1887

Chapter 6 : Use of Commercial Amplification Tests in the Clinical Microbiology Laboratory: Test Selection and Quality Assurance

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

Preview this chapter:
Zoom in
Zoomout

Use of Commercial Amplification Tests in the Clinical Microbiology Laboratory: Test Selection and Quality Assurance, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555816834/9781555814977_Chap06-1.gif /docserver/preview/fulltext/10.1128/9781555816834/9781555814977_Chap06-2.gif

Abstract:

Molecular approaches to the detection of infectious-disease agents in the clinical microbiology laboratory can be performed through the use of commercially available products or by using in-house or “home-brew” procedures. Both types of assays are currently used for the diagnosis of two sexually transmitted organisms, and , for screening of Group B in pregnancy, for nasal screening of methicillin-resistant (MRSA) and detection of both methicillin-resistant (MRSA) and methicillin-susceptible (MSSA) in wounds and positive blood culture vials, for detection of toxigenic in stool samples, and for the detection of . A description of how to choose and implement a commercially available assay for these agents is provided in this chapter. The chapter talks about implementation of the new assay, and use of commercial assays for amplification. Three commercial PCR-based amplification assays have been cleared by Food and Drug Administration (FDA) for the detection of the toxin B gene in stool samples. All of the principles for implementation of a molecular test that have been described in this chapter will also need to be performed for amplification assays. After implementation of a molecular assay, monitoring the process and results to be assured of the expected performance of the assay should be ongoing.

Citation: Hall G, Katanik M, Tuohy M, Sholtis M. 2011. Use of Commercial Amplification Tests in the Clinical Microbiology Laboratory: Test Selection and Quality Assurance, p 107-116. In Persing D, Tenover F, Tang Y, Nolte F, Hayden R, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555816834.ch6

Key Concept Ranking

Aptima Combo 2 Assay
0.45961034
0.45961034
Highlighted Text: Show | Hide
Loading full text...

Full text loading...

References

/content/book/10.1128/9781555816834.ch06
1. Bergmann, J. S.,, W. E. Keating, and, G. L. Woods. 2000. Clinical evaluation of the BDProbeTec ET system for rapid detection of Mycobacterium tuberculosis. J. Clin. Microbiol. 38:863865.
2. Brown, T. J.,, E. G. M. Power, and, G. L. French. 1999. Evaluation of three commercial detection systems for Mycobacterium tuberculosis where clinical diagnosis is difficult. J. Clin. Pathol. 52:193197.
3. Catanzaro, A.,, S. Perry,, J. E. Clarridge,, S. Dunbar,, S. Goodnight-White,, P. A. LoBue,, C. Peter,, G. E. Pfyffer,, M. F. Sierra,, R. Weber,, G. Woods,, G. Matthews,, V. Jonas,, K. Smith, and, P. Della-Latta. 2000. The role of clinical suspicion in evaluating a new diagnostic test for active tuberculosis. JAMA 283:639645.
4. Centers for Disease Control and Prevention. 2002. Sexually transmitted disease treatment guidelines 2002. MMWR Recommend. Rep. 51(RR-6):178.
5. Centers for Disease Control and Prevention. 2002. Screening tests to detect Chlamydia trachomatis and Neisseria gonorrhoeae infections. MMWR Recommend. Rep. 51(RR-15):127.
6. Chernesky, M.,, E. L. Ciemins,, L. A. Borenstein,, I. E. Dyer,, E. Cordero,, J. G. Courtney,, S. M. Harvey, and, G. A. Richwald. 1997. Comparisons of cost and accuracy of DNA probe test and culture for the detection of Neisseria gonorrhoeae in patients attending public sexually transmitted disease clinics in Los Angeles County. Sex. Transm. Dis. 24:422428.
7. Della-Latta, P.,, and S. Whittier. 1998. Comprehensive evaluation of performance, laboratory application, and clinical usefulness of two direct amplification technologies for the detection of Mycobacterium tuberculosis complex. Am. J. Clin. Pathol. 110:301310.
8. Dimech, W.,, D. S. Bowden,, B. Brestovac,, K. Byron,, G. James,, D. Jardine,, T. Sloots, and, E. M. Dax. 2004. Validation of assembled nucleic acid-based tests in diagnostic microbiology laboratories. Pathology 36:4550.
9. Doern, G. V. 1996. Diagnostic mycobacteriology: where are we today? J. Clin. Microbiol. 35:10411042.
10. Elder, B. L.,, S. A. Hansen,, J. A. Kellogg,, F. J. Marsik, and, R. J. Zabransky. 1997. Cumitech 31, Verification and Validation in the Clinical Microbiology Laboratory. Coordinating ed., B. W. McCurdy. American Society for Microbiology, Washington, DC.
11. Farrell, D. J. 1999. Evaluation of AMPLICOR Neisseria gonorrhoeae PCR using cppB nested PCR and 16S rRNA PCR. J. Clin. Microbiol. 37:386390.
12. [Reference deleted.]
13. Forbes, B. A. 1997. Critical assessment of gene amplification approaches on the diagnosis of tuberculosis. Immunol. Investig. 26:105116.
14. Gamboa, F.,, J. M. Manterola,, J. Lonca,, B. Vinado,, L. Matas,, M. Gimenez,, J. R. Manzano,, C. Rodrigo,, P. J. Cardona,, E. Padilla,, J. Dominguez, and, V. Ausina. 1997. Rapid detection of Mycobacterium tuberculosis in respiratory specimens, blood and other non-respiratory specimens by amplification of rRNA. Int. J. Tuberc. Lung Dis. 1:542555.
15. [Reference deleted.]
16. Gorwitz, R. J.,, D. Kruszon-Moran,, S. K. McAllister,, G. McQuillan,, L. K. McDougal,, G. E. Fosheim,, B. J. Jensen,, G. Killgore,, F. C. Tenover, and, M. J. Kuehnert. 2008. Changes in the prevalence of nasal colonization with Staphylococcus aureus in the United States, 2001-2004. J. Infect. Dis. 197:12261234.
17. Helb, D.,, M. Jones,, E. Story,, C. Boehme,, E. Wallace,, K. Ho,, J. Kop,, M. R. Owens,, R. Rodgers,, P. Banada,, H. Safi,, R. Blakemore,, N. T. Lan,, E. C. Jones-Lopez,, M. Levi,, M. Burday,, I. Ayakaka,, R. D. Mugerwa,, B. McMillan,, E. Winn-Deen,, L. Christel,, P. Dailey,, M. D. Perkins,, D. H. Persing, and, D. Alland. 2010. Rapid detection of Mycobacterium tuberculosis and rifampin resistance by use of on-demand, near-patient technology. J. Clin. Microbiol. 48:229237.
18. Hillier, S. L.,, and A. Schuchat. 1997. Preventing neonatal Group B streptococcal disease: the role of the clinical microbiology laboratory. Clin. Microbiol. Newsl. 19:113116.
19. Katila, M. L.,, P. Katila, and, R. Erkinjuntti-Pekkanen. 2000. Accelerated detection and identification of mycobacteria with MGIT 960 and COBAS AMPLICOR systems. J. Clin. Microbiol. 38:960964.
20. Kellogg, J. A.,, J. W. Seiple,, J. L. Klinedinst,, E. S. Stroll, and, S. H. Cavanaugh. 1995. Improved PCR detection of Chlamydia trachomatis by using an altered method of specimen transport and high quality endocervical specimens. J. Clin. Microbiol. 33:27652767.
21. Koumans, E. H.,, R. E. Johnson,, J. S. Knapp, and, M. E. St. Louis. 1998. Laboratory testing for Neisseria gonorrhoeae by recently introduced nonculture tests: a performance review with clinical and public health considerations. Clin. Infect. Dis. 27:11711180.
22. Lang, A. M.,, J. Feris-Iglesias,, C. Pena,, J. F. Sanchez,, L. Stockman,, P. Rys,, G. D. Roberts,, N. K. Henry,, D. H. Persing, and, F. R. Cockerill. 1998. Clinical evaluation of the Gen-Probe amplified direct test for detection of Mycobacterium tuberculosis complex organisms in cerebrospinal fluid. J. Clin. Microbiol. 36:21912194.
23. Lauderdale, T. L.,, L. Landers,, I. Thorneycroft, and, K. Chapin. 1999. Comparison of the PACE 2 assay, two amplification assays and Clearview EIA for detection of Chlamydia trachomatis in female endocervical and urine specimens. J. Clin. Microbiol. 37:22232229.
24. Mahony, J.,, S. Chong,, D. Jang,, K. Luinstra,, M. Faught,, D. Dalby,, J. Sellors, and, M. Chernesky. 1998. Urine specimens from pregnant and nonpregnant women inhibitory to amplification of Chlamydia trachomatis nucleic acid by PCR, ligase chain reaction, and transcription-mediated amplification: identification of urinary substances associated with inhibition and removal of inhibitory activity. J. Clin. Microbiol. 36:31223126.
25. Mahony, J. B.,, X. Song,, S. Chong,, M. Faught,, T. Salonga, and, J. Kapala. 2001. Evaluation of the NucliSens Basic Kit for detection of Chlamydia trachomatis and Neisseria gonorrhoeae in genital tract specimens using nucleic acid sequence-based amplification of 16S rRNA. J. Clin. Microbiol. 39:14291435.
26. Makinen, J., et al. 2006. Evaluation of a novel strip test, GenoType Mycobacterium CM/AS, for species identification of mycobacterial cultures. Clin. Microbiol. Infect. 12:481483.
27. McDonald, L. C.,, M. Owings, and, D. B. Jernigan. 2006. Clostridium difficile infection in patients discharged from US short-stay hospitals, 1996-2003. Emerg. Infect. Dis. 12:409415.
28. Miller, N.,, S. Infante, and, T. Cleary. 2000. Evaluation of the LiPA Mycobacteria assay for identification of mycobacterial species from BACTEC 12B bottles. J. Clin. Microbiol. 38:19151919.
29. Moore, D. F.,, and J. L. Curry. 1998. Detection and identification of Mycobacterium tuberculosis directly from sputum sediments by ligase chain reaction. J. Clin. Microbiol. 36:10281031.
30. Novak-Weekley, S. M.,, E. M. Marlowe,, J. M. Miller,, J. Cumpio,, J. H. Nomura,, P. H. Vance, and, A. Weissfeld. 2010. Clostridium difficile testing in the clinical laboratory using multiple testing algorithms. J. Clin. Microbiol. 48:889893.
31. Parta, M.,, M. Goebel,, M. Matloobi,, C. Stager, and, D. M. Musher. 2009. Identification of methicillin-resistant or methicillin-susceptible Staphylococcus aureus in blood cultures and wound swabs by GeneXpert. J. Clin. Microbiol. 47:16091610.
32. Pasternack, R.,, P. Vuorinen,, T. Pitkajarvi,, M. Koskela, and, A. Miettinen. 1997. Comparison of manual AMPLICOR PCR, Cobas AMPLICOR PCR, and LCx assays for detection of Chlamydia trachomatis infection in women by using urine specimens. J. Clin. Microbiol. 35:402405.
33. Piersimoni, C.,, A. Callegaro,, C. Scarparo,, V. Penati,, D. Nista,, S. Bornigia,, C. Lacchini,, M. Scagnelli,, G. Santini, and, G. D. Sio. 1998. Comparative evaluation of the new Gen-Probe Mycobacterium tuberculosis Amplified Direct test and the semiautomated Abbott LCx Mycobacterium tuberculosis assay for direct detection of Mycobacterium tuberculosis complex in respiratory and extrapulmonary specimens. J. Clin. Microbiol. 36:36013604.
34. Reischl, U.,, N. Lehn,, H. Wolf, and, L. Neumann. 1998. Clinical evaluation of the automated COBAS AMPLICOR MTB assay for testing respiratory and nonrespiratory specimens. J. Clin. Microbiol. 36:28532860.
35. Stamper, P. D.,, R. Alcabasa,, D. Aird,, W. Babiker,, J. Wehrlin,, I. Ikpeama, and, K. C. Carroll. 2009. Comparison of a commercial real-time PCR assay for tcdB detection to a cell culture cytotoxicity assay and toxigenic culture for direct detection of toxin-producing Clostridium difficile in clinical samples. J. Clin. Microbiol. 47:373378.
36. Stamper, P. D.,, W. Babiker,, R. Alcabasa,, D. Aird,, J. Wehrlin,, I. Ikpeama,, L. Gluck, and, K. C. Carroll. 2009. Evaluation of a new commercial TaqMan PCR assay for direct detection of the Clostridium difficile toxin B gene in clinical stool specimens. J. Clin. Microbiol. 47:38463850.
37. Tenover, F. C.,, J. T. Crawford,, R. E. Huebner,, L. J. Geiter,, C. R. Horsburgh, and, R. C. Good. 1999. The resurgence of tuberculosis: is your laboratory ready? J. Clin. Microbiol. 31:767770.
38. van der Pol, B.,, D. V. Ferrero,, L. Buck-Barrington,, E. Hook,, C. Lenderman,, T. Quinn,, C. A. Gaydos,, J. Lovchik,, J. Schachter,, J. Moncada,, G. Hall,, M. J. Tuohy, and, R. B. Jones. 2001. Multicenter evaluation of the BDProbeTec ET system for detection of Chlamydia trachomatis and Neisseria gonorrhoeae in urine specimens, female endocervical swabs, and male urethral swabs. J. Clin. Microbiol. 39:10081016.
39. van Doornum, G. J. J.,, L. M. Schouls,, A. Pijl,, I. Cairo,, M. Buimer, and, S. Bruisten. 2001. Comparison between the LCx probe system and the COBAS AMPLICOR system for detection of Chlamydia trachomatis and Neisseria gonorrhoeae infections in patients attending a clinic for treatment of sexually transmitted diseases in Amsterdam, The Netherlands. J. Clin. Microbiol. 39:829835.
40. Watterson, S. A.,, and F. A. Drobniewski. 2000. Modern laboratory diagnosis of mycobacterial infections. J. Clin. Pathol. 53:727732.
41. Wolk, D. M.,, E. Picton,, D. Johnson,, T. Davis,, P. Pancholi,, C. C. Ginocchio,, S. Finegold,, D. F. Welch,, M. de Boer,, D. Fuller,, M. C. Solomon,, B. Rogers,, M. S. Mehta, and, L. R. Peterson. 2009. Multicenter evaluation of the Cepheid Xpert methicillin-resistant Staphylococcus aureus (MRSA) test as a rapid screening method for detection of MRSA in nares. J. Clin. Microbiol. 47:758764.
42. Wolk, D. M.,, M. J. Struelens,, P. Pancholi,, T. Davis,, P. Della-Latta,, D. Fuller,, E. Picton,, R. Dickenson,, O. Denis,, D. Johnson, and, K. Chapin. 2009. Rapid detection of Staphylococcus aureus and methicillin-resistant S. aureus (MRSA) in wound specimens and blood cultures: multicenter preclinical evaluation of the Cepheid Xpert MRSA/SA skin and soft tissue and blood culture assays. J. Clin. Microbiol. 47:823826.
43. Woods, G. L.,, J. S. Bergmann, and, N. Williams-Bouyer. 2001. Clinical evaluation of the Gen-Probe Amplified Mycobacterium tuberculosis Direct test for rapid detection of Mycobacterium tuberculosis in select nonrespiratory specimens. J. Clin. Microbiol. 39:747749.
44. Zwadyk, P.,, J. A. Down,, N. Myers, and, M. S. Dey. 1994. Rendering of mycobacteria safe for molecular diagnostic studies and development of a lysis method for strand displacement amplification and PCR. J. Clin. Microbiol. 32:21402146.

Tables

Generic image for table
TABLE 1

Reporting of amplification results

Citation: Hall G, Katanik M, Tuohy M, Sholtis M. 2011. Use of Commercial Amplification Tests in the Clinical Microbiology Laboratory: Test Selection and Quality Assurance, p 107-116. In Persing D, Tenover F, Tang Y, Nolte F, Hayden R, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555816834.ch6
Generic image for table
TABLE 2

Reporting of amplification results

Citation: Hall G, Katanik M, Tuohy M, Sholtis M. 2011. Use of Commercial Amplification Tests in the Clinical Microbiology Laboratory: Test Selection and Quality Assurance, p 107-116. In Persing D, Tenover F, Tang Y, Nolte F, Hayden R, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555816834.ch6
Generic image for table
TABLE 3

Comparison of methods for detection of

Citation: Hall G, Katanik M, Tuohy M, Sholtis M. 2011. Use of Commercial Amplification Tests in the Clinical Microbiology Laboratory: Test Selection and Quality Assurance, p 107-116. In Persing D, Tenover F, Tang Y, Nolte F, Hayden R, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555816834.ch6
Generic image for table
TABLE 4

Comparison of methods for detection of

Citation: Hall G, Katanik M, Tuohy M, Sholtis M. 2011. Use of Commercial Amplification Tests in the Clinical Microbiology Laboratory: Test Selection and Quality Assurance, p 107-116. In Persing D, Tenover F, Tang Y, Nolte F, Hayden R, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555816834.ch6
Generic image for table
TABLE 5

Issues that need to be addressed before and after implementation of a NAAT for and

Citation: Hall G, Katanik M, Tuohy M, Sholtis M. 2011. Use of Commercial Amplification Tests in the Clinical Microbiology Laboratory: Test Selection and Quality Assurance, p 107-116. In Persing D, Tenover F, Tang Y, Nolte F, Hayden R, van Belkum A (ed), Molecular Microbiology. ASM Press, Washington, DC. doi: 10.1128/9781555816834.ch6

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error