Laboratory diagnosis of respiratory tract infections in children - The state of the art

Frontiers in Microbiology

Volumn 9, Issue OCT, 2018, Pages

  Das, Shubhagata ^a   Dunbar, Sherry ^a   Tang, Yi Wei ^b  

^a LUMINEX CORPORATION   (United States)

^b WEILL CORNELL MEDICAL COLLEGE   (United States)

Author keywords

Pediatric population; Respiratory infection diagnosis molecular diagnostics; Respiratory tract infection; Respiratory virus

Indexed keywords

EID: 85055113712     PISSN: None     EISSN: 1664302X     Source Type: Journal    
DOI: 10.3389/fmicb.2018.02478     Document Type: Review

References (102)

1. Abanses, J. C., Dowd, M. D., Simon, S. D., and Sharma, V. (2006). Impact of rapid influenza testing at triage on management of febrile infants and young children. Pediatr. Emerg. Care 22, 145-149. doi: 10.1097/01.pec.0000202454.19237.b0 PubMed Abstract | CrossRef Full Text | Google Scholar
2. Akers, I. E., Weber, R., Sax, H., Boni, J., Trkola, A., and Kuster, S. P. (2017). Influence of time to diagnosis of severe influenza on antibiotic use, length of stay, isolation precautions, and mortality: a retrospective study. Influenza Other Respir. Viruses 11, 337-344. doi: 10.1111/irv.12454 PubMed Abstract | CrossRef Full Text | Google Scholar
3. Andrews, D., Chetty, Y., Cooper, B. S., Virk, M., Glass, S. K., Letters, A., et al. (2017). Multiplex PCR point of care testing versus routine, laboratory-based testing in the treatment of adults with respiratory tract infections: a quasi-randomised study assessing impact on length of stay and antimicrobial use. BMC Infect. Dis. 17:671. doi: 10.1186/s12879-017-2784-z PubMed Abstract | CrossRef Full Text | Google Scholar
4. Aslanzadeh, J., Zheng, X., Li, H., Tetreault, J., Ratkiewicz, I., Meng, S., et al. (2008). Prospective evaluation of rapid antigen tests for diagnosis of respiratory syncytial virus and human metapneumovirus infections. J. Clin. Microbiol. 46, 1682-1685. doi: 10.1128/jcm.00008-08 PubMed Abstract | CrossRef Full Text | Google Scholar
5. ATS and IDSA (2005). Guidelines for the management of adults with hospital-acquired, ventilator-associated, and healthcare-associated pneumonia. Am. J. Respir. Crit. Care Med. 171, 388-416. doi: 10.1164/rccm.200405-644ST PubMed Abstract | CrossRef Full Text | Google Scholar
6. Azar, M. M., and Landry, M. L. (2018). Detection of influenza A and B viruses and respiratory syncytial virus using CLIA-waived point-of-care assays: a paradigm shift to molecular tests. J. Clin. Microbiol. 56:e00367-18. doi: 10.1128/jcm.00367-18 PubMed Abstract | CrossRef Full Text | Google Scholar
7. Babady, N. E., England, M. R., Jurcic Smith, K. L., He, T., Wijetunge, D. S., Tang, Y. W., et al. (2018). Multicenter evaluation of the ePlex respiratory pathogen panel for the detection of viral and bacterial respiratory tract pathogens in nasopharyngeal swabs. J. Clin. Microbiol. 56, e01658-17. doi: 10.1128/jcm.01658-17 PubMed Abstract | CrossRef Full Text | Google Scholar
8. Barenfanger, J., Drake, C., Leon, N., Mueller, T., and Troutt, T. (2000). Clinical and financial benefits of rapid detection of respiratory viruses: an outcomes study. J. Clin. Microbiol. 38, 2824-2828. PubMed Abstract | Google Scholar
9. Beckmann, C., and Hirsch, H. H. (2016). Comparing luminex NxTAG-respiratory pathogen panel and RespiFinder-22 for multiplex detection of respiratory pathogens. J. Med. Virol. 88, 1319-1324. doi: 10.1002/jmv.24492 PubMed Abstract | CrossRef Full Text | Google Scholar
10. Beersma, M. F., Dirven, K., van Dam, A. P., Templeton, K. E., Claas, E. C., and Goossens, H. (2005). Evaluation of 12 commercial tests and the complement fixation test for Mycoplasma pneumoniae-specific immunoglobulin G (IgG) and IgM antibodies, with PCR used as the "gold standard". J. Clin. Microbiol. 43, 2277-2285. doi: 10.1128/jcm.43.5.2277-2285.2005 PubMed Abstract | CrossRef Full Text | Google Scholar
11. Bell, J., Bonner, A., Cohen, D. M., Birkhahn, R., Yogev, R., Triner, W., et al. (2014). Multicenter clinical evaluation of the novel AlereTM I Influenza A&B isothermal nucleic acid amplification test. J. Clin. Virol. 61, 81-86. doi: 10.1016/j.jcv.2014.06.001 PubMed Abstract | CrossRef Full Text | Google Scholar
12. Blaschke, A. J., Shapiro, D. J., Pavia, A. T., Byington, C. L., Ampofo, K., Stockmann, C., et al. (2014). A national study of the impact of rapid influenza testing on clinical care in the emergency department. J. Pediatr. Infect Dis. Soc. 3, 112-118. doi: 10.1093/jpids/pit071 PubMed Abstract | CrossRef Full Text | Google Scholar
13. Brealey, J. C., Sly, P. D., Young, P. R., and Chappell, K. J. (2015). Viral bacterial co-infection of the respiratory tract during early childhood. FEMS Microbiol. Lett. 362:fnv062. doi: 10.1093/femsle/fnv062 PubMed Abstract | CrossRef Full Text | Google Scholar
14. Brendish, N. J., Malachira, A. K., Armstrong, L., Houghton, R., Aitken, S., Nyimbili, E., et al. (2017). Routine molecular point-of-care testing for respiratory viruses in adults presenting to hospital with acute respiratory illness (ResPOC): a pragmatic, open-label, randomised controlled trial. Lancet Respir. Med. 5, 401-411. doi: 10.1016/S2213-2600(17)30120-0 PubMed Abstract | CrossRef Full Text | Google Scholar
15. Brendish, N. J., Schiff, H. F., and Clark, T. W. (2015). Point-of-care testing for respiratory viruses in adults: the current landscape and future potential. J. Infect. 71, 501-510. doi: 10.1016/j.jinf.2015.07.008 PubMed Abstract | CrossRef Full Text | Google Scholar
16. Brotons, P., Henares, D., Latorre, I., Cepillo, A., Launes, C., and Munoz-Almagro, C. (2016). Comparison of NxTAG respiratory pathogen panel and anyplex II RV16 tests for multiplex detection of respiratory pathogens in hospitalized children. J. Clin. Microbiol. 54, 2900-2904. doi: 10.1128/jcm.01243-16 PubMed Abstract | CrossRef Full Text | Google Scholar
17. Bryce, J., Boschi-Pinto, C., Shibuya, K., and Black, R. E. (2005). WHO estimates of the causes of death in children. Lancet 365, 1147-1152. doi: 10.1016/s0140-6736(05)71877-8 CrossRef Full Text | Google Scholar
18. Bryce, L., Koenig, M., and Jerke, K. H. (2012). A large-scale study of respiratory virus infection over 2 years using the Luminex xTAGRVP assay. Mil. Med. 177, 1533-1538. doi: 10.7205/MILMED-D-12-00277 PubMed Abstract | CrossRef Full Text | Google Scholar
19. Busson, L., Mahadeb, B., De Foor, M., Vandenberg, O., and Hallin, M. (2017). Contribution of a rapid influenza diagnostic test to manage hospitalized patients with suspected influenza. Diagn. Microbiol. Infect. Dis. 87, 238-242. doi: 10.1016/j.diagmicrobio.2016.11.015 PubMed Abstract | CrossRef Full Text | Google Scholar
20. Byington, C. L., Castillo, H., Gerber, K., Daly, J. A., Brimley, L. A., Adams, S., et al. (2002). The effect of rapid respiratory viral diagnostic testing on antibiotic use in a children's hospital. Arch. Pediatr. Adolesc. Med. 156, 1230-1234. doi: 10.1001/archpedi.156.12.1230 CrossRef Full Text | Google Scholar
21. Caliendo, A. M. (2011). Multiplex PCR and emerging technologies for the detection of respiratory pathogens. Clin. Infect. Dis. 52(Suppl. 4), S326-S330. doi: 10.1093/cid/cir047 PubMed Abstract | CrossRef Full Text | Google Scholar
22. Chartrand, C., Tremblay, N., Renaud, C., and Papenburg, J. (2015). Diagnostic accuracy of rapid antigen detection tests for respiratory syncytial virus infection: systematic review and meta-analysis. J. Clin. Microbiol. 53, 3738-3749. doi: 10.1128/jcm.01816-15 PubMed Abstract | CrossRef Full Text | Google Scholar
23. Chkhaidze, I., Manjavidze, N., and Nemsadze, K. (2006). Serodiagnosis of acute respiratory infections in children in Georgia. Indian J. Pediatr. 73, 569-572. doi: 10.1007/BF02759919 CrossRef Full Text | Google Scholar
24. Crawford, J. M., Stallone, R., Zhang, F., Gerolimatos, M., Korologos, D. D., Sweetapple, C., et al. (2010). Laboratory surge response to pandemic (H1N1) 2009 outbreak, New York City metropolitan area, USA. Emerg. Infect. Dis. 16, 8-13. doi: 10.3201/eid1601.091167 PubMed Abstract | CrossRef Full Text | Google Scholar
25. Davis, S., Allen, A. J., O'Leary, R., Power, M., Price, D. A., Simpson, A. J., et al. (2017). Diagnostic accuracy and cost analysis of the AlereTM I Influenza A&B near-patient test using throat swabs. J. Hosp. Infect. 97, 301-309. doi: 10.1016/j.jhin.2017.05.017 PubMed Abstract | CrossRef Full Text | Google Scholar
26. Dilnessa, T., and Zeleke, H. (2017). Cell culture, cytopathic effect and immunofluorescence diagnosis of viral infection. J. Microbiol. Mod. Tech. 2, 102-110. Google Scholar
27. Dugas, A. F., Valsamakis, A., Gaydos, C. A., Forman, M., Hardick, J., Kidambi, P., et al. (2014). Evaluation of the Xpert Flu rapid PCR assay in high-risk emergency department patients. J. Clin. Microbiol. 52, 4353-4355. doi: 10.1128/jcm.02343-14 PubMed Abstract | CrossRef Full Text | Google Scholar
28. Dunn, J. J. (2015). "Specimen collection, transport, and processing: virology, " in Manual of Clinical Microbiology, 11th Edn, eds J. H. Jorgensen, M. A. Pfaller, K. C. Carroll, G. Funke, S. S. Richter, M. L. Landry, et al. (Washington, DC: American Society of Microbiology), 1405-1421. Google Scholar
29. Englund, J. A., Piedra, P. A., Jewell, A., Patel, K., Baxter, B. B., and Whimbey, E. (1996). Rapid diagnosis of respiratory syncytial virus infections in immunocompromised adults. J. Clin. Microbiol. 34, 1649-1653. Google Scholar
30. Falsey, A. R., and Walsh, E. E. (2003). Novel coronavirus and severe acute respiratory syndrome. Lancet 361, 1312-1313. doi: 10.1016/s0140-6736(03)13084-x CrossRef Full Text | Google Scholar
31. FDA (2018a). 510(k) Premarket Notification [Online]. Available at: https://www.accessdata.fda.gov/scripts/cdrh/cfdocs/cfpmn/pmn.cfm [accessed June 24, 2018].
32. FDA (2018b). CLIA Categorizations [Online]. Available at: https://www.fda.gov/MedicalDevices/DeviceRegulationandGuidance/IVDRegulatoryAssistance/ucm393229.htm [accessed June 24, 2018].
33. FDA (2018c). Nucleic Acid Based Tests [Online]. Available at: https://www.fda.gov/MedicalDevices/ProductsandMedicalProcedures/InVitroDiagnostics/ucm330711.htm [accessed June 24, 2018].
34. Feikin, D. R., Njenga, M. K., Bigogo, G., Aura, B., Gikunju, S., Balish, A., et al. (2013). Additional diagnostic yield of adding serology to PCR in diagnosing viral acute respiratory infections in Kenyan patients 5 years of age and older. Clin. Vaccine Immunol. 20, 113-114. doi: 10.1128/cvi.00325-12 PubMed Abstract | CrossRef Full Text | Google Scholar
35. Gharabaghi, F., Hawan, A., Drews, S. J., and Richardson, S. E. (2011). Evaluation of multiple commercial molecular and conventional diagnostic assays for the detection of respiratory viruses in children. Clin. Microbiol. Infect. 17, 1900-1906. doi: 10.1111/j.1469-0691.2011.03529.x PubMed Abstract | CrossRef Full Text | Google Scholar
36. Gibson, J., Schechter-Perkins, E. M., Mitchell, P., Mace, S., Tian, Y., Williams, K., et al. (2017). Multi-center evaluation of the cobas® Liat® Influenza A/B & RSV assay for rapid point of care diagnosis. J. Clin. Virol. 95, 5-9. doi: 10.1016/j.jcv.2017.08.004 PubMed Abstract | CrossRef Full Text | Google Scholar
37. Ginocchio, C. C. (2007). Detection of respiratory viruses using non-molecular based methods. J. Clin. Virol. 40(Suppl. 1), S11-S14. doi: 10.1016/s1386-6532(07)70004-5 CrossRef Full Text | Google Scholar
38. Ginocchio, C. C., Zhang, F., Manji, R., Arora, S., Bornfreund, M., Falk, L., et al. (2009). Evaluation of multiple test methods for the detection of the novel 2009 influenza A (H1N1) during the New York City outbreak. J. Clin. Virol. 45, 191-195. doi: 10.1016/j.jcv.2009.06.005 PubMed Abstract | CrossRef Full Text | Google Scholar
39. Goldsmith, C. S., and Miller, S. E. (2009). Modern uses of electron microscopy for detection of viruses. Clin. Microbiol. Rev. 22, 552-563. doi: 10.1128/cmr.00027-09 PubMed Abstract | CrossRef Full Text | Google Scholar
40. Graf, E. H., Simmon, K. E., Tardif, K. D., Hymas, W., Flygare, S., Eilbeck, K., et al. (2016). Unbiased detection of respiratory viruses using RNA-seq-based metagenomics: a systematic comparison to a commercial PCR panel. J. Clin. Microbiol. 54, 1000-1007. doi: 10.1128/JCM.03060-15 PubMed Abstract | CrossRef Full Text | Google Scholar
41. Gray, G. C., McCarthy, T., Lebeck, M. G., Schnurr, D. P., Russell, K. L., Kajon, A. E., et al. (2007). Genotype prevalence and risk factors for severe clinical adenovirus infection, United States 2004-2006. Clin. Infect. Dis. 45, 1120-1131. doi: 10.1086/522188 PubMed Abstract | CrossRef Full Text | Google Scholar
42. Green, D. A., Hitoaliaj, L., Kotansky, B., Campbell, S. M., and Peaper, D. R. (2016). Clinical utility of on-demand multiplex respiratory pathogen testing among adult outpatients. J. Clin. Microbiol. 54, 2950-2955. doi: 10.1128/jcm.01579-16 PubMed Abstract | CrossRef Full Text | Google Scholar
43. Greninger, A. L., Waghmare, A., Adler, A., Qin, X., Crowley, J. L., Englund, J. A., et al. (2017). Rule-out outbreak: 24-hour metagenomic next-generation sequencing for characterizing respiratory virus source for infection prevention. J. Pediatr. Infect. Dis. Soc. 6, 168-172. doi: 10.1093/jpids/pix019 PubMed Abstract | CrossRef Full Text | Google Scholar
44. Grys, T. E., and Smith, T. F. (2009). "Specimen requirements: selection, collection, transport, and processing, " in Clinical Virology Manual, 4th Edn, eds M. J. Loeffelholz, R. L. Hodinka, S. A. Young, and B. A. Pinsky (Washington, DC: American Society of Microbiology), 18-35. Google Scholar
45. Hall, C. B., Walsh, E. E., Long, C. E., and Schnabel, K. C. (1991). Immunity to and frequency of reinfection with respiratory syncytial virus. J. Infect. Dis. 163, 693-698. doi: 10.1093/infdis/163.4.693 CrossRef Full Text | Google Scholar
46. Hammitt, L. L., Murdoch, D. R., Scott, J. A. G., Driscoll, A., Karron, R. A., Levine, O. S., et al. (2012). Specimen collection for the diagnosis of pediatric pneumonia. Clin. Infect. Dis. 54(Suppl. 2), S132-S139. doi: 10.1093/cid/cir1068 PubMed Abstract | CrossRef Full Text | Google Scholar
47. Harris, A. M., Bramley, A. M., Jain, S., Arnold, S. R., Ampofo, K., Self, W. H., et al. (2017). Influence of antibiotics on the detection of bacteria by culture-based and culture-independent diagnostic tests in patients hospitalized with community-acquired pneumonia. Open Forum Infect. Dis. 4:ofx014. doi: 10.1093/ofid/ofx014 PubMed Abstract | CrossRef Full Text | Google Scholar
48. Hematian, A., Sadeghifard, N., Mohebi, R., Taherikalani, M., Nasrolahi, A., Amraei, M., et al. (2016). Traditional and modern cell culture in virus diagnosis. Osong Public Health Res. Perspect. 7, 77-82. doi: 10.1016/j.phrp.2015.11.011 PubMed Abstract | CrossRef Full Text | Google Scholar
49. Hodinka, R. L. (2013). Point: is the era of viral culture over in the clinical microbiology laboratory? J. Clin. Microbiol. 51, 2-4. doi: 10.1128/jcm.02593-12 PubMed Abstract | CrossRef Full Text | Google Scholar
50. Ieven, M., and Goossens, H. (1997). Relevance of nucleic acid amplification techniques for diagnosis of respiratory tract infections in the clinical laboratory. Clin. Microbiol. Rev. 10, 242-256. Google Scholar
51. Jokela, P., Vuorinen, T., Waris, M., and Manninen, R. (2015). Performance of the Alere I influenza A&B assay and mariPOC test for the rapid detection of influenza A and B viruses. J. Clin. Virol. 70, 72-76. doi: 10.1016/j.jcv.2015.07.294 PubMed Abstract | CrossRef Full Text | Google Scholar
52. Juretschko, S., Mahony, J., Buller, R. S., Manji, R., Dunbar, S., Walker, K., et al. (2017). Multicenter clinical evaluation of the luminex Aries Flu A/B & RSV assay for pediatric and adult respiratory tract specimens. J. Clin. Microbiol. 55, 2431-2438. doi: 10.1128/jcm.00318-17 PubMed Abstract | CrossRef Full Text | Google Scholar
53. Kallander, K., Hildenwall, H., Waiswa, P., Galiwango, E., Peterson, S., and Pariyo, G. (2008). Delayed care seeking for fatal pneumonia in children aged under five years in Uganda: a case-series study. Bull. World Health Organ. 86, 332-338. doi: 10.2471/BLT.07.049353 PubMed Abstract | CrossRef Full Text | Google Scholar
54. Kawai, N., Ikematsu, H., Iwaki, N., Kawashima, T., Maeda, T., Mitsuoka, S., et al. (2007). Longer virus shedding in influenza B than in influenza A among outpatients treated with oseltamivir. J. Infect. 55, 267-272. doi: 10.1016/j.jinf.2007.05.176 PubMed Abstract | CrossRef Full Text | Google Scholar
55. Krunic, N., Merante, F., Yaghoubian, S., Himsworth, D., and Janeczko, R. (2011). Advances in the diagnosis of respiratory tract infections: role of the Luminex xTAG respiratory viral panel. Ann. N. Y. Acad. Sci. 1222, 6-13. doi: 10.1111/j.1749-6632.2011.05964.x PubMed Abstract | CrossRef Full Text | Google Scholar
56. Ksiazek, T. G., Erdman, D., Goldsmith, C. S., Zaki, S. R., Peret, T., Emery, S., et al. (2003). A novel coronavirus associated with severe acute respiratory syndrome. N. Engl. J. Med. 348, 1953-1966. doi: 10.1056/NEJMoa030781 PubMed Abstract | CrossRef Full Text | Google Scholar
57. Kuypers, J., Wright, N., Ferrenberg, J., Huang, M. L., Cent, A., Corey, L., et al. (2006). Comparison of real-time PCR assays with fluorescent-antibody assays for diagnosis of respiratory virus infections in children. J. Clin. Microbiol. 44, 2382-2388. doi: 10.1128/jcm.00216-06 PubMed Abstract | CrossRef Full Text | Google Scholar
58. Landry, M. L., and Ferguson, D. (2000). SimulFluor respiratory screen for rapid detection of multiple respiratory viruses in clinical specimens by immunofluorescence staining. J. Clin. Microbiol. 38, 708-711. PubMed Abstract | Google Scholar
59. LaSala, P. R., Bufton, K. K., Ismail, N., and Smith, M. B. (2007). Prospective comparison of R-mixTM shell vial system with direct antigen tests and conventional cell culture for respiratory virus detection. J. Clin. Virol. 38, 210-216. doi: 10.1016/j.jcv.2006.12.015 PubMed Abstract | CrossRef Full Text | Google Scholar
60. Leland, D. S., and Ginocchio, C. C. (2007). Role of cell culture for virus detection in the age of technology. Clin. Microbiol. Rev. 20, 49-78. doi: 10.1128/cmr.00002-06 PubMed Abstract | CrossRef Full Text | Google Scholar
61. Lin, B., Vora, G. J., Thach, D., Walter, E., Metzgar, D., Tibbetts, C., et al. (2004). Use of oligonucleotide microarrays for rapid detection and serotyping of acute respiratory disease-associated adenoviruses. J. Clin. Microbiol. 42, 3232-3239. doi: 10.1128/jcm.42.7.3232-3239.2004 PubMed Abstract | CrossRef Full Text | Google Scholar
62. Ling, L., Kaplan, S. E., Lopez, J. C., Stiles, J., Lu, X., and Tang, Y. W. (2018). Parallel validation of three molecular devices for simultaneous detection and identification of influenza A and B and respiratory syncytial viruses. J. Clin. Microbiol. 56:e01691-17. doi: 10.1128/jcm.01691-17 PubMed Abstract | CrossRef Full Text | Google Scholar
63. Loeffelholz, M., and Chonmaitree, T. (2010). Advances in diagnosis of respiratory virus infections. Int. J. Microbiol. 2010:126049. doi: 10.1155/2010/126049 PubMed Abstract | CrossRef Full Text | Google Scholar
64. Mahony, J. B. (2008). Detection of respiratory viruses by molecular methods. Clin. Microbiol. Rev. 21, 716-747. doi: 10.1128/cmr.00037-07 PubMed Abstract | CrossRef Full Text | Google Scholar
65. Mahony, J. B., Petrich, A., and Smieja, M. (2011). Molecular diagnosis of respiratory virus infections. Crit. Rev. Clin. Lab. Sci. 48, 217-249. doi: 10.3109/10408363.2011.640976 PubMed Abstract | CrossRef Full Text | Google Scholar
66. Landry, M. L., and Ferguson, D. (2000). SimulFluor respiratory screen for rapid detection of multiple respiratory viruses in clinical specimens by immunofluorescence staining. J. Clin. Microbiol. 38, 708-711. PubMed Abstract | Google Scholar
67. LaSala, P. R., Bufton, K. K., Ismail, N., and Smith, M. B. (2007). Prospective comparison of R-mixTM shell vial system with direct antigen tests and conventional cell culture for respiratory virus detection. J. Clin. Virol. 38, 210-216. doi: 10.1016/j.jcv.2006.12.015 PubMed Abstract | CrossRef Full Text | Google Scholar
68. Leland, D. S., and Ginocchio, C. C. (2007). Role of cell culture for virus detection in the age of technology. Clin. Microbiol. Rev. 20, 49-78. doi: 10.1128/cmr.00002-06 PubMed Abstract | CrossRef Full Text | Google Scholar
69. Lin, B., Vora, G. J., Thach, D., Walter, E., Metzgar, D., Tibbetts, C., et al. (2004). Use of oligonucleotide microarrays for rapid detection and serotyping of acute respiratory disease-associated adenoviruses. J. Clin. Microbiol. 42, 3232-3239. doi: 10.1128/jcm.42.7.3232-3239.2004 PubMed Abstract | CrossRef Full Text | Google Scholar
70. Ling, L., Kaplan, S. E., Lopez, J. C., Stiles, J., Lu, X., and Tang, Y. W. (2018). Parallel validation of three molecular devices for simultaneous detection and identification of influenza A and B and respiratory syncytial viruses. J. Clin. Microbiol. 56:e01691-17. doi: 10.1128/jcm.01691-17 PubMed Abstract | CrossRef Full Text | Google Scholar
71. Loeffelholz, M., and Chonmaitree, T. (2010). Advances in diagnosis of respiratory virus infections. Int. J. Microbiol. 2010:126049. doi: 10.1155/2010/126049 PubMed Abstract | CrossRef Full Text | Google Scholar
72. Mahony, J. B. (2008). Detection of respiratory viruses by molecular methods. Clin. Microbiol. Rev. 21, 716-747. doi: 10.1128/cmr.00037-07 PubMed Abstract | CrossRef Full Text | Google Scholar
73. Mahony, J. B., Petrich, A., and Smieja, M. (2011). Molecular diagnosis of respiratory virus infections. Crit. Rev. Clin. Lab. Sci. 48, 217-249. doi: 10.3109/10408363.2011.640976 PubMed Abstract | CrossRef Full Text | Google Scholar
74. McMullen, P., Boonlayangoor, S., Charnot-Katsikas, A., Beavis, K. G., and Tesic, V. (2017). The performance of Luminex ARIES® Flu A/B & RSV and Cepheid Xpert® Flu/RSV XC for the detection of influenza A, influenza B, and respiratory syncytial virus in prospective patient samples. J. Clin. Virol. 95, 84-85. doi: 10.1016/j.jcv.2017.08.018 PubMed Abstract | CrossRef Full Text | Google Scholar
75. Nie, S., Roth, R. B., Stiles, J., Mikhlina, A., Lu, X., Tang, Y. W., et al. (2014). Evaluation of Alere I influenza A&B for rapid detection of influenza viruses A and B. J. Clin. Microbiol. 52, 3339-3344. doi: 10.1128/jcm.01132-14 PubMed Abstract | CrossRef Full Text | Google Scholar
76. Ohm-Smith, M. J., Nassos, P. S., and Haller, B. L. (2004). Evaluation of the Binax NOW, BD Directigen, and BD Directigen EZ assays for detection of respiratory syncytial virus. J. Clin. Microbiol. 42, 2996-2999. doi: 10.1128/jcm.42.7.2996-2999.2004 PubMed Abstract | CrossRef Full Text | Google Scholar
77. Olsen, M. A., Shuck, K. M., Sambol, A. R., Flor, S. M., O'Brien, J., and Cabrera, B. J. (1993). Isolation of seven respiratory viruses in shell vials: a practical and highly sensitive method. J. Clin. Microbiol. 31, 422-425. PubMed Abstract | Google Scholar
78. Peters, R. M., Schnee, S. V., Tabatabai, J., Schnitzler, P., and Pfeil, J. (2017). Evaluation of Alere I RSV for rapid detection of respiratory syncytial virus in children hospitalized with acute respiratory tract infection. J. Clin. Microbiol. 55, 1032-1036. doi: 10.1128/jcm.02433-16 PubMed Abstract | CrossRef Full Text | Google Scholar
79. Popowitch, E. B., and Miller, M. B. (2015). Performance characteristics of Xpert Flu/RSV XC assay. J. Clin. Microbiol. 53, 2720-2721. doi: 10.1128/jcm.00972-15 PubMed Abstract | CrossRef Full Text | Google Scholar
80. Popowitch, E. B., O'Neill, S. S., and Miller, M. B. (2013). Comparison of the Biofire FilmArray RP, Genmark eSensor RVP, Luminex xTAG RVPv1, and Luminex xTAG RVP fast multiplex assays for detection of respiratory viruses. J. Clin. Microbiol. 51, 1528-1533. doi: 10.1128/jcm.03368-12 PubMed Abstract | CrossRef Full Text | Google Scholar
81. Poritz, M. A., Blaschke, A. J., Byington, C. L., Meyers, L., Nilsson, K., Jones, D. E., et al. (2011). FilmArray, an automated nested multiplex PCR system for multi-pathogen detection: development and application to respiratory tract infection. PLoS One 6:e26047. doi: 10.1371/journal.pone.0026047 PubMed Abstract | CrossRef Full Text | Google Scholar
82. Ramanan, P., Bryson, A. L., Binnicker, M. J., Pritt, B. S., and Patel, R. (2018). Syndromic panel-based testing in clinical microbiology. Clin. Microbiol. Rev. 31:e00024-17. doi: 10.1128/cmr.00024-17 PubMed Abstract | CrossRef Full Text | Google Scholar
83. Reijans, M., Dingemans, G., Klaassen, C. H., Meis, J. F., Keijdener, J., Mulders, B., et al. (2008). RespiFinder: a new multiparameter test to differentially identify fifteen respiratory viruses. J. Clin. Microbiol. 46, 1232-1240. doi: 10.1128/jcm.02294-07 PubMed Abstract | CrossRef Full Text | Google Scholar
84. Rocholl, C., Gerber, K., Daly, J., Pavia, A. T., and Byington, C. L. (2004). Adenoviral infections in children: the impact of rapid diagnosis. Pediatrics 113(1 Pt 1), e51-e56. Google Scholar
85. Rogers, B. B., Shankar, P., Jerris, R. C., Kotzbauer, D., Anderson, E. J., Watson, J. R., et al. (2015). Impact of a rapid respiratory panel test on patient outcomes. Arch. Pathol. Lab. Med. 139, 636-641. doi: 10.5858/arpa.2014-0257-OA PubMed Abstract | CrossRef Full Text | Google Scholar
86. Roingeard, P. (2008). Viral detection by electron microscopy: past, present and future. Biol. Cell 100, 491-501. doi: 10.1042/bc20070173 PubMed Abstract | CrossRef Full Text | Google Scholar
87. Sails, A. D., Eltringham, G., Valappil, M., Waugh, S., and Saunders, D. (2017). Comparison of the Luminex NxTAG respiratory pathogen panel and a multiplex in-house real-time PCR panel for the detection of respiratory viruses in symptomatic patients. J. Med. Microbiol. doi: 10.1099/jmm.0.000562 [Epub ahead of print]. PubMed Abstract | CrossRef Full Text | Google Scholar
88. Sawatwong, P., Chittaganpitch, M., Hall, H., Peruski, L. F., Xu, X., Baggett, H. C., et al. (2012). Serology as an adjunct to polymerase chain reaction assays for surveillance of acute respiratory virus infections. Clin. Infect. Dis. 54, 445-446. doi: 10.1093/cid/cir710 PubMed Abstract | CrossRef Full Text | Google Scholar
89. Schreckenberger, P. C., and McAdam, A. J. (2015). Point-counterpoint: large multiplex PCR panels should be first-line tests for detection of respiratory and intestinal pathogens. J. Clin. Microbiol. 53, 3110-3115. doi: 10.1128/jcm.00382-15 PubMed Abstract | CrossRef Full Text | Google Scholar
90. Selvaraju, S. B., Bambach, A. V., Leber, A. L., Patru, M.-M., Patel, A., and Menegus, M. A. (2014). Comparison of the SimplexaTM Flu A/B & RSV kit (nucleic acid extraction-dependent assay) and the Prodesse ProFlu + TM assay for detecting influenza and respiratory syncytial viruses. Diagn. Microbiol. Infect. Dis. 80, 50-52. doi: 10.1016/j.diagmicrobio.2013.11.015 PubMed Abstract | CrossRef Full Text | Google Scholar
91. Shafik, C. F., Mohareb, E. W., and Youssef, F. G. (2011). Comparison of direct fluorescence assay and real-time rt-PCR as diagnostics for respiratory syncytial virus in young children. J. Trop. Med. 2011:781919. doi: 10.1155/2011/781919 PubMed Abstract | CrossRef Full Text | Google Scholar
92. Slinger, R., Milk, R., Gaboury, I., and Diaz-Mitoma, F. (2004). Evaluation of the QuickLab RSV test, a new rapid lateral-flow immunoassay for detection of respiratory syncytial virus antigen. J. Clin. Microbiol. 42, 3731-3733. doi: 10.1128/jcm.42.8.3731-3733.2004 PubMed Abstract | CrossRef Full Text | Google Scholar
93. Tang, Y. W., Gonsalves, S., Sun, J. Y., Stiles, J., Gilhuley, K. A., Mikhlina, A., et al. (2016). Clinical evaluation of the Luminex NxTAG respiratory pathogen panel. J. Clin. Microbiol. 54, 1912-1914. doi: 10.1128/jcm.00482-16 PubMed Abstract | CrossRef Full Text | Google Scholar
94. Tenover, F. C. (2011). Developing molecular amplification methods for rapid diagnosis of respiratory tract infections caused by bacterial pathogens. Clin. Infect. Dis. 52(Suppl. 4), S338-S345. doi: 10.1093/cid/cir049 PubMed Abstract | CrossRef Full Text | Google Scholar
95. Vinh, D. C., Newby, D., Charest, H., and McDonald, J. (2008). Evaluation of a commercial direct fluorescent-antibody assay for human metapneumovirus in respiratory specimens. J. Clin. Microbiol. 46, 1840-1841. doi: 10.1128/jcm.01554-07 PubMed Abstract | CrossRef Full Text | Google Scholar
96. Weinberg, A., and Walker, M. L. (2005). Evaluation of three immunoassay kits for rapid detection of influenza virus A and B. Clin. Diagn. Lab. Immunol. 12, 367-370. doi: 10.1128/cdli.12.3.367-370.2005 PubMed Abstract | CrossRef Full Text | Google Scholar
97. Wellinghausen, N., Straube, E., Freidank, H., von Baum, H., Marre, R., and Essig, A. (2006). Low prevalence of Chlamydia pneumoniae in adults with community-acquired pneumonia. Int. J. Med. Microbiol. 296, 485-491. doi: 10.1016/j.ijmm.2006.05.003 PubMed Abstract | CrossRef Full Text | Google Scholar
98. WHO (2005). WHO Recommendations on the use of Rapid Testing for Influenza Diagnosis [Online]. Available at: http://www.who.int/influenza/resources/documents/RapidTestInfluenza-WebVersion.pdf [accessed June 24, 2018].
99. Winn, W. C., and Koneman, E. W. (2006). Koneman's Color Atlas and Textbook of Diagnostic Microbiology. Philadelphia, PA: Lippincott Williams & Wilkins. Google Scholar
100. Woodhead, M., Blasi, F., Ewig, S., Huchon, G., Ieven, M., Ortqvist, A., et al. (2005). Guidelines for the management of adult lower respiratory tract infections. Eur. Respir. J. 26, 1138-1180. doi: 10.1183/09031936.05.00055705 PubMed Abstract | CrossRef Full Text | Google Scholar
101. Zhang, Y., Hung, T., Song, J., and He, J. (2013). Electron microscopy: essentials for viral structure, morphogenesis and rapid diagnosis. Sci. China Life Sci. 56, 421-430. doi: 10.1007/s11427-013-4476-2 PubMed Abstract | CrossRef Full Text | Google Scholar
102. Zhang, Y., Sakthivel, S. K., Bramley, A., Jain, S., Haynes, A., Chappell, J. D., et al. (2017). Serology enhances molecular diagnosis of respiratory virus infections other than influenza in children and adults hospitalized with community-acquired pneumonia. J. Clin. Microbiol. 55, 79-89. doi: 10.1128/jcm.01701-16 PubMed Abstract | CrossRef Full Text | Google Scholar