Development of two real-time multiplex PCR assays for the detection and quantification of eight key bacterial pathogens in lower respiratory tract infections

Clinical Microbiology and Infection

Volumn 21, Issue 8, 2015, Pages 788.e1-788.e13

  Gadsby, N J ^a   McHugh, M P ^a   Russell, C D ^a   Mark, H ^a   Conway Morris, A ^b   Laurenson, I F ^a   Hill, A T ^a   Templeton, K E ^a  

^a ROYAL INFIRMARY OF EDINBURGH   (United Kingdom)

^b UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

Bacteria; Molecular diagnostics; PCR; Quantitative; Respiratory infection

Indexed keywords

ACINETOBACTER BAUMANNII; ARTICLE; BACTERIAL LOAD; BACTERIUM CULTURE; BACTERIUM DETECTION; BACTERIUM ISOLATE; COLONY FORMING UNIT; ESCHERICHIA COLI; HAEMOPHILUS INFLUENZAE; HUMAN; KLEBSIELLA PNEUMONIAE; LOWER RESPIRATORY TRACT INFECTION; LUNG LAVAGE; MORAXELLA CATARRHALIS; MULTIPLEX POLYMERASE CHAIN REACTION; NONHUMAN; POLYMERASE CHAIN REACTION SYSTEM; PRIORITY JOURNAL; PSEUDOMONAS AERUGINOSA; REAL TIME POLYMERASE CHAIN REACTION; SPUTUM CULTURE; STAPHYLOCOCCUS AUREUS; STREPTOCOCCUS PNEUMONIAE; BACTERIAL INFECTIONS; BACTERIUM; BRONCHOPNEUMONIA; CLASSIFICATION; EVALUATION STUDY; GENETICS; ISOLATION AND PURIFICATION; MICROBIOLOGY; MOLECULAR DIAGNOSIS; PROCEDURES; SENSITIVITY AND SPECIFICITY; SPUTUM;

ACINETOBACTER BAUMANNII; BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; HAEMOPHILUS INFLUENZAE; KLEBSIELLA PNEUMONIAE; MORAXELLA CATARRHALIS; PSEUDOMONAS AERUGINOSA; STAPHYLOCOCCUS AUREUS; STREPTOCOCCUS PNEUMONIAE;

BACTERIAL DNA;

BACTERIA; BACTERIAL INFECTIONS; BACTERIAL LOAD; BRONCHOPNEUMONIA; DNA, BACTERIAL; HUMANS; MOLECULAR DIAGNOSTIC TECHNIQUES; MULTIPLEX POLYMERASE CHAIN REACTION; REAL-TIME POLYMERASE CHAIN REACTION; SENSITIVITY AND SPECIFICITY; SPUTUM;

EID: 84937521558     PISSN: 1198743X     EISSN: 14690691     Source Type: Journal    
DOI: 10.1016/j.cmi.2015.05.004     Document Type: Article

References (47)

1. Public Health England. Investigation of bronchoalveolar lavage, sputum and associated specimens. UK Standards for Microbiology Investigations 2014; B 57: Issue 2.5. http://www.hpa.org.uk/SMI/pdf.
2. Chalmers J.D., Taylor J.K., Singanayagam A., Fleming G.B., Akram A.R., Mandal P., et al. Epidemiology, antibiotic therapy, and clinical outcomes in health care-associated pneumonia: QA UK cohort study. Clin Infect Dis 2011, 53:107-113.
3. Johansson N., Kalin M., Tiveljung-Lindell A., Giske C.G., Hedlund J. Etiology of community-acquired pneumonia: Increased microbiological yield with new diagnostic methods. Clin Infect Dis 2010, 50:202-209.
4. Templeton K.E., Scheltinga S.A., Beersma M.F., Kroes A.C., Claas E.C. 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 2004, 42:1564-1569.
5. Abdeldaim G.M., Stralin K., Korsgaard J., Blomberg J., Welinder-Olsson C., Herrmann B. Multiplex quantitative PCR for detection of lower respiratory tract infection and meningitis caused by Streptococcus pneumoniae, Haemophilus influenzae and Neisseria meningitidis. BMC Microbiol 2010, 10:310.
6. Curran T., Coyle P.V., McManus T.E., Kidney J., Coulter W.A. Evaluation of real-time PCR for the detection and quantification of bacteria in chronic obstructive pulmonary disease. FEMS Immunol Med Microbiol 2007, 50:112-118.
7. Kais M., Spindler C., Kalin M., Ortqvist A., Giske C.G. Quantitative detection of Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis in lower respiratory tract samples by real-time PCR. Diagn Microbiol Infect Dis 2006, 55:169-178.
8. Rice L.M., Reis A.H., Mistry R., Khan H., Khosla P., Bharya S., et al. Design and construction of a single tube, quantitative endpoint, LATE-PCR multiplex assay for ventilator-associated pneumonia. J Appl Microbiol 2013, 115:818-827.
9. Rios-Licea M.M., Bosques F.J., Arroliga A.C., Galindo-Galindo J.O., Garza-Gonzalez E. Quadruplex real-time quantitative PCR assay for the detection of pathogens related to late-onset ventilator-associated pneumonia: a preliminary report. J Microbiol Methods 2010, 81:232-234.
10. Stralin K., Backman A., Holmberg H., Fredlund H., Olcen P. Design of a multiplex PCR for Streptococcus pneumoniae, Haemophilus influenzae, Mycoplasma pneumoniae and Chlamydophila pneumoniae to be used on sputum samples. APMIS 2005, 113:99-111.
11. Benson R., Tondella M.L., Bhatnagar J., Carvalho Mda G., Sampson J.S., Talkington D.F., et al. Development and evaluation of a novel multiplex PCR technology for molecular differential detection of bacterial respiratory disease pathogens. J Clin Microbiol 2008, 46:2074-2077.
12. Bogaerts P., Hamels S., de Mendonca R., Huang F.D., Roisin S., Remacle J., et al. Analytical validation of a novel high multiplexing real-time PCR array for the identification of key pathogens causative of bacterial ventilator-associated pneumonia and their associated resistance genes. J Antimicrob Chemother 2013, 68:340-347.
13. Jamal W., Al Roomi E., AbdulAziz L.R., Rotimi V.O. Evaluation of Curetis Unyvero, a multiplex PCR-based testing system, for rapid detection of bacteria and antibiotic resistance and impact of the assay on management of severe nosocomial pneumonia. J Clin Microbiol 2014, 52:2487-2492.
14. Vallone P.M., Butler J.M. AutoDimer: a screening tool for primer-dimer and hairpin structures. Biotechniques 2004, 37:226-231.
15. Niesters H.G.M. Quantification of viral load using real-time amplification techniques. Methods 2001, 25:419-429.
16. Saunders N., Zambon M., Sharp I., Siddiqui R., Bermingham A., Ellis J. Guidance on the development and validation of diagnostic tests that depend on nucleic acid amplification and detection. J Clin Virol 2013, 56:260-270.
17. Carvalho Mda G., Tondella M.L., McCaustland K., Weidlich L., McGee L., Mayer L.W. Evaluation and improvement of real-time PCR assays targeting lytA, ply, and psaA genes for detection of pneumococcal DNA. J Clin Microbiol 2007, 45:2460-2466.
18. Wessels E., Schelfaut J.J., Bernards A.T., Claas E.C. Evaluation of several biochemical and molecular techniques for identification of Streptococcus pneumoniae and Streptococcus pseudopneumoniae and their detection in respiratory samples. J Clin Microbiol 2012, 50:1171-1177.
19. Wang X., Mair R., Hatcher C., Theodore M.J., Edmond K., Wu H.M., et al. Detection of bacterial pathogens in Mongolia meningitis surveillance with a new real-time PCR assay to detect Haemophilus influenzae. Int J Med Microbiol 2011, 301:303-309.
20. Meyler K.L., Meehan M., Bennett D., Cunney R., Cafferkey M. Development of a diagnostic real-time polymerase chain reaction assay for the detection of invasive Haemophilus influenzae in clinical samples. Diagn Microbiol Infect Dis 2012, 74:356-362.
21. Zhang B., Kunde D., Tristram S. Haemophilus haemolyticus is infrequently misidentified as Haemophilus influenzae in diagnostic specimens in Australia. Diagn Microbiol Infect Dis 2014, 80:272-273.
22. Pichon B., Hill R., Laurent F., Larsen A.R., Skov R.L., Holmes M., et al. Development of a real-time quadruplex PCR assay for simultaneous detection of nuc, Panton-Valentine leucocidin (PVL), mecA and homologue mecALGA251. J Antimicrob Chemother 2012, 67:2338-2341.
23. Dunne E.M., Manning J., Russell F.M., Robins-Browne R.M., Mulholland E.K., Satzke C. Effect of pneumococcal vaccination on nasopharyngeal carriage of Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, and Staphylococcus aureus in Fijian children. J Clin Microbiol 2012, 50:1034-1038.
24. Clifford R.J., Milillo M., Prestwood J., Quintero R., Zurawski D.V., Kwak Y.I., et al. Detection of bacterial 16S rRNA and identification of four clinically important bacteria by real-time PCR. PLoS One 2012, 7:e48558.
25. Anuj S.N., Whiley D.M., Kidd T.J., Bell S.C., Wainwright C.E., Nissen M.D., et al. Identification of Pseudomonas aeruginosa by a duplex real-time polymerase chain reaction assay targeting the ecfX and the gyrB genes. Diagn Microbiol Infect Dis 2009, 63:127-131.
26. Kidd T.J., Ramsay K.A., Hu H., Bye P.T.P., Elkins M.R., Grimwood K., et al. Low rates of Pseudomonas aeruginosa misidentification in isolates from cystic fibrosis patients. J Clin Microbiol 2009, 47:1503-1509.
27. Le Gall F., Le Berre R., Rosec S., Hardy J., Gouriou S., Boisame-Gastrin S., et al. Proposal of a quantitative PCR-based protocol for an optimal Pseudomonas aeruginosa detection in patients with cystic fibrosis. BMC Microbiol 2013, 13:143.
28. Chuang Y.C., Chang S.C., Wang W.K. High and increasing Oxa-51 DNA load predict mortality in Acinetobacter baumannii bacteremia: implication for pathogenesis and evaluation of therapy. PLoS One 2010, 5:e14133.
29. Turton J.F., Woodford N., Glover J., Yarde S., Kaufmann M.E., Pitt T.L. Identification of Acinetobacter baumannii by detection of the blaOXA-51-like carbapenemase gene intrinsic to this species. J Clin Microbiol 2006, 44:2974-2976.
30. Zander E., Higgins P.G., Fernandez-Gonzalez A., Seifert H. Detection of intrinsic blaOXA-51-like by multiplex PCR on its own is not reliable for the identification of Acinetobacter baumannii. Int J Med Microbiol 2013, 303:88-89.
31. Paule S.M., Pasquariello A.C., Hacek D.M., Fisher A.G., Thomson R.B., Kaul K.L., et al. Direct detection of Staphylococcus aureus from adult and neonate nasal swab specimens using real-time polymerase chain reaction. J Mol Diagn 2004, 6:191-196.
32. Greiner O., Day P.J., Altwegg M., Nadal D. Quantitative detection of Moraxella catarrhalis in nasopharyngeal secretions by real-time PCR. J Clin Microbiol 2003, 41:1386-1390.
33. Hirama T., Yamaguchi T., Miyazawa H., Tanaka T., Hashikita G., Kishi E., et al. Prediction of the pathogens that are the cause of pneumonia by the battlefield hypothesis. PLoS One 2011, 6:e24474.
34. Smith-Vaughan H., Byun R., Nadkarni M., Jacques N.A., Hunter N., Halpin S., et al. Measuring nasal bacterial load and its association with otitis media. BMC Ear Nose Throat Disord 2006, 6:10.
35. Sakwinska O., Bastic Schmid V., Berger B., Bruttin A., Keitel K., Lepage M., et al. Nasopharyngeal microbiota in healthy children and pneumonia patients. J Clin Microbiol 2014, 52:1590-1594.
36. Obasi C.N., Barrett B., Brown R., Vrtis R., Barlow S., Muller D., et al. Detection of viral and bacterial pathogens in acute respiratory infections. J Infect 2014, 68:125-130.
37. Stralin K., Korsgaard J., Olcen P. Evaluation of a multiplex PCR for bacterial pathogens applied to bronchoalveolar lavage. Eur Respir J 2006, 28:568-575.
38. Goddard A.F., Staudinger B.J., Dowd S.E., Joshi-Datar A., Wolcott R.D., Aitken M.L. Direct sampling of cystic fibrosis lungs indicates that DNA-based analyses of upper-airway specimens can misrepresent lung microbiota. Proc Natl Acad Sci USA 2012, 109:13769-13774.
39. Wurzel D.F., Marchant J.M., Clark J.E., Mackay I.M., Wang C.Y.T., Sloots T.P., et al. Respiratory virus detection in nasopharyngeal aspirate versus bronchoalveolar lavage is dependent on virus type in children with chronic respiratory symptoms. J Clin Virol 2013, 58:683-688.
40. Huijskens E.G., Rossen J.W., Kluytmans J.A., van der Zanden A.G., Koopmans M. Evaluation of yield of currently available diagnostics by sample type to optimize detection of respiratory pathogens in patients with a community-acquired pneumonia. Influenza Other Respir Viruses 2014, 8:243-249.
41. Abdeldaim G.M., Stralin K., Olcen P., Blomberg J., Herrmann B. Toward a quantitative DNA-based definition of pneumococcal pneumonia: a comparison of Streptococcus pneumoniae target genes, with special reference to the Spn9802 fragment. Diagn Microbiol Infect Dis 2008, 60:143-150.
42. Albrich W.C., Madhi S.A., Adrian P.V., van Nierkerk N., Mareletsi T., Cutland C., et al. Use of a rapid test of pneumococcal colonization density to diagnose pneumococcal pneumonia. Clin Infect Dis 2012, 54:601-609.
43. Stralin K., Herrmann B., Abdeldaim G., Olcen P., Holmberg H., Molling P. Comparison of sputum and nasopharyngeal aspirate samples and of the PCR gene targets lytA and Spn9802 for quantitative PCR for rapid detection of pneumococcal pneumonia. J Clin Microbiol 2014, 52:83-89.
44. Chastre J., Fagon J.Y. Ventilator-associated pneumonia. Am J Respir Crit Care Med 2002, 165:867-903.
45. Peters R.P., de Boer R.F., Schuurman T., Gierveld S., Kooistra-Smid M., van Agtmael M.A., et al. Streptococcus pneumoniae DNA load in blood as a marker of infection in patients with community-acquired pneumonia. J Clin Microbiol 2009, 47:3308-3312.
46. Rello J., Lisboa T., Lujan M., Gallego M., Kee C., Kay I., et al. Severity of pneumococcal pneumonia associated with genomic bacterial load. Chest 2009, 136:832-840.
47. Werno A.M., Anderson T.P., Murdoch D.R. Association between pneumococcal load and disease severity in adults with pneumonia. J Med Microbiol 2012, 61:1129-1135.