Skip to main content

Advertisement

SpringerLink
Log in

16S-ribosomal DNA to diagnose culture-negative endocarditis

  • Published:
Current Infectious Disease Reports Aims and scope Submit manuscript

Abstract

Culture-negative endocarditis (CNE) accounts for 2.5% to 48% of all cases of infectious endocarditis (IE). Prior or concurrent antibiotic treatment at the time blood cultures are taken accounts for 45% to 60% cases of CNE; the remainder are caused by slow-growing and fastidious organisms. Although limited in sensitivity because of potential contaminating bacterial DNA, detection of bacterial 16S ribosomal (r) DNA (from the 16S rRNA gene) is nevertheless more sensitive than culture. It is accomplished by using polymerase chain reaction (PCR) that targets highly conserved regions of the 16S rRNA gene. The identity of noncultivated infecting agents can then be determined by sequencing PCR products and comparing them with known 16S rDNA sequences from a wide range of bacteria. This has served to broaden the etiologic diagnosis of CNE. We review the benefits and limitations of PCR to diagnose IE and we propose advances that will be necessary to secure a place for PCR in guiding 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

Similar content being viewed by others

References and Recommended Reading

  1. Syed FF, Millar BC, Prendergast BD: Molecular technology in context: a current review of diagnosis and management of infective endocarditis. Prog Cardiovasc Dis 2007, 50:181–197.

    Article  PubMed  CAS  Google Scholar 

  2. Prendergast BD: The changing face of infective endocarditis. Heart 2006, 92:879–885.

    Article  PubMed  CAS  Google Scholar 

  3. Von Reyn CF, Levy BS, Arbeit RD, et al.: Infective endocarditis: an analysis based on strict case definitions. Ann Intern Med 94:505–518.

  4. Durack DT, Lukes AS, Bright DK: New criteria for diagnosis of infective endocarditis: utilization of specific echocardiographic findings. Duke endocarditis service. Am J Med 1994, 96:200–209.

    Article  PubMed  CAS  Google Scholar 

  5. Brouqui P, Raoult D: New insight into the diagnosis of fastidious bacterial endocarditis. FEMS Immunol Med Microbiol 2006, 47:1–13.

    Article  PubMed  CAS  Google Scholar 

  6. Li JS, Sexton DJ, Mick N, et al.: Proposed modifications to the Duke criteria for the diagnosis of infective endocarditis. Clin Infect Dis 2000, 30:633–638.

    Article  PubMed  CAS  Google Scholar 

  7. Rice PA, Madico GE: Polymerase chain reaction to diagnose infective endocarditis: will it replace blood cultures? Circulation 2005, 111:1352–1354.

    Article  PubMed  Google Scholar 

  8. Lamas CC, Eykyn SJ: Suggested modifications to the Duke criteria for the clinical diagnosis of native valve and prosthetic valve endocarditis: analysis of 118 pathologically proven cases. Clin Infect Dis 1997, 25:713–719.

    Article  PubMed  CAS  Google Scholar 

  9. Habib G, Derumeaux G, Avierinos JF, et al.: Value and limitations of the Duke criteria for the diagnosis of infective endocarditis. J Am Coll Cardiol 1999, 33:2023–2029.

    Article  PubMed  CAS  Google Scholar 

  10. Shapiro SM, Young E, De Guzman S, et al.: Transesophageal echocardiography in diagnosis of infective endocarditis. Chest 1994, 105:377–382.

    Article  PubMed  CAS  Google Scholar 

  11. Fowler VG, Li J, Corey GR, et al.: Role of echocardiography in evaluation of patients with Staphylococcus aureus bacteremia: experience in 103 patients. J Amer Col Cardiol 1997, 30:1072–1078.

    Article  Google Scholar 

  12. Koegelenberg CF, Doubell AF, Orth H, Reuter H: Infective endocarditis: improving the diagnostic yield. Cardiovasc J S Afr 2004, 15:14–20.

    PubMed  CAS  Google Scholar 

  13. Tariq M, Alam M, Munir G, et al.: Infective endocarditis: a five-year experience at a tertiary care hospital in Pakistan. Int J Infect Dis 2004, 8:163–170.

    Article  PubMed  Google Scholar 

  14. Goldenberger D, Kunzli A, Vogt P, et al.: Molecular diagnosis of bacterial endocarditis by broad-range PCR amplification and direct sequencing. J Clin Microbiol 1997, 35:2733–2739.

    PubMed  CAS  Google Scholar 

  15. Lamas CC, Eykyn SJ: Blood culture negative endocarditis: analysis of 63 cases presenting over 25 years. Heart 2003, 89:258–262.

    Article  PubMed  CAS  Google Scholar 

  16. Werner M, Andersson R, Olaison L, Hogevik H: A clinical study of culture-negative endocarditis. Medicine (Baltimore) 2003, 82:263–273.

    Article  Google Scholar 

  17. Tunkel AR, Kaye D: Endocarditis with negative blood cultures. N Engl J Med 1992, 326:1215–1217.

    PubMed  CAS  Google Scholar 

  18. Fournier PE, Lelievre H, Eykyn SJ, et al.: Epidemiologic, clinical characteristics of Bartonella quintana and Bartonella henselae endocarditis: a study of 48 patients. Medicine (Baltimore) 2001, 80:245–251.

    Article  CAS  Google Scholar 

  19. Maurin M, Raoult D: Bartonella (Rochalimaea) quintana infections. Clin Microbiol 1996, 9:273–292.

    CAS  Google Scholar 

  20. Lang S, Watkin RW, Lambert PA, et al.: Detection of bacterial DNA in cardiac vegetations by PCR after the completion of antimicrobial treatment for endocarditis. Clin Microbiol Infect 2004, 10:579–581.

    Article  PubMed  CAS  Google Scholar 

  21. Gauduchon V, Chalabreysse L, Etienne J, et al.: Molecular diagnosis of infective endocarditis by PCR amplification and direct sequencing of DNA from valve tissue. J Clin Microbiol 2003, 41:763–766.

    Article  PubMed  CAS  Google Scholar 

  22. Casalta JP, Habib G, La Scola B, et al.: Molecular diagnosis of Granulicatella elegans on the cardiac valve of a patient with culture-negative endocarditis. J Clin Microbiol 2002, 40:1845–1847.

    Article  PubMed  CAS  Google Scholar 

  23. Mueller NJ, Kaplan V, Zbinden R, Altwegg M: Diagnosis of Cardiobacterium hominis endocarditis by broad-range PCR from arterio-embolic tissue. Infection 1999, 27:278–279.

    Article  PubMed  CAS  Google Scholar 

  24. Rothman RE, Majmudar MD, Kelen GD, et al.: Detection of bacteremia in emergency department patients at risk for infective endocarditis using universal 16S rRNA primers in a decontaminated polymerase chain reaction assay. J Infect Dis 2002, 186:1677–1681.

    Article  PubMed  CAS  Google Scholar 

  25. Greisen K, Loeffelholz M, Purohit A, Leong D: PCR primers and probes for the 16S rRNA gene of most species of pathogenic bacteria, including bacteria found in cerebrospinal fluid. J Clin Microbiol 1994, 32:335–351.

    PubMed  CAS  Google Scholar 

  26. Meier A, Persing D, Finken M, Bottger EC: Elimination of contaminating DNA within polymerase chain reaction reagents: implication for a general approach to detection of uncultured pathogens. J Clin Microbiol 1993, 31:646–652.

    PubMed  CAS  Google Scholar 

  27. Relman DA, Loutit JS, Schmidt TM, et al.: The agent of bacillary angiomatosis: an approach to the identification of uncultured pathogens. N Engl J Med 1990, 323:1573–1580.

    PubMed  CAS  Google Scholar 

  28. Anderson BE, Dawson JE, Jones DC, Wilson KH: Ehrlichia chaffeensis, a new species associated with human ehrlichiosis. J Clin Microbiol 1991, 29:2838–2842.

    PubMed  CAS  Google Scholar 

  29. Woese CR, Magrun LJ, Gupta R, et al.: Secondary structure model for bacterial 16S ribosomal RNA: phylogenetic, enzymatic and chemical evidence. Nucleic Acids Res 1980, 8:2275–2293.

    Article  PubMed  CAS  Google Scholar 

  30. Corless CE, Guiver M, Borrow R, et al.: Contamination and sensitivity issues with a real-time universal 16S rRNA PCR. J Clin Microbiol 2000, 38:1747–1752.

    PubMed  CAS  Google Scholar 

  31. Podglajen I, Bellery F, Poyart C, et al.: Comparative molecular and microbiologic diagnosis of bacterial endocarditis. Emerg Infect Dis 2003, 9:1543–1547.

    PubMed  Google Scholar 

  32. Millar B, Moore J, Mallon P, et al.: Molecular diagnosis of infective endocarditis—a new Duke’s criterion. Scand J Infect 2001, 33:673–680.

    Article  CAS  Google Scholar 

  33. Bosshard PP, Kronenberg A, Zbinden R, et al.: Etiologic diagnosis of infective endocarditis by broad-range polymerase chain reaction: a 3-year experience. Clin Infect Dis 2003, 37:167–172.

    Article  PubMed  Google Scholar 

  34. Greub G, Lepidi H, Rovery C, et al.: Diagnosis of infectious endocarditis in patients undergoing valve surgery. Am J Med 2005, 118:230–238.

    Article  PubMed  Google Scholar 

  35. Breitkopf C, Hammel D, Scheld HH, et al.: Impact of a molecular approach to improve the microbiological diagnosis of infective heart valve endocarditis. Circulation 2005, 111:1415–1421.

    Article  PubMed  CAS  Google Scholar 

  36. Qin X, Urdahl KB: PCR and sequencing of independent genetic targets for the diagnosis of culture negative bacterial endocarditis. Diagn Microbiol Infect Dis 2001, 40:145–149.

    Article  PubMed  CAS  Google Scholar 

  37. Jaspers E, Overmann J: Ecological significance of microdiversity: identical 16S rRNA gene sequences can be found in bacteria with highly divergent genomes and ecophysiologies. Appl Environ Microbiol 2004, 70:4831–4939.

    Article  PubMed  CAS  Google Scholar 

  38. Wilson KH, Blitchington RB, Greene RC: Amplification of bacterial 16S ribosomal DNA with polymerase chain reaction. J Clin Microbiol 1990, 28:1942–1946.

    PubMed  CAS  Google Scholar 

  39. Houpikian P, Raoult D: Diagnostic methods. Current best practices and guidelines for identification of difficult-to-culture pathogens in infective endocarditis. Cardiol Clin 2003, 21:207–217.

    Article  PubMed  Google Scholar 

  40. Brouqui P, Raoult D: Endocarditis due to rare and fastidious bacteria. Clin Microbiol 2001, 14:177–207.

    Article  CAS  Google Scholar 

  41. Kotilainen P, Jalava J, Meurman O, et al.: Diagnosis of meningococcal meningitis by broad-range bacterial PCR with cerebrospinal fluid. J Clin Microbiol 1998, 36:2205–2209.

    PubMed  CAS  Google Scholar 

  42. Lang S, Watkin RW, Lambert PA, et al.: Evaluation of PCR in the molecular diagnosis of endocarditis. J Infect 2004, 48:269–275.

    Article  PubMed  CAS  Google Scholar 

  43. Marín M, Muñoz P, Sánchez M, et al.: Molecular diagnosis of infective endocarditis by real-time broad-range polymerase chain reaction (PCR) and sequencing directly from heart valve tissue. Medicine (Baltimore) 2007, 86:195–202.

    Article  Google Scholar 

  44. Grijalva M, Horvath R, Dendis M, et al.: Molecular diagnosis of culture negative infective endocarditis: clinical validation in a group of surgically treated patients. Heart 2003, 89:263–268.

    Article  PubMed  CAS  Google Scholar 

  45. Kotilainen P, Heiro M, Jalava J, et al.: Aetiological diagnosis of infective endocarditis by direct amplification of rRNA genes from surgically removed valve tissue. An 11-year experience in a Finnish teaching hospital. Ann Med 2006, 38:263–273.

    Article  PubMed  CAS  Google Scholar 

  46. Hilali F, Saulnier P, Chachaty E, Andremont A: Decontamination of polymerase chain reaction reagents for detection of low concentration of 16S rRNA genes. Mol Biotechnol 1997, 7:207–216.

    Article  PubMed  CAS  Google Scholar 

  47. Carroll NM, Adamson P, Okhravi N: Elimination of bacterial DNA from Taq DNA polymerases by restriction endonuclease digestion. J Clin Microbiol 1999, 37:3402–3404.

    PubMed  CAS  Google Scholar 

  48. Branger S, Casalta JP, Habib G, et al.: Streptococcus pneumoniae endocarditis: persistence of DNA on heart valve material 7 years after infectious episode. J Clin Microbiol 2003, 41:4435–4437.

    Article  PubMed  CAS  Google Scholar 

  49. Rovery C, Greub G, Lepidi H, et al.: PCR detection of bacteria on cardiac valves of patients with treated bacterial endocarditis. J Clin Microbiol 2005, 43:163–167.

    Article  PubMed  CAS  Google Scholar 

  50. van Doorn R, Szemes M, Bonants P, et al.: Quantitative multiplex detection of plant pathogens using a novel ligation probe-based system coupled with universal, high-throughput real-time PCR on Open Arrays. BMC Genomics 2007, 8:276.

    Article  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Medicine, Section of Infectious Diseases, Boston University School of Medicine, Evans Biomedical Research Center Building, Room 616, 650 Albany Street, Boston, MA, 02118, USA

    Guillermo E. Madico

Authors
  1. Guillermo E. Madico
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Peter A. Rice
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Guillermo E. Madico.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Madico, G.E., Rice, P.A. 16S-ribosomal DNA to diagnose culture-negative endocarditis. Curr Infect Dis Rep 10, 280–286 (2008). https://doi.org/10.1007/s11908-008-0046-3

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11908-008-0046-3

Keywords

Search

Navigation