Prospects for molecular point-of-care diagnosis of lower respiratory infections at the hospital's doorstep

Future Virology

Volumn 8, Issue 1, 2013, Pages 43-56

  Cohen Bacrie, Stéphan ^a   Halfon, Philippe ^a  

^a Laboratoire Alphabio   (France)

Author keywords

adults; bronchiolitis; children; emergency; molecular; PCR; pneumonia; point of care; respiratory; virus

Indexed keywords

ANTIINFECTIVE AGENT;

ADULT; BRONCHIOLITIS; COMMUNITY ACQUIRED ACUTE BRONCHIOLITIS; COMMUNITY ACQUIRED PNEUMONIA; DISEASE SEVERITY; HOSPITAL CARE; HUMAN; INFLUENZA; LOWER RESPIRATORY TRACT INFECTION; MAJOR CLINICAL STUDY; MICROBIOLOGICAL EXAMINATION; MOLECULAR DIAGNOSIS; MORBIDITY; MORTALITY; NONHUMAN; POINT OF CARE TESTING; PRIORITY JOURNAL; RESPIRATORY VIRUS; REVIEW;

EID: 84871543741     PISSN: 17460794     EISSN: 17460808     Source Type: Journal    
DOI: 10.2217/fvl.12.124     Document Type: Review

References (90)

1. Willsher K. France's next president faces tough decisions on health. Lancet 379(9825), 1473-1474 (2012).
2. Fuchs VR, Schaeffer LD. If accountable care organizations are the answer, who should create them? JAMA 307(21), 2261-2262 (2012).
3. Porter ME. What is value in health care? N. Engl. J. Med. 363(26), 2477-2481 (2010).
4. Kocher R, Sahni NR. Physicians versus hospitals as leaders of accountable care organizations. N. Engl. J. Med. 363(27), 2579-2582 (2010).
5. Jartti T, Jartti L, Ruuskanen O, Soderlund- Venermo M. New respiratory viral infections. Curr. Opin. Pulm. Med. 18(3), 271-278 (2012).
6. Huguenin A, Moutte L, Renois F et al. Broad respiratory virus detection in infants hospitalized for bronchiolitis by use of a multiplex RT-PCR DNA microarray system. J. Med. Virol. 84(6), 979-985 (2012).
7. Mills JM, Harper J, Broomfield D, Templeton KE. Rapid testing for respiratory syncytial virus in a paediatric emergency department: Benefits for infection control and bed management. J. Hosp. Infect. 77(3), 248-251 (2011).
8. Nougairede A, Ninove L, Zandotti C et al. Point of care strategy for rapid diagnosis of novel A/H1N1 influenza virus. PLoS One 5(2), e9215 (2010).
9. 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. 18(4), E81-E83 (2012).
10. Pierce VM, Elkan M, Leet M, McGowan KL, Hodinka RL. Comparison of the Idaho Technology FilmArray system to real-time PCR for detection of respiratory pathogens in children. J. Clin. Microbiol. 50(2), 364-371 (2012).
11. Cohen-Bacrie S, Ninove L, Nougairede A et al. Revolutionizing clinical microbiology laboratory organization in hospitals with in situ point-of-care. PLoS One 6(7), e22403 (2011).
12. Agence Nationale d'Acréditation et d'Evaluation en Santé et URML-Union Régionale des Médecins Libéraux d'Ile de France. [Care of bronchiolitis in infants. September 21 2000, Salle Louis Armand, Cite des Sciences et de l'Industrie del la Villette, Paris. A.N.A.E.S. National Agency of Accreditation and Evaluation of Health and URMLYRegional Union of Independent Physicians of the Ile de France]. Therapie 56(2), 175-185 (2001).
13. WHO. Cough or difficult breathing. In: Pocket Book of Hospital Care for Children. Guidelines for the Management of Common Illnessess With Limited Resources. WHO Press, Switzerland, 69-108 (2005).
14. American Academy of Pediatrics Subcommittee on Diagnosis and Management of Bronchiolitis. Diagnosis and management of bronchiolitis. Pediatrics 118(4), 1774-1793 (2006).
15. Harris M, Clark J, Coote N et al. British Thoracic Society guidelines for the management of community acquired pneumonia in children: Update 2011. Thorax 66(Suppl. 2), ii1-ii23 (2011).
16. Lim WS, Baudouin SV, George RC et al. BTS guidelines for the management of community acquired pneumonia in adults: Update 2009. Thorax 64(Suppl. 3), iii1-iii55 (2009).
17. Neumaier M, Braun A, Wagener C. Fundamentals of quality assessment of molecular amplification methods in clinical diagnostics. International Federation of Clinical Chemistry Scientific Division Committee on Molecular Biology Techniques. Clin. Chem. 44(1), 12-26 (1998).
18. Richard N, Komurian-Pradel F, Javouhey E et al. The impact of dual viral infection in infants admitted to a pediatric intensive care unit associated with severe bronchiolitis. Pediatr. Infect. Dis. J. 27(3), 213-217 (2008).
19. Miron D, Srugo I, Kra-Oz Z et al. Sole pathogen in acute bronchiolitis: Is there a role for other organisms apart from respiratory syncytial virus? Pediatr. Infect. Dis. J. 29(1), e7-e10 (2010).
20. Frobert E, Escuret V, Javouhey E et al. Respiratory viruses in children admitted to hospital intensive care units: Evaluating the CLART(R) Pneumovir DNA array. J. Med. Virol. 83(1), 150-155 (2011).
21. Stempel HE, Martin ET, Kuypers J, Englund JA, Zerr DM. Multiple viral respiratory pathogens in children with bronchiolitis. Acta Paediatr. 98(1), 123-126 (2009).
22. Brand HK, De Groot R, Galama JM et al. Infection with multiple viruses is not associated with increased disease severity in children with bronchiolitis. Pediatr. Pulmonol. 47(4), 393-400 (2012).
23. Papoff P, Moretti C, Cangiano G et al. Incidence and predisposing factors for severe disease in previously healthy term infants experiencing their first episode of bronchiolitis. Acta Paediatr. 100(7), e17-e23 (2011).
24. Semple MG, Cowell A, Dove W et al. Dual infection of infants by human metapneumovirus and human respiratory syncytial virus is strongly associated with severe bronchiolitis. J. Infect. Dis. 191(3), 382-386 (2005).
25. Mermond S, Zurawski V, D'ortenzio E et al. Lower respiratory infections among hospitalized children in New Caledonia: A pilot study for the Pneumonia Etiology Research for Child Health project. Clin. Infect. Dis. 54(Suppl. 2), S180-S189 (2012).
26. Xepapadaki P, Psarras S, Bossios A et al. Human metapneumovirus as a causative agent of acute bronchiolitis in infants. J. Clin. Virol. 30(3), 267-270 (2004).
27. Marguet C, Lubrano M, Gueudin M et al. In very young infants severity of acute bronchiolitis depends on carried viruses. PLoS One 4(2), e4596 (2009).
28. Helminen M, Nuolivirta K, Virta M et al. IL-10 gene polymorphism at -1082 A/G is associated with severe rhinovirus bronchiolitis in infants. Pediatr. Pulmonol. 43(4), 391-395 (2008).
29. Bouscambert-Duchamp M, Lina B, Trompette A, Moret H, Motte J, Andreoletti L. Detection of human metapneumovirus RNA sequences in nasopharyngeal aspirates of young French children with acute bronchiolitis by real-time reverse transcriptase PCR and phylogenetic analysis. J. Clin. Microbiol. 43(3), 1411-1414 (2005).
30. Honkinen M, Lahti E, Osterback R, Ruuskanen O, Waris M. Viruses and bacteria in sputum samples of children with community-acquired pneumonia. Clin. Microbiol. Infect. 18(3), 300-307 (2012).
31. Cevey-Macherel M, Galetto-Lacour A, Gervaix A et al. Etiology of community-acquired pneumonia in hospitalized children based on WHO clinical guidelines. Eur. J. Pediatr. 168(12), 1429-1436 (2009).
32. Wolf DG, Greenberg D, Shemer-Avni Y, Givon-Lavi N, Bar-Ziv J, Dagan R. Association of human metapneumovirus with radiologically diagnosed community-acquired alveolar pneumonia in young children. J. Pediatr. 156(1), 115-120 (2010).
33. Xiang Z, Gonzalez R, Xie Z et al. Human rhinovirus C infections mirror those of human rhinovirus A in children with community-acquired pneumonia. J. Clin. Virol. 49(2), 94-99 (2010).
34. Werno AM, Anderson TP, Jennings LC, Jackson PM, Murdoch DR. Human metapneumovirus in children with bronchiolitis or pneumonia in New Zealand. J. Paediatr. Child Health 40(9-10), 549-551 (2004).
35. Tsolia MN, Psarras S, Bossios A et al. Etiology of community-acquired pneumonia in hospitalized school-age children: Evidence for high prevalence of viral infections. Clin. Infect. Dis. 39(5), 681-686 (2004).
36. Juven T, Mertsola J, Waris M et al. Etiology of community-acquired pneumonia in 254 hospitalized children. Pediatr. Infect. Dis. J. 19(4), 293-298 (2000).
37. Franz A, Adams O, Willems R et al. Correlation of viral load of respiratory pathogens and co-infections with disease severity in children hospitalized for lower respiratory tract infection. J. Clin. Virol. 48(4), 239-245 (2010).
38. Johnstone J, Majumdar SR, Fox JD, Marrie TJ. Viral infection in adults hospitalized with community-acquired pneumonia: Prevalence, pathogens, and presentation. Chest 134(6), 1141-1148 (2008).
39. Mermond S, Berlioz-Arthaud A, Estivals M, Baumann F, Levenes H, Martin PM. Aetiology of community-acquired pneumonia in hospitalized adult patients in New Caledonia. Trop. Med. Int. Health 15(12), 1517-1524 (2010).
40. Johansson N, Kalin M, Tiveljung-Lindell A, Giske CG, Hedlund J. Etiology of community-acquired pneumonia: Increased microbiological yield with new diagnostic methods. Clin. Infect. Dis. 50(2), 202-209 (2010).
41. Lieberman D, Shimoni A, Shemer-Avni Y, Keren-Naos A, Shtainberg R. Respiratory viruses in adults with community-acquired pneumonia. Chest 138(4), 811-816 (2010).
42. Templeton KE, Scheltinga SA, Van Den Eeden WC, Graffelman AW, Van Den Broek PJ, Claas EC. Improved diagnosis of the etiology of community-acquired pneumonia with real-time polymerase chain reaction. Clin. Infect. Dis. 41(3), 345-351 (2005).
43. Jennings LC, Anderson TP, Beynon KA et al. Incidence and characteristics of viral community-acquired pneumonia in adults. Thorax 63(1), 42-48 (2008).
44. Diederen BM, Van Der Eerden MM, Vlaspolder F, Boersma WG, Kluytmans JA, Peeters MF. Detection of respiratory viruses and Legionella spp. by real-time polymerase chain reaction in patients with community acquired pneumonia. Scand. J. Infect. Dis. 41(1), 45-50 (2009).
45. Hohenthal U, Vainionpaa R, Nikoskelainen J, Kotilainen P. The role of rhinoviruses and enteroviruses in community acquired pneumonia in adults. Thorax 63(7), 658-659 (2008).
46. Grimprel E. [Epidemiology of infant bronchiolitis in France]. Arch. Pediatr. 8(Suppl. 1), 83SY92S (2001).
47. Che D, Nicolau J, Bergounioux J, Perez T, Bitar D. Bronchiolitis among infants under 1 year of age in France: Epidemiology and factors associated with mortality. Arch. Pediatr. 19(7), 700-706 (2012).
48. Clark JE, Hammal D, Hampton F, Spencer D, Parker L. Epidemiology of community-acquired pneumonia in children seen in hospital. Epidemiol. Infect. 135(2), 262-269 (2007).
49. Klapdor B, Ewig S, Pletz MW et al. Community-acquired pneumonia in younger patients is an entity on its own. Eur. Respir. J. 39(5), 1156-1161 (2012).
50. Fitzwater SP, Chandran A, Santosham M, Johnson HL. The worldwide impact of the seven-valent pneumococcal conjugate vaccine. Pediatr. Infect. Dis. J. 31(5), 501-508 (2012).
51. Lee GE, Lorch SA, Sheffler-Collins S, Kronman MP, Shah SS. National hospitalization trends for pediatric pneumonia and associated complications. Pediatrics 126(2), 204-213 (2010).
52. Miller E, Andrews NJ, Waight PA, Slack MP, George RC. Herd immunity and serotype replacement 4 years after seven-valent pneumococcal conjugate vaccination in England and Wales: An observational cohort study. Lancet Infect. Dis. 11(10), 760-768 (2011).
53. Smith KJ, Wateska AR, Nowalk MP, Raymund M, Nuorti JP, Zimmerman RK. Cost-effectiveness of adult vaccination strategies using pneumococcal conjugate vaccine compared with pneumococcal polysaccharide vaccine. JAMA 307(8), 804-812 (2012).
54. Hall CB, Weinberg GA, Iwane MK et al. The burden of respiratory syncytial virus infection in young children. N. Engl. J. Med. 360(6), 588-598 (2009).
55. Madge P, Paton JY, Mccoll JH, Mackie PL. Prospective controlled study of four infection-control procedures to prevent nosocomial infection with respiratory syncytial virus. Lancet 340(8827), 1079-1083 (1992).
56. Dizdar EA, Aydemir C, Erdeve O et al. Respiratory syncytial virus outbreak defined by rapid screening in a neonatal intensive care unit. J. Hosp. Infect. 75(4), 292-294 (2010).
57. Halasa NB, Williams JV, Wilson GJ, Walsh WF, Schaffner W, Wright PF. Medical and economic impact of a respiratory syncytial virus outbreak in a neonatal intensive care unit. Pediatr. Infect. Dis. J. 24(12), 1040-1044 (2005).
58. Hall CB. Nosocomial respiratory syncytial virus infections: The 'Cold War' has not ended. Clin. Infect. Dis. 31(2), 590-596 (2000).
59. Enstone JE, Myles PR, Openshaw PJ et al. Nosocomial pandemic (H1N1) 2009, United Kingdom, 2009-2010. Emerg. Infect. Dis. 17(4), 592-598 (2011).
60. Maltezou HC, Drancourt M. Nosocomial influenza in children. J. Hosp. Infect. 55(2), 83-91 (2003).
61. Poehling KA, Edwards KM, Weinberg GA et al. The underrecognized burden of influenza in young children. N. Engl. J. Med. 355(1), 31-40 (2006).
62. Influenza-associated pediatric deaths Y United States, September 2010-August 2011. MMWR Morb. Mortal. Wkly Rep. 60(36), 1233-1238 (2011).
63. Weinberger DM, Simonsen L, Jordan R, Steiner C, Miller M, Viboud C. Impact of the 2009 influenza pandemic on pneumococcal pneumonia hospitalizations in the United States. J. Infect. Dis. 205(3), 458-465 (2012).
64. Finelli L, Fiore A, Dhara R et al. Influenza-associated pediatric mortality in the United States: Increase of Staphylococcus aureus coinfection. Pediatrics 122(4), 805-811 (2008).
65. Scaber J, Saeed S, Ihekweazu C, Efstratiou A, McCarthy N, O'Moore E. Group A streptococcal infections during the seasonal influenza outbreak 2010/11 in South East England. Euro Surveill. 16(5), 19780 (2011).
66. Palacios G, Hornig M, Cisterna D et al. Streptococcus pneumoniae coinfection is correlated with the severity of H1N1 pandemic influenza. PLoS One 4(12), e8540 (2009).
67. Severe coinfection with seasonal influenza A (H3N2) virus and Staphylococcus aureus Y Maryland, FebruaryYMarch 2012. MMWR Morb. Mortal. Wkly Rep. 61(16), 289-291 (2012).
68. Fiore AE, Fry A, Shay D, Gubareva L, Bresee JS, Uyeki TM. Antiviral agents for the treatment and chemoprophylaxis of influenza Y recommendations of the Advisory Committee on Immunization Practices (ACIP). MMWR Recomm. Rep. 60(1), 1-24 (2011).
69. Thorlund K, Awad T, Boivin G, Thabane L. Systematic review of influenza resistance to the neuraminidase inhibitors. BMC Infect. Dis. 11, 134 (2011).
70. Hernan MA, Lipsitch M. Oseltamivir and risk of lower respiratory tract complications in patients with flu symptoms: A meta-analysis of eleven randomized clinical trials. Clin. Infect. Dis. 53(3), 277-279 (2011).
71. Cochrane Neuraminidase Inhibitors Review Team. Does oseltamivir really reduce complications of influenza? Clin. Infect. Dis. 53(12), 1302-1303; author reply 1303-1304 (2011).
72. Wang K, Shun-Shin M, Gill P, Perera R, Harnden A. Neuraminidase inhibitors for preventing and treating influenza in children. Cochrane Database Syst. Rev. (3), CD002744 (2012).
73. Viasus D, Pano-Pardo JR, Pachon J et al. Pneumonia complicating pandemic (H1N1) 2009: Risk factors, clinical features, and outcomes. Medicine (Baltimore) 90(5), 328-336 (2011).
74. Bowles SK, Lee W, Simor AE et al. Use of oseltamivir during influenza outbreaks in Ontario nursing homes, 1999-2000. J. Am. Geriatr. Soc. 50(4), 608-616 (2002).
75. Gagneur A, Vallet S, Talbot PJ et al. Outbreaks of human coronavirus in a pediatric and neonatal intensive care unit. Eur. J. Pediatr. 167(12), 1427-1434 (2008).
76. Lynch T, Bialy L, Kellner JD et al. A systematic review on the diagnosis of pediatric bacterial pneumonia: When gold is bronze. PLoS One 5(8), e11989 (2010).
77. Hazir T, Nisar YB, Abbasi S et al. Comparison of oral amoxicillin with placebo for the treatment of world health organization-defined nonsevere pneumonia in children aged 2-59 months: A multicenter, double-blind, randomized, placebo-controlled trial in pakistan. Clin. Infect. Dis. 52(3), 293-300 (2011).
78. Esposito S, Tagliabue C, Picciolli I et al. Procalcitonin measurements for guiding antibiotic treatment in pediatric pneumonia. Respir. Med. 105(12), 1939-1945 (2011).
79. Schuetz P, Christ-Crain M, Thomann R et al. Effect of procalcitonin-based guidelines vs standard guidelines on antibiotic use in lower respiratory tract infections: The ProHOSP randomized controlled trial. JAMA 302(10), 1059-1066 (2009).
80. Che D, Caillere N, Josseran L. [Surveillance and epidemiology of infant bronchiolitis in France]. Arch. Pediatr. 15(3), 327-328 (2008).
81. Mansbach JM, Clark S, Christopher NC et al. Prospective multicenter study of bronchiolitis: Predicting safe discharges from the emergency department. Pediatrics 121(4), 680-688 (2008).
82. Garcia CG, Bhore R, Soriano-Fallas A et al. Risk factors in children hospitalized with RSV bronchiolitis versus non-RSV bronchiolitis. Pediatrics 126(6), e1453-e1460 (2010).
83. Holman RC, Shay DK, Curns AT, Lingappa JR, Anderson LJ. Risk factors for bronchiolitis-associated deaths among infants in the United States. Pediatr. Infect. Dis. J. 22(6), 483-490 (2003).
84. Panickar JR, Dodd SR, Smyth RL, Couriel JM. Trends in deaths from respiratory illness in children in England and Wales from 1968 to 2000. Thorax 60(12), 1035-1038 (2005).
85. Moineddin R, Nie JX, Domb G, Leong AM, Upshur RE. Seasonality of primary care utilization for respiratory diseases in Ontario: A time-series analysis. BMC Health Serv. Res. 8, 160 (2008).
86. Kronman MP, Hersh AL, Feng R, Huang YS, Lee GE, Shah SS. Ambulatory visit rates and antibiotic prescribing for children with pneumonia, 1994-2007. Pediatrics 127(3), 411-418 (2011).
87. Black RE, Cousens S, Johnson HL et al. Global, regional, and national causes of child mortality in 2008: A systematic analysis. Lancet 375(9730), 1969-1987 (2010).
88. Ochoa-Gondar O, Vila-Corcoles A, De Diego C et al. The burden of community-acquired pneumonia in the elderly: The Spanish EVAN 65 study. BMC Public Health 8, 222 (2008).
89. Trotter CL, Stuart JM, George R, Miller E. Increasing hospital admissions for pneumonia, England. Emerg. Infect. Dis. 14(5), 727-733 (2008).
90. Ewig S, Klapdor B, Pletz MW et al. Nursing-home-acquired pneumonia in Germany: An 8-year prospective multicentre study. Thorax 67(2), 132-138 (2012).