Multiplex PCR and emerging technologies for the detection of respiratory pathogens

Clinical Infectious Diseases

Volumn 52, Issue SUPPL. 4, 2011, Pages

  Caliendo, Angela M ^a  

^a EMORY UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOVIRUS; ARTICLE; BACTERIUM DETECTION; BOCAVIRUS; BORDETELLA PERTUSSIS; CAPILLARY ELECTROPHORESIS; CHLAMYDOPHILA PNEUMONIAE; CORONAVIRUS; ELECTROSPRAY MASS SPECTROMETRY; ENTEROVIRUS; FUNGAL DETECTION; HAEMOPHILUS INFLUENZAE; INFLUENZA VIRUS A H1N1; INFLUENZA VIRUS A H5N1; INFLUENZA VIRUS B; LEGIONELLA PNEUMOPHILA; METAPNEUMOVIRUS; MICROARRAY ANALYSIS; MULTIPLEX POLYMERASE CHAIN REACTION; MYCOPLASMA PNEUMONIAE; NEISSERIA MENINGITIDIS; NONHUMAN; PARAINFLUENZA VIRUS; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; RESPIRATORY SYNCYTIAL PNEUMOVIRUS; RESPIRATORY TRACT INFECTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RHINOVIRUS; SENSITIVITY AND SPECIFICITY; STREPTOCOCCUS PNEUMONIAE; VIRUS DETECTION; VIRUS IDENTIFICATION;

BACTERIAL INFECTIONS; HUMANS; MOLECULAR DIAGNOSTIC TECHNIQUES; POLYMERASE CHAIN REACTION; RESPIRATORY TRACT INFECTIONS; VIRUS DISEASES;

EID: 79953785400     PISSN: 10584838     EISSN: 15376591     Source Type: Journal    
DOI: 10.1093/cid/cir047     Document Type: Article

References (64)

1. Barenfanger J, Drake C, Leon N, Mueller T, Troutt T. Clinical and financialbenefits of rapid detection ofrespiratoryviruses: an outcomes study. J Clin Microbiol 2000; 38:2824-8. (Pubitemid 30640557)
2. Woo PC, Chiu SS, Seto WH, Peiris M. Costeffectiveness of rapid diagnosis ofviral respiratory tract infections in pediatric patients.J Clin Microbiol 1997; 35:1579-81. (Pubitemid 27216837)
3. Zou S, Han J, Wen L, et al. Human influenza A virus (H5N1) detection by a novel multiplex PCR typing method. J Clin Microbiol 2007; 45:1889-92. (Pubitemid 46933922)
4. Brunstein JD, Cline CL, McKinney S, Thomas E. Evidence from multiplex molecular assays for complex multipathogen interactions in acute respiratory infections. J Clin Microbiol 2008; 46:97-102.
5. Li H, McCormac MA, Estes RW, et al. Simultaneous detection and highthroughput identification of a panel of RNA viruses causing respiratory tract infections. J Clin Microbiol 2007; 45:2105-9. (Pubitemid 47203777)
6. Benson R, Tondella ML, Bhatnagar J, et al. Development and evalua-tion of a novel multiplex PCR technology for molecular differential detection of bacterial respiratory disease pathogens. J Clin Microbiol 2008; 46:2074-7. (Pubitemid 351831846)
7. Raymond F, Carbonneau J, Boucher N, et al. Comparison of auto-mated microarray detection with realtime PCR assays for detection of respiratory viruses in specimens obtained from children. J Clin Microbiol 2009; 47:743-50.
8. Beck ET, Jurgens LA, Kehl SC, et al. Development of a rapid automated influenza A, influenza B, and respiratory syncytial virus A/B multiplex realtime RTPCR assay and its use during the 2009 H1N1 swineorigin influenza virus epidemic in Milwaukee, Wisconsin.J Mol Diagn 2010; 12:74-81.
9. Chen, et al. PCR and electrospray ionization mass spectrometry (PCR/ESI-MS) for identifying viral respiratory infections [abstract D-2256]. Presented at: 48th Annual Interscience Conference on Antimicrobial Agents and Chemotherapy/46th Annual Meeting of the Infectious Diseases Society of America; 2008.
10. Ecker DJ, Sampath R, Blyn LB, et al. Rapid identification and strain-typing of respiratory pathogens for epidemic surveillance. Proc Natl Acad Sci USA 2005; 102:8012-7. (Pubitemid 40781054)
11. Sampath R, Hofstadler SA, Blyn LB, et al. Rapid identification of emerging pathogens: coronavirus. Emerg Infect Dis 2005; 11:373-9. (Pubitemid 40315721)
12. Mandell LA, Wunderink RG, Anzueto A, et al. Infectious Diseases Society of America/American Thoracic Society consensus guidelines on the management of communityacquired pneumonia in adults. Clin Infect Dis 2007; 44(Suppl. 2):S27-72. (Pubitemid 46290553)
13. Werno AM, Murdoch DR. Medical microbiology: laboratory diagnosis ofinvasive pneumococcal disease. Clin Infect Dis 2008; 46:926-32. (Pubitemid 351417200)
14. Johansson N, Kalin M, TiveljungLindell A, Giske CG, Hedlund J. Etiology of communityacquired pneumonia: increased microbiolog-ical yield with new diagnostic methods. Clin Infect Dis 2010; 50:202-9.
15. Michelow IC, Olsen K, Lozano J, et al. Epidemiology and clinical characteristics of communityacquired pneumonia in hospitalized children. Pediatrics 2004; 113:701-7. (Pubitemid 38437371)
16. Musher D. Streptococcus pneumoniae. In: Mandell GL, Bennett JE, Dolin R, eds. Principals and practice of infectious diseases. 7th ed. Vol. 2. Philadelphia: Churchill Livingstone, 2010: 2623-42.
17. Kellogg JA, Bankert DA, Elder CJ, Gibbs JL, Smith MC. Identification of Streptococcus pneumoniae revisited. J Clin Microbiol 2001; 39: 3373-5. (Pubitemid 32830345)
18. Klugman KP, Madhi SA, Albrich WC. Novel approaches to the iden-tification of Streptococcus pneumoniae as the cause of community-acquired pneumonia. Clin Infect Dis 2008; 47(Suppl. 3):S202-6.
19. Gutierrez F, Masia M, Rodriguez JC, et al. Evaluation of the im-munochromatographic Binax NOW assay for detection of Streptococ-cus pneumoniae urinary antigen in a prospective study of community-acquired pneumonia in Spain. Clin Infect Dis 2003; 36:286-92. (Pubitemid 36169663)
20. Smith MD, Sheppard CL, Hogan A, et al. Diagnosis of Streptococcus pneumoniae infections in adults with bacteremia and community-acquired pneumonia: clinical comparison of pneumococcal PCR and urinary antigen detection.J Clin Microbiol 2009; 47:1046-9.
21. Murdoch DR, Laing RT, Cook JM. The Now S. pneumoniae urinary antigen test positivity rate 6 weeks after pneumonia onset, among patients with COPD. Clin Infect Dis 2003; 37:153-4. (Pubitemid 36836663)
22. Esposito S, Bosis S, Colombo R, et al. Evaluation of rapid assay for detection of Streptococcus pneumoniae urinary antigen among infants and young children with possible invasive pneumococcal disease. Pe-diatr Infect Dis J 2004; 23:365-7. (Pubitemid 38508896)
23. Ploton C, Freydiere AM, Benito Y, et al. Streptococcus pneumoniae thoracic empyema in children: rapid diagnosis by using the Binax NOW immunochromatographic membrane test in pleural fluids. Pathol Biol (Paris) 2006; 54:498-501. (Pubitemid 44794357)
24. Porcel JM, Ruiz-Gonzalez A, Falguera M, et al. Contribution of a pleural antigen assay (Binax NOW) to the diagnosis ofpneumococcal pneumonia. Chest 2007; 131:1442-7. (Pubitemid 46762350)
25. Jacobs JA, Stobberingh EE, Cornelissen EI, Drent M. Detection of Streptococcus pneumoniae antigen in bronchoalveolar lavage fluid samples by a rapid immunochromatographic membrane assay. J Clin Microbiol 2005; 43:4037-40. (Pubitemid 41129696)
26. Petti CA, Woods CW, Reller LB. Streptococcuspneumoniae antigen test using positive blood culture bottles as an alternative method to diagnose pneumococcal bacteremia.J Clin Microbiol 2005; 43:2510-2. (Pubitemid 40656282)
27. Cima-Cabal MD, Vazquez F, de los Toyos JR, Mendez FJ. Rapid and reliable identification ofStreptococcus pneumoniae isolates by pneumolysin-mediated agglutination.J Clin Microbiol 1999; 37:1964-6. (Pubitemid 29235254)
28. Nohynek H, Eskola J, Kleemola M, Jalonen E, Saikku P, Leinonen M. Bacterial antibody assays in the diagnosis of acute lower respiratory tract infection in children. Pediatr Infect Dis J 1995; 14:478-84.
29. Wheeler J, Freeman R, Steward M, et al. Detection of pneumolysin in sputum. J Med Microbiol 1999; 48:863-6. (Pubitemid 29476422)
30. Murdoch DR, Anderson TP, Beynon KA, et al. Evaluation of a PCR assay for detection of Streptococcus pneumoniae in respiratory and nonrespiratory samples from adults with communityacquired pneu-monia. J Clin Microbiol 2003; 41:63-6. (Pubitemid 36098554)
31. Lahti E, Mertsola J, Kontiokari T, Eerola E, Ruuskanen O, Jalava J. Pneumolysin polymerase chain reaction for diagnosis ofpneumococcal pneumonia and empyema in children. Eur J Clin Microbiol Infect Dis 2006; 25:783-9. (Pubitemid 44786654)
32. Rudolph KM, Parkinson AJ, Black CM, Mayer LW. Evaluation of polymerase chain reaction for diagnosis of pneumococcal pneumonia. J Clin Microbiol 1993; 31:2661-6. (Pubitemid 23284898)
33. Salo P, Ortqvist A, Leinonen M. Diagnosis of bacteremic pneumo-coccal pneumonia by amplification of pneumolysin gene fragment in serum. J Infect Dis 1995; 171:479-82.
34. Toikka P, Nikkari S, Ruuskanen O, Leinonen M, Mertsola J. Pneu-molysin PCR-based diagnosis of invasive pneumococcal infection in children. J Clin Microbiol 1999; 37:633-7. (Pubitemid 29091277)
35. Carvalho Mda G, Tondella ML, McCaustland K, et al. Evaluation and improvement of realtime PCR assays targeting lytA, ply, and psaA genes for detection of pneumococcal DNA. J Clin Microbiol 2007; 45:2460-6. (Pubitemid 47295474)
36. Neeleman C, Klaassen CH, Klomberg DM, de Valk HA, Mouton JW. Pneumolysin is a key factor in misidentification ofmacrolideresistant Streptococcus pneumoniae and is a putative virulence factor of S. mitis and other streptococci. J Clin Microbiol 2004; 42:4355-7. (Pubitemid 39296176)
37. Ronda C, Garcia JL, Garcia E, Sanchez-Puelles JM, Lopez R. Biological role of the pneumococcal amidase. Cloning of the lytA gene in Strep-tococcuspneumoniae. Eur J Biochem 1987; 164:621-4. (Pubitemid 17072818)
38. Rajam G, Anderton JM, Carlone GM, Sampson JS, Ades EW. Pneumo-coccal surface adhesin A (psaA): a review. Crit Rev Microbiol 2008; 34:131-42.
39. Suzuki N, Seki M, Nakano Y, Kiyoura Y, Maeno M, Yamashita Y. Discrimination of Streptococcus pneumoniae from Viridans group streptococci by genomic subtractive hybridization. J Clin Microbiol 2005; 43:4528-34. (Pubitemid 41298238)
40. Sheppard CL, Harrison TG, Morris R, Hogan A, George RC. Autolysin-targeted LightCycler assay including internal process control for de-tection of Streptococcus pneumoniae DNA in clinical samples. J Med Microbiol 2004; 53:189-95. (Pubitemid 38340117)
41. Byington CL, Spencer LY, Johnson TA, et al. An epidemiological in-vestigation of a sustained high rate of pediatric parapneumonic em-pyema: risk factors and microbiological associations. Clin Infect Dis 2002; 34:434-40. (Pubitemid 34112262)
42. Rello J, Lisboa T, Lujan M, et al. Severity ofpneumococcal pneumonia associated with genomic bacterial load. Chest 2009; 136:832-40.
43. Peters RP, de Boer RF, Schuurman T, et al. Streptococcus pneumoniae DNA load in blood as a marker of infection in patients with communityacquired pneumonia. J Clin Microbiol 2009; 47:3308-12.
44. Azzari C, Moriondo M, Indolfi G, et al. Molecular detection methods and serotyping performed directly on clinical samples improve di-agnostic sensitivity and reveal increased incidence ofinvasive disease by Streptococcus pneumoniae in Italian children. J Med Microbiol 2008; 57:1205-12.
45. Kee C, Palladino S, Kay I, et al. Feasibility of realtime polymerase chain reaction in whole blood to identify Streptococcus pneumoniae in pa-tients with communityacquired pneumonia. Diagn Microbiol Infect Dis 2008; 61:72-5. (Pubitemid 351509748)
46. Le Monnier A, Carbonnelle E, Zahar JR, et al. Microbiological di-agnosis of empyema in children: comparative evaluations by culture, polymerase chain reaction, and pneumococcal antigen detection in pleural fluids. Clin Infect Dis 2006; 42:1135-40.
47. Tarrago D, Fenoll A, SanchezTatay D, et al. Identification of pneu-mococcal serotypes from culturenegative clinical specimens by novel realtime PCR. Clin Microbiol Infect 2008; 14:828-34.
48. Musher DM, Montoya R, Wanahita A. Diagnostic value ofmicroscopic examination of Gramstained sputum and sputum cultures in patients with bacteremic pneumococcal pneumonia. Clin Infect Dis 2004; 39:165-9. (Pubitemid 38971484)
49. Ghaffar F, Friedland IR, McCracken GH Jr. Dynamics of nasopha-ryngeal colonization by Streptococcus pneumoniae. Pediatr Infect Dis J 1999; 18:638-46. (Pubitemid 29350335)
50. Palacios G, Hornig M, Cisterna D, et al. Streptococcus pneumoniae coinfection is correlatedwith the severityofH1N1 pandemic influenza. PLoS One 2009; 4:e8540.
51. Kais M, Spindler C, Kalin M, Ortqvist A, Giske CG. Quantitative de-tection of Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis in lower respiratory tract samples by real-time PCR. Diagn Microbiol Infect Dis 2006; 55:169-78. (Pubitemid 43949456)
52. Morozumi M, Nakayama E, Iwata S, et al. Simultaneous detection of pathogens in clinical samples from patients with communityacquired pneumonia by real-time PCR with pathogen-specific molecular beacon probes.J Clin Microbiol 2006; 44:1440-6.
53. Johansson N, Kalin M, Giske CG, Hedlund J. Quantitative detection of Streptococcus pneumoniae from sputum samples with real-time quantitative polymerase chain reaction for etiologic diagnosis of communityacquired pneumonia. Diagn Microbiol Infect Dis 2008; 60:255-61. (Pubitemid 351253612)
54. Nolte FS. Molecular diagnostics for detection of bacterial and viral pathogens in communityacquired pneumonia. Clin Infect Dis 2008; 47(Suppl. 3):S123-6.
55. Pai R, Gertz RE, Beall B. Sequential multiplex PCR approach for de-termining capsular serotypes of Streptococcus pneumoniae isolates. J Clin Microbiol 2006; 44:124-31. (Pubitemid 43100590)
56. Harris KA, Turner P, Green EA, Hartley JC. Dulpex real-time PCR assay for detection of Streptococcus pneumoniae in clinical samples and de-termination of penicillin susceptibility.J Clin Microbiol 2008; 46:2751-8.
57. Pisani G, Cristiano K, Marino F, et al. Quantification of hepatitis C virus (HCV) RNA in a multicenter study: implications for management of HCV genotype 1-infected patients. J Clin Microbiol 2009; 47:2931-6.
58. Preiksaitis JK, Pang XL, Fox JD, Fenton JM, Caliendo AM, Miller GG. Interlaboratory comparison of Epstein-Barr virus viral load assays. Am J Transpl 2009; 9:269-79.
59. Yang S, Lin S, Khalil A, et al. Quantitative PCR assay using sputum samples for rapid diagnosis of pneumococcal pneumonia in adult emergencydepartment patients. J Clin Microbiol 2005; 43:3221-6. (Pubitemid 40981327)
60. Peters RP, van Agtmael MA, Danner SA, Savelkoul PH, Vanden-brouckeGrauls CM. New developments in the diagnosis of blood-stream infections. Lancet Infect Dis 2004; 4:751-60. (Pubitemid 39574347)
61. Niederman MS. Biological markers to determine eligibility in trials for communityacquired pneumonia: a focus on procalcitonin. Clin Infect Dis 2008; 47(Suppl. 3):S127-32.
62. Schuetz P, ChristCrain M, Thomann R, et al. Effect ofprocalcitonin-based guidelines vs standard guidelines on antibiotic use in lower re-spiratory tract infections: the ProHOSP randomized controlled trial. JAMA 2009; 302:1059-66.
63. de Roux A, Marcos MA, Garcia E, et al. Viral communityacquired pneumonia in nonimmunocompromised adults. Chest 2004; 125: 1343-51. (Pubitemid 38501348)
64. Templeton KE, Scheltinga SA, van den Eeden WC, Graffelman AW, van den Broek PJ, Claas EC Improved diagnosis of the etiology of communityacquired pneumonia with realtime polymerase chain re-action. Clin Infect Dis 2005; 41:345-51. (Pubitemid 41022112)