Sample-to-result molecular infectious disease assays: Clinical implications, limitations and potential

Expert Review of Molecular Diagnostics

Volumn 16, Issue 3, 2016, Pages 323-341

  Beal, Stacy G ^a   Assarzadegan, Naziheh ^a   Rand, Kenneth H ^a  

^a UNIVERSITY OF FLORIDA COLLEGE OF MEDICINE   (United States)

Author keywords

Infectious disease testing; microbiology; molecular testing; nucleic acid tests; rapid testing; sample to answer; sample to result; undeveloped countries

Indexed keywords

ASSAY; CENTRAL NERVOUS SYSTEM; GASTROINTESTINAL INFECTION; GASTROINTESTINAL TRACT; HUMAN; INFECTION; LUNG TUBERCULOSIS; MOLECULAR BIOLOGY; MOLECULAR DIAGNOSIS; MOLECULAR INFECTIOUS DISEASE ASSAY; NOROVIRUS; PATIENT CARE; PEPTOCLOSTRIDIUM DIFFICILE; RESPIRATORY SYSTEM; RESPIRATORY TRACT DISEASE; RESPIRATORY TRACT EXAMINATION; REVIEW; SENSITIVITY AND SPECIFICITY; SEXUALLY TRANSMITTED DISEASE; UROGENITAL SYSTEM; DEVELOPING COUNTRY; ECONOMICS; MASS SCREENING; POLYMERASE CHAIN REACTION; PROCEDURES; STANDARDS;

DEVELOPING COUNTRIES; HUMANS; INFECTION; MASS SCREENING; MOLECULAR DIAGNOSTIC TECHNIQUES; POLYMERASE CHAIN REACTION; SENSITIVITY AND SPECIFICITY;

EID: 84959346407     PISSN: 14737159     EISSN: 17448352     Source Type: Journal    
DOI: 10.1586/14737159.2016.1134325     Document Type: Review

References (103)

1. Fakruddin M, Mannan KS, Chowdhury A., et al. Nucleic acid amplification: alternative methods of polymerase chain reaction. J Pharm Bioallied Sci. 2013 Oct; 5 (4): 245-252.
2. Gill P, Ghaemi A. Nucleic acid isothermal amplification technologies: a review. Nucleosides Nucleotides Nucleic Acids. 2008 Mar; 27 (3): 224-243.
3. Cepheid. Cepheid website [Internet]. [cited 2015 Dec 7]. Available from: http://www.cepheid.com/us/.
4. Dugas AF, Valsamakis A, Gaydos CA., et al. Evaluation of the Xpert Flu rapid PCR assay in high-risk emergency department patients. J Clin Microbiol. 2014 Dec; 52 (12): 4353-4355.
5. Salez N, Ninove L, Thirion L., et al. Evaluation of the Xpert Flu test and comparison with in-house real-time RT-PCR assays for detection of influenza virus from 2008 to 2011 in Marseille, France. Clin Microbiol Infect. 2012 Apr; 18 (4): E81-83.
6. Li M, Brenwald N, Bonigal S., et al. Rapid diagnosis of influenza: an evaluation of two commercially available RT-PCR assays. J Infect. 2012 Jul; 65 (1): 60-63.
7. Popowitch EB, Miller MB. Performance characteristics of Xpert Flu/RSV XC assay. J Clin Microbiol. 2015 May 27;53(8):2720-2721.
8. Salez N, Nougairede A, Ninove L., et al. Prospective and retrospective evaluation of the Cepheid Xpert(R) Flu/RSV XC assay for rapid detection of influenza A, influenza B, and respiratory syncytial virus. Diagn Microbiol Infect Dis. 2015 Apr; 81 (4): 256-258.
9. Salez N, De Lamballerie X, Zandotti C., et al. Improved sensitivity of the novel Xpert flu test for detection of influenza B virus. J Clin Microbiol. 2013 Dec; 51 (12): 4277-4278.
10. Woodberry MW, Shankar R, Cent A., et al. Comparison of the Simplexa FluA/B & RSV direct assay and laboratory-developed real-time PCR assays for detection of respiratory virus. J Clin Microbiol. 2013 Nov; 51 (11): 3883-3885.
11. Doern CD, Lacey D, Huang R., et al. Evaluation and implementation of FilmArray version 1.7 for improved detection of adenovirus respiratory tract infection. J Clin Microbiol. 2013 Dec; 51 (12): 4036-4039.
12. Couturier MR, Barney T, Alger G., et al. Evaluation of the FilmArray(R) Respiratory Panel for clinical use in a large childrens hospital. J Clin Lab Anal. 2013 Mar; 27 (2): 148-154.
13. Jerris RC, Williams SR, MacDonald HJ., et al. Testing implications of varying targets for Bordetella pertussis: comparison of the FilmArray Respiratory Panel and the Focus B. pertussis PCR assay. J Clin Pathol. 2015 May; 68 (5): 394-396.
14. Branche AR, Walsh EE, Formica MA., et al. Detection of respiratory viruses in sputum from adults by use of automated multiplex PCR. J Clin Microbiol. 2014 Oct; 52 (10): 3590-3596.
15. Ruggiero P, McMillen T, Tang YW., et al. Evaluation of the BioFire FilmArray respiratory panel and the GenMark eSensor respiratory viral panel on lower respiratory tract specimens. J Clin Microbiol. 2014 Jan; 52 (1): 288-290.
16. Xu M, Qin X, Astion ML., et al. Implementation of filmarray respiratory viral panel in a core laboratory improves testing turnaround time and patient care. Am J Clin Pathol. 2013 Jan; 139 (1): 118-123.
17. Rand KH, Rampersaud H, Houck HJ. Comparison of two multiplex methods for detection of respiratory viruses: FilmArray RP and xTAG RVP. J Clin Microbiol. 2011 Jul; 49 (7): 2449-2453.
18. Butt SA, Maceira VP, McCallen ME., et al. Comparison of three commercial RT-PCR systems for the detection of respiratory viruses. J Clin Virol. 2014 Nov; 61 (3): 406-410.
19. Cho HJ, Jang JW, Ko SY., et al. Evaluation and verification of the nanosphere Verigene RV+ assay for detection of influenza A/B and H1/H3 subtyping. J Med Virol. 2015 Jan; 87 (1): 18-24.
20. Boku S, Naito T, Murai K., et al. Near point-of-care administration by the attending physician of the rapid influenza antigen detection immunochromatography test and the fully automated respiratory virus nucleic acid test: contribution to patient management. Diagn Microbiol Infect Dis. 2013 Aug; 76 (4): 445-449.
21. Van Wesenbeeck L, Meeuws H, Van Immerseel A., et al. Comparison of the FilmArray RP, Verigene RV+, and Prodesse ProFLU+/FAST+ multiplex platforms for detection of influenza viruses in clinical samples from the 2011-2012 influenza season in Belgium. J Clin Microbiol. 2013 Sep; 51 (9): 2977-2985.
22. Chu HY, Englund JA, Huang D., et al. Impact of rapid influenza PCR testing on hospitalization and antiviral use: A retrospective cohort study. J Med Virol. 2015 May 27;87(12):2021-2026.
23. Rogers BB, Shankar P, Jerris RC., et al. Impact of a rapid respiratory panel test on patient outcomes. Arch Pathol Lab Med. 2015 May; 139 (5): 636-641.
24. Hammond SP, Gagne LS, Stock SR., et al. Respiratory virus detection in immunocompromised patients with FilmArray respiratory panel compared to conventional methods. J Clin Microbiol. 2012 Oct; 50 (10): 3216-3221.
25. Alere Scarborough, Inc. Alere i package insert. Scarborough., ME: Alere Scarborough, Inc.; 2014.
26. Bell J, Bonner A, Cohen DM., et al. Multicenter clinical evaluation of the novel Alere™ i Influenza A&B isothermal nucleic acid amplification test. J Clin Virol. 2014 9; 61 (1): 81-86.
27. Alere Scarborough, Inc. Alere i Influenza A & B brochure. Scarborough, ME: Alere Scarborough, Inc.; 2015.
28. Beckmann C, Hirsch HH. Diagnostic performance of near-patient testing for influenza. J Clin Virol. 2015 Jun; 67: 43-46.
29. Bell JJ, Selvarangan R. Evaluation of the Alere I influenza A&B nucleic acid amplification test by use of respiratory specimens collected in viral transport medium. J Clin Microbiol. 2014 Nov; 52 (11): 3992-3995.
30. Nie S, Roth RB, Stiles J., et al. Evaluation of Alere i Influenza A&B for rapid detection of influenza viruses A and B. J Clin Microbiol. 2014 Sep; 52 (9): 3339-3344.
31. Hazelton B, Gray T, Ho J., et al. Detection of influenza A and B with the Alere i Influenza A & B: a novel isothermal nucleic acid amplification assay. Influenza Other Respir Viruses. 2015 May; 9 (3): 151-154.
32. Chapin KC, Flores-Cortez EJ. Performance of the molecular Alere I influenza A&B test compared to that of the xpert flu A/B assay. J Clin Microbiol. 2015 Feb; 53 (2): 706-709.
33. FDA. Class 2 device recall. Washington., DC: U.S. Food and Drug Administration; 2015. (Recall Number Z-1677-2015).
34. Binnicker MJ, Espy MJ, Irish CL., et al. Direct detection of influenza A and B viruses in less than 20 minutes using a commercially available rapid PCR assay. J Clin Microbiol. 2015 Jul; 53 (7): 2353-2354.
35. World health organization global tuberculosis report. 2014. Available from: http://www.who.int/tb/publications/global-report/gtbr14-main-text.pdf
36. Parsons LM, Somoskovi A, Gutierrez C., et al. Laboratory diagnosis of tuberculosis in resource-poor countries: challenges and opportunities. Clin Microbiol Rev. 2011 Apr; 24 (2): 314-350.
37. World Health Organization. Media center, tuberculosis. 2015 [cited 2015 Dec 11]. Available from: http://www.who.int/mediacentre/factsheets/fs104/en/.
38. World Health Organization. Global tuberculosis control: epidemiology, strategy, financing: WHO report. Geneva (Switzerland): World Health Organization; 2009.
39. Lawn SD, Nicol MP. Xpert(R) MTB/RIF assay: development, evaluation and implementation of a new rapid molecular diagnostic for tuberculosis and rifampicin resistance. Future Microbiol. 2011 Sep; 6 (9): 1067-1082.
40. World Health Organization recommendations. Tuberculosis diagnostics Xpert MTB/RIF test. 2013 [cited 2015 Dec 11]. Available from: http://who.int/tb/features-archive/factsheet-xpert.pdf
41. Diagnosis of tuberculosis disease. In: Centers for disease control and prevention, core curriculum on tuberculosis: what the clinician should know. 6th ed. Atlanta, GA: Centers for Disease Control and Prevention; 2013.
42. Centers for Disease Control and Prevention. A new tool to diagnose Tuberculosis: the Xpert MTB/RIF assay [Internet]. 2014 [cited 2015 Dec 11]. Available from: http://www.cdc.gov/tb/publications/factsheets/pdf/xpertmtbrifassayfactsheet-final.pdf.
43. Boehme CC, Nabeta P, Hillemann D., et al. Rapid molecular detection of tuberculosis and rifampin resistance. N Engl J Med. 2010 Sep 9; 363 (11): 1005-1015.
44. El-Hajj HH, Marras SA, Tyagi S., et al. Detection of rifampin resistance in Mycobacterium tuberculosis in a single tube with molecular beacons. J Clin Microbiol. 2001 Nov; 39 (11): 4131-4137.
45. World Health Organization. Roadmap for rolling out Xpert MTB/RIF for rapid diagnosis of TB and MDR-TB. Washington, DC: World Health Organization; 2010.
46. Xpert MTB/RIF. Implementation manual: technical and operational How-To; practical considerations. Washington, DC: WHO; 2014.
47. Helb D, Jones M, Story E., et al. Rapid detection of Mycobacterium tuberculosis and rifampin resistance by use of on-demand, near-patient technology. J Clin Microbiol. 2010 Jan; 48 (1): 229-237.
48. Banada PP, Sivasubramani SK, Blakemore R., et al. Containment of bioaerosol infection risk by the Xpert MTB/RIF assay and its applicability to point-of-care settings. J Clin Microbiol. 2010 Oct; 48 (10): 3551-3557.
49. Centers for Disease Control and Prevention. Report of an expert consultation on the uses of nucleic acid amplification tests for the diagnosis of tuberculosis, general consideration [Internet]. 2012 [cited 2015 Dec 11]. Available from: http://www.cdc.gov/tb/publications/guidelines/amplification-tests/default.htm
50. Millman AJ, Dowdy DW, Miller CR., et al. Rapid molecular testing for TB to guide respiratory isolation in the U.S.: a cost-benefit analysis. PLoS One. 2013; 8 (11): 1-8.
51. World Health Organization. Tuberculosis diagnostics automated DNA test. WHO endorsement and recommendations. Geneva: WHO; 2010.
52. Foundation for innovative new diagnostics, xpert MTB/DIF instrument price [Internet]. 2013 [cited 2015 Dec 11]. Available from: http://www.finddiagnostics.org/about/what-we-do/successes/find-negotiatedprices/xpert-mtb-rif.html
53. Cepheid announces first phase of Xpert MTB/RIF buy-down for high burden developing countries [news release]. Sunnyvale (CA). 2012 Aug 6 [cited 2015 Dec 11]. Available from: http://ir.cepheid.com/releasedetail.cfm?releaseid=698417.
54. Abu-Raddad LJ, Sabatelli L, Achterberg JT. Epidemiological benefits of more-effective tuberculosis vaccines, drugs, and diagnostics. Proc Natl Acad Sci USA. 2009 Aug 18; 106 (33): 13980-13985.
55. Lee BE, Davies HD. Aseptic meningitis. Curr Opin Infect Dis. 2007 Jun; 20 (3): 272-277.
56. Giulieri SG, Chapuis-Taillard C, Manuel O., et al. Rapid detection of enterovirus in cerebrospinal fluid by a fully-automated PCR assay is associated with improved management of aseptic meningitis in adult patients. J Clin Virol. 2015 Jan; 62: 58-62.
57. Marlowe EM, Novak SM, Dunn JJ., et al. Performance of the GeneXpert enterovirus assay for detection of enteroviral RNA in cerebrospinal fluid. J Clin Virol. 2008 Sep; 43 (1): 110-113.
58. Kost CB, Rogers B, Oberste MS., et al. Multicenter beta trial of the GeneXpert enterovirus assay. J Clin Microbiol. 2007 Apr; 45 (4): 1081-1086.
59. Nolte FS, Rogers BB, Tang YW., et al. Evaluation of a rapid and completely automated real-time reverse transcriptase PCR assay for diagnosis of enteroviral meningitis. J Clin Microbiol. 2011 Feb; 49 (2): 528-533.
60. Raschilas F, Wolff M, Delatour F., et al. Outcome of and prognostic factors for herpes simplex encephalitis in adult patients: results of a multicenter study. Clin Infect Dis. 2002 Aug 1; 35 (3): 254-260.
61. Debiasi RL, Tyler KL. Molecular methods for diagnosis of viral encephalitis. Clin Microbiol Rev. 2004 Oct; 17 (4): 903-925. table of contents
62. FilmArray. Meningitis (ME) panel. 2015 [cited 2015 Dec 7]. Available from: http://filmarray.com/the-panels/.
63. Liu L, Johnson HL, Cousens S., et al. Global, regional, and national causes of child mortality: an updated systematic analysis for 2010 with time trends since 2000. Lancet. 2012 Jun 9; 379 (9832): 2151-2161.
64. U.S. Department of Health and Human Services. National statistics on intestinal infections. 2015 [cited 2015 Dec 11]. Available from: http://hcupnet.ahrq.gov.
65. Khare R, Espy MJ, Cebelinski E., et al. Comparative evaluation of two commercial multiplex panels for detection of gastrointestinal pathogens by use of clinical stool specimens. J Clin Microbiol. 2014 Oct; 52 (10): 3667-3673.
66. Buss SN, Leber A, Chapin K., et al. Multicenter evaluation of the BioFire FilmArray gastrointestinal panel for etiologic diagnosis of infectious gastroenteritis. J Clin Microbiol. 2015 Mar; 53 (3): 915-925.
67. Scallan E, Hoekstra RM, Angulo FJ., et al. Foodborne illness acquired in the United States-major pathogens. Emerg Infect Dis. 2011 Jan; 17 (1): 7-15.
68. De Boer RF, Ott A, Kesztyus B., et al. Improved detection of five major gastrointestinal pathogens by use of a molecular screening approach. J Clin Microbiol. 2010 Nov; 48 (11): 4140-4146.
69. Reddington K, Tuite N, Minogue E., et al. A current overview of commercially available nucleic acid diagnostics approaches to detect and identify human gastroenteritis pathogens. Biomol Detect Quantification. 2014; 1 (1): 3-7.
70. Jangi S, Lamont JT. Asymptomatic colonization by Clostridium difficile in infants: implications for disease in later life. J Pediatr Gastroenterol Nutr. 2010 Jul; 51 (1): 2-7.
71. Mengelle C, Mansuy JM, Prere MF., et al. Simultaneous detection of gastrointestinal pathogens with a multiplex Luminex-based molecular assay in stool samples from diarrhoeic patients. Clin Microbiol Infect. 2013 Oct; 19 (10): E458-465.
72. Rand KH, Tremblay EE, Hoidal M., et al. Multiplex gastrointestinal pathogen panels: implications for infection control. Diagn Microbiol Infect Dis. 2015 Jun; 82 (2): 154-157.
73. Pancholi P, Kelly C, Raczkowski M., et al. Detection of toxigenic Clostridium difficile: comparison of the cell culture neutralization, Xpert C. difficile, Xpert C. difficile/Epi, and Illumigene C. difficile assays. J Clin Microbiol. 2012 Apr; 50 (4): 1331-1335.
74. Buss SN, Alter R, Iwen PC., et al. Implications of culture-independent panel-based detection of Cyclospora cayetanensis. J Clin Microbiol. 2013 Nov; 51 (11): 3909.
75. Prakash VP, LeBlanc L, Alexander-Scott NE., et al. Use of a culture-independent gastrointestinal multiplex PCR panel during a Shigellosis outbreak: considerations for clinical laboratories and public health. J Clin Microbiol. United States 2015; 53: 1048-1049.
76. Prevention CfDCa. Norovirus. [. Updated 2015 Sept 30; cited 2015 Dec 8]. Available from: http://www.cdc.gov/norovirus/index.html
77. Gonzalez MD, Langley LC, Buchan BW., et al. Multi-center evaluation of the Xpert norovirus assay for detection of norovirus GI and GII in fecal specimens. J Clin Microbiol. 2015 Nov 11. [Epub ahead of print].
78. Berry N, Sewell B, Jafri S., et al. Real-time polymerase chain reaction correlates well with clinical diagnosis of Clostridium difficile infection. J Hosp Infect. 2014 Jun; 87 (2): 109-114.
79. Centers for disease control and prevention(CDC). Frequently asked questions about clostridium difficile for healthcare providers. [. Updated 2012; cited 2015 Dec 11]. Available from: http://www.cdc.gov/HAI/organisms/cdiff/Cdiff-faqs-HCP.html
80. Carroll KC, Bartlett JG. Biology of Clostridium difficile: implications for epidemiology and diagnosis. Annu Rev Microbiol. 2011; 65: 501-521.
81. Novak-Weekley SM, Marlowe EM, Miller JM., et al. Clostridium difficile testing in the clinical laboratory by use of multiple testing algorithms. J Clin Microbiol. 2010 Mar; 48 (3): 889-893.
82. Chapin KC, Dickenson RA, Wu F., et al. Comparison of five assays for detection of Clostridium difficile toxin. J Mol Diagn. 2011 Jul; 13 (4): 395-400.
83. Carroll KC, Buchan BW, Tan S., et al. Multicenter evaluation of the Verigene Clostridium difficile nucleic acid assay. J Clin Microbiol. 2013 Dec; 51 (12): 4120-4125.
84. Sewell B, Rees E, Thomas I., et al. Cost and impact on patient length of stay of rapid molecular testing for clostridium difficile. Infect Dis Ther. 2014 Dec;3(2):281-293.
85. Society for Healthcare Epidemiology of America. Patient isolation tied to dissatisfaction with care. 2013 [cited 2015 Dec 11]. Available from: http://www.shea-online.org/View/ArticleId/238/Patient-Isolation-Tied-to-Dissatisfaction-with-Care.aspx.
86. Deshpande A, Pasupuleti V, Rolston DD., et al. Diagnostic accuracy of real-time polymerase chain reaction in detection of Clostridium difficile in the stool samples of patients with suspected Clostridium difficile Infection: a meta-analysis. Clin Infect Dis. 2011 Oct; 53 (7): e81-90.
87. Eckert C, Jones G, Barbut F. Diagnosis of Clostridium difficile infection: the molecular approach. Future Microbiol. 2013 Dec; 8 (12): 1587-1598.
88. Dubberke ER, Han Z, Bobo L., et al. Impact of clinical symptoms on interpretation of diagnostic assays for Clostridium difficile infections. J Clin Microbiol. 2011 Aug; 49 (8): 2887-2893.
89. Tomas ME, Getman D, Donskey CJ., et al. Overdiagnosis of urinary tract infection and underdiagnosis of sexually transmitted infection in adult women presenting to an emergency department. J Clin Microbiol. 2015 Aug; 53 (8): 2686-2692.
90. Centers for Disease Control and Prevention. Recommendations for the laboratory-based detection of Chlamydia trachomatis and Neisseria gonorrhoeae-2014. MMWR Recomm Rep. 2014 Mar 14; 63 (Rr-02): 1-19.
91. Prevention CfDCa. Trichomoniasis-2015 sexually transmitted diseases treatment guidelines. 2015 [cited 2015 Dec 11]. Available from: http://www.cdc.gov/std/tg2015/trichomoniasis.htm
92. Causer LM, Hengel B, Natoli L., et al. A field evaluation of a new molecular-based point-of-care test for chlamydia and gonorrhoea in remote Aboriginal health services in Australia. Sex Health. 2014 Nov 27. [Epub ahead of print].
93. Gaydos CA. Review of use of a new rapid real-time PCR, the Cepheid GeneXpert(R) (Xpert) CT/NG assay, for Chlamydia trachomatis and Neisseria gonorrhoeae: results for patients while in a clinical setting. Expert Rev Mol Diagn. 2014 Mar; 14 (2): 135-137.
94. Wingrove I, McOwan A, Nwokolo N., et al. Diagnostics within the clinic to test for gonorrhoea and chlamydia reduces the time to treatment: a service evaluation. Sex Transm Infect. England 2014; 90: 474.
95. Chernesky M, Jang D, Gilchrist J., et al. Head-to-head comparison of second-generation nucleic acid amplification tests for detection of Chlamydia trachomatis and Neisseria gonorrhoeae on urine samples from female subjects and self-collected vaginal swabs. J Clin Microbiol. 2014 Jul; 52 (7): 2305-2310.
96. Cheng A, Kirby JE. Evaluation of the Hologic gen-probe PANTHER, APTIMA Combo 2 assay in a tertiary care teaching hospital. Am J Clin Pathol. 2014 Mar; 141 (3): 397-403.
97. Ratnam S, Jang D, Gilchrist J., et al. Workflow and maintenance characteristics of five automated laboratory instruments for the diagnosis of sexually transmitted infections. J Clin Microbiol. 2014 Jul; 52 (7): 2299-2304.
98. Allawi HT, Lyamichev VI. Compositions and methods for analysis of nucleic acid molecules during amplification reactions. Google Patents. 2009.
99. Hill CS. Molecular diagnostic testing for infectious diseases using TMA technology. Expert Rev Mol Diagn. 2001 Nov; 1 (4): 445-455.
100. Jenson A, Dize L, Mkocha H., et al. Field evaluation of the Cepheid GeneXpert Chlamydia trachomatis assay for detection of infection in a trachoma endemic community in Tanzania. PLoS Negl Trop Dis. 2013; 7 (7): e2265.
101. Goldenberg SD, Finn J, Sedudzi E., et al. Performance of the GeneXpert CT/NG assay compared to that of the Aptima AC2 assay for detection of rectal Chlamydia trachomatis and Neisseria gonorrhoeae by use of residual Aptima Samples. J Clin Microbiol. 2012 Dec; 50 (12): 3867-3869.
102. Focus Diagnostics, Inc. Simplexa HSV 1 & 2 direct package. insert. Cypress, CA: Focus Diagnostics, Inc.; 2015.
103. Luminex. ARIES system resources [Internet]. 2015 [cited 2015 Dec 9]. Available from: https://www.luminexcorp.com/clinical/instruments/aries/resources/.