Standardization of nucleic acid tests for clinical measurements of bacteria and viruses

Journal of Clinical Microbiology

Volumn 53, Issue 7, 2015, Pages 2008-2014

  Pavšič, Jernej ^a,b   Devonshire, Alison S ^c   Parkes, Helen ^c   Schimmel, Heinz ^d   Foy, Carole A ^c   Karczmarczyk, Maria ^d   Gutiérrez Aguirre, Ion ^a   Honeyborne, Isobella ^e   Huggett, Jim F ^c   McHugh, Timothy D ^e   Milavec, Mojca ^a   Zeichhardt, Heinz ^f   Žela, Jana ^a  

^a NATIONAL INSTITUTE OF BIOLOGY   (Slovenia)

^b JO EF STEFAN INSTITUTE   (Slovenia)

^c LGC   (United Kingdom)

^d JOINT RESEARCH CENTRE   (Italy)

^e UNIVERSITY COLLEGE LONDON   (United Kingdom)

^f CHARITÉ UNIVERSITÄTSMEDIZIN BERLIN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

VIRUS DNA;

ANALYTIC METHOD; ARTICLE; BACTERIUM EXAMINATION; BACTERIUM IDENTIFICATION; BK VIRUS; CONTROLLED STUDY; DIAGNOSTIC ACCURACY; DIAGNOSTIC TEST; DIAGNOSTIC TEST ACCURACY STUDY; EPSTEIN BARR VIRUS; HUMAN; HUMAN CYTOMEGALOVIRUS; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; INFLUENZA; INFLUENZA VIRUS; LABORATORY DIAGNOSIS; LIMIT OF DETECTION; LIMIT OF QUANTITATION; MOLECULAR DIAGNOSIS; MULTIDRUG RESISTANT TUBERCULOSIS; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; NUCLEIC ACID AMPLIFICATION; PNEUMOCYSTIS JIROVECI; POINT OF CARE TESTING; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; QUALITY CONTROL; REPRODUCIBILITY; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SENSITIVITY AND SPECIFICITY; SPUTUM SMEAR; STANDARDIZATION; VIRUS EXAMINATION; VIRUS IDENTIFICATION; VIRUS LOAD; BACTERIAL INFECTION; BACTERIAL LOAD; BACTERIUM; ISOLATION AND PURIFICATION; MICROBIOLOGY; PROCEDURES; STANDARD; STANDARDS; VIROLOGY; VIRUS; VIRUS INFECTION;

BK POLYOMAVIRUS; HUMAN HERPESVIRUS 4; HUMAN HERPESVIRUS 5; MYCOBACTERIUM TUBERCULOSIS; ORTHOMYXOVIRIDAE;

BACTERIA; BACTERIAL INFECTIONS; BACTERIAL LOAD; HUMANS; MOLECULAR DIAGNOSTIC TECHNIQUES; REFERENCE STANDARDS; VIRAL LOAD; VIRUS DISEASES; VIRUSES;

EID: 84932627774     PISSN: 00951137     EISSN: 1098660X     Source Type: Journal    
DOI: 10.1128/JCM.02136-14     Document Type: Article

References (49)

1. Kotton CN, Kumar D, Caliendo AM, Asberg A, Chou S, Danziger-Isakov L, Humar A; Transplantation Society International CMV Consensus Group. 2013. Updated international consensus guidelines on the management of cytomegalovirus in solid-organ transplantation. Transplantation 96:333-360. http://dx.doi.org/10.1097/TP.0b013e31829df29d.
2. Lawn SD, Mwaba P, Bates M, Piatek A, Alexander H, Marais BJ, Cuevas LE, McHugh TD, Zijenah L, Kapata N, Abubakar I, McNerney R, Hoelscher M, Memish ZA, Migliori GB, Kim P, Maeurer M, Schito M, Zumla A. 2013. Advances in tuberculosis diagnostics: the Xpert MTB/RIF assay and future prospects for a point-of-care test. Lancet Infect Dis 13: 349-361. http://dx.doi.org/10.1016/S1473-3099(13)70008-2.
3. Hayden RT, Yan X, Wick MT, Rodriguez AB, Xiong X, Ginocchio CC, Mitchell MJ, Caliendo AM; College of American Pathologists Microbiology Resource Committee. 2012. Factors contributing to variability of quantitative viral PCR results in proficiency testing samples: a multivariate analysis. J Clin Microbiol 50:337-345. http://dx.doi.org/10.1128/JCM.01287-11.
4. Pang XL, Fox JD, Fenton JM, Miller GG, Caliendo AM, Preiksaitis JK; American Society of Transplantation Infectious Diseases Community of Practice; Canadian Society of Transplantation. 2009. Interlaboratory comparison of cytomegalovirus viral load assays. Am J Transplant 9:258-268. http://dx.doi.org/10.1111/j.1600-6143.2008.02513.x.
5. Antonenka U, Hofmann-Thiel S, Turaev L, Esenalieva A, Abdulloeva M, Sahalchyk E, Alnour T, Hoffmann H. 2013. Comparison of Xpert MTB/RIF with ProbeTec ET DTB and COBAS TaqMan MTB for direct detection of M. tuberculosis complex in respiratory specimens. BMC Infect Dis 13:280. http://dx.doi.org/10.1186/1471-2334-13-280.
6. International Organization of Standardization. 2003. In vitro diagnostic medical devices - measurement of quantities in biological samples - metrological traceability of values assigned to calibrators and control materials. International standard ISO 17511:2003. ISO, Geneva, Switzerland.
7. Armbruster D, Miller RR. 2007. The Joint Committee for Traceability in Laboratory Medicine (JCTLM): a global approach to promote the standardisation of clinical laboratory test results. Clin Biochem Rev 28:105-113.
8. Vesper HW, Thienpont LM. 2009. Traceability in laboratory medicine. Clin Chem 55:1067-1075. http://dx.doi.org/10.1373/clinchem.2008.107052.
9. White GH. 2011. Metrological traceability in clinical biochemistry. Ann Clin Biochem 48:393-409. http://dx.doi.org/10.1258/acb.2011.011079.
10. Kraft CS, Armstrong WS, Caliendo AM. 2012. Interpreting quantitative cytomegalovirus DNA testing: understanding the laboratory perspective. Clin Infect Dis 54:1793-1797. http://dx.doi.org/10.1093/cid/cis212.
11. Bravo D, lari MÁ, Costa E, Muñoz-Cobo B, Solano C, José Remigia M, Navarro D. 2011. Comparative evaluation of three automated systems for DNA extraction in conjunction with three commercially available realtime PCR assays for quantitation of plasma Cytomegalovirus DNAemia in allogeneic stem cell transplant recipients. J Clin Microbiol 49:2899-2904. http://dx.doi.org/10.1128/JCM.00785-11.
12. Caliendo AM, Shahbazian MD, Schaper C, Ingersoll J, Abdul-Ali D, Boonyaratanakornkit J, Pang X-L, Fox J, Preiksaitis J, Schönbrunner ER. 2009. A commutable cytomegalovirus calibrator is required to improve the agreement of viral load values between laboratories. Clin Chem 55:1701-1710. http://dx.doi.org/10.1373/clinchem.2009.124743.
13. Przybylski M, Dzieciatkowski T, Les K, Mucha MA, Wroblewska M, Mlynarczyk G. 2012. Comparison of real-time PCR quantitative analysis of the cytomegalovirus DNA level using LightCycler 2.0 and LightCycler 480 instruments. J Clin Virol 55:270-273. http://dx.doi.org/10.1016/j.jcv.2012.08.005.
14. Zeichhardt H, Mantke OD . 5 June 2014, posting date. Report, external quality assessment scheme, group 365, virus genome detection-cytomegalovirus, March/April 2014. http://www.instandev.de /uploads/tx-nfextinstandpdf/365-EN-Cytomegalovirus-Genome-EQAS-March-April-2014-20140605.pdf.
15. Schnepf N, Scieux C, Resche-Riggon M, Feghoul L, Xhaard A, Gallien S, Molina J-M, Socié G, Viglietti D, Simon F, Mazeron M-C, Legoff J. 2013. Fully automated quantification of cytomegalovirus (CMV) in whole blood with the new sensitive Abbott RealTime CMV assay in the era of the CMV international standard. J Clin Microbiol 51:2096-2102. http://dx.doi.org/10.1128/JCM.00067-13.
16. Gulley ML, Tang W. 2010. Using Epstein-Barr viral load assays to diagnose, monitor, and prevent posttransplant lymphoproliferative disorder. Clin Microbiol Rev 23:350-366. http://dx.doi.org/10.1128/CMR.00006-09.
17. Bechert CJ, Schnadig VJ, Payne DA, Dong J. 2010. Monitoring of BK viral load in renal allograft recipients by real-time PCR assays. Am J Clin Pathol 133:242-250. http://dx.doi.org/10.1309/AJCP63VDFCKCRUUL.
18. Ruf S, Behnke-Hall K, Gruhn B, Bauer J, Horn M, Beck J, Reiter A, Wagner HJ. 2012. Comparison of six different specimen types for Epstein-Barr viral load quantification in peripheral blood of pediatric patients after heart transplantation or after allogeneic hematopoietic stem cell transplantation. J Clin Virol 53:186-194. http://dx.doi.org/10.1016/j.jcv.2011.11.010.
19. Hoffman NG, Cook L, Atienza EE, Limaye AP, Jerome KR. 2008. Marked variability of BK virus load measurement using quantitative realtime PCR among commonly used assays. J Clin Microbiol 46:2671-2680. http://dx.doi.org/10.1128/JCM.00258-08.
20. Germi R, Lupo J, Semenova T, Larrat S, Magnat N, Grossi L, Seigneurin J-M, Morand P. 2012. Comparison of commercial extraction systems and PCR assays for quantification of Epstein-Barr virus DNA load in whole blood. J Clin Microbiol 50:1384-1389. http://dx.doi.org/10.1128/JCM.05593-11.
21. Zeichhardt H, Mantke OD. 15 July 2014, posting date. Report, external quality assessment scheme, group 364, virus genome detection, BK virus, March/April 2014. http://www.instandev.de/uploads/tx-nfextinstandpdf/364-EN-BK-virus-Genome-EQAS-March-April-2014-20140715.pdf.
22. Zeichhardt H, Mantke OD. 10 September 2014, posting date. Report, external quality assessment scheme, group 376, virus genome detection- Epstein Barr virus, June 2014. http://www.instandev.de/uploads/tx-nfextinstandpdf/376-EN-Epstein-Barr-Virus-Genome-June-2014-20140910.pdf.
23. Trofe-Clark J, Sparkes T, Gentile C, Van Deerlin V, Sawinski D, Bloom RD. 2013. BK virus genotype variance and discordant BK viremia PCR assay results. Am J Transplant 13:1112-1113. http://dx.doi.org/10.1111/ajt.12169.
24. Maillet M, Maubon D, Brion JP, François P, Molina L, Stahl JP, Epaulard O, Bosseray A, Pavese P. 2014. Pneumocystis jirovecii (Pj) quantitative PCR to differentiate Pj pneumonia from Pj colonization in immunocompromised patients. Eur J Clin Microbiol Infect Dis 33:331-336. http://dx.doi.org/10.1007/s10096-013-1960-3.
25. van Zyl-Smit RN, Binder A, Meldau R, Mishra H, Semple PL, Theron G, Peter J, Whitelaw A, Sharma SK, Warren R, Bateman ED, Dheda K. 2011. Comparison of quantitative techniques including Xpert MTB/RIF to evaluate mycobacterial burden. PLoS One 6:e28815. http://dx.doi.org /10.1371/journal.pone.0028815.
26. Aryan E, Makvandi M, Farajzadeh A, Huygen K, Alvandi A-H, Gouya M-M, Sadrizadeh A, Romano M. 2013. Clinical value of IS6110-based loop-mediated isothermal amplification for detection of Mycobacterium tuberculosis complex in respiratory specimens. J Infect 66:487-493. http: //dx.doi.org/10.1016/j.jinf.2013.02.005.
27. Seagar A-L, Neish B, Laurenson IF. 2012. Comparison of two in-house real-time PCR assays with MTB Q-PCR Alert and GenoType MTBDRplus for the rapid detection of mycobacteria in clinical specimens. J Med Microbiol 61:1459-1464. http://dx.doi.org/10.1099/jmm.0.043166-0.
28. Dorman SE, Chihota VN, Lewis JJ, Shah M, Clark D, Grant AD, Churchyard GJ, Fielding KL. 2012. Performance characteristics of the Cepheid Xpert MTB/RIF test in a tuberculosis prevalence survey. PLoS One 7:e43307. http://dx.doi.org/10.1371/journal.pone.0043307.
29. Steingart K, Schiller I, Horne D, Pai M, Boehme C, Denkuri N. 2014. Xpert® MTB/RIF assay for pulmonary tuberculosis and rifampicin resistance in adults. Cochrane Database Syst Rev 1:CD009593. http://dx.doi .org/10.1002/14651858.CD009593.pub3.
30. Molinari N-AM, Ortega-Sanchez IR, Messonnier ML, Thompson WW, Wortley PM, Weintraub E, Bridges CB. 2007. The annual impact of seasonal influenza in the US: measuring disease burden and costs. Vaccine 25:5086-5096. http://dx.doi.org/10.1016/j.vaccine.2007.03.046.
31. Biere B, Schweiger B, Nitsche A. 2009. Influenza A H1N1 diagnostics: the first, the fastest, and the most reliable. Lancet Infect Dis 9:721-722. http: //dx.doi.org/10.1016/S1473-3099(09)70301-9.
32. van Elden LJR, Nijhuis M, Schipper P, Schuurman R, Loon Van AM. 2001. Simultaneous detection of influenza viruses A and B using real-time quantitative PCR. J Clin Microbiol 39:196-200. http://dx.doi.org/10.1128/JCM.39.1.196-200.2001.
33. Lalle E, Bordi L, Meschi S, Selleri M, Valli MB, Patella E, Capobianchi MR. 2011. Comparison of two real-time RT-PCR-based systems for the detection and typing of the pandemic influenza A virus, 2009. J Virol Methods 177:193-196. http://dx.doi.org/10.1016/j.jviromet.2011.07.004.
34. Templeton KE, Scheltinga SA, Beersma MFC, Kroes ACM, Claas ECJ. 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. http://dx.doi.org/10.1128/JCM.42.4.1564-1569.2004.
35. Yang G, Erdman DE, Kodani M, Kools J, Bowen MD, Fields BS. 2011. Comparison of commercial systems for extraction of nucleic acids from DNA/RNA respiratory pathogens. J Virol Methods 171:195-199. http://dx.doi.org/10.1016/j.jviromet.2010.10.024.
36. Sanders R, Mason DJ, Foy CA, Huggett JF. 2013. Evaluation of digital PCR for absolute RNA quantification. PLoS One 8:e75296. http://dx.doi.org/10.1371/journal.pone.0075296.
37. Van Wesenbeeck L, Meeuws H, Van Immerseel A, Ispas G, Schmidt K, Houspie L, Van Ranst M, Stuyver L. 2013. Comparison of the FilmArray RP, Verigene RVô, and Prodesse ProFLU+/FAST6+ multiplex platforms for detection of influenza viruses in clinical samples from the 2011-2012 influenza season in Belgium. J Clin Microbiol 51:2977-2985. http://dx.doi.org/10.1128/JCM.00911-13.
38. Piralla A, Daleno C, Pariani E, Conaldi P, Esposito S, Zanetti A, Baldanti F. 2013. Virtual quantification of influenza A virus load by realtime RT-PCR. J Clin Virol 56:65- 68. http://dx.doi.org/10.1016/j.jcv.2012.09.011.
39. Rheem I, Park J, Kim T, Kim JW. 2012. Evaluation of a multiplex real-time PCR assay for the detection of respiratory viruses in clinical specimens. Ann Lab Med 32:399- 406. http://dx.doi.org/10.3343/alm.2012.32.6.399.
40. Huber I, Campe H, Sebah D, Hartberger C, Konrad R, Bayer M, Busch U, Sing A. 2011. A multiplex one-step real-time RT-PCR assay for influenza surveillance. Euro Surveill 16:pii=19798. http://www.eurosurveillance.org/ViewArticle.aspx?ArticleId=19798.
41. Zeichhardt H, Mantke OD. 13 August 2014, posting date. Report, external quality assessment scheme, group 370, virus genome detection - influenza A and B viruses, March/April 2014. http://www.instandev.de/uploads/tx-nfextinstandpdf/370-EN-Influenza-EQAS-March-April-2014-20140813a.pdf.
42. Razonable RR, Åsberg A, Rollag H, Duncan J, Boisvert D, Yao JD, Caliendo AM, Humar A, Do TD. 2013. Virologic suppression measured by a cytomegalovirus (CMV) DNA test calibrated to the World Health Organization international standard is predictive of CMV disease resolution in transplant recipients. Clin Infect Dis 56:1546-1553. http://dx.doi.org/10.1093/cid/cit096.
43. Bhat S, Curach N, Mostyn T, Bains GS, Griffiths KR, Emslie KR. 2010. Comparison of methods for accurate quantification of DNA mass concentration with traceability to the international system of units. Anal Chem 82:7185-7192. http://dx.doi.org/10.1021/ac100845m.
44. Hayden RT, Gu Z, Ingersoll J, Abdul-Ali D, Shi L, Pounds S, Caliendo AM. 2013. Comparison of droplet digital PCR to real-time PCR for quantitative detection of cytomegalovirus. J Clin Microbiol 51:540-546. http://dx.doi.org/10.1128/JCM.02620-12.
45. Morisset D, Štebih D, Milavec M, Gruden K, Žel J. 2013. Quantitative analysis of food and feed samples with droplet digital PCR. PLoS One 8:e62583. http://dx.doi.org/10.1371/journal.pone.0062583.
46. Kelley K, Cosman A, Belgrader P, Chapman B, Sullivan DC. 2013. Detection of methicillin-resistant Staphylococcus aureus by a duplex droplet digital PCR assay. J Clin Microbiol 51:2033-2039. http://dx.doi.org/10.1128/JCM.00196-13.
47. Rački N, Morisset D, Gutierrez-Aguirre I, Ravnikar M. 2014. One-step RT-droplet digital PCR: a breakthrough in the quantification of waterborne RNA viruses. Anal Bioanal Chem 406:661-667. http://dx.doi.org/10.1007/s00216-013-7476-y.
48. Sedlak RH, Cook L, Cheng A, Magaret A, Jerome KR. 2014. Evaluation of the clinical utility of droplet digital PCR for human cytomegalovirus. J Clin Microbiol 52:2844-2848. http://dx.doi.org/10.1128/JCM.00803-14.
49. Joint Committee for Guides in Metrology. 2012. International vocabulary of metrology - basic and general concepts and associated terms (VIM) JCGM 200:2012. http://www.bipm.org/utils/common/documents/jcgm/JCGM-200-2012.pdf.