,, I. Hazan,, E. Leibovitz,, D. Greenberg,, F. Schlaeffer, and, R. Levy. 1998. Prospective study to determine clinical relevance of detection of pneumococcal DNA in sera of children by PCR. J. Clin. Microbiol. 36: 669673.
41. Della-Latta, P.,, and S. Whittier. 1998. Comprehensive evaluation of performance, laboratory application, and clinical usefulness of two direct amplification technologies for the detection of Mycobacterium tuberculosis complex. Am. J. Clin. Pathol. 110: 301310.
42. Duck, P.,, G. Alvarado-Urbina,, B. Burdick, and, B. Collier. 1990. Probe amplifier system based on chimeric cycling oligonucleotides. BioTechniques 9: 142148.
43. Dunne, A. L.,, and S. M. Crowe. 1997. Comparison of branched DNA and reverse transcriptase polymerase chain reaction for quantifying six different HIV-1 subtypes in plasma. AIDS 11: 126127.
44. Eckert, K. A.,, and T. A. Kunkel. 1991. DNA polymerase fidelity and the polymerase chain reaction. PCR Methods Appl. 1: 1724.
45. Eckert, K. A.,, and T. A. Kunkel. 1993. Effect of reaction pH on the fidelity and processivity of exonuclease-deficient Klenow polymerase. J. Biol. Chem. 268: 1346213471.
46. Einsele, H.,, H. Hebart,, G. Roller,, J. Loffler,, I. Rothenhofer,, C. A. Muller,, R. A. Bowden,, J. van Burik,, D. Engelhard,, L. Kanz, and, U. Schumacher. 1997. Detection and identification of fungal pathogens in blood by using molecular probes. J. Clin. Microbiol. 35: 13531360.
47. Eis, P. S.,, M. C. Olson,, T. Takova,, M. L. Curtis,, S. M. Olson,, T. I. Vener,, H. S. Ip,, K. L. Vedvik,, C. T. Bartholomay,, H. T. Allawi,, W. P. Ma,, J. G. Hall,, M. D. Morin,, T. H. Rushmore,, V. I. Lyamichev, and, R. W. Kwiatkowski. 2001. An invasive cleavage assay for direct quantitation of specific RNAs. Nat. Biotechnol. 19: 673676.
48. Elnifro, E. M.,, A. M. Ashshi,, R. J. Cooper, and, P. E. Klapper. 2000. Multiplex PCR: optimization and application in diagnostic virology. Clin. Microbiol. Rev. 13: 559570.
49. Enosawa, M.,, S. Kageyama,, K. Sawai,, K. Watanabe,, T. Notomi,, S. Onoe,, Y. Mori, and, Y. Yokomizo. 2003. Use of loop-mediated isothermal amplification of the IS900 sequence for rapid detection of cultured Mycobacterium avium subsp. paratuberculosis. J. Clin. Microbiol. 41: 43594365.
50. Eom, S. H.,, J. Wang, and, T. A. Steitz. 1996. Structure of Taq polymerase with DNA at the polymerase active site. Nature 382: 278281.
51. Espy, M. J.,, T. F. Smith, and, D. H. Persing. 1993. Dependence of polymerase chain reaction product inactivation protocols on amplicon length and sequence composition. J. Clin. Microbiol. 31: 23612365.
52. Fahy, E.,, D. Y. Kwoh, and, T. R. Gingeras. 1991. Self-sustained sequence replication (3SR): an isothermal transcription-based amplification system alternative to PCR. PCR Methods Appl. 1: 2533.
53. Fairfax, M. R.,, M. A. Metcalf, and, R. W. Cone. 1991. Slow inactivation of dry PCR templates by UV light. PCR Methods Appl. 1: 142143.
54. Ferreira-Gonzalez, A.,, and C. T. Garrett. 1996. Pitfalls in establishing a molecular diagnostic laboratory. Hum. Pathol. 27: 437440.
55. Fire, A.,, and S. Q. Xu. 1995. Rolling replication of short DNA circles. Proc. Natl. Acad. Sci. USA 92: 46414645.
56. Fluit, A. C.,, M. R. Visser, and, F. J. Schmitz. 2001. Molecular detection of antimicrobial resistance. Clin. Microbiol. Rev. 14: 836871.
57. Fong, W. K.,, Z. Modrusan,, J. P. McNevin,, J. Marostenmaki,, B. Zin, and, F. Bekkaoui. 2000. Rapid solid-phase immunoassay for detection of methicillin-resistant Staphylococcus aureus using cycling probe technology. J. Clin. Microbiol. 38: 25252529.
58. Food and Drug Administration. 2010. Vaccines, Blood & Biologics. Food and Drug Administration, Rockville, MD. http://www.fda.gov/BiologicsBloodVaccines/BloodBloodProducts/ApprovedProducts/.
59. Fox, G. E.,, E. Stackebrandt,, R. B. Hespell,, J. Gibson,, J. Maniloff,, T. A. Dyer,, R. S. Wolfe,, W. E. Balch,, R. S. Tanner,, L. J. Magrum,, L. B. Zablen,, R. Blakemore,, R. Gupta,, L. Bonen,, B. J. Lewis,, D. A. Stahl,, K. R. Luehrsen,, K. N. Chen, and, C. R. Woese. 1980. The phylogeny of prokaryotes. Science 209: 457463.
60. Fox, G. E.,, J. D. Wisotzkey, and, P. Jurtshuk, Jr. 1992. How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity. Int. J. Syst. Bacteriol. 42: 166170.
61. Foy, C. A.,, and H. C. Parkes. 2001. Emerging homogeneous DNA-based technologies in the clinical laboratory. Clin. Chem. 47: 9901000.
62. Fredericks, D. N.,, and D. A. Relman. 1996. Sequence-based identification of microbial pathogens: a reconsideration of Koch’s postulates. Clin. Microbiol. Rev. 9: 1833.
63. Fredricks, D. N.,, and D. A. Relman. 1999. Application of polymerase chain reaction to the diagnosis of infectious diseases. Clin. Infect. Dis. 29: 475486.
64. Garrino, M. G.,, Y. Glupczynski,, J. Degraux,, H. Nizet, and, M. Delmee. 1999. Evaluation of the Abbott LCx Mycobacterium tuberculosis assay for direct detection of Mycobacterium tuberculosis complex in human samples. J. Clin. Microbiol. 37: 229232.
65. Geha, D. J.,, J. R. Uhl,, C. A. Gustaferro, and, D. H. Persing. 1994. Multiplex PCR for identification of methicillin-resistant staphylococci in the clinical laboratory. J. Clin. Microbiol. 32: 17681772.
66. Germer, J. J.,, D. W. Majewski,, B. Yung,, P. S. Mitchell, and, J. D. Yao. 2006. Evaluation of the invader assay for genotyping hepatitis C virus. J. Clin. Microbiol. 44: 318323.
67. Gherardi, G.,, F. D’Ambrosio,, M. Monaco,, R. Camilli,, L. De Florio,, F. D’Ancona,, G. Dicuonzo, and, A. Pantosti. 2009. Population structure of invasive Streptococcus pneumoniae isolates in Italy prior to the implementation of the 7-valent conjugate vaccine (1999-2003). Eur. J. Clin. Microbiol. Infect. Dis. 28: 99103.
68. Gibson, U. E.,, C. A. Heid, and, P. M. Williams. 1996. A novel method for real time quantitative RT-PCR. Genome Res. 6: 9951001.
69. Gingeras, T. R.,, and D. Y. Kwoh. 1992. In vitro nucleic acid target amplification techniques: issues and benefits. Praxis Biotechnol. 4: 403429.
70. Gingeras, T. R.,, P. Prodanovich,, T. Latimer,, J. C. Guatelli,, D. D. Richman, and, K. J. Barringer. 1991. Use of self-sustained sequence replication amplification reaction to analyze and detect mutations in zidovudine-resistant human immunodeficiency virus. J. Infect. Dis. 164: 10661074.
71. Graber, J. H.,, M. J. O’Donnell,, C. L. Smith, and, C. R. Cantor. 1998. Advances in DNA diagnostics. Curr. Opin. Biotechnol. 9: 1418.
72. Hall, J. G.,, P. S. Eis,, S. M. Law,, L. P. Reynaldo,, J. R. Prudent,, D. J. Marshall,, H. T. Allawi,, A. L. Mast,, J. E. Dahlberg,, R. W. Kwiatkowski,, M. de Arruda,, B. P. Neri, and, V. I. Lyamichev. 2000. Sensitive detection of DNA polymorphisms by the serial invasive signal amplification reaction. Proc. Natl. Acad. Sci. USA 97: 82728277.
73. Hamilton, S. C.,, J. W. Farchaus, and, M. C. Davis. 2001. DNA polymerases as engines for biotechnology. BioTechniques 31: 370376, 378-380, 382–383.
74. Haqqi, T. M.,, G. Sarkar,, C. S. David, and, S. S. Sommer. 1988. Specific amplification with PCR of a refractory segment of genomic DNA. Nucleic Acids Res. 16: 11844.
75. Hatch, A.,, T. Sano,, J. Misasi, and, C. L. Smith. 1999. Rolling circle amplification of DNA immobilized on solid surfaces and its application to multiplex mutation detection. Genet. Anal. 15: 3540.
76. Hawkins, A.,, F. Davidson, and, P. Simmonds. 1997. Comparison of plasma virus loads among individuals infected with hepatitis C virus (HCV) genotypes 1, 2, and 3 by quantiplex HCV RNA assay versions 1 and 2, Roche Monitor assay, and an in-house limiting dilution method. J. Clin. Microbiol. 35: 187192.
77. Hayden, R. T.,, K. M. Hokanson,, S. B. Pounds,, M. J. Bankowski,, S. W. Belzer,, J. Carr,, D. Diorio,, M. S. Forman,, Y. Joshi,, D. Hillyard,, R. L. Hodinka,, M. N. Nikiforova,, C. A. Romain,, J. Stevenson,, A. Valsamakis, and, H. H. Balfour, Jr. 2008. Multicenter comparison of different real-time PCR assays for quantitative detection of Epstein-Barr virus. J. Clin. Microbiol. 46: 157163.
78. Heid, C. A.,, J. Stevens,, K. J. Livak, and, P. M. Williams. 1996. Real time quantitative PCR. Genome Res. 6: 986994.
79. Henegariu, O.,, N. A. Heerema,, S. R. Dlouhy,, G. H. Vance, and, P. H. Vogt. 1997. Multiplex PCR: critical parameters and step-by-step protocol. BioTechniques 23: 504511.
80. Henrickson, K. J. 2005. Cost-effective use of rapid diagnostic techniques in the treatment and prevention of viral respiratory infections. Pediatr. Ann. 34: 2431.
81. Hill, C. S. 2001. Molecular diagnostic testing for infectious diseases using TMA technology. Expert Rev. Mol. Diagn. 1: 445455.
82. Hilscher, C.,, W. Vahrson, and, D. P. Dittmer. 2005. Faster quantitative real-time PCR protocols may lose sensitivity and show increased variability. Nucleic Acids Res. 33: e182.
83. Hodinka, R. L. 1998. The clinical utility of viral quantitation using molecular methods. Clin. Diagn. Virol. 10: 2547.
84. Hofmann, W. P.,, V. Dries,, E. Herrmann,, B. Gartner,, S. Zeuzem, and, C. Sarrazin. 2005. Comparison of transcription mediated amplification (TMA) and reverse transcription polymerase chain reaction (RT-PCR) for detection of hepatitis C virus RNA in liver tissue. J. Clin. Virol. 32: 289293.
85. Holland, P. M.,, R. D. Abramson,, R. Watson, and, D. H. Gelfand. 1991. Detection of specific polymerase chain reaction product by utilizing the 5′-3′ exonuclease activity of Thermus aquaticus DNA polymerase. Proc. Natl. Acad. Sci. USA 88: 72767280.
86. Hymas, W. C.,, W. K. Aldous,, E. W. Taggart,, J. B. Stevenson, and, D. R. Hillyard. 2008. Description and validation of a novel real-time RT-PCR enterovirus assay. Clin. Chem. 54: 406413.
87. Ibrahim, M. S.,, R. S. Lofts,, P. B. Jahrling,, E. A. Henchal,, V. W. Weedn,, M. A. Northrup, and, P. Belgrader. 1998. Real-time microchip PCR for detecting single-base differences in viral and human DNA. Anal. Chem. 70: 20132017.
88. Ieven, M. 2007. Currently used nucleic acid amplification tests for the detection of viruses and atypicals in acute respiratory infections. J. Clin. Virol. 40: 259276.
89. Imai, M.,, A. Ninomiya,, H. Minekawa,, T. Notomi,, T. Ishizaki,, M. Tashiro, and, T. Odagiri. 2006. Development of H5-RT-LAMP (loop-mediated isothermal amplification) system for rapid diagnosis of H5 avian influenza virus infection. Vaccine 24: 66796682.
90. Isaacs, S. T.,, J. W. Tessman,, K. C. Metchette,, J. E. Hearst, and, G. D. Cimino. 1991. Post-PCR sterilization: development and application to an HIV-1 diagnostic assay. Nucleic Acids Res. 19: 109116.
91. Jandreski, M. A. 1995. Novel methods of DNA analysis. Clin. Lab. Med. 15: 817837.
92. Jung, R.,, K. Soondrum, and, M. Neumaier. 2000. Quantitative PCR. Clin. Chem. Lab Med. 38: 833836.
93. Jungkind, D. 2001. Automation of laboratory testing for infectious diseases using the polymerase chain reaction—our past, our present, our future. J. Clin. Virol. 20: 16.
94. Katcher, H. L.,, and I. Schwartz. 1994. A distinctive property of Tth DNA polymerase: enzymatic amplification in the presence of phenol. BioTechniques 16: 8492.
95. Kebelmann-Betzing, C.,, K. Seeger,, S. Dragon,, G. Schmitt,, A. Moricke,, T. A. Schild,, G. Henze, and, B. Beyermann. 1998. Advantages of a new Taq DNA polymerase in multiplex PCR and time-release PCR. BioTechniques 24: 154158.
96. Kessler, H. H.,, G. Muhlbauer,, B. Rinner,, E. Stelzl,, A. Berger,, H. W. Dorr,, B. Santner,, E. Marth, and, H. Rabenau. 2000. Detection of herpes simplex virus DNA by real-time PCR. J. Clin. Microbiol. 38: 26382642.
97. Kiehn, T. E. 1993. The diagnostic mycobacteriology laboratory of the 1990s. Clin. Infect. Dis. 17 (Suppl. 2): 447454.
98. Kitchin, P. A.,, Z. Szotyori,, C. Fromholc, and, N. Almond. 1990. Avoidance of PCR false positives. Nature 344: 201. (Letter.) (Erratum, 344:388.)
99. Kleppe, K.,, E. Ohtsuka,, R. Kleppe,, I. Molineux, and, H. G. Khorana. 1971. Studies on polynucleotides. XCVI. Repair replications of short synthetic DNA’s as catalyzed by DNA polymerases. J. Mol. Biol. 56: 341361.
100. Kojima, T.,, N. Shibata,, M. Ikedo, and, Y. Arakawa. 2006. Development and evaluation of novel loop-mediated isothermal amplification for rapid detection of bla(IMP-1) and bla(VIM-2) genes. Kansenshogaku Zasshi 80: 405412. (In Japanese.)
101. Kolbert, C. P.,, and D. H. Persing. 1999. Ribosomal DNA sequencing as a tool for identification of bacterial pathogens. Curr. Opin. Microbiol. 2: 299305.
102. Krunic, N.,, T. D. Yager,, D. Himsworth,, F. Merante,, S. Yaghoubian, and, R. Janeczko. 2007. xTAG RVP assay: analytical and clinical performance. J. Clin. Virol. 40 (Suppl. 1): S39S46.
103. Kwoh, D. Y.,, G. R. Davis,, K. M. Whitfield,, H. L. Chappelle,, L. J. DiMichele, and, T. R. Gingeras. 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: 11731177.
104. Kwok, S.,, and R. Higuchi. 1989. Avoiding false positives with PCR. Nature 339: 237238. (Erratum, 339: 490.)
105. Lander, E. S.,, L. M. Linton,, B. Birren,, C. Nusbaum,, M. C. Zody,, J. Baldwin,, K. Devon,, K. Dewar,, M. Doyle,, W. FitzHugh,, R. Funke,, D. Gage,, K. Harris,, A. Heaford,, J. Howland,, L. Kann,, J. Lehoczky,, R. LeVine,, P. McEwan,, K. McKernan,, J. Meldrim,, J. P. Mesirov,, C. Miranda,, W. Morris,, J. Naylor,, C. Raymond,, M. Rosetti,, R. Santos,, A. Sheridan,, C. Sougnez,, N. Stange-Thomann,, N. Stojanovic,, A. Subramanian,, D. Wyman,, J. Rogers,, J. Sulston,, R. Ainscough,, S. Beck,, D. Bentley,, J. Burton,, C. Clee,, N. Carter,, A. Coulson,, R. Deadman,, P. Deloukas,, A. Dunham,, I. Dunham,, R. Durbin,, L. French,, D. Grafham,, S. Gregory,, T. Hubbard,, S. Humphray,, A. Hunt,, M. Jones,, C. Lloyd,, A. McMurray,, L. Matthews,, S. Mercer,, S. Milne,, J. C. Mullikin,, A. Mungall,, R. Plumb,, M. Ross,, R. Shownkeen,, S. Sims,, R. H. Waterston,, R. K. Wilson,, L. W. Hillier,, J. D. McPherson,, M. A. Marra,, E. R. Mardis,, L. A. Fulton,, A. T. Chinwalla,, K. H. Pepin,, W. R. Gish,, S. L. Chissoe,, M. C. Wendl,, K. D. Delehaunty,, T. L. Miner,, A. Delehaunty,, J. B. Kramer,, L. L. Cook,, R. S. Fulton,, D. L. Johnson,, P. J. Minx,, S. W. Clifton,, T. Hawkins,, E. Branscomb,, P. Predki,, P. Richardson,, S. Wenning,, T. Slezak,, N. Doggett,, J. F. Cheng,, A. Olsen,, S. Lucas,, C. Elkin,, E. Uberbacher, and, M. Frazier. 2001. Initial sequencing and analysis of the human genome. Nature 409: 860921.
106. Lane, D. J.,, B. Pace,, G. J. Olsen,, D. A. Stahl,, M. L. Sogin, and, N. R. Pace. 1985. Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc. Natl. Acad. Sci. USA 82: 69556959.
107. Laurent, F. J.,, F. Provost, and, P. Boiron. 1999. Rapid identification of clinically relevant Nocardia species to genus level by 16S rRNA gene PCR. J. Clin. Microbiol. 37: 99102.
108. LeBar, W. D. 1996. Keeping up with new technology: new approaches to diagnosis of Chlamydia infection. Clin. Chem. 42: 809812.
109. Ledford, M.,, K. D. Friedman,, M. J. Hessner,, C. Moehlenkamp,, T. M. Williams, and, R. S. Larson. 2000. A multi-site study for detection of the factor V (Leiden) mutation from genomic DNA using a homogeneous invader microtiter plate fluorescence resonance energy transfer (FRET) assay. J. Mol. Diagn. 2: 97104.
110. Lefrere, J. J.,, J. Lerable,, M. Mariotti,, M. Bogard,, V. Thibault,, L. Frangeul,, P. Loiseau,, F. Bouchardeau,, S. Laperche,, J. M. Pawlotsky,, J. F. Cantaloube,, P. Biagini,, X. de Lamballerie,, J. Izopet,, C. Defer,, I. Lepot,, J. D. Poveda,, E. Dussaix,, V. Gerolami,, P. Halfon,, C. Buffet-Janvresse,, C. Ferec,, B. Mercier,, P. Marcellin,, M. Martinot-Peignoux, and, M. Gassain. 2000. Lessons from a multicentre study of the detectability of viral genomes based on a two-round quality control of GB virus C (GBV-C)/hepatitis G virus (HGV) polymerase chain reaction assay. J. Virol. Methods 85: 117124.
111. Ley, B. E.,, C. J. Linton,, D. M. Bennett,, H. Jalal,, A. B. Foot, and, M. R. Millar. 1998. Detection of bacteraemia in patients with fever and neutropenia using 16S rRNA gene amplification by polymerase chain reaction. Eur. J. Clin. Microbiol. Infect. Dis. 17: 247253.
112. Lindsley, M. D.,, S. F. Hurst,, N. J. Iqbal, and, C. J. Morrison. 2001. Rapid identification of dimorphic and yeast-like fungal pathogens using specific DNA probes. J. Clin. Microbiol. 39: 35053511.
113. Liolios, L.,, A. Jenney,, D. Spelman,, T. Kotsimbos,, M. Catton, and, S. Wesselingh. 2001. Comparison of a multiplex reverse transcription-PCR-enzyme hybridization assay with conventional viral culture and immunofluorescence techniques for the detection of seven viral respiratory pathogens. J. Clin. Microbiol. 39: 27792783.
114. Lipuma, J. J. 1998. Molecular tools for epidemiologic study of infectious diseases. Pediatr. Infect. Dis. J. 17: 667675.
115. Lisby, G. 1998. Application of nucleic acid amplification in clinical microbiology. Methods Mol. Biol. 92: 129.
116. Lisby, G.,, and R. Dessau. 1994. Construction of a DNA amplification assay for detection of Legionella species in clinical samples. Eur. J. Clin. Microbiol. Infect. Dis. 13: 225231.
117. Little, M. C.,, J. Andrews,, R. Moore,, S. Bustos,, L. Jones,, C. Embres,, G. Durmowicz,, J. Harris,, D. Berger,, K. Yanson,, C. Rostkowski,, D. Yursis,, J. Price,, T. Fort,, A. Walters,, M. Collis,, O. Llorin,, J. Wood,, F. Failing,, C. O’Keefe,, B. Scrivens,, B. Pope,, T. Hansen,, K. Marino, and, K. Williams. 1999. Strand displacement amplification and homogeneous real-time detection incorporated in a second-generation DNA probe system, BDProbeTecET. Clin. Chem. 45: 777784.
118. Liu, J. 1997. Clinical uses of polymerase chain reaction in infectious diseases. Zhonghua Yi Xue Za Zhi 77: 725726. (In Chinese.)
119. Livak, K. J.,, S. J. Flood,, J. Marmaro,, W. Giusti, and, K. Deetz. 1995. Oligonucleotides with fluorescent dyes at opposite ends provide a quenched probe system useful for detecting PCR product and nucleic acid hybridization. PCR Methods Appl. 4: 357362.
120. Lizardi, P. M.,, X. Huang,, Z. Zhu,, P. Bray-Ward,, D. C. Thomas, and, D. C. Ward. 1998. Mutation detection and single-molecule counting using isothermal rolling-circle amplification. Nat. Genet. 19: 225232.
121. Louie, M.,, L. Louie, and, A. E. Simor. 2000. The role of DNA amplification technology in the diagnosis of infectious diseases. CMAJ 163: 301309.
122. Lu, J. J.,, C. L. Perng,, S. Y. Lee, and, C. C. Wan. 2000. Use of PCR with universal primers and restriction endonuclease digestions for detection and identification of common bacterial pathogens in cerebrospinal fluid. J. Clin. Microbiol. 38: 20762080.
123. Ludwig, W.,, O. Strunk,, S. Klugbauer,, N. Klugbauer,, M. Weizenegger,, J. Neumaier,, M. Bachleitner, and, K. H. Schleifer. 1998. Bacterial phylogeny based on comparative sequence analysis. Electrophoresis 19: 554568.
124. Lui, D.,, S. L. Daubendiek,, M. A. Zillman,, K. Ryan, and, E. T. Kool. 1996. Rolling circle DNA synthesis: small circular oligonucleotides as efficient templates for DNA polymerase. Am. Chem. Soc. 118: 15871594.
125. Lyamichev, V.,, A. L. Mast,, J. G. Hall,, J. R. Prudent,, M. W. Kaiser,, T. Takova,, R. W. Kwiatkowski,, T. J. Sander,, M. de Arruda,, D. A. Arco,, B. P. Neri, and, M. A. Brow. 1999. Polymorphism identification and quantitative detection of genomic DNA by invasive cleavage of oligonucleotide probes. Nat. Biotechnol. 17: 292296.
126. Manger, I. D.,, and D. A. Relman. 2000. How the host “sees” pathogens: global gene expression responses to infection. Curr. Opin. Immunol. 12: 215218.
127. Markoulatos, P.,, N. Siafakas, and, M. Moncany. 2002. Multiplex polymerase chain reaction: a practical approach. J. Clin. Lab. Anal. 16: 4751.
128. Marshall, A.,, and J. Hodgson. 1998. DNA chips: an array of possibilities. Nat. Biotechnol. 16: 2731.
129. Martell, M.,, J. Gomez,, J. I. Esteban,, S. Sauleda,, J. Quer,, B. Cabot,, R. Esteban, and, J. Guardia. 1999. High-throughput real-time reverse transcription-PCR quantitation of hepatitis C virus RNA. J. Clin. Microbiol. 37: 327332.
130. McCabe, K. M.,, and E. R. McCabe. 1997. Molecular genetic diagnosis of infectious diseases. Pediatr. Ann. 26: 547552.
131. McDowell, D. 1999. PCR: Factors Affecting Reliability and Validity. The Royal Society of Chemistry, London, United Kingdom.
132. McGlennen, R. C. 2001. Miniaturization technologies for molecular diagnostics. Clin. Chem. 47: 393402.
133. Meier, A.,, D. H. Persing,, M. Finken, and, E. C. Bottger. 1993. Elimination of contaminating DNA within polymerase chain reaction reagents: implications for a general approach to detection of uncultured pathogens. J. Clin. Microbiol. 31: 646652.
134. Mizuguchi, H.,, M. Nakatsuji,, S. Fujiwara,, M. Takagi, and, T. Imanaka. 1999. Characterization and application to hot start PCR of neutralizing monoclonal antibodies against KOD DNA polymerase. J. Biochem. 126: 762768.
135. Modrusan, Z.,, C. Marlowe,, D. Wheeler,, M. Pirseyedi, and, R. N. Bryan. 2000. CPT-EIA assays for the detection of vancomycin resistant vanA and vanB genes in enterococci. Diagn. Microbiol. Infect. Dis. 37: 4550.
136. Modrusan, Z.,, C. Marlowe,, D. Wheeler,, M. Pirseyedi, and, R. N. Bryan. 1999. Detection of vancomycin resistant genes vanA and vanB by cycling probe technology. Mol. Cell Probes 13: 223231.
137. Moretti, T.,, B. Koons, and, B. Budowle. 1998. Enhancement of PCR amplification yield and specificity using AmpliTaq Gold DNA polymerase. BioTechniques 25: 716722.
138. 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: 150154.
139. Mukhopadhyay, A. K.,, S. Garg,, R. Mitra,, A. Basu,, K. Rajendran,, D. Dutta,, S. K. Bhattacharya,, T. Shimada,, T. Takeda,, Y. Takeda, and, G. B. Nair. 1996. Temporal shifts in traits of Vibrio cholerae strains isolated from hospitalized patients in Calcutta: a 3-year (1993 to 1995) analysis. J. Clin. Microbiol. 34: 25372543.
140. Mullis, K. B. 1990. The unusual origin of the polymerase chain reaction. Sci. Am. 262: 5661, 64–65.
141. Mullis, K. B.,, and F. A. Faloona. 1987. Specific synthesis of DNA in vitro via a polymerase-catalyzed chain reaction. Methods Enzymol. 155: 335350.
142. Murali, R.,, M. Helmer-Citterich,, D. J. Sharkey,, E. R. Scalice,, J. L. Daiss,, M. A. Sullivan, and, H. M. Krishna Murthy. 1998. Structural studies on an inhibitory antibody against Thermus aquaticus DNA polymerase suggest mode of inhibition. Protein Eng. 11: 7986.
143. Myers, T. W.,, and D. H. Gelfand. 1991. Reverse transcription and DNA amplification by a Thermus thermophilus DNA polymerase. Biochemistry 30: 76617666.
144. Mylonakis, E.,, M. Paliou, and, J. D. Rich. 2001. Plasma viral load testing in the management of HIV infection. Am. Fam. Physician 63: 483486.
145. Niemeyer, D. M. 1998. Polymerase chain reaction: a link to the future. Mil. Med. 163: 226228.
146. Nilsson, M.,, H. Malmgren,, M. Samiotaki,, M. Kwiatkowski,, B. P. Chowdhary, and, U. Landegren. 1994. Padlock probes: circularizing oligonucleotides for localized DNA detection. Science 265: 20852088.
147. Nolte, F. S. 1998. Branched DNA signal amplification for direct quantitation of nucleic acid sequences in clinical specimens. Adv. Clin. Chem. 33: 201235.
148. Notomi, T.,, H. Okayama,, H. Masubuchi,, T. Yonekawa,, K. Watanabe,, N. Amino, and, T. Hase. 2000. Loop-mediated isothermal amplification of DNA. Nucleic Acids Res. 28: E63.
149. Nucci, M.,, T. Akiti,, G. Barreiros,, F. Silveira,, S. G. Revankar,, B. L. Wickes,, D. A. Sutton, and, T. F. Patterson. 2002. Nosocomial outbreak of Exophiala jeanselmei fungemia associated with contamination of hospital water. Clin. Infect. Dis. 34: 14751480.
150. Olivier, M.,, A. Aggarwal,, J. Allen,, A. A. Almendras,, E. S. Bajorek,, E. M. Beasley,, S. D. Brady,, J. M. Bushard,, V. I. Bustos,, A. Chu,, T. R. Chung,, A. DeWitte,, M. E. Denys,, R. Dominguez,, N. Y. Fang,, B. D. Foster,, R. W. Freudenberg,, D. Hadley,, L. R. Hamilton,, T. J. Jeffrey,, L. Kelly,, L. Lazzeroni,, M. R. Levy,, S. C. Lewis,, X. Liu,, F. J. Lopez,, B. Louie,, J. P. Marquis,, R. A. Martinez,, M. K. Matsuura,, N. S. Misherghi,, J. A. Norton,, A. Olshen,, S. M. Perkins,, A. J. Perou,, C. Piercy,, M. Piercy,, F. Qin,, T. Reif,, K. Sheppard,, V. Shokoohi,, G. A. Smick,, W. L. Sun,, E. A. Stewart,, J. Fernando,, Tejeda,, N. M. Tran,, T. Trejo,, N. T. Vo,, S. C. Yan,, D. L. Zierten,, S. Zhao,, R. Sachidanandam,, B. J. Trask,, R. M. Myers, and, D. R. Cox. 2001. A high-resolution radiation hybrid map of the human genome draft sequence. Science 291: 12981302.
151. Olsen, G. J.,, D. J. Lane,, S. J. Giovannoni,, N. R. Pace, and, D. A. Stahl. 1986. Microbial ecology and evolution: a ribosomal RNA approach. Annu. Rev. Microbiol. 40: 337365.
152. Orlando, C.,, P. Pinzani, and, M. Pazzagli. 1998. Developments in quantitative PCR. Clin. Chem. Lab. Med. 36: 255269.
153. Osiowy, C. 1998. Direct detection of respiratory syncytial virus, parainfluenza virus, and adenovirus in clinical respiratory specimens by a multiplex reverse transcription-PCR assay. J. Clin. Microbiol. 36: 31493154.
154. Ostergaard, L. 1999. Diagnosis of urogenital Chlamydia trachomatis infection by use of DNA amplification. APMIS Suppl. 89: 536.
155. Ou, C. Y.,, S. Kwok,, S. W. Mitchell,, D. H. Mack,, J. J. Sninsky,, J. W. Krebs,, P. Feorino,, D. Warfield, and, G. Schochetman. 1988. DNA amplification for direct detection of HIV-1 in DNA of peripheral blood mononuclear cells. Science 239: 295297.
156. Pasternack, R.,, P. Vuorinen,, A. Kuukankorpi,, T. Pitkajarvi, and, A. Miettinen. 1996. Detection of Chlamydia trachomatis infections in women by Amplicor PCR: comparison of diagnostic performance with urine and cervical specimens. J. Clin. Microbiol. 34: 995998.
157. Patel, J. B.,, D. G. Leonard,, X. Pan,, J. M. Musser,, R. E. Berman, and, I. Nachamkin. 2000. Sequence-based identification of Mycobacterium species using the MicroSeq 500 16S rDNA bacterial identification system. J. Clin. Microbiol. 38: 246251.
158. Patel, R.,, J. R. Uhl,, P. Kohner,, M. K. Hopkins, and, F. R. Cockerill III. 1997. Multiplex PCR detection of vanA, vanB, vanC-1, and vanC-2/3 genes in enterococci. J. Clin. Microbiol. 35: 703707.
159. Pawlotsky, J. M. 1999. Diagnostic tests for hepatitis C. J. Hepatol. 31: 7179.
160. Pawlotsky, J. M. 1997. Measuring hepatitis C viremia in clinical samples: can we trust the assays? Hepatology 26: 14.
161. Persing, D. H. 1991. Polymerase chain reaction: trenches to benches. J. Clin. Microbiol. 29: 12811285.
162. Pfaller, M. A. 2001. Molecular approaches to diagnosing and managing infectious diseases: practicality and costs. Emerg. Infect. Dis. 7: 312318.
163. Pfaller, M. A. 1999. Molecular epidemiology in the care of patients. Arch. Pathol. Lab. Med. 123: 10071010.
164. Pfyffer, G. E.,, P. Funke-Kissling,, E. Rundler, and, R. Weber. 1999. Performance characteristics of the BDProbeTec system for direct detection of Mycobacterium tuberculosis complex in respiratory specimens. J. Clin. Microbiol. 37: 137140.
165. Pitt, T. L.,, and N. A. Saunders. 2000. Molecular bacteriology: a diagnostic tool for the millennium. J. Clin. Pathol. 53: 7175.
166. Pittaluga, F.,, T. Allice,, M. L. Abate,, A. Ciancio,, F. Cerutti,, S. Varetto,, G. Colucci,, A. Smedile, and, V. Ghisetti. 2008. Clinical evaluation of the COBAS Ampliprep/COBAS TaqMan for HCV RNA quantitation in comparison with the branched-DNA assay. J. Med. Virol. 80: 254260.
167. Poddar, S. K.,, M. H. Sawyer, and, J. D. Connor. 1998. Effect of inhibitors in clinical specimens on Taq and Tth DNA polymerase-based PCR amplification of influenza A virus. J. Med. Microbiol. 47: 11311135.
168. Poddar, S. K.,, M. H. Sawyer, and, J. D. Connor. 1998. Evaluation of PCR assays in presence of antibody to thermostable DNA polymerases for detection of microbial agents: avoiding false negative results for specimen containing low-titer agent. J. Clin. Lab. Anal. 12: 238241.
169. Post, J. C.,, and G. D. Ehrlich. 2000. The impact of the polymerase chain reaction in clinical medicine. JAMA 283: 15441546.
170. Rachlis, A. R.,, D. P. Zarowny, et al. 1998. Guidelines for antiretroviral therapy for HIV infection. CMAJ 158: 496505.
171. Raja, S.,, J. Ching,, L. Xi,, S. J. Hughes,, R. Chang,, W. Wong,, W. McMillan,, W. E. Gooding,, K. S. McCarty, Jr.,, M. Chestney,, J. D. Luketich, and, T. E. Godfrey. 2005. Technology for automated, rapid, and quantitative PCR or reverse transcription-PCR clinical testing. Clin. Chem. 51: 882890.
172. Relman, D. A. 1998. Detection and identification of previously unrecognized microbial pathogens. Emerg. Infect. Dis. 4: 382389.
173. Relman, D. A. 1993. The identification of uncultured microbial pathogens. J. Infect. Dis. 168: 18.
174. Relman, D. A.,, and S. Falkow. 1992. Identification of uncultured microorganisms: expanding the spectrum of characterized microbial pathogens. Infect. Agents Dis. 1: 245253.
175. Relman, D. A.,, J. S. Loutit,, T. M. Schmidt,, S. Falkow, and, L. S. Tompkins. 1990. The agent of bacillary angiomatosis. An approach to the identification of uncultured pathogens. N. Engl. J. Med. 323: 15731580.
176. Ririe, K. M.,, R. P. Rasmussen, and, C. T. Wittwer. 1997. Product differentiation by analysis of DNA melting curves during the polymerase chain reaction. Anal. Biochem. 245: 154160.
177. Roberts, T. C.,, and G. A. Storch. 1997. Multiplex PCR for diagnosis of AIDS-related central nervous system lymphoma and toxoplasmosis. J. Clin. Microbiol. 35: 268269.
178. Ross, J. S. 1999. Financial determinants of outcomes in molecular testing. Arch. Pathol. Lab. Med. 123: 10711075.
179. Ross, J. S. 1998. Molecular pathology and managed care: challenges and opportunities. Diagn. Mol. Pathol. 7: 189191.
180. Ryan, D.,, B. Nuccie, and, D. Arvan. 1999. Non-PCR-dependent detection of the factor V Leiden mutation from genomic DNA using a homogeneous invader microtiter plate assay. Mol. Diagn. 4: 135144.
181. Rys, P. N.,, and D. H. Persing. 1993. Preventing false positives: quantitative evaluation of three protocols for inactivation of polymerase chain reaction amplification products. J. Clin. Microbiol. 31: 23562360.
182. Saiki, R. K.,, D. H. Gelfand,, S. Stoffel,, S. J. Scharf,, R. Higuchi,, G. T. Horn,, K. B. Mullis, and, H. A. Erlich. 1988. Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239: 487491.
183. Saiki, R. K.,, S. Scharf,, F. Faloona,, K. B. Mullis,, G. T. Horn,, H. A. Erlich, and, N. Arnheim. 1985. Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. Science 230: 13501354.
184. Salfinger, M.,, Y. M. Hale, and, J. R. Driscoll. 1998. Diagnostic tools in tuberculosis. Present and future. Respiration 65: 163170.
185. Sanchez-Pescador, R.,, M. S. Stempien, and, M. S. Urdea. 1988. Rapid chemiluminescent nucleic acid assays for detection of TEM-1 beta-lactamase-mediated penicillin resistance in Neisseria gonorrhoeae and other bacteria. J. Clin. Microbiol. 26: 19341938.
186. Sarkar, G.,, and S. S. Sommer. 1990. Shedding light on PCR contamination. Nature 343: 27. (Letter.)
187. Schachter, J.,, W. E. Stamm,, T. C. Quinn,, W. W. Andrews,, J. D. Burczak, and, H. H. Lee. 1994. Ligase chain reaction to detect Chlamydia trachomatis infection of the cervix. J. Clin. Microbiol. 32: 25402543.
188. Schiffman, M. H.,, N. B. Kiviat,, R. D. Burk,, K. V. Shah,, R. W. Daniel,, R. Lewis,, J. Kuypers,, M. M. Manos,, D. R. Scott, and, M. E. Sherman. 1995. Accuracy and interlaboratory reliability of human papillomavirus DNA testing by hybrid capture. J. Clin. Microbiol. 33: 545550.
189. Schmidt, B.,, R. R. Muellegger,, C. Stockenhuber,, H. P. Soyer,, S. Hoedl,, A. Luger, and, H. Kerl. 1996. Detection of Borrelia burgdorferi-specific DNA in urine specimens from patients with erythema migrans before and after antibiotic therapy. J. Clin. Microbiol. 34: 13591363.
190. Schmitt, Y. 2001. Performance characteristics of quantification assays for human immunodeficiency virus type 1 RNA. J. Clin. Virol. 20: 3133.
191. Schumacher, W.,, E. Frick,, M. Kauselmann,, V. Maier-Hoyle,, R. van der Vliet, and, R. Babiel. 2007. Fully automated quantification of human immunodeficiency virus (HIV) type 1 RNA in human plasma by the COBAS AmpliPrep/COBAS TaqMan system. J. Clin. Virol. 38: 304312.
192. Schutten, M. 2008. Comparison of the Abbott Realtime HIV-1 and HCV viral load assays with commercial competitor assays. Expert Rev. Mol. Diagn. 8: 369377.
193. Schuurman, R.,, D. Descamps,, G. J. Weverling,, S. Kaye,, J. Tijnagel,, I. Williams,, R. van Leeuwen,, R. Tedder,, C. A. Boucher,, F. Brun-Vezinet, and, C. Loveday. 1996. Multicenter comparison of three commercial methods for quantification of human immunodeficiency virus type 1 RNA in plasma. J. Clin. Microbiol. 34: 30163022.
194. Schweitzer, B.,, and S. Kingsmore. 2001. Combining nucleic acid amplification and detection. Curr. Opin. Biotechnol. 12: 2127.
195. Schweitzer, B.,, S. Wiltshire,, J. Lambert,, S. O’Malley,, K. Kukanskis,, Z. Zhu,, S. F. Kingsmore,, P. M. Lizardi, and, D. C. Ward. 2000. Immunoassays with rolling circle DNA amplification: a versatile platform for ultrasensitive antigen detection. Proc. Natl. Acad. Sci. USA 97: 1011310119.
196. Sharkey, D. J.,, E. R. Scalice,, K. G. Christy, Jr.,, S. M. Atwood, and, J. L. Daiss. 1994. Antibodies as thermolabile switches: high temperature triggering for the polymerase chain reaction. Bio/Technology 12: 506509.
197. Sia, I. G.,, and R. Patel. 2000. New strategies for prevention and therapy of cytomegalovirus infection and disease in solid-organ transplant recipients. Clin. Microbiol. Rev. 13: 83121.
198. Soll, D. R. 2000. The ins and outs of DNA fingerprinting the infectious fungi. Clin. Microbiol. Rev. 13: 332370.
199. Spargo, C. A.,, M. S. Fraiser,, M. Van Cleve,, D. J. Wright,, C. M. Nycz,, P. A. Spears, and, G. T. Walker. 1996. Detection of M. tuberculosis DNA using thermophilic strand displacement amplification. Mol. Cell. Probes 10: 247256.
200. Spears, P. A.,, C. P. Linn,, D. L. Woodard, and, G. T. Walker. 1997. Simultaneous strand displacement amplification and fluorescence polarization detection of Chlamydia trachomatis DNA. Anal. Biochem. 247: 130137.
201. Springer, B.,, L. Stockman,, K. Teschner,, G. D. Roberts, and, E. C. Bottger. 1996. Two-laboratory collaborative study on identification of mycobacteria: molecular versus phenotypic methods. J. Clin. Microbiol. 34: 296303.
202. Stary, A.,, S. F. Ching,, L. Teodorowicz, and, H. Lee. 1997. Comparison of ligase chain reaction and culture for detection of Neisseria gonorrhoeae in genital and extragenital specimens. J. Clin. Microbiol. 35: 239242.
203. Stockman, L.,, K. A. Clark,, J. M. Hunt, and, G. D. Roberts. 1993. Evaluation of commercially available acridinium ester-labeled chemiluminescent DNA probes for culture identification of Blastomyces dermatitidis, Coccidioides immitis, Cryptococcus neoformans, and Histoplasma capsulatum. J. Clin. Microbiol. 31: 845850.
204. Syrmis, M. W.,, D. M. Whiley,, M. Thomas,, I. M. Mackay,, J. Williamson,, D. J. Siebert,, M. D. Nissen, and, T. P. Sloots. 2004. A sensitive, specific, and cost-effective multiplex reverse transcriptase-PCR assay for the detection of seven common respiratory viruses in respiratory samples. J. Mol. Diagn. 6: 125131.
205. Takagi, M.,, M. Nishioka,, H. Kakihara,, M. Kitabayashi,, H. Inoue,, B. Kawakami,, M. Oka, and, T. Imanaka. 1997. Characterization of DNA polymerase from Pyrococcus sp. strain KOD1 and its application to PCR. Appl. Environ. Microbiol. 63: 45044510.
206. Tang, Y.-W.,, and D. H. Persing. 1999. Molecular detection and identification of microorganisms, p. 215–244. In P. R. Murray,, E. J. Baron,, M. A. Pfaller,, F. C. Tenover, and, R. H. Yolken (ed.), Manual of Clinical Microbiology, 7th ed. ASM Press, Washington, DC.
207. Tang, Y. W.,, N. M. Ellis,, M. K. Hopkins,, D. H. Smith,, D. E. Dodge, and, D. H. Persing. 1998. Comparison of phenotypic and genotypic techniques for identification of unusual aerobic pathogenic gram-negative bacilli. J. Clin. Microbiol. 36: 36743679.
208. Tang, Y. W.,, M. K. Hopkins,, C. P. Kolbert,, P. A. Hartley,, P. J. Severance, and, D. H. Persing. 1998. Bordetella holmesii-like organisms associated with septicemia, endocarditis, and respiratory failure. Clin. Infect. Dis. 26: 389392.
209. Tang, Y. W.,, P. S. Mitchell,, M. J. Espy,, T. F. Smith, and, D. H. Persing. 1999. Molecular diagnosis of herpes simplex virus infections in the central nervous system. J. Clin. Microbiol. 37: 21272136.
210. Tang, Y. W.,, G. W. Procop, and, D. H. Persing. 1997. Molecular diagnostics of infectious diseases. Clin. Chem. 43: 20212038.
211. Tang, Y. W.,, A. Von Graevenitz,, M. G. Waddington,, M. K. Hopkins,, D. H. Smith,, H. Li,, C. P. Kolbert,, S. O. Montgomery, and, D. H. Persing. 2000. Identification of coryneform bacterial isolates by ribosomal DNA sequence analysis. J. Clin. Microbiol. 38: 16761678.
212. Taylor, G. R.,, and P. Robinson. 1998. The polymerase chain reaction: from functional genomics to high-school practical classes. Curr. Opin. Biotechnol. 9: 3542.
213. Templeton, K.,, J. Roberts,, D. Jeffries,, G. Forster, and, C. Aitken. 2001. The detection of Chlamydia trachomatis by DNA amplification methods in urine samples from men with urethritis. Int. J. STD AIDS 12: 793796.
214. Tenover, F. C.,, J. T. Crawford,, R. E. Huebner,, L. J. Geiter,, C. R. Horsburgh, Jr., and, R. C. Good. 1993. The resurgence of tuberculosis: is your laboratory ready? J. Clin. Microbiol. 31: 767770.
215. Thomas, D. C.,, G. A. Nardone, and, S. K. Randall. 1999. Amplification of padlock probes for DNA diagnostics by cascade rolling circle amplification or the polymerase chain reaction. Arch. Pathol. Lab. Med. 123: 11701176.
216. Tomita, N.,, Y. Mori,, H. Kanda, and, T. Notomi. 2008. Loop-mediated isothermal amplification (LAMP) of gene sequences and simple visual detection of products. Nat. Protoc. 3: 877882.
217. Tyagi, S.,, and F. R. Kramer. 1996. Molecular beacons: probes that fluoresce upon hybridization. Nat. Biotechnol. 14: 303308.
218. Urdea, M. S.,, T. Horn,, T. J. Fultz,, M. Anderson,, J. A. Running,, S. Hamren,, D. Ahle, and, C. A. Chang. 1991. Branched DNA amplification multimers for the sensitive, direct detection of human hepatitis viruses. Nucleic Acids Symp. Ser. 1991: 197200.
219. Ushio, M.,, I. Yui,, N. Yoshida,, M. Fujino,, T. Yonekawa,, Y. Ota,, T. Notomi, and, T. Nakayama. 2005. Detection of respiratory syncytial virus genome by subgroups-A, B specific reverse transcription loop-mediated isothermal amplification (RT-LAMP). J. Med. Virol. 77: 121127.
220. Vandamme, A. M.,, K. Fransen,, L. Debaisieux,, D. Marissens,, S. Sprecher,, D. Vaira,, A. T. Vandenbroucke,, C. Verhofstede, et al. 1995. Standardisation of primers and an algorithm for HIV-1 diagnostic PCR evaluated in patients harbouring strains of diverse geographical origin. The Belgian AIDS Reference Laboratories. J. Virol. Methods 51: 305316.
221. Vandamme, P.,, B. Pot,, M. Gillis,, P. de Vos,, K. Kersters, and, J. Swings. 1996. Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol. Rev. 60: 407438.
222. VanDevanter, D. R.,, P. Warrener,, L. Bennett,, E. R. Schultz,, S. Coulter,, R. L. Garber, and, T. M. Rose. 1996. Detection and analysis of diverse herpesviral species by consensus primer PCR. J. Clin. Microbiol. 34: 16661671.
223. Walker, G. T.,, M. S. Fraiser,, J. L. Schram,, M. C. Little,, J. G. Nadeau, and, D. P. Malinowski. 1992. Strand displacement amplification—an isothermal, in vitro DNA amplification technique. Nucleic Acids Res. 20: 16911696.
224. Walker, G. T.,, M. C. Little,, J. G. Nadeau, and, D. D. Shank. 1992. Isothermal in vitro amplification of DNA by a restriction enzyme/DNA polymerase system. Proc. Natl. Acad. Sci. USA 89: 392396.
225. 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: 556561.
226. Whitcombe, D.,, J. Brownie,, H. L. Gillard,, D. McKechnie,, J. Theaker,, C. R. Newton, and, S. Little. 1998. A homogeneous fluorescence assay for PCR amplicons: its application to real-time, single-tube genotyping. Clin. Chem. 44: 918923.
227. Whitcombe, D.,, C. R. Newton, and, S. Little. 1998. Advances in approaches to DNA-based diagnostics. Curr. Opin. Biotechnol. 9: 602608.
228. White, T. J.,, R. Madej, and, D. H. Persing. 1992. The polymerase chain reaction: clinical applications. Adv. Clin. Chem. 29: 161196.
229. Wiedmann, M.,, W. J. Wilson,, J. Czajka,, J. Luo,, F. Barany, and, C. A. Batt. 1994. Ligase chain reaction (LCR)—overview and applications. PCR Methods Appl. 3: S51S64.
230. Wilson, K. H.,, R. B. Blitchington, and, R. C. Greene. 1990. Amplification of bacterial 16S ribosomal DNA with polymerase chain reaction. J. Clin. Microbiol. 28: 19421946. (Erratum, 29:666, 1991.)
231. Wilton, S.,, and D. Cousins. 1992. Detection and identification of multiple mycobacterial pathogens by DNA amplification in a single tube. PCR Methods Appl. 1: 269273.
232. Witt, D. J.,, M. Kemper,, A. Stead,, P. Sillekens,, C. C. Ginocchio,, M. J. Espy,, C. V. Paya,, T. F. Smith,, F. Roeles, and, A. M. Caliendo. 2000. Analytical performance and clinical utility of a nucleic acid sequence-based amplification assay for detection of cytomegalovirus infection. J. Clin. Microbiol. 38: 39943999.
233. Wittwer, C. T.,, K. M. Ririe,, R. V. Andrew,, D. A. David,, R. A. Gundry, and, U. J. Balis. 1997. The LightCycler: a microvolume multisample fluorimeter with rapid temperature control. BioTechniques 22: 176181.
234. Woese, C. R. 1987. Bacterial evolution. Microbiol. Rev. 51: 221271.
235. Wolff, D.,, and A. Gerritzen. 2007. Comparison of the Roche COBAS Amplicor Monitor, Roche COBAS Ampliprep/COBAS Taqman and Abbott RealTime Test assays for quantification of hepatitis C virus and HIV RNA. Clin. Chem. Lab. Med. 45: 917922.
236. Wolk, D.,, P. S. Mitchell, and, R. Patel. 2001. Principles of molecular microbiology testing methods. Infect. Dis. Clin. N. Am. 15: 11571204.
237. Wong, A. K.,, R. C. Chan,, W. S. Nichols, and, S. Bose. 2008. Human papillomavirus (HPV) in atypical squamous cervical cytology: the Invader HPV test as a new screening assay. J. Clin. Microbiol. 46: 869875.
238. Wu, D. Y.,, and R. B. Wallace. 1989. The ligation amplification reaction (LAR)—amplification of specific DNA sequences using sequential rounds of templatedependent ligation. Genomics 4: 560569.
239. Yao, J.,, Z. Liu,, L. S. Ko,, G. Pan, and, Y. Jiang. 2005. Quantitative detection of HIV-1 RNA using NucliSens EasyQ HIV-1 assay. J. Virol. Methods 129: 4046.
240. Yen-Lieberman, B. 2001. Diagnosis of human cytomegalovirus disease. Clin. Microbiol. Newsl. 22: 105109.
241. Yoda, T.,, Y. Suzuki,, K. Yamazaki,, N. Sakon,, M. Kanki,, I. Aoyama, and, T. Tsukamoto. 2007. Evaluation and application of reverse transcription loop-mediated isothermal amplification for detection of noroviruses. J. Med. Virol. 79: 326334.
242. Yoshino, M.,, T. Annaka,, T. Kojima, and, M. Ikedo. 2008. Sensitive and rapid detection of Mycoplasma pneumoniae by loop-mediated isothermal amplification. Kansenshogaku Zasshi 82: 168176. (In Japanese.)
243. Young, K. K.,, R. M. Resnick, and, T. W. Myers. 1993. Detection of hepatitis C virus RNA by a combined reverse transcription-polymerase chain reaction assay. J. Clin. Microbiol. 31: 882886.
244. Yourno, J. 1992. A method for nested PCR with single closed reaction tubes. PCR Methods Appl. 2: 6065.
245. Yox, S. B. 1999. The laboratory on a chip: the future of miniaturization and automation. Lab. Med. 30: 456461.
246. Zetola, N. M.,, A. Mintie,, S. Liska,, E. Wong,, J. D. Williams,, M. P. Busch, and, J. D. Klausner. 2007. Performance of a transcription-mediated-amplification HIV-1 RNA assay in pooled specimens. J. Clin. Virol. 40: 6870.


Generic image for table

NAA methods

Citation: Datta V, Hayden R. 2011. In Vitro Nucleic Acid Amplification Techniques, p 33-61. 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.ch3
Generic image for table

Amplification methods as analogs of artificial media

Citation: Datta V, Hayden R. 2011. In Vitro Nucleic Acid Amplification Techniques, p 33-61. 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.ch3
Generic image for table

FDA-approved molecular diagnostic tests for infectious disease

Citation: Datta V, Hayden R. 2011. In Vitro Nucleic Acid Amplification Techniques, p 33-61. 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.ch3
Generic image for table

Noncommercial nucleic acid-based tests for clinically important viral and bacterial pathogens

Citation: Datta V, Hayden R. 2011. In Vitro Nucleic Acid Amplification Techniques, p 33-61. 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.ch3