The bacteriology in adult patients with pneumonia and parapneumonic effusions: increased yield with DNA sequencing method

  • Niclas JohanssonEmail author
  • Martin Vondracek
  • Carolina Backman-Johansson
  • Magnus C. Sköld
  • Karin Andersson-Ydsten
  • Jonas HedlundEmail author
Original Article


The aim of this study was to use a 16S rDNA sequencing method in combination with conventional culture in patients with parapneumonic effusions (PPE) to evaluate the methods, study the microbiological spectrum, and examine the presence of bacteria within the different stages of PPE. Adults with community-acquired pneumonia (CAP) and PPE (n = 197) admitted to the Departments of Infectious Diseases at four hospitals in Stockholm County during 2011–2014 were prospectively studied. All patients underwent thoracentesis. Twenty-seven non-infectious pleural effusions were used as controls. The pleural samples were analyzed with culture, 16S rDNA sequencing, pH, glucose, and lactate dehydrogenase. Microbiological etiology was found in 99/197 (50%) of the patients with mixed infections in 20 cases. The most common pathogens were viridans streptococci (n = 37) and anaerobic bacteria (n = 40). Among the 152 patients with both methods performed, 26/152 (17%) and 94/152 (62%) had bacteria identified with culture and 16S rDNA sequencing respectively (p < 0.001). In 24/26 (92%) culture-positive cases, the same organism was identified by 16S rDNA. All controls were negative in both methods. Among the patients with complicated PPE and complete sampling, bacteria were found in 69/74 patients (93%), all detected with 16S rDNA sequencing, compared to 23/74 (31%) culture-positive samples (p < 0.001). Compared with culture, 16S rDNA sequencing substantially improved the microbiological yield, a microbiological diagnosis was achieved in almost all patients with complicated PPE, and the specificity seemed to be high. 16S rDNA sequencing should be used together with culture in patients with PPE to guide antibiotic therapy.


Pneumonia Etiology PCR Parapneumonic effusion Pleuritis 



The authors thank the staff at Danderyd Hospital and Södersjukhuset for sample collection of the patients with parapneumonic effusion admitted to their units, the Lung-Allergy Clinic staff (Gunnel de Forest, Mari Pettersson, Camilla Mattsson, and Ulli Klaile-Hammarberg) for identifying and sampling the control group, and Christian Giske, Professor, Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska Institutet, for valuable comments on the manuscript.


This work was supported by ALF Grants, Stockholm County [grant number 20110088].

Compliance with ethical standards

Written informed consent was obtained from enrolled patients or from their nearest relative. The study was approved by the regional ethics committee, Stockholm, Sweden, nr 2010/2066-31.

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

10096_2018_3426_MOESM1_ESM.doc (61 kb)
ESM 1 (DOC 61 kb)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Department of Medicine, Solna, Infectious Diseases UnitKarolinska University Hospital, Karolinska InstitutetStockholmSweden
  2. 2.Department of Infectious DiseasesKarolinska University Hospital SolnaStockholmSweden
  3. 3.Department of Clinical Microbiology, Department of Microbiology, Tumor and Cell BiologyKarolinska University Hospital, Karolinska InstitutetStockholmSweden
  4. 4.Department of Clinical ChemistryKarolinska University Hospital SolnaSolnaSweden
  5. 5.Respiratory Medicine Unit, Department of Medicine Solna and Center for Molecular MedicineKarolinska InstitutetStockholmSweden
  6. 6.Lung-Allergy ClinicKarolinska University Hospital SolnaStockholmSweden

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