Utility of oropharyngeal real-time PCR for S. pneumoniae and H. influenzae for diagnosis of pneumonia in adults.
A lack of sensitive tests and difficulties obtaining representative samples contribute to the challenge in identifying etiology in pneumonia. Upper respiratory tract swabs can be easily collected and analyzed with real-time PCR (rtPCR). Common pathogens such as S. pneumoniae and H. influenzae can both colonize and infect the respiratory tract, complicating the interpretation of positive results. Oropharyngeal swabs were collected (n = 239) prospectively from adults admitted to hospital with pneumonia. Analysis with rtPCR targeting S. pneumoniae and H. influenzae was performed and results compared with sputum cultures, blood cultures, and urine antigen testing for S. pneumoniae. Different Ct cutoff values were applied to positive tests to discern colonization from infection. Comparing rtPCR with conventional testing for S. pneumoniae in patients with all tests available (n = 57) resulted in: sensitivity 87 %, specificity 79 %, PPV 59 % and NPV 94 %, and for H. influenzae (n = 67): sensitivity 75 %, specificity 80 %, PPV 45 % and NPV 94 %. When patients with prior antimicrobial exposure were excluded sensitivity improved: 92 % for S. pneumoniae and 80 % for H. influenzae. Receiver operating characteristic curve analysis demonstrated for S. pneumoniae: AUC = 0.65 (95 % CI 0.51-0.80) and for H. influenzae: AUC = 0.86 (95 % CI 0.72-1.00). Analysis of oropharyngeal swabs using rtPCR proved both reasonably sensitive and specific for diagnosing pneumonia caused by S. pneumoniae and H. influenzae. This method may be a useful diagnostic adjunct to other methods and of special value in patients unable to provide representative lower airway samples.
Faculty of Medicine, University of Iceland, Reykjavik, Vatnsmyrarvegi 16, 101, Reykjavik, Iceland.|Departments of Medicine, Microbiology and Virology, Landspitali University Hospital, 101, Reykjavik, Iceland.
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Bjarnason
Department of Infectious Diseases/Clinical Virology, University of Gothenburg, Medicinaregatan 3a-5b, 40530, Gothenburg, Sweden.
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Lindh
Department of Infectious Diseases/Clinical Virology, University of Gothenburg, Medicinaregatan 3a-5b, 40530, Gothenburg, Sweden.
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Westin
Department of Infectious Diseases/Clinical Virology, University of Gothenburg, Medicinaregatan 3a-5b, 40530, Gothenburg, Sweden.
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Andersson
Departments of Medicine, Microbiology and Virology, Landspitali University Hospital, 101, Reykjavik, Iceland.
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Baldursson
Faculty of Medicine, University of Iceland, Reykjavik, Vatnsmyrarvegi 16, 101, Reykjavik, Iceland.|Departments of Medicine, Microbiology and Virology, Landspitali University Hospital, 101, Reykjavik, Iceland.
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Kristinsson
Faculty of Medicine, University of Iceland, Reykjavik, Vatnsmyrarvegi 16, 101, Reykjavik, Iceland. magnusgo@landspitali.is.|Departments of Medicine, Microbiology and Virology, Landspitali University Hospital, 101, Reykjavik, Iceland. magnusgo@landspitali.is.|Division of Infectious Diseases, Landspitali University Hospital, Fossvogur, 108, Reykjavik, Iceland. magnusgo@landspitali.is.
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Gottfredsson
D000328:Adult; D000368:Aged; D005260:Female; D006193:Haemophilus influenzae / Q000235:genetics / Q000302:isolation & purification*; D006801:Humans; D008297:Male; D008875:Middle Aged; D025202:Molecular Diagnostic Techniques / Q000379:methods*; D009960:Oropharynx / Q000382:microbiology*; D018410:Pneumonia, Bacterial / Q000175:diagnosis* / Q000382:microbiology; D011237:Predictive Value of Tests; D011446:Prospective Studies; D012372:ROC Curve; D060888:Real-Time Polymerase Chain Reaction / Q000379:methods*; D012680:Sensitivity and Specificity; D013296:Streptococcus pneumoniae / Q000235:genetics / Q000302:isolation & purification*