Broad-range 16S rRNA gene polymerase chain reaction for diagnosis of culture-negative bacterial infections

Clin Infect Dis. 2011 Dec;53(12):1245-51. doi: 10.1093/cid/cir692. Epub 2011 Oct 5.


Background: Broad-range 16S ribosomal RNA (rRNA) gene polymerase chain reaction (PCR) is used for detection and identification of bacterial pathogens in clinical specimens from patients with a high suspicion for infection. However, prospective studies addressing the impact and clinical value of broad-range bacterial 16S rRNA gene amplification for diagnosis of acute infectious diseases in nonselected patient populations are lacking.

Methods: We first assessed the diagnostic performance of 16S rRNA gene PCR compared with routine bacterial culture. Second, we addressed prospectively the impact and clinical value of broad-range PCR for the diagnosis of acute infections using samples that tested negative by routine bacterial culture; the corresponding patients' data were evaluated by detailed medical record reviews.

Results: Results from 394 specimens showed a high concordance of >90% for 16S rRNA gene PCR and routine bacterial culture, indicating that the diagnostic performance of PCR for acute bacterial infections is comparable to that of bacterial culture, which is currently considered the gold standard. In thisprospective study, 231 specimens with a negative result on routine bacterial culture were analyzed with PCR, and patients' clinical data were reviewed. We found that broad-range 16S rRNA gene PCR showed a sensitivity, specificity, positive predictive value, and negative predictive value of 42.9%, 100%, 100%, and 80.2% for culture-negative bacterial infections.

Conclusions: This study defines the role of 16S rRNA gene PCR for diagnosis of culture-negative bacterial infections. Our data show that 16S rRNA gene PCR is particularly useful for identification of bacterial pathogens in patients pretreated with antibiotics.

Publication types

  • Comparative Study
  • Evaluation Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacteria / classification*
  • Bacteria / genetics*
  • Bacteria / growth & development
  • Bacteria / isolation & purification
  • Bacterial Infections / diagnosis*
  • Bacteriological Techniques / methods*
  • Humans
  • Molecular Diagnostic Techniques / methods*
  • Polymerase Chain Reaction / methods*
  • Predictive Value of Tests
  • Prospective Studies
  • RNA, Bacterial / genetics
  • RNA, Ribosomal, 16S / genetics*
  • Sensitivity and Specificity


  • RNA, Bacterial
  • RNA, Ribosomal, 16S