Molecular Microbiology

Frederick S. Nolte; Angela M. Caliendo

doi:10.1128/9781555816728.ch4

Chapter 4 : Molecular Microbiology

Authors: Frederick S. Nolte, Angela M. Caliendo

Content Type: Reference

Publication Year: 2011

Category: Clinical Microbiology

Book DOI: 10.1128/9781555816728

Chapter DOI: 10.1128/9781555816728.ch4

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Molecular Microbiology, Page 1 of 2

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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: 0.69145083
Antimicrobial Susceptibility Testing: 0.5331986
Human immunodeficiency virus 1: 0.4980995
Reverse Transcriptase PCR: 0.47679815

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Molecular Microbiology

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FIGURE 1

bDNA signal amplification. Reprinted with permission of Elsevier from reference 182 .

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FIGURE 1

bDNA signal amplification. Reprinted with permission of Elsevier from reference 182 .

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FIGURE 2

PCR target amplification. Reprinted with permission of Elsevier from reference 182 .

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FIGURE 2

PCR target amplification. Reprinted with permission of Elsevier from reference 182 .

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FIGURE 3

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

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FIGURE 3

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FIGURE 4

5′ exonuclease chemistry for real-time PCR applications. Reprinted with permission of Elsevier from reference 182 .

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FIGURE 4

5′ exonuclease chemistry for real-time PCR applications. Reprinted with permission of Elsevier from reference 182 .

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FIGURE 5

Dual hybridization probes for real-time PCR applications. Reprinted with permission of Elsevier from reference 182 .

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FIGURE 5

Dual hybridization probes for real-time PCR applications. Reprinted with permission of Elsevier from reference 182 .

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FIGURE 6

Molecular beacon probes for real-time amplification applications. Reprinted with permission of Elsevier from reference 182 .

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FIGURE 6

Molecular beacon probes for real-time amplification applications. Reprinted with permission of Elsevier from reference 182 .

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FIGURE 7

Transcription-based target amplification. NASBA and TMA are examples of transcription- based amplification systems. Reprinted with permission of Elsevier from reference 182 .

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FIGURE 7

Transcription-based target amplification. NASBA and TMA are examples of transcription- based amplification systems. Reprinted with permission of Elsevier from reference 182 .

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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. B1 and B2, bumper primers; S1 and S2, amplification primers. Modified from reference 91 .

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FIGURE 8

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FIGURE 9

Cleavase-invader probe-based amplification. Reprinted with permission of Elsevier from reference 182 .

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FIGURE 9

Cleavase-invader probe-based amplification. Reprinted with permission of Elsevier from reference 182 .

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

Molecular Microbiology

/content/10.1128/9781555816728.chap4.tab4-1

TABLE 1

Comparison of next-generation and Sanger sequencing platforms

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10.1128/9781555816728/tab4-1.gif

TABLE 1

Comparison of next-generation and Sanger sequencing platforms

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TABLE 2

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

a 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 in situ hybridization; SSTI, skin and soft tissue infection; TC, target capture.

b Five Candida species directly from positive blood cultures, including C. albicans and/or C. parapsilosis, C. tropicalis, and C. glabrata and/or C. krusei.

c Mycobacteria include M. avium, M. intracellulare, M. avium complex, M. gordonae, M. kansasii, and M. tuberculosis complex. Fungi include Blastomyces dermatitidis, Coccidioides immitis, Cryptococcus neoformans, and Histoplasma capsulatum. Bacteria include Campylobacter spp., Enterococcus spp., group A Streptococcus, group B Streptococcus, H. influenzae, L. monocytogenes, N. gonorrhoeae, S. pneumoniae, and S. aureus.

d 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.

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

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

10.1128/9781555816728/tab4-2_thmb.gif

10.1128/9781555816728/tab4-2.gif

TABLE 2

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

b Five Candida species directly from positive blood cultures, including C. albicans and/or C. parapsilosis, C. tropicalis, and C. glabrata and/or C. krusei.

d 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.

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

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