Clinical validation of a real-time polymerase chain reaction detection of Neisseria gonorrheae porA pseudogene versus culture techniques

Sex Transm Dis. 2008 May;35(5):517-20. doi: 10.1097/OLQ.0b013e3181644bc9.


Background: Diagnosing Neisseria gonorrheae using nucleic acid amplification tests (NAATs) might increase the sensitivity, compared to cultivation. However, using NAATs has also been problematic mainly due to the close genetic relationships between different Neisseria species, resulting in false positive diagnoses. This study was conducted to clinically validate a previously published real-time polymerase chain reaction (PCR) method targeting the porA pseudogene in N. gonorrheae in comparison to culture techniques.

Methods: In total, 360 samples, urethra (n = 109), rectum (n = 84), pharynx (n = 119), and cervix (n = 48) from 185 males and 57 females, were analyzed using porA pseudogene PCR and cultivation. Sequencing of the entire porA pseudogene and the 16S rRNA gene were used to resolve discrepant results.

Results: Of the 360 samples, 37 were positive by both culture and PCR, however, the PCR identified 15 additional confirmed positive samples. The PCR method showed a sensitivity, specificity, positive predictive value, and negative predictive value of 100% in a preselected population. The preselected population had a true gonorrhea prevalence of 17.4%.

Conclusions: The present porA pseudogene real-time PCR comprises a valuable supplement to the traditional culture techniques for diagnosis of N. gonorrheae, especially for samples from extragenital sites such as pharynx and rectum.

Publication types

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

MeSH terms

  • Culture Techniques / methods*
  • DNA, Bacterial / analysis
  • Female
  • Gonorrhea / diagnosis*
  • Gonorrhea / microbiology
  • Humans
  • Male
  • Neisseria gonorrhoeae / genetics*
  • Polymerase Chain Reaction / methods*
  • Porins / genetics*
  • Predictive Value of Tests
  • Pseudogenes / genetics


  • DNA, Bacterial
  • Porins
  • porin protein, Neisseria