title: Diagnostic implications of 16S ribosomal assay for gonorrhoea.
abstract: OBJECTIVE
  In the absence of a single nucleic acid amplification test (NAAT) that is both highly specific and sensitive for gonorrhoea, many have put forward the 16S-based assay as a confirmatory test for Neisseria gonorrhoeae. This study was undertaken to evaluate the performance of PCR based on 16S ribosomal gene in comparison with a porA pseudogene-based assay.
  
  
  METHODS
  The specificity of both the porA pseudogene-based PCR and 16S ribosomal gene PCR was checked against a panel of strains comprising of non N gonorrhoeae Neisseria sp (NgNS) and other gram-negative and gram-positive bacteria. The sensitivity studies were performed using different dilutions of N gonorrhoeae DNA. PCRs were also done on endocervical and urethral swab samples collected from a total of 100 female and 50 male patients presenting to sexually transmitted disease clinics, Dermatology OPD of AIIMS and Safdarjang Hospital, New Delhi, India, recruited as per inclusion criteria.
  
  
  RESULTS
  PCR assay based on 16S ribosomal gene showed cross-reactivity with three of six strains of N sicca. The porA pseudogene-based PCR was highly specific. Analytical sensitivity of 16S-based ribosomal assay was more than that of porA pseudogene-based assay. In clinical samples, for female patients, sensitivity, specificity, positive predictive value and negative predictive value of 16S ribosomal assay was 100% (95% CI 51.7% to 100%), 91.5% (95% CI 83.4% to 96%), 42.9% (95% CI 18.8% to 70.4%) and 100% (95% CI 94.7% to 100%), respectively, while for the male patients it was 100% (95% CI 85% to 100%), 95.5% (95% CI 75.1% to 99.8%), 96.6% (95% CI 80.4% to 99.8%) and 100% (95% CI 80.8% to 100%), respectively.
  
  
  CONCLUSIONS
  The data presented in this report supports use of 16S ribosomal assay as a screening assay only. The porA pseudogene target is highly specific for N gonorrhoeae and may be used as a supplemental assay.
authors.affiliation: Department of Microbiology, AIIMS, Ansari Nagar, New Delhi 110029, India.
authors.forename: Rachna
authors.initials: R
authors.lastname: Verma
authors.forename: Seema
authors.initials: S
authors.lastname: Sood
authors.forename: Manju
authors.initials: M
authors.lastname: Bala
authors.forename: Arti
authors.initials: A
authors.lastname: Kapil
authors.forename: Bimal Kumar
authors.initials: BK
authors.lastname: Das
authors.forename: Vinod Kumar
authors.initials: VK
authors.lastname: Sharma
authors.forename: Jyotish Chandra
authors.initials: JC
authors.lastname: Samantaray
mesh_terms: D015746:Abdominal Pain / Q000382:microbiology*; D000293:Adolescent; D000328:Adult; D005260:Female; D006069:Gonorrhea / Q000175:diagnosis*; D006801:Humans; D008297:Male; D008826:Microbial Sensitivity Tests; D008875:Middle Aged; D009344:Neisseria gonorrhoeae / Q000235:genetics / Q000302:isolation & purification; D016133:Polymerase Chain Reaction / Q000379:methods; D018272:Porins / Q000235:genetics; D011544:Pseudogenes / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D012680:Sensitivity and Specificity; D014526:Urethritis / Q000175:diagnosis* / Q000382:microbiology; D002577:Uterine Cervical Diseases / Q000175:diagnosis* / Q000382:microbiology; D019522:Vaginal Discharge / Q000175:diagnosis* / Q000382:microbiology; D055815:Young Adult
chemical_list: D018272:Porins; D012336:RNA, Ribosomal, 16S; C057699:porin protein, Neisseria