1586. Utility of Upper Airway PCR for Diagnosing S. pneumoniae and H. influenza Pneumonia in Adults
Session: Poster Abstract Session: Community Acquired Pneumonia
Saturday, October 10, 2015
Room: Poster Hall

Determining the etiology of pneumonia can be challenging. Obtaining lower airway samples is often difficult; analysis of upper airway swabs with PCR testing is therefore an attractive option. Two causative agents Streptococcus pneumoniae and Haemophilus influenzae can colonize the human respiratory tract, complicating the interpretation of results.


Adult patients admitted with pneumonia were prospectively recruited provided they had a new x-ray infiltrate and clinical symptoms of pneumonia. Etiologic testing with standard methods was performed (blood and sputum cultures, antigen testing of urine for S. pneumoniae). A multiplex real-time PCR was performed on upper airway swabs with primers specific for S. pneumoniae and H. influenzae. Results were analyzed for three cut-off threshold cycle (Ct) values. Only S. pneumoniae patients with available PCR results who were also tested with any combination of urinary antigen test, sputum or blood culture were examined. Only H. influenzaepatients with PCR results and either sputum and/or blood culture were included. As no gold standard exists; PCR results were compared with the sum result of other diagnostic methods.


A total of 363 patients were included. For S. pneumoniae, data was available for 192 patients, 23 of which were positive in ≥1 standard test and 49 were PCR positive with Ct 40. For H. influenzae, data was available for 179 patients, 14 tested positive in ≥1 standard test and 22 with PCR. Sensitivity decreased markedly with lower Ct values which may have been affected by the low sensitivity of our reference method in the absence of a true gold standard. Results of calculations for specificity and sensitivity of the PCR results were:




S. pneumoniae



Ct 40



Ct 35



Ct 30



H. influenzae



Ct 40



Ct 35



Ct 30




These results demonstrate the utility of PCR testing of upper airway samples for etiologic diagnosis of pneumonia. Upper airway samples had good specificity but lacked sensitivity when compared with conventional etiologic testing.

Analysis of upper airway swabs for S. pneumoniae and H. influenzae may increase diagnostic yield for pneumonia patients and may be of special utility as an addition to multiplex PCR tests and in patients who are unable to provide lower airway samples.

Agnar Bjarnason, MD1,2, Magnus Lindh, MD, PhD3, Johan Westin, MD, PhD3, Lars-Magnus Andersson, MD, PhD3, Olafur Baldursson, MD, PhD4, Karl G. Kristinsson, MD, PhD1,5 and Magnus Gottfredsson, MD, PhD1,6, (1)Faculty of Medicine, University of Iceland, Reykjavik, Iceland, (2)Dept of Infectious Diseases, Sahlgrenska University Hospital, Gothenburg, Sweden, (3)Dept of Infectious Diseases/Virology, Sahlgrenska University Hospital, Gothenburg, Sweden, (4)Pulmonary Medicine, Landspitali University Hospital, Reykjavik, Iceland, (5)Clinical Microbiology, Landspitali University Hospital, Reykjavik, Iceland, (6)Infectious Diseases, Landspitali University Hospital, Reykjavik, Iceland


A. Bjarnason, None

M. Lindh, None

J. Westin, None

L. M. Andersson, None

O. Baldursson, None

K. G. Kristinsson, None

M. Gottfredsson, None

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