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J Hosp Med. 2012 Jan;7(1):8-13. doi: 10.1002/jhm.911. Epub 2011 Oct 12.

Broad-range bacterial polymerase chain reaction in the microbiologic diagnosis of complicated pneumonia.

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  • 1Division of Infectious Diseases, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.



A bacterial cause is not frequently identified in children with pneumonia complicated by parapneumonic effusion (ie, complicated pneumonia).


To determine the frequency of positive blood and pleural fluid cultures in children with complicated pneumonia and to determine whether broad-range 16S rRNA polymerase chain reaction (PCR) improves identification of a microbiologic cause.


This prospective cohort study included children 1-18 years of age hospitalized with complicated pneumonia.


Pleural fluid drainage was performed in 64 (51.6%) of 124 children with complicated pneumonia. A microbiologic cause was identified in 11 of 64 patients (17.2%; 95% confidence interval [CI]: 8.9%-28.7%). Bacteria were isolated from pleural fluid culture in 6 of 64 patients (9.4 %; 95% CI: 3.5%-19.3%) undergoing pleural drainage; the causative bacteria were Staphylococcus aureus (n = 5) and Streptococcus pneumoniae (n = 1). Blood culture identified a bacterial cause in 3 of 44 cases (6.8%; 95% CI: 1.4%-18.7%) undergoing pleural fluid drainage; S. pneumoniae (n = 1), Haemophilus influenzae (n = 1), and S. aureus (n = 1) were isolated. Only 3 of the 19 pleural fluid samples (15.8%; 95% CI: 3.4%-39.6%) analyzed with 16S rRNA PCR were positive. S. pneumoniae was the only organism detected in all three samples; two of these three had negative pleural fluid cultures and absence of bacteria on Gram stain. S. aureus was isolated from pleural fluid culture in one patient with a negative 16S rRNA PCR test.


Causative bacteria were infrequently identified in children with complicated pneumonia. Broad-range 16S rRNA PCR only modestly improved the microbiologic yield over conventional culture methods.


Staphylococcus aureus; Streptococcus pneumoniae; empyema; molecular diagnostic techniques; pneumonia, bacterial; polymerase chain reaction

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