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Chapter 4 : Molecular Microbiology

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Abstract:

Technological advances in realtime PCR techniques, automation, nucleic acid sequencing, multiplex analysis, and mass spectrometry have reinvigorated the field and created new opportunities for growth. Molecular microbiology is the leading area in molecular pathology in terms of both the numbers of tests performed and clinical relevance. This chapter covers amplified- and nonamplified-probe techniques, postamplification detection and analysis, clinical applications of these techniques. It also discusses the special challenges and opportunities that these techniques provide for the clinical laboratory. Although probes can range from 15 to thousands of nucleotides in size, synthetic oligonucleotides of less than 50 nucleotides are commonly incorporated into commercial kits. In most clinical applications, formalin-fixed, paraffin-embedded tissue sections are used. Nonamplified-probe techniques are used most effectively in culture confirmation assays for mycobacteria and systemic dimorphic fungi. Strategies other than PCR, are based on signal, target, or probe amplification, and have sensitivity unparalleled in laboratory medicine, have created new opportunities for the clinical laboratory to have an effect on patient care, and have become the new “gold standards” for laboratory diagnosis of many infectious diseases. In signal amplification methods, the concentration of the probe or target does not increase. Signal amplification assays have several advantages over target amplification assays. The target amplification systems share certain fundamental characteristics. They use enzyme-mediated processes, in which a single enzyme or multiple enzymes synthesize copies of target nucleic acid. In these techniques, the amplification products are detected by two oligonucleotide primers that bind to complementary sequences on opposite strands of double-stranded targets.

Citation: Nolte F, Caliendo A. 2011. Molecular Microbiology, p 27-59. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch4

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Nucleic Acid Amplification Techniques
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Antimicrobial Susceptibility Testing
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Human immunodeficiency virus 1
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Reverse Transcriptase PCR
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FIGURE 1

bDNA signal amplification. Reprinted with permission of Elsevier from reference .

Citation: Nolte F, Caliendo A. 2011. Molecular Microbiology, p 27-59. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch4
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Image of FIGURE 2
FIGURE 2

PCR target amplification. Reprinted with permission of Elsevier from reference .

Citation: Nolte F, Caliendo A. 2011. Molecular Microbiology, p 27-59. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch4
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Image of FIGURE 3
FIGURE 3

Real-time PCR amplification plot with commonly used terms and abbreviations. R, normalized fluorescent signal from reporter dye. From , p. 5–94 (Applied Biosystems, Foster City, CA, 2002). Reprinted with permission.

Citation: Nolte F, Caliendo A. 2011. Molecular Microbiology, p 27-59. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch4
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Image of FIGURE 4
FIGURE 4

5′ exonuclease chemistry for real-time PCR applications. Reprinted with permission of Elsevier from reference .

Citation: Nolte F, Caliendo A. 2011. Molecular Microbiology, p 27-59. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch4
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Image of FIGURE 5
FIGURE 5

Dual hybridization probes for real-time PCR applications. Reprinted with permission of Elsevier from reference .

Citation: Nolte F, Caliendo A. 2011. Molecular Microbiology, p 27-59. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch4
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Image of FIGURE 6
FIGURE 6

Molecular beacon probes for real-time amplification applications. Reprinted with permission of Elsevier from reference .

Citation: Nolte F, Caliendo A. 2011. Molecular Microbiology, p 27-59. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch4
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Image of FIGURE 7
FIGURE 7

Transcription-based target amplification. NASBA and TMA are examples of transcription- based amplification systems. Reprinted with permission of Elsevier from reference .

Citation: Nolte F, Caliendo A. 2011. Molecular Microbiology, p 27-59. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch4
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Image of FIGURE 8
FIGURE 8

Strand displacement target amplification. The process is shown for only one strand of a dsDNA target, but amplification occurs on both strands simultaneously. B and B, bumper primers; S and S, amplification primers. Modified from reference .

Citation: Nolte F, Caliendo A. 2011. Molecular Microbiology, p 27-59. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch4
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Image of FIGURE 9
FIGURE 9

Cleavase-invader probe-based amplification. Reprinted with permission of Elsevier from reference .

Citation: Nolte F, Caliendo A. 2011. Molecular Microbiology, p 27-59. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch4
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References

/content/book/10.1128/9781555816728.chap4
1. American Medical Association. 2009. CPT 2009, Current Procedural Terminology. AMA Press, Chicago, IL.
2. Arnold, C.,, L. Westland,, G. Mowat,, A. Underwood,, J. Magee,, and S. Gharbia. 2005. Single-nucleotide polymorphism- based differentiation and drug resistance detection in Mycobacterium tuberculosis from isolates or directly from sputum. Clin. Microbiol. Infect. 11: 122 130.
3. Arnold, L. J., Jr.,, P. W. Hammond,, W. A. Wiese,, and N. C. Nelson. 1989. Assay formats involving acridinium esterlabeled DNA probes. Clin. Chem. 35: 1588 1594.
4. Barbeau, J. M.,, J. Goforth,, A. M. Caliendo,, and F. S. Nolte. 2004. Performance characteristics of a quantitative TaqMan hepatitis C virus RNA analyte-specific reagent. J. Clin. Microbiol. 42: 3739 3746.
5. Beutler, E.,, T. Gelbart,, and W. Kuhl. 1990. Interference of heparin with the polymerase chain reaction. BioTechniques 9: 166.
6. Blin, N.,, and D. W. Stafford. 1976. A general method for isolation of high molecular weight DNA from eukaryotes. Nucleic Acids Res. 3: 2303 2308.
7. Boom, R.,, C. Sol,, M. Salimans,, C. Jansen,, P. M. Wertheimvan Dillen,, and J. van der Noordaa. 1990. Rapid and simple method for purification of nucleic acids. J. Clin. Microbiol. 28: 495 503.
8. Boriskin, Y. S.,, P. S. Rice,, R. A. Stabler,, J. Hinds,, H. Al-Ghusein,, K. Vass,, and P. D. Butcher. 2004. DNA microarrays for virus detection in cases of central nervous system infection. J. Clin. Microbiol. 42: 5811 5818.
9. Briese, T.,, G. Palacios,, M. Kokoris,, O. Jabado,, Z. Liu,, and N. Renwick. 2005. Diagnostic system for rapid and sensitive differential detection of pathogens. Emerg. Infect. Dis. 11: 310 313.
10. Brunstein, J. D.,, C. L. Cline,, S. McKinney,, and E. Thomas. 2008. Evidence from multiplex molecular assays for complex multipathogen interactions in acute respiratory infections. J. Clin. Microbiol. 46: 97 102.
11. Caliendo, A. M.,, K. St. George,, S. Y. Kao,, J. Allega,, B. H. Tan,, R. LaFontaine,, L. Bui,, and C. R. Rinaldo. 2000. Comparison of quantitative cytomegalovirus (CMV) PCR in plasma and CMV antigenemia assay: clinical utility of the prototype AMPLICOR CMV MONITOR test in transplant recipients. J. Clin. Microbiol. 38: 2122 2127.
12. Capaul, S. E.,, and M. Georgievski-Hirsoho. 2005. Detection of enterovirus RNA in cerebrospinal fluid (CSF) using NuclioSens Easy Q Enterovirus assay. J. Clin. Virol. 32: 236 240.
13. Chamberlain, J. S.,, R. A. Gibbs,, J. E. Rainer,, P. N. Nguyen,, and C. T. Caskey. 1988. Deletion screening of the Duchenne muscular dystrophy locus via multiplex DNA amplification. Nucleic Acids Res. 16: 11141 11156.
14. Chin, C. Y.,, A. Urisman,, S. Grenhow,, S. Rouskin,, S. Yagi,, D. Schnurr,, C. Wright,, W. L. Drew,, D. Wang,, P. S. Weintrub,, J. L. Derisi,, and D. Ganem. 2008. Utility of DNA microarrays for detection of viruses in acute respiratory tract infections in children. J. Pediatr. 153: 76 83.
15. Chomczynski, P.,, and N. Sacchi. 1987. Single-step method of RNA isolation by acid guanidinium thiocyanate-phenolchloroform extraction. Anal. Biochem. 62: 156 159.
16. Choo, Q. L.,, G. Kuo,, A. J. Weiner,, L. R. Overby,, D. W. Bradley,, and M. Houghton. 1989. Isolation of a cDNA clone derived from a blood-borne non-A, non-B viral hepatitis genome. Science 244: 359 362.
17. Chow, W. H. A.,, C. McCloskey,, Y. Tong,, L. Hu,, Q. You,, C. P. Kelly,, H. Kong,, Y. Tang,, and W. Tang. 2008. Application of isothermal helicase-dependent amplification with a disposable detection device in a simple sensitive stool test for toxigenic Clostridium difficile. J. Mol. Diagn. 10: 452 458.
18. Clementi, M.,, S. Menzo,, P. Bagnarelli,, A. Manzin,, A. Valenza,, and P. E. Varaldo. 1993. Quantitative PCR and RT-PCR in virology. PCR Methods Appl. 2: 191 196.
19. Clinical and Laboratory Standards Institute. 2006. Collection, Transport, Preparation, and Storage of Specimens and Samples for Molecular Methods; Approved Guideline. CLSI document MM13-A. Clinical and Laboratory Standards Institute, Wayne, PA.
20. Clinical and Laboratory Standards Institute. 2005. Diagnostic Nucleic Acid Microarrays; Proposed Guideline. CLSI document MMP12-P. Clinical and Laboratory Standards Institute, Wayne, PA.
21. Clinical and Laboratory Standards Institute. 2006. Genotyping for Infectious Diseases: Identification and Characterizations; Approved Guideline. CLSI document MM10-A. Clinical and Laboratory Standards Institute, Wayne, PA.
22. Clinical and Laboratory Standards Institute. 2006. Molecular Diagnostic Methods for Infectious Diseases; Approved Guideline, 2nd ed. CLSI document MM3-A2. Clinical and Laboratory Standards Institute, Wayne, PA.
23. Collins, M. L.,, C. Zayati,, J. J. Detmer,, B. Daly,, J. A. Kolberg,, T. Cha,, B. D. Irvine,, J. Tucker,, and M. S. Urdea. 1995. Preparation and characterization of RNA standards for use in quantitative branched-DNA hybridization assays. Anal. Biochem. 226: 120 129.
24. Compton, J. 1991. Nucleic acid sequence-based amplification. Nature 350: 91 92.
25. Cope, J. J.,, A. Hildesheim,, M. H. Schiffman,, M. M. Manos,, A. T. Lorincz,, R. D. Burk,, A. G. Glass,, C. Greer,, J. Burkland,, K. Helgesen,, D. R. Scott,, M. E. Sherman,, R. J. Kurman,, and K. L. Liaw. 1997. Comparison of the hybrid capture tube test and PCR for detection of human papillomavirus DNA in cervical specimens. J. Clin. Microbiol. 35: 2262 2265.
26. Corless, C. E.,, M. Guiver,, R. Borrow,, V. Edwards-Jones,, A. J. Fox,, and E. B. Kaczmarski. 2001. Simultaneous detection of Neisseria meningitidis, Haemophilus influenzae, and Streptococcus pneumoniae in suspected cases of meningitis and septicemia using real-time PCR. J. Clin. Microbiol. 39: 1553 1558.
27. Diaz, M. R.,, and J. W. Fell. 2004. High-throughput detection of pathogenic yeasts of the genus Trichosporon. J. Clin. Microbiol. 42: 3696 3706.
28. Dienstag, J. L.,, and J. G. Hutchinson. 2006. American Gastroenterological Association Medical Position Statement on the management of hepatitis C. Gastroenterology 130: 225 230.
29. Diggle, M. A.,, and S. C. Clarke. 2004. Pyrosequencing: sequence typing at the speed of light. Mol. Biotechnol. 28: 129 137.
30. Dunbar, S. A.,, C. A. Vander Zee,, K. G. Oliver,, K. L. Karem,, and J. W. Jacobson. 2003. Quantitative, multiplexed detection of bacterial pathogens: DNA and protein applications of the Luminex LabMAP system. J. Microbiol. Methods 53: 245 252.
31. Ecker, D.,, J. J. Drader,, J. Gutierrez,, A. Gutierrez,, J. C. Hannis,, A. Schink,, R. Sampath,, L. B. Blyn,, M. W. Eshoo,, T. A. Hall,, M. Tobarmosquera,, Y. Jiang,, K. A. Sannes- Lowery,, L. L. Cummins,, B. Libby,, D. J. Walcott,, C. Massire,, R. Ranken,, S. Manalili,, C. Ivy,, R. Melton,, H. Levene,, V. Harpin,, F. Li,, N. White,, M. Pear,, J. A. Ecker,, V. Samant,, D. Knize,, D. Robbins,, K. Rudnick,, F. Hajjar,, and S. A. Hofstadler. 2006. The Ibis T5000 Universal Biosensor: an automated platform for pathogen identification and strain typing. J. Assoc. Lab. Automation 11: 341 351.
32. Ecker, D. J.,, R. Sampath,, L. B. Blyn,, M. W. Eshoo,, C. Ivy,, J. A. Ecker,, B. Libby,, V. Samant,, K. A. Sannes-Lowery,, R. E. Melton,, K. Russel,, N. Freed,, C. Barrozo,, J. Wu,, K. Rudnick,, A. Desai,, E. Moradi,, D. J. Knize,, D. W. Robbins,, J. C. Hannis,, P. M. Harrell,, C. Massire,, T. A. Hall,, Y. Jiang,, R. Rankin,, J. J. Drader,, N. White,, J. A. McNeil,, S. T. Crooke,, and S. A. Hoftadler. 2005. Rapid identification and strain-typing of respiratory pathogens for epidemic surveillance. Proc. Natl. Acad. Sci. USA 102: 8012 8017.
33. Emery, V. C.,, C. A. Sabin,, A. V. Cope,, D. Gor,, A. F. Hassan-Walker,, and P. D. Griffiths. 2000. Application of viral-load kinetics to identify patients who develop cytomegalovirus disease after transplantation. Lancet 355: 2032 2036.
34. 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: 2361 2365.
35. Farrell, D. J. 1999. Evaluation of AMPLICOR Neisseria gonorrhoeae PCR using cppB nested PCR and 16S rRNA PCR. J. Clin. Microbiol. 37: 386 390.
36. Felmlee, T. A.,, R. P. Oda,, D. A. Persing,, and J. P. Landers. 1995. Capillary electrophoresis of DNA potential utility for clinical diagnoses. J. Chromatogr. A 717: 127 137.
37. 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: 2525 2529.
38. Fried, M. W.,, M. L. Shiffman,, K. R. Reddy,, C. Smith,, G. Marinos,, F. L. Goncales, Jr.,, D. Haussinger,, M. Diago,, G. Carosi,, D. Dhumeaux,, A. Craxi,, A. Lin,, J. Hoffman,, and J. Yu. 2002. Peginterferon alfa-2a plus ribavirin for chronic hepatitis C virus infection. N. Engl. J. Med. 347: 975 982.
39. Furukawa, K.,, and V. P. Bhavanandan. 1983. Influences of anionic polysaccharides on DNA synthesis in isolated nuclei and by DNA polymerase alpha: correlation of observed effects with properties of the polysaccharides. Biochim. Biophys. Acta 740: 466 475.
40. Garcia, E. P.,, L. A. Dowding,, L. W. Stanton,, and V. I. Slepnev. 2005. Scalable transcriptional analysis routinemultiplexed quantitative real-time polymerase chain reaction platform for gene expression analysis and molecular diagnostics. J. Mol. Diagn. 7: 444 454.
41. Gaydos, C. A.,, K. A. Crotchfelt,, M. R. Howell,, S. Kralian,, P. Hauptman,, and T. C. Quinn. 1998. Molecular amplification assays to detect chlamydial infections in urine specimens from high school female students and to monitor the persistence of chlamydial DNA after therapy. J. Infect. Dis. 177: 417 424.
42. Gaynor, A. M.,, M. D. Nissenz,, D. M. Whiley,, I. M. Mackay,, S. B. Lambert,, G. Wu,, D. C. Brennan,, G. A. Storch,, T. P. Sloots,, and D. Wang. 2007. Identification of a novel polyomavirus from patients with acute repiratory tract infections. PLOS Pathog. 3: 595 604.
43. Gerna, G.,, D. Zipeto,, M. Parea,, M. G. Revello,, E. Silini,, E. Percivalle,, M. Zavattoni,, P. Grossi,, and G. Milanesi. 1991. Monitoring of human cytomegalovirus infections and ganciclovir treatment in heart transplant recipients by determination of viremia, antigenemia, and DNAemia. J. Infect. Dis. 164: 488 498.
44. Gharizadeh, B.,, E. Norberg,, J. Loffler,, S. Jalal,, J. Tollemar,, H. Einsele,, L. Klingspor,, and P. Nyren. 2004. Identification of medically important fungi by the Pyrosequencing technology. Mycoses 47: 29 33.
45. Ginocchio, C. C.,, D. Barth,, and F. Zhang. 2008. Comparison of the Third Wave Invader human papillomavirus (HPV) assay and the Digene HPV Hybrid Capture 2 assay for detection of high-risk HPV DNA. J. Clin. Microbiol. 46: 1641 1646.
46. Goldmeyer, J.,, H. Li,, M. McCormac,, S. Cook,, C. Stratton,, B. Lemieux,, H. Kong,, W. Tang,, and Y. Tang. 2008. Identification of Staphylococcus aureus and determination of methicillin resistance directly from positive blood cultures by isothermal amplification and a disposable detection device. J. Clin. Microbiol. 46: 1534 1536.
47. Gross-Bellard, M.,, P. Oudet,, and P. Chambon. 1973. Isolation of high-molecular-weight DNA from mammalian cells. Eur. J. Biochem. 36: 32 38.
48. Guatelli, J. C.,, K. M. Whitfield,, D. Y. Kwoh,, K. J. Barringer,, D. D. Richman,, and T. R. Gingeras. 1990. Isothermal in vitro amplification of nucleic acids by multi-enzyme reaction modeled after retroviral replication. Proc. Natl. Acad. Sci. USA 87: 1874 1878.
49. Haanpera, M.,, P. Huovinen,, and J. Jalava. 2005. Detection and quantification of macrolide resistance mutations at positions 2058 and 2059 of the 23S rRNA gene by pyrosequencing. Antimicrob. Agents Chemother. 49: 457 460.
50. Hadiyannis, S. J.,, H. Sette, Jr.,, T. R. Morgan,, V. Balan,, M. Diago,, P. Marcellin,, G. Ramdori,, H. Bodenheimer, Jr.,, D. Bernstein,, M. Rizzetto,, S. Zeuzem,, P. J. Pockros,, A. Lin,, and A. M. Ackrill for the PEGASYS International Study Group. 2004. Peginterferon-a2a and ribavirin combination therapy in chronic hepatitis C: a randomized study of treatment duration and ribavirin dose. Ann. Intern. Med. 140: 346 355.
51. Halfon, P.,, M. Bourlière,, G. Halimi,, H. Khiri,, P. Bertezene,, I. Portal,, D. Botta-Fridlund,, A. P. Gauthier,, M. Jullien,, J. M. Feryn,, V. Gerolami,, and G. Cartouzou. 1998. Assessment of spontaneous fluctuations of viral load in utreated patient with chonic hepatitis C with two standardized quatitation methods: branched DNA and Amplicor Monitor. J. Clin. Microbiol. 36: 2073 2075.
52. Hall, L.,, S. Wohlfiel,, and G. D. Roberts. 2003. Experience with the MicroSeq D2 large-subunit ribosomal DNA sequencing kit for identification of commonly encountered, clinically important yeast species. J. Clin. Microbiol. 41: 5099 5102.
53. Hall, L.,, S. Wohlfiel,, and G. D. Roberts. 2004. Experience with the MicroSeq D2 large-subunit ribosomal DNA sequencing kit for identification of filamentous fungi encountered in the clinical laboratory. J. Clin. Microbiol. 42: 622 626.
54. Hammer, S. M.,, J. J. Eron,, P. Reiss,, R. T. Schooley,, M. A. Thompson,, S. Walmsley,, P. Cahn,, M. A. Fischl,, J. M. Gatel,, M. S. Hirsch,, D. M. Jacobsen,, J. S. G. Montaner,, D. D. Richman,, P. G. Yeni,, and P. A. Volberding. 2008. Antiretroviral treatment of adult HIV infection. Recommendations of the International AIDS Society-USA panel. JAMA 300: 555 570.
55. Hankin, R. C. 1992. In situ hybridization: principles and applications. Lab. Med. 23: 764 770.
56. 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.
57. Heid, C.,, J. Stevens,, K. J. Livak,, and P. M. Williams. 1996. Real time quantitative PCR. Genome Res. 6: 986 994.
58. Higuchi, R. 1989. Simple and Rapid Preparation of Samples for PCR. Stockton Press, New York, NY.
59. Higuchi, R.,, C. Fockler,, G. Dollinger,, and R. Watson. 1993. Kinetic PCR analysis: real-time monitoring of DNA amplification reactions. Bio/Technology 11: 1026 1030.
60. Hirsch, H. H.,, D. C. Brennan,, C. B. Drachenberg,, F. Ginevri,, J. Gordon,, A. P. Limaye,, M. J. Mihatsch,, V. Nickeleit,, E. Ramos,, P. Randhawa,, E. Shapiro,, J. Steiger,, M. J. Suthanthiran,, and J. Trofe. 2005. Polyomarvirus-associated nephropathy in renal transplantation: interdisciplinary analyses and recommendations. Transplantation 79: 1277 1286.
61. Holland, P. M.,, R. D. Abramson,, R. Watson,, and D. H. Gelfand. 1991. Detection of specific polymerase chain reaction product by utilizing the 59→ 39 exonuclease activity of Thermus aquaticus DNA polymerase. Proc. Natl. Acad. Sci. USA 88: 7276 7280.
62. Honish, C.,, Y. Chen,, C. Moritmer,, C. Arnold,, O. Schmidt,, D. van den Boom,, C. R. Cantor,, H. N. Shah,, and S. E. Gharbia. 2007. Automated comparative sequence analysis by base-specific cleavage and mass spectrometry for nucleic acid-based microbial typing. Proc. Natl. Acad. Sci. USA 104: 10649 10654.
63. Humar, A.,, D. Gregson,, A. M. Caliendo,, A. McGeer,, G. Malkan,, M. Krajden,, P. Corey,, P. Greig,, S. Walmsley,, G. Levy,, and T. Mazzulli. 1999. Clinical utility of quantitative cytomegalovirus viral load determination for predicting cytomegalovirus disease in liver transplant recipients. Transplantation 68: 1305 1311.
64. Ihira, M.,, T. Yoshikawa,, Y. Enomoto,, S. Akimoto,, M. Ohashi,, S. Suga,, N. Nishimura,, T. Ozaki,, Y. Nishiyama,, T. Notomi,, Y. Ohta,, and Y. Asano. 2004. Rapid diagnosis of human herpesvirus 6 infection by a novel DNA amplification method, loop-mediated isothermal amplification. J. Clin. Microbiol. 42: 140 145.
65. Innis, M. A.,, K. B. Myambo,, D. H. Gelfand,, and M. A. Brow. 1998. DNA sequencing with Thermus aquaticus DNA polymerase and direct sequencing of polymerase chain reactionamplified DNA. Proc. Natl. Acad. Sci. USA 85: 9436 9440.
66. Iwamoto, T.,, T. Sonobe,, and K. Hayashi. 2003. Loop-mediated isothermal amplification for direct detection of Mycobacterium tuberculosis complex, M. avium, and M. intracellulare in sputum samples. J. Clin. Microbiol. 41: 2616 2622.
67. Izreli, S.,, C. Pfleiderer,, and T. Lion. 1991. Detection of gene expression by PCR amplification of RNA derived from frozen heparinized whole blood. Nucleic Acids Res. 19: 6051.
68. Kalinina, O.,, J. Brown,, and J. Silver. 1997. Nanoliter scale PCR with TaqMan detection. Nucleic Acids Res. 25: 1999 2004.
69. Kern, D.,, M. Collins,, T. Fultz,, J. Detmer,, S. Hamren,, J. J. Peterkin,, P. Sheridan,, M. Urdea,, R. White,, T. Yeghiazarian,, and J. Todd. 1996. An enhanced-sensitivity branched-DNA assay for quantification of human immunodeficiency virus type 1 RNA in plasma. J. Clin. Microbiol. 34: 3196 3202.
70. Khanna, M.,, J. Fan,, K. Pehler-Harrington,, C. Waters,, P. Douglass,, J. Stallock,, S. Kehl,, and K. J. Henrickson. 2005. The Pneumoplex assays, a multiplex PCR-enzyme hybridization assay that allows simultaneous detection of five organisms, Mycoplasma pneumoniae, Chlamydia (Chlamydophila) pneumoniae, Legionella pneumophila, Legionella micdadei, and Bordetella pertussis, and its real-time counterpart. J. Clin. Microbiol. 43: 565 571.
71. Kim, S. R.,, C. Ki,, and N. Y. Lee. 2009. Rapid detection and identification of 12 respiratory viruses using a dual priming oligonucleotide system-based multiplex PCR assay. J. Virol. Methods 156: 111 116.
72. Klugman, K. P.,, S. A. Madhi,, and W. C. Albrich 2008. Novel approaches to the identification of Steptococcus pneumoniae as the cause of community-acquired pneumonia. Clin. Infect. Dis. 47: 202 206.
73. Korimbocus, J.,, N. Scaramozzino,, B. Lecroix,, J. M. Crance,, D. Garin,, and G. Vermet. 2005. DNA probe array for the simultaneous identification of herpesviruses, enteroviruses, and flaviviruses. J. Clin. Microbiol. 43: 3779 3787.
74. Kricka, L. J. 1999. Nucleic acid detection technologies— labels, strategies, and formats. Clin. Chem. 45: 453 458.
75. Kricka, L. J. 2002. Stains, labels and detection strategies for nucleic acids assays. Ann. Clin. Biochem. 39: 114 129.
76. Ksiazek, T. G.,, D. Erdman,, C. S. Goldsmith,, S. R. Zaki,, T. Peret,, S. Emery,, S. Tong,, C. Urbani,, J. A. Comer,, W. Lim,, P. E. Rollin,, S. F. Dowell,, A. E. Ling,, C. D. Humphrey,, W. J. Shieh,, J. Guarner,, C. D. Paddock,, P. Rota,, B. Fields,, J. DeRisi,, J. Y. Yang,, N. Cox,, J. M. Hughes,, J. W. LeDuc,, W. J. Bellini,, L. J. Anderson, and the SARS Working Group. 2003. A novel coronavirus associated with severe acute respiratory syndrome. N. Engl. J. Med. 348: 1953 1966.
77. Kurtzman, C. P.,, and C. J. Robnett. 1997. Identification of clinically important ascomycetous yeasts based on nucleotide divergence in the 59 end of the large-subunit (26S) ribosomal DNA gene. J. Clin. Microbiol. 35: 1216 1223.
78. Kutyavin, I. V.,, I. A. Afonina,, A. Mills,, V. V. Gorn,, E. A. Lukhtanov,, E. S. Belousov,, M. J. Singer,, D. K. Walburger,, S. G. Lokhov,, A. A. Gall,, R. Dempcy,, M. W. Reed,, R. B. Meyer,, and J. Hedgpeth. 2000. 39-Minor groove binder- DNA probes increase sequence specificity at PCR extension temperatures. Nucleic Acids Res. 28: 655 661.
79. Kwoh, D. Y.,, G. R. David,, K. M. Whitfield,, H. L. Chapelle,, L. J. DiMichele,, and T. R. Gingeras. 1989. Transcriptionbased 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 1177.
80. Lakeman, F. D.,, R.J. Whitley, and the National Institute of Allergy and Infectious Diseases Collaborative Antiviral Study Group. 1995. Diagnosis of herpes simplex encephalitis: application of polymerase chain reaction to cerebrospinal fluid from brain-biopsied patients and correlation with disease. J. Infect. Dis. 171: 857 863.
81. Lay, M. J.,, and C. T. Wittwer. 1997. Real-time fluorescence genotyping of factor V Leiden during rapid cycle PCR. Clin. Chem. 43: 2262 2267.
82. Le, B. M.,, L. M. Demertzis,, G. Wu,, R. J. Tibbits,, R. Buller,, M. Q. Arens,, A. M. Gaynor,, G. A. Storch,, and D. Wang. 2007. Clinical and epidemiologic characterization of WU polyomavirus infection, St. Louis, Missouri. Emerg. Infect. Dis. 13: 1936 1938.
83. Lee, H. H.,, M. A. Chernesky,, J. Schachter,, J. D. Burczak,, W. W. Andrews,, S. Muldoon,, G. Leckie,, and W. E. Stamm. 1995. Diagnosis of Chlamydia trachomatis genitourinary infection in women by ligase chain reaction assay of urine. Lancet 345: 213 216.
84. Lefmann, M.,, C. Honisch,, S. Böcker,, N. Storm,, F. van Wintzingerode,, C. Schlötelberg,, A. Moter,, D. van den Boom,, and U. B. Göbel. 2004. Novel mass spectrometry-based tool for genotypic identification of mycobacteria. J. Clin. Microbiol. 42: 339 346.
85. LeGoff, J.,, R. Kara,, F. Moulin,, A. Si-Mohammed,, A. Krivine,, L. Bélec,, and P. Lebon. 2008. Evaluation of the one-step multiplex real-time reverse transcription-PCR ProFlu-1 assay for detection of influenza A and B viruses and respiratory syncytial viruses in children. J. Clin. Microbiol. 46: 789 791.
86. Leone, G.,, H. Van Schijndel,, B. Van Gemen,, F. R. Kramer,, and C. D. Schoen. 1998. Molecular beacon probes combined with amplification by NASBA enable homogeneous, realtime detection of RNA. Nucleic Acids Res. 26: 2150 2155.
87. LeRoux, C. A.,, T. Kubo,, A. A. Grobbelaar,, P. J. van Vuren,, J. Weyer,, L. H. Nel,, R. Swanepoel,, K. Morita,, and J. T. Paweska. 2009. Development and evaluation of a real-time reverse transcription-loop-mediated isothermal amplification assay for rapid detection of Rift Valley fever virus in clinical specimens. J. Clin. Microbiol. 47: 645 651.
88. Lieber, M. R. 1997. The FEN-1 family of structure-specific nucleases in eukaryotic DNA replication, recombination and repair. Bioessays 19: 233 240.
89. Lim, S. G.,, T. M. Ng,, N. Kung,, Z. Krastev,, M. Volfova,, P. Husa,, S. S. Lee,, S. Chan,, M. L. Shiffman,, M. K. Washington,, A. Rigney,, J. Anderson,, E. Mondou,, A. Snow,, J. Sorbel,, R. Guan,, and F. Rosseau for the Emtricitabine FTCB-301 Study Group. 2006. A double-blind placebo-controlled study of emtricitabine in chronic hepatitis B. Arch. Intern. Med. 166: 49 56.
90. Lin, B.,, Z. Wang,, G. J. Vora,, J. A. Thornton,, J. M. Schnur,, D. C. Thach,, K. M. Blaney,, A. G. Ligler,, A. P. Malanoski,, J. Santiago,, E. A. Walter,, B. K. Agan,, D. Metzgar,, D. Seto,, L. T. Daum,, R. Kruzelock,, R. K. Rowley,, E. H. Hanson,, C. Tibbetts,, and D. A. Stenger. 2006. Broad-spectrum respiratory tract pathogen identification using resequencing DNA microarrays. Genome Res. 16: 527 535.
91. 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: 777 784.
92. Liu, J.,, S. L. Lim,, Y. Ruan,, A. E. Ling,, F. P. Ng,, C. Dosten,, E. T. Liu,, L. W. Stanton,, and M. L. Hibberd. 2005. SARS transmission pattern in Singapore reassessed by viral sequence variation analysis. PLoS Med. 2: 43.
93. Liu, R. H.,, W. A. Coty,, M. Reed,, and G. Gust. 2008. Electrochemical detection-based DNA microarrays. IVD Technol. 14: 31 38.
94. Loeffelholz, M. J.,, C. A. Lewinski,, S. R. Silver,, A. Purohit,, S. A. Herman,, D. A. Buonagurio,, and E. A. Dragon. 1992. Detection of Chlamydia trachomatis in endocervical specimens by polymerase chain reaction. J. Clin. Microbiol. 30: 2847 2851.
95. Longo, M. C.,, M. S. Berninger,, and J. L. Hartley. 1990. Use of uracil DNA glycosylase to control carry-over contamination in polymerase chain reactions. Gene 93: 125 128.
96. Lyamichev, V.,, A. Mast,, J. G. Hall,, J. R. Prudent,, M. W. Kaiser,, T. Takova,, R. K. Kwiatkowski,, T. J. Sander,, M. de Arruda,, D. Arco,, B. P. Weri,, and M. A. D. Brow. 1999. Polymorphism identification and quantitative detection from genomic DNA by invasive cleavage of oligonucleotide probes. Nat. Biotechnol. 17: 292 296.
97. Lyamichev, V.,, and B. Neri. 2003. Invader assay for SNP genotyping. Methods Mol. Biol. 212: 229 240.
98. Mahony, J.,, S. Chong,, F. Merante,, S. Yaghoubian,, T. Sinha,, C. Lisle,, and R. Janeczko. 2007. Development of a respiratory virus panel test for detection of twenty human respiratory viruses by use of multiplex PCR and a fluid microbead-based assay. J. Clin. Microbiol. 45: 2965 2970.
99. Manns, M. P.,, J. G. McHutchison,, S. C. Gordon,, V. K. Rutsgi,, M. Shiffman,, R. Reindollar,, Z. D. Goodman,, K. Koury,, M. H. Ling,, J. K. Albrecht, and the International Hepatitis Interventional Therapy Group. 2001. Peginterferon alfa-2b plus ribavirin compared with interferon alfa-2b plus ribavirin for initial treatment of chronic hepatitis C: a randomised trial. Lancet 358: 958 965.
100. Mantero, G.,, A. Zonaro,, A. Albertini,, P. Bertolo,, and D. Primi. 1991. DNA enzyme immunoassay: general method for detecting products of polymerase chain reaction. Clin. Chem. 37: 422 429.
101. Mardis, E. R. 2008. Next-generation DNA sequencing methods. Annu. Rev. Genomics Hum. Genet. 9: 387 402.
102. Mazzulli, T.,, L. W. Drew,, B. Yen-Lieberman,, D. Jekic- McMullen,, D. J. Kohn,, C. Isada,, G. Moussa,, R. Chua,, and S. Walmsley. 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: 958 963.
103. Mellors, J. W.,, C. R. Rinaldo, Jr.,, P. Gupta,, R. M. White,, J. A. Todd,, and L. A. Kingsley. 1996. Prognosis in HIV-1 infection predicted by the quantity of virus in plasma. Science 272: 1167 1170.
104. Mitchell, P. S.,, M. J. Espy,, T. F. Smith,, D. R. Toal,, P. N. Rys,, E. F. Berbari,, D. R. Osmon,, and D. H. Persing. 1997. Laboratory diagnosis of central nervous system infections with herpes simplex virus by PCR performed with cerebrospinal fluid specimens. J. Clin. Microbiol. 35: 2873 2877.
105. Mitchell, P. S.,, J. J. Germer,, and J. D. C. Yao,. 2011. Laboratory design and operations, p. 127 141. In D. H. Persing,, F. C. Tenover,, Y.-W. Tang,, F. S. Nolte,, R. T. Hayden,, and A. van Belkum (ed.), Molecular Microbiology: Diagnostic Principles and Practice, 2nd ed. ASM Press, Washington, DC.
106. Montague, N. S.,, T. J. Cleary,, O. V. Martines,, and G. W. Procop. 2008. Detection of group B streptococci in Lim broth by use of group B Streptococcus peptide nucleic acid fluorescent in situ hybridization and selective and nonselective agars. J. Clin. Microbiol. 46: 3470 3472.
107. Morrison, T.,, J. J. Weiss,, and C. T. Wittwer. 1998. Quantification of low copy transcripts by continuous SYBR green I dye monitoring during amplification. BioTechniques 24: 954 958.
108. Mulligan, E. K.,, J. J. Germer,, M. Q. Arens,, K. L. D’Amore,, A. D. Bisceglie,, N. A. Ledboer,, M. J. Moser,, A. C. Newman,, A. K. O’Guin,, P. D. Olivo,, D. S. Podzorski,, K. A. Vaughan,, J. D. Yao,, S. A. Elagin,, and S. C. Johnson. 2009. Detection of quantification of hepatitis C virus (HCV) by MultiCode-RTx PCR targeting the HCV 39 untranslated region. J. Clin. Microbiol. 47: 2635 2638.
109. Myers, T. W.,, and D. H. Gelfand. 1991. Reverse transcription and DNA amplification by a Thermus thermophilus DNA polymerase. Biochemistry 30: 7661 7666.
110. Nakagawa, N.,, and M. Ito. 2006. Rapid subtyping of influenza A virus by loop-mediated isothermal amplification: two cases of influenza patients who returned from Thailand. Jpn. Infect. Dis. 59: 200 201.
111. NCCLS. 2001. Quantitative Molecular Methods for Infectious Diseases. NCCLS document MM6-A. NCCLS, Wayne, PA.
112. NCCLS. 2004. Nucleic Acid Sequencing Methods in Diagnostic Laboratory Medicine. NCCLS document MM9-A. NCCLS, Wayne, PA.
113. Nolte, F. S.,, D. J. Marshall,, C. Rasberry,, S. Schievelbein,, G. G. Banks,, G. A. Storch,, M. Q. Arens,, R. S. Buller,, and J. R. Prudent. 2007. MultiCode-PLx system for multiplexed detection of seventeen respiratory viruses. J. Clin. Microbiol. 45: 2779 2786.
114. Nolte, F. S. 1999. Branched DNA signal amplification for direct quantitation of nucleic acid sequences in clinical specimens. Adv. Clin. Chem. 33: 201 235.
115. Nolte, F. S.,, R. K. Emmens,, C. Thurmond,, P. S. Mitchell,, C. Pascuzzi,, S. M. Devine,, R. Saral,, and J. R. Wingard. 1995. Early detection of human cytomegalovirus viremia in bone marrow transplant recipients by DNA amplification. J. Clin. Microbiol. 33: 1263 1266.
116. Notomi, T.,, H. Okayama,, H. Masubuchi,, T. Yonekawa,, K. Wananabe,, N. Amino,, and T. Hase. 2000. Loop-mediated isothermal amplification of DNA. Nucleic Acids Res. 28: 63.
117. Nycz, C. M.,, C. H. Dean,, P. D. Haaland,, C. A. Spargo,, and G. T. Walker. 1998. Quantitative reverse transcription strand displacement amplification; quantitation of nucleic acids using an isothermal amplification technique. Anal. Biochem. 259: 226 234.
118. Office of the Federal Register. 2004. Code of Federal Regulations. Clinical Laboratory Improvement Act Regulations, part 493, subpart K, section 1253. U.S. Government Printing Office and Office of the Federal Register, Washington, DC. http://www.phppo.cdc.gov/clia/regs/subpart_k.aspx.
119. Okamoto, S.,, T. Yoshikawa,, M. Ihira,, K. Suszuki,, K. Shimokata,, Y. Nishiyama,, and Y. Asano. 2004. Rapid detection of varicella-zoster virus infection by a loop-mediated isothermal amplification method. J. Med. Virol. 74: 677 682.
120. Oliveira, K.,, S. M. Brecher,, A. Durbin,, D. S. Shapiro,, D. R. Schwartz,, P. C. De Girolami,, J. Dakos,, G. W. Procop,, D. Wilson,, C. S. Hanna,, G. Haase,, H. Peltroche-Llacsahuanga,, K. C. Chapin,, M. C. Musgnug,, M. H. Levi,, C. Shoemaker,, and H. Stender. 2003. Direct identification of Staphylococcus aureus from positive blood culture bottles. J. Clin. Microbiol. 41: 889 891.
121. O’Meara, D.,, K. Wilbe,, T. Leitner,, B. Hejdeman,, J. Albert,, and J. Lundeberg. 2001. Monitoring resistance to human immunodeficiency virus type 1 protease inhibitors by pyrosequencing. J. Clin. Microbiol. 39: 464 473.
122. Orita, M.,, H. Iwahana,, H. Kanazawa,, K. Hayashi,, and T. Sekiya. 1989. Detection of polymorphism of human DNA by gel electrophoresis as single-strand conformation polymorphisms. Proc. Natl. Acad. Sci. USA 86: 2766 2770.
123. Palacios, G.,, P. Quan,, O. J. Jabado,, S. Conlan,, D. L. Hirschberg,, Y. Liu,, J. Zhai,, N. Renwick,, J. Hui,, H. Hegy,, A. Grolla,, J. E. Strong,, J. S. Towner,, T. W. Geisbert,, P. B. Jahrling,, C. Büchen-Osmond,, H. Ellerbrok,, M. P. Sanchez-Seco,, Y. Lussier,, P. Formenty,, S. T. Nichol,, H. Feldman,, T. Briese,, and W. Lipkin. 2007. Panmicrobial oligonucleotide array for diagnosis of infectious diseases. Emerg. Infect. Dis. 13: 73 81.
124. Pang, J.,, J. Modlin,, and R. Yolken. 1992. Use of modified nucleotides and uracil-DNA glycosylase (UNG) for the control of contamination in the PCR-based amplification of RNA. Mol. Cell. Probes 6: 251 256.
125. Pang, X. L.,, J. D. Fox,, J. M. Fenton,, G. G. Miller,, A. M. Caliendo,, and J. K. Preiksaitis. 2009. Interlaboratory comparison of cytomegalovirus viral load assays. Am. J. Transplant. 9: 258 268.
126. Parida, M.,, K. Horioke,, H. Ishida,, P. K. Dash,, P. Saxena,, A. M. Jana,, S. Islam,, N. Inoue,, N. Hosaka,, and K. Morita. 2005. Rapid detection and differentiation of dengue virus serotypes by a real-time reverse transcription-loop-mediated isothermal amplification assay. J. Clin. Microbiol. 43: 2895 2903.
127. Pease, A. C.,, D. Solas,, E. J. Sullivan,, M. T. Cronin,, C. P. Holmes,, and S. P. Fodor. 1994. Light-generated oligonucleotide arrays for rapid DNA sequence analysis. Proc. Natl. Acad. Sci. USA 91: 5022 5026.
128. Peiris, J. S. M.,, S. T. Lai,, L. L. M. Poon,, Y. Guan,, L. Y. C. Yam,, W. Lim,, J. Nicholls,, W. K. S. Yee,, W. W. Yan,, M. T. Cheung,, V. C. C. Cheng,, K. H. Chan,, D. N. C. Tsang,, R. W. H. Yung,, T. K. Ng,, K. Y. Yuen, and members of the SARS study group. 2003. Coronavirus as a possible cause of severe acute respiratory syndrome. Lancet 361: 1319 1325.
129. Persing, D. H.,, F. C. Tenover,, Y.-W. Tang,, F. S. Nolte,, R. T. Hayden,, and A. van Belkum (ed.). 2011. Molecular Microbiology: Diagnostic Principles and Practice, 2nd ed. ASM Press, Washington, DC.
130. Piccirilli, J. A.,, T. Krauch,, S. E. Moroney,, and S. A. Benner. 1990. Enzymatic incorporation of a new base pair into DNA and RNA extends the genetic alphabet. Nature 343: 33 37.
131. Poljak, M.,, and K. Seme. 1996. Rapid detection and typing of human papillomaviruses by consensus polymerase chain reaction and enzyme-linked immunosorbent assay. J. Virol. Methods 56: 231 238.
132. Procop, G. W. 2007. Molecular diagnostics for the detection and characterization of microbial pathogens. Clin. Infect. Dis. 45: 99 111.
133. Reid, R.,, M. Greenberg,, A. B. Jensen,, M. Husain,, J. Willett,, Y. Daoud,, G. Temple,, C. R. Stanhope,, A. Sherman,, and D. G. Phibbs. 1987. Sexually transmitted papillomaviral infections. I. The anatomic distribution and pathologic grade of neoplastic lesions associated with different viral types. Am. J. Obstet. Gynecol. 156: 212 222.
134. Relman, D. A.,, T. M. Schmidt,, R. P. MacDermott,, and S. Falkow. 1992. Identification of the uncultured bacillus of Whipple’s disease. N. Engl. J. Med. 327: 293 301.
135. Rigby, S.,, G. W. Procop,, G. Haase,, D. Wilson,, G. Hall,, C. Kurtzman,, K. Oliveira,, S. Von Oy,, J. J. Hyldig-Nielsen,, J. Coull,, and H. Stender. 2002. Fluorescence in situ hybridization with peptide nucleic acid probes for rapid identification of Candida albicans directly from blood culture bottles. J. Clin. Microbiol. 40: 2182 2186.
136. Ririe, K.,, R. P. Rasmussen,, and C. T. Wittwer. 1997. Product differentiation by analysis of DNA melting curves during the polymerase chain reaction. Anal. Biochem. 245: 154 160.
137. Rosenstraus, M.,, Z. Wang,, S.Y. Chang,, D. DeBonville,, and J. P. Spadoro. 1998. An internal control for routine diagnostic PCR: design, properties, and effect on clinical performance. J. Clin. Microbiol. 36: 191 197.
138. Rossau, R.,, H. Traore,, H. De Beenhouwer,, W. Mijs,, G. Jannes,, P. De Rijk,, and F. Portaels. 1997. Evaluation of the INNO-LiPA Rif. TB assay, a reverse hybridization assay for the simultaneous detection of Mycobacterium tuberculosis complex and its resistance to rifampin. Antimicrob. Agents Chemother. 41: 2093 2098.
139. Saag, M. S.,, M. Holodniy,, D. R. Kuritzkes,, W. A. O’Brien,, R. Coombs,, M. E. Poscher,, D. M. Jacobsen,, G. M. Shaw,, D. D. Richman,, and P. A. Volberding. 1996. HIV viral load markers in clinical practice. Nat. Med. 2: 625 629.
140. Saiki, R. K.,, D. H. Gelfand,, S. Stoffel,, S. J. Scharf,, R. Higuchi,, K. B. Mullis,, G. Horn,, and H. A. Ehrlich. 1988. Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239: 487 491.
141. Sampath, R.,, T. A. Hall,, C. Massire,, L. Feng,, L. B. Blyn,, M. W. Eshoo,, S. A. Hofstadler,, and D. J. Ecker. 2007. Rapid identification of emerging infectious agents using PCR and electrospray ionization mass spectrometry. Ann. N. Y. Acad. Sci. 1102: 109 120.
142. Sampath, R.,, K. L. Russell,, C. Massiere,, M. W. Eshoo,, V. Harpin,, L. B. Blyn,, R. Melton,, C. Ivy,, T. Pennella,, F. Li,., H. Levene,, T. A. Hall,, B. Libby,, N. Fan,, D. J. Walcott,, R. Ranken,, M. Pear,, A. Schink,, J. Gutierrez,, J. Drader,, D. Moore,, D. Metzgar,, L. Addington,, R. Rothman,, C. A. Gaydos,, S. Yang,, K. St. George,, M. E. Fuschino,, A. B. Dean,, D. E. Stallknecht,, G. Goekjian,, S. Yingst,, M. Montevelle,, M. D. Saad,, C. A. Whitehouse,, C. Baldwin,, K. H. Rudnick,, S. A. Hofstadler,, S. M. Lemon,, and D. J. Ecker. 2007. Global surveillance of emerging influenza virus genotypes by mass spectrometry. PLoS ONE 5: 489.
143. 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: 2540 2543.
144. Schena, M.,, D. Shalon,, R. Heller,, A. Chai,, P. O. Brown,, and R. W. Davis. 1996. Parallel human genome analysis: microarray-based expression monitoring of 1000 genes. Proc. Natl. Acad. Sci. USA 93: 10614 10619.
145. Shepard, J. R.,, R. M. Addison,, B. D. Alexander,, P. Della-Latta,, M. Gherna,, G. Haase,, G. Hall,, J. K. Johnson,, W. G. Merz,, H. Peltroche-Llacsahuanga,, H. Stender,, R. A. Venezia,, D. Wilson,, G. W. Procop,, F. Wu,, and M. J. Fiandaca. 2008. Multicenter evaluation of the Candida albicans/Candida glabrata peptide nucleic acid fluorescent in situ hybridization method for simultaneous dual-color identification of C. albicans and C. glabrata directly from blood culture bottles. J. Clin. Microbiol. 46: 50 55.
146. Sherrill, C. B.,, D. J. Marshall,, M. J. Moser,, C. A. Larsen,, L. Daude-Snow,, and J. R. Prudent. 2004. Nucleic acid analysis using an expanded genetic alphabet to quench fluorescence. J. Am. Chem. Soc. 126: 4550 4556.
147. Simen, B. B.,, J. F. Simons,, K. H. Hullsiek,, R. M. Novak,, R. D. Macarther,, J. D. Baxter,, C. Hugan,, C. Lubeski,, G. S. Turenchalk,, M. S. Braverman,, B. Desany,, J. M. Rothberg,, M. Egholm,, M. J. Kozai, and Terry Beirn Community Programs for Clinical Research on AIDS. 2009. Lowabundance drug-resistant viral variants in chronically HIVinfected, antiretroviral treatment-naïve patients significantly impact treatment outcomes. J. Infect. Dis. 199: 610 612.
148. Smith, P. L.,, C. R. Walker Peach,, R. J. Fulton,, and D. B. DuBois. 1998. A rapid, sensitive, multiplexed assay for detection of viral nucleic acids using the FlowMetrix system. Clin. Chem. 44: 2054 2056.
149. Söderlund-Strand, A.,, J. Dillner,, and J. Carlson. 2008. Highthroughput genotyping of oncogenic human papilloma viruses with MALDI-TOF mass spectrometry. Clin. Chem. 54: 86 92.
150. Sogaard, M.,, H. Stender,, and H. C. Schonheyder. 2005. Direct identification of major blood culture pathogens, including Pseudomonas aeruginosa and Escherichia coli, by a panel of fluorescence in situ hybridization assays using peptide nucleic acid probes. J. Clin. Microbiol. 43: 1947 1949.
151. Solomon, D.,, M. Schiffman,, R. Tarone, et al. 2001. Comparison of three management strategies for patients with atypical squamous cells of undetermined significance: baseline results from a randomized trial. J. Natl. Cancer Inst. 93: 293 299.
152. Steinau, M.,, D. C. Swan,, and E. R. Unger. 2008. Typespecific reproducibility of the Roche linear array HPV genotyping test. J. Clin. Virol. 42: 412 414.
153. Stender, H.,, M. Fiandaca,, J. J. Hyldig-Nielsen,, and J. Coull. 2002. PNA for rapid microbiology. J. Microbiol. Methods 48: 1 17.
154. Stender, H.,, T. A. Mollerup,, K. Lund,, K. H. Petersen,, P. Hongmanee,, and S. E. Godtfredsen. 1999. Direct detection and identification of Mycobacterium tuberculosis in smearpositive sputum samples by fluorescence in situ hybridization (FISH) using peptide nucleic acid (PNA) probes. Int. J. Tuberc. Lung Dis. 3: 830 837.
155. Stürenburg, E.,, N. Storm,, I. Sobottka,, M. A. Horstkotte,, S. Scherpe,, M. Aepfelbacher,, and S. Müller. 2006. Detection and genotyping of SHV b-lactamase variants by mass spectrometry after base-specific cleavage of in vitro-generated RNA transcripts. J. Clin. Microbiol. 44: 909 915.
156. Stuyver, L.,, A. Wyseur,, A. Rombout,, J. Louwagie,, T. Scarcez,, C. Verhofstede,, D. Rimland,, R. F. Schinazi,, and R. Rossau. 1997. Line probe assay for rapid detection of drug-selected mutations in the human immunodeficiency virus type 1 reverse transcriptase gene. Antimicrob. Agents Chemother. 41: 284 291.
157. Stuyver, L.,, A. Wyseur,, W. van Arnhem,, F. Hernandez,, and G. Maertens. 1996. Second-generation line probe assay for hepatitis C virus genotyping. J. Clin. Microbiol. 34: 2259 2266.
158. Svarovskaia, E. S.,, M. J. Moser,, A. S. Bae,, J. R. Prudent,, M. D. Miller,, and K. Borroto-Esoda. 2006. MultiCode- RTx real-time PCR system for detection of subpopulations of K65R human immunodeficiency virus type 1 reverse transcriptase mutant viruses in clinical samples. J. Clin. Microbiol. 44: 4237 4241.
159. Sykes, P. J .,, S. H. Neoh,, M. J. Brisco,, E. Hughes,, J. Condon,, and A. A. Morley. 1992. Quantitation of targets for PCR by use of limiting dilution. BioTechniques 13: 444 449.
160. 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: 3674 3679.
161. Telenti, A.,, P. Imboden,, F. Marchesi,, T. Schmidheini,, and T. Bodmer. 1993. Direct, automated detection of rifampinresistant Mycobacterium tuberculosis by polymerase chain reaction and single-strand conformation polymorphism analysis. Antimicrob. Agents Chemother. 37: 2054 2058.
162. Templeton, K. E.,, S. A. Scheltinga,, M. F. Beersma,, A. C. Kroes,, and E. C. Claas. 2004. Rapid and sensitive method using multiplex real-time PCR for diagnosis of infections by influenza A and influenza B viruses, respiratory syncytial virus, and parainfluenza viruses 1, 2, 3, and 4. J. Clin. Microbiol. 42: 1564 1569.
163. ten Bosch, J. R.,, and W. W. Grody. 2008. Keeping up with the next generation: massively parallel sequencing in clinical diagnostics. J. Mol. Diagn. 10: 484 492.
164. Tenover, F. C. 1988. Diagnostic deoxyribonucleic acid probes for infectious diseases. Clin. Microbiol. Rev. 1: 82 101.
165. Tenover, F. C.,, and J. K. Rasheed,. 2011. Detection of antimicrobial resistance genes and mutations associated with antimicrobial resistance in bacteria, p. 507 524. In D. H. Persing,, F. C. Tenover,, Y.-W. Tang,, F. S. Nolte,, R. T. Hayden,, and A. van Belkum (ed.), Molecular Microbiology: Diagnostic Principles and Practice, 2nd ed. ASM Press, Washington, DC.
166. Thai, H .T. C.,, M. Q. Le,, C. D. Vuong,, M. Parida,, H. Minekawa,, T. Notomi,, F. Hasebe,, and K. Morita. 2004. Development and evaluation of a novel loop-mediated isothermal amplification method for rapid detection of severe acute respiratory syndrome coronavirus. J. Clin. Microbiol. 42: 1956 1961.
167. Thelwell, N.,, S. Millington,, A. Solinas,, J. Booth,, and T. Brown. 2000. Mode of action and application of Scorpion primers to mutation detection. Nucleic Acids Res. 28: 3752 3761.
168. Thornton, C. G.,, J. L. Hartley,, and A. Rashtchian. 1992. Utilizing uracil DNA glycosylase to control carryover contamination in PCR: characterization of residual UDG activity following thermal cycling. BioTechniques 13: 180 184.
169. Tong, Y.,, W. Tang,, H. Kim,, X. Pan,, T.A. Ranall,, and T. Kong. 2008. Development of isothermal TaqMan assays for detection of biothreat organisms. BioTechniques 45: 543 557.
170. Touhy, M. J.,, G. S. Hall,, M. Sholtis,, and G. W. Procop. 2005. Pyrosequencing™ as a tool for the identification of common isolates of Mycobacterium. Diagn. Microbiol. Infect. Dis. 51: 245 250.
171. Tyagi, S.,, D. P. Bratu,, and F. R. Kramer. 1998. Multicolor molecular beacons for allele discrimination. Nat. Biotechnol. 16: 49 53.
172. Vincent, M.,, Y. Xu,, and H. Kong. 2004. Helicasedependent isothermal DNA amplification. EMBO Rep. 5: 795 800.
173. Vogelstein, B.,, and K. W. Kinzler. 1999. Digital PCR. Proc. Natl. Acad. Sci. USA 96: 9236 9241.
174. 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: 1691 1696.
175. Wallace, J.,, B. A. Woda,, and G. Pihan. 2005. Facile, comprehensive, high-throughput genotyping of human genital papillomaviruses using spectrally addressable liquid bead microarrays. J. Mol. Diagn. 7: 72 80.
176. Walsh, E. E.,, K. M. McConnochie,, C. E. Long,, and C. B. Hall. 1997. Severity of respiratory syncytial virus infection is related to virus strain. J. Infect. Dis. 175: 814 820.
177. Wang, C.,, Y. Mitsuya,, and B. Gharizadeh. 2007. Characterization of mutation spectra with ultra-deep pyrosequencing: application to HIV-1 drug resistance. Genome Res. 17: 1195 1201.
178. Wang, D.,, L. Coscoy,, M. Zylberberg,, P.C. Avila,, H. A. Boushey,, D. Ganem,, and J. L. DeRisi. 2002. Microarraybased detection and genotyping of viral pathogens. Proc. Natl. Acad. Sci. USA 99: 15687 15692.
179. Wang, D.,, A. Urisman,, Y. T. Liu,, M. Springer,, T. G. Ksiazek,, D. D. Erdman,, E. R. Mardis,, M. M. Hickenbotham,, V. Magrini,, J. Eldred,, J. P. Latreille,, R. K. Wilson,, D. Ganem,, and J. L. DeRisi. 2003. Viral discovery and sequence recovery using DNA microarrays. PLOS Biol. 1: 2.
180. Whitcombe, D.,, J. Theaker,, S. P. Guy,, T. Brown,, and S. Little. 1999. Detection of PCR products using self-probing amplicons and fluorescence. Nat. Biotechnol. 17: 804 807.
181. Woese, C. R. 1987. Bacterial evolution. Microbiol. Rev. 51: 221 271.
182. Wolk, D.,, S. Mitchell,, and R. Patel. 2001. Principles of molecular microbiology testing methods. Infect. Dis. Clin. N. Am. 15: 1157 1204.
183. Wong, C. W.,, C. L. Heng,, L. Wan Yee,, S. W. Soh,, C. B. Kartasasmita,, E. A. Simoes,, M. L. Hibberd,, W. K. Sung,, and L. D. Miller. 2007. Optimization and clinical validation of a pathogen detection microarray. Genome Biol. 8: 93.
184. Wright, T. C., Jr.,, M. Schiffman,, D. Solomon,, J. T. Cox,, F. Garcia,, S. Goldie,, K. Hatch,, K. L. Noller,, N. Roach,, C. Runowicz,, and D. Saslow. 2004. Interim guidance for the use of human papillomavirus DNA testing as an adjunct to cervical cytology for screening. Obstet. Gynecol. 103: 304 309.
185. Wu, D. Y.,, and R. B. Wallace. 1989. The ligation amplification reaction (LAR)—amplification of specific DNA sequences using sequential rounds of template-dependent ligation. Genomics 4: 560 569.
186. 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: 326 334.
187. Zeuzem, S.,, M. Rizzetto,, P. Ferenci,, and M. L. Shiffman. 2009. Management of hepatitis C virus genotype 2 or 3 infection: treatment optimization on the basis of virological response. Antivir. Ther. 14: 143 154.

Tables

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TABLE 1

Comparison of next-generation and Sanger sequencing platforms

Citation: Nolte F, Caliendo A. 2011. Molecular Microbiology, p 27-59. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch4
Generic image for table
TABLE 2

FDA-cleared or -approved molecular diagnostic tests for infectious diseases as of 10 December 2009

Modified from http://www.amp.org. Abbreviations: ASPE, allele-specific primer extension; HC, hybrid capture; HPA, hybridization protection assay; HR, high risk; JBAIDS, Joint Biological Agent Identification and Diagnostic System; PNA FISH, peptide nucleic acid fluorescent hybridization; SSTI, skin and soft tissue infection; TC, target capture.

Five species directly from positive blood cultures, including and/or , , and and/or .

Mycobacteria include , , complex, , , and complex. Fungi include , , , and . Bacteria include spp., spp., group , group , , , , , and .

Viruses include influenza A (H1, H3) virus; influenza B virus; adenovirus; respiratory syncytial viruses A and B; metapneumovirus; parainfluenza virus types 1, 2, and 3; and rhinovirus.

Viruses include influenza A and B viruses and respiratory syncytial virus.

Viruses include influenza A and B viruses and respiratory syncytial virus.

Citation: Nolte F, Caliendo A. 2011. Molecular Microbiology, p 27-59. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch4

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