Skip to main content

Advertisement

SpringerLink
Log in

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

  • Original Article
  • Published:
European Journal of Clinical Microbiology & Infectious Diseases Aims and scope Submit manuscript

Abstract

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.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1

Similar content being viewed by others

References

  1. Koegelenberg CF, Diacon AH, Bolliger CT (2008) Parapneumonic pleural effusion and empyema. Respiration 75(3):241–250. https://doi.org/10.1159/000117172

    Article  PubMed  Google Scholar 

  2. Davies HE, Davies RJ, Davies CW, Group BTSPDG (2010) Management of pleural infection in adults: British Thoracic Society pleural disease guideline 2010. Thorax 65(Suppl 2):ii41–ii53. https://doi.org/10.1136/thx.2010.137000

    Article  PubMed  Google Scholar 

  3. Light RW, Girard WM, Jenkinson SG, George RB (1980) Parapneumonic effusions. Am J Med 69(4):507–512

    Article  CAS  PubMed  Google Scholar 

  4. Foster S, Maskell N (2007) Bacteriology of complicated parapneumonic effusions. Curr Opin Pulm Med 13(4):319–323. https://doi.org/10.1097/MCP.0b013e3281864691

    Article  PubMed  Google Scholar 

  5. Meyer CN, Rosenlund S, Nielsen J, Friis-Moller A (2011) Bacteriological aetiology and antimicrobial treatment of pleural empyema. Scand J Infect Dis 43(3):165–169. https://doi.org/10.3109/00365548.2010.536162

    Article  PubMed  Google Scholar 

  6. Ahmed RA, Marrie TJ, Huang JQ (2006) Thoracic empyema in patients with community-acquired pneumonia. Am J Med 119(10):877–883. https://doi.org/10.1016/j.amjmed.2006.03.042

    Article  PubMed  Google Scholar 

  7. Sahn SA (2007) Diagnosis and management of parapneumonic effusions and empyema. Clin Infect Dis 45(11):1480–1486. https://doi.org/10.1086/522996

    Article  CAS  PubMed  Google Scholar 

  8. Everts RJ, Reller LB (1999) Pleural space infections: microbiology and antimicrobial therapy. Semin Respir Infect 14(1):18–30

    CAS  PubMed  Google Scholar 

  9. Mohanty S, Kapil A, Das BK (2007) Bacteriology of parapneumonic pleural effusions in an Indian hospital. Trop Dr 37(4):228–229. https://doi.org/10.1258/004947507782333152

    Article  Google Scholar 

  10. Insa R, Marin M, Martin A, Martin-Rabadan P, Alcala L, Cercenado E, Calatayud L, Linares J, Bouza E (2012) Systematic use of universal 16S rRNA gene polymerase chain reaction (PCR) and sequencing for processing pleural effusions improves conventional culture techniques. Medicine (Baltimore) 91(2):103–110. https://doi.org/10.1097/MD.0b013e31824dfdb0

    Article  CAS  Google Scholar 

  11. Gollomp K, Rankin SC, White C, Mattei P, Harris MC, Kilpatrick LE, Sheffler-Collins S, McGowan KL, Shah SS (2012) Broad-range bacterial polymerase chain reaction in the microbiologic diagnosis of complicated pneumonia. J Hosp Med 7(1):8–13. https://doi.org/10.1002/jhm.911

    Article  PubMed  Google Scholar 

  12. Saglani S, Harris KA, Wallis C, Hartley JC (2005) Empyema: the use of broad range 16S rDNA PCR for pathogen detection. Arch Dis Child 90(1):70–73. https://doi.org/10.1136/adc.2003.042176

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Menezes-Martins LF, Menezes-Martins JJ, Michaelsen VS, Aguiar BB, Ermel T, Machado DC (2005) Diagnosis of parapneumonic pleural effusion by polymerase chain reaction in children. J Pediatr Surg 40(7):1106–1110. https://doi.org/10.1016/j.jpedsurg.2005.03.057

    Article  PubMed  Google Scholar 

  14. Blaschke AJ, Heyrend C, Byington CL, Obando I, Vazquez-Barba I, Doby EH, Korgenski EK, Sheng X, Poritz MA, Daly JA, Mason EO, Pavia AT, Ampofo K (2011) Molecular analysis improves pathogen identification and epidemiologic study of pediatric parapneumonic empyema. Pediatr Infect Dis J 30(4):289–294. https://doi.org/10.1097/INF.0b013e3182002d14

    Article  PubMed  PubMed Central  Google Scholar 

  15. Krenke K, Sadowy E, Podsiadly E, Hryniewicz W, Demkow U, Kulus M (2016) Etiology of parapneumonic effusion and pleural empyema in children. The role of conventional and molecular microbiological tests. Respir Med 116:28–33. https://doi.org/10.1016/j.rmed.2016.05.009

    Article  PubMed  Google Scholar 

  16. Utine GE, Pinar A, Ozcelik U, Sener B, Yalcin E, Dogru D, Menemenlioglu D, Gur D, Kiper N, Gocmen A (2008) Pleural fluid PCR method for detection of Staphylococcus aureus, Streptococcus pneumoniae and Haemophilus influenzae in pediatric parapneumonic effusions. Respiration 75(4):437–442. https://doi.org/10.1159/000107741

    Article  CAS  PubMed  Google Scholar 

  17. Le Monnier A, Carbonnelle E, Zahar JR, Le Bourgeois M, Abachin E, Quesne G, Varon E, Descamps P, De Blic J, Scheinmann P, Berche P, Ferroni A (2006) Microbiological diagnosis of empyema in children: comparative evaluations by culture, polymerase chain reaction, and pneumococcal antigen detection in pleural fluids. Clin Infect Dis 42(8):1135–1140. https://doi.org/10.1086/502680

    Article  PubMed  Google Scholar 

  18. Maskell NA, Batt S, Hedley EL, Davies CW, Gillespie SH, Davies RJ (2006) The bacteriology of pleural infection by genetic and standard methods and its mortality significance. Am J Respir Crit Care Med 174(7):817–823. https://doi.org/10.1164/rccm.200601-074OC

    Article  PubMed  Google Scholar 

  19. Kommedal O, Kvello K, Skjastad R, Langeland N, Wiker HG (2009) Direct 16S rRNA gene sequencing from clinical specimens, with special focus on polybacterial samples and interpretation of mixed DNA chromatograms. J Clin Microbiol 47(11):3562–3568. https://doi.org/10.1128/JCM.00973-09

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Vondracek M, Sartipy U, Aufwerber E, Julander I, Lindblom D, Westling K (2011) 16S rDNA sequencing of valve tissue improves microbiological diagnosis in surgically treated patients with infective endocarditis. The Journal of infection 62(6):472–478. https://doi.org/10.1016/j.jinf.2011.04.010

    Article  PubMed  Google Scholar 

  21. Light RW (1995) A new classification of parapneumonic effusions and empyema. Chest 108(2):299–301

    Article  CAS  Google Scholar 

  22. Kawanami T, Fukuda K, Yatera K, Kido M, Mukae H, Taniguchi H (2011) A higher significance of anaerobes: the clone library analysis of bacterial pleurisy. Chest 139(3):600–608. https://doi.org/10.1378/chest.10-0460

    Article  PubMed  Google Scholar 

  23. Munoz-Almagro C, Gala S, Selva L, Jordan I, Tarrago D, Pallares R (2011) DNA bacterial load in children and adolescents with pneumococcal pneumonia and empyema. Eur J Clin Microbiol Infect Dis 30(3):327–335. https://doi.org/10.1007/s10096-010-1086-9

    Article  PubMed  Google Scholar 

  24. Johansson N, Kalin M, Giske CG, Hedlund J (2008) Quantitative detection of Streptococcus pneumoniae from sputum samples with real-time quantitative polymerase chain reaction for etiologic diagnosis of community-acquired pneumonia. Diagn Microbiol Infect Dis 60(3):255–261

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

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.

Funding

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

Author information

Authors and Affiliations

  1. Department of Medicine, Solna, Infectious Diseases Unit, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden

    Niclas Johansson, Karin Andersson-Ydsten & Jonas Hedlund

  2. Department of Infectious Diseases, Karolinska University Hospital Solna, SE-171 76, Stockholm, Sweden

    Niclas Johansson, Karin Andersson-Ydsten & Jonas Hedlund

  3. Department of Clinical Microbiology, Department of Microbiology, Tumor and Cell Biology, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden

    Martin Vondracek

  4. Department of Clinical Chemistry, Karolinska University Hospital Solna, Solna, Sweden

    Carolina Backman-Johansson

  5. Respiratory Medicine Unit, Department of Medicine Solna and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden

    Magnus C. Sköld

  6. Lung-Allergy Clinic, Karolinska University Hospital Solna, Stockholm, Sweden

    Magnus C. Sköld

Authors
  1. Niclas Johansson
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Martin Vondracek
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Carolina Backman-Johansson
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Magnus C. Sköld
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Karin Andersson-Ydsten
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Jonas Hedlund
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Niclas Johansson or Jonas Hedlund.

Ethics declarations

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.

Additional information

Publisher’s note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Summary of the article’s main point

Among patients with parapneumonic effusions, bacteria were often detected in pleural fluid, with viridans streptococci and anaerobic species as the most frequently findings. Compared with culture, 16S rDNA sequencing improved the microbiological yield and the specificity seemed to be high.

Electronic supplementary material

ESM 1

(DOC 61 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Johansson, N., Vondracek, M., Backman-Johansson, C. et al. The bacteriology in adult patients with pneumonia and parapneumonic effusions: increased yield with DNA sequencing method. Eur J Clin Microbiol Infect Dis 38, 297–304 (2019). https://doi.org/10.1007/s10096-018-3426-0

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10096-018-3426-0

Keywords

Search

Navigation