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Urine based nucleic acid amplification testing in STD

Three Part Question

In [sexually active males presenting to the emergency department with urethral discharge] is [urine based nucleic acid amplification testing alone] enough to [give an accurate diagnosis]?

Clinical Scenario

A 16-year-old male presents to the emergency department on a Friday night with a one-day history of urethral discharge following unprotected sex. The GUM clinic is closed. You wonder if urine based nucleic acid amplification testing will be sufficient to give an accurate diagnosis.

Search Strategy

Medline - 1966 to June week 2 2006
Embase - 1980 to 2006 Week 24
CINAHL - 1982 to June Week 2 2006
The Cochrane Library 2006 Issue 2
Medline/Embase/CINAHL - [exp Chlamydia trachomatis/ OR exp Gonorrhea/ OR exp Chlamydia Infections/ OR exp Urethritis/ OR exp Neisseria gonorrhoeae/ OR exp Sexually Transmitted Diseases/ OR OR OR (urethra$ adj discharge).mp.] AND [exp Urinalysis/ OR nucleic acid amplification test$.mp. OR OR first pass OR urine OR urine] limit to humans, English language and males.
Cochrane: (Chlamydia [MESH] OR chlamydia trachomatis OR non gonococcal OR NGU OR Neisseria gonorrhoeae [MESH] OR gonorrhoea OR gonococcal OR urethritis [MESH]) AND (nucleic acid amplification techniques OR NAAT OR PCR OR LCR)

Search Outcome

Altogether, 134 papers were found in Medline, 409 in Embase, 50 in CINAHL and 16 in Cochrane. Of these, 10 were relevant in Medline, an additional 12 in Embase and none in CINAHL or Cochrane. I relevant paper was a systematic review from 2005, no other relevant papers were published after this.

Relevant Paper(s)

Author, date and country Patient group Study type (level of evidence) Outcomes Key results Study Weaknesses
Cook RL, Hutchison SL, Ostergaard L, Braithwaite RS, Ness RB.
June 2005
29 articles published from 1 January 1991 to 31 December 2004, including symptomatic and asymptomatic persons from several countries.Systematic ReviewPolymerase chain reaction (PCR) testing in men for chlamydiaPooled sensitivity = 84.0% (95% CI, 78.5-89.4) urine sample v. 87.5% (95% CI, 82.4-92.5) urethral sample. Pooled specificity = 99.3% (95% CI, 98.9-99.7) urine sample v. 99.2% (95% CI, 98.8-99.6) urethral sample.Search methods used to locate relevant studies were not fully comprehensive. Did not find any articles which looked at NAATs other than PCR for testing for N.gonorrhoeae.
Transcription-mediated amplification (TMA) testing in men for chlamydiaPooled sensitivity = 87.7% (95% CI, 80.1-95.2) urine sample v. 95.9% (95% CI, 91.3-100) urethral sample. Pooled specificity = 99.4% (95% CI, 98.7-100) urine sample v. 99.4% (95% CI, 98.7-100) urethral sample.
Strand-displacement amplification (SDA) testing in men for chlamydia.Sensitivity = 93.1 (95% CI, 87.7-96.7) urine sample v. 92.4% (95% CI, 86.8-96.2) urethral sample. Specificity = 93.8% (95% CI, 90.7-95.1) urine sample v. 96.3% (95% CI, 94.3-97.8) urethral sample.
PCR testing in men for gonorrhoea.Pooled sensitivity = 90.4% (95% CI, 87.9-92.9) urine sample v. 96.1% (95% CI, 94.4-97.7) urethral sample. Pooled specificity = 99.7% (95% CI, 99.4-100) urine sample v. 99.0% (95% CI, 98.2-99.8) urethral sample.


This study is a good quality systematic review and so gives a high level of evidence. It found that for each of the three tests for C.trachomatis, the sensitivity and specificity was nearly identical when performed on urine samples compared to urethral samples. The only test looked at for gonoorrhoea was PCR and the results for this test were again similar for urine and urethral samples. More research is needed to determine the specificity and sensitivity of other commercially available NAATs when testing for gonorrhoea.

Clinical Bottom Line

Urine-based NAATs are an ideal choice for testing men presenting with urethral discharge in the emergency department.


  1. Cook RL, Hutchison SL, Ostergaard L, Braithwaite RS, Ness RB. Systematic review: noninvasive testing for Chlamydia trachomatis and Neisseria gonorrhoeae. Annals of Internal Medicine. 2005;142(11):914-25