Specimen Collection for Urethral Discharge and Discolored Urine
Obtain a first-void urine specimen using nucleic acid amplification testing (NAAT) rather than a urethral swab, as this is the CDC-recommended approach for both symptomatic and asymptomatic men with suspected urethritis. 1
Rationale for First-Void Urine Over Urethral Swab
The CDC explicitly recommends against urethral swabs for screening when urine NAAT is available, citing poor patient acceptability with no diagnostic advantage. 1
First-void urine NAAT demonstrates sensitivity of 86-100% and specificity of 97-100% for detecting chlamydia and gonorrhea in men. 1
Urethral swabs cause significant patient discomfort without improving diagnostic yield compared to modern NAAT testing on urine. 2
Clinical Algorithm for This Patient
Step 1: Collect first-void urine specimen
- Instruct the patient to collect the first 10-20 mL of urine after holding for at least 2 hours without voiding 2, 3
- This specimen should be tested using NAAT for both Chlamydia trachomatis and Neisseria gonorrhoeae 1
Step 2: Consider additional testing based on sexual history
- Even though the patient denies current sexual activity, discolored urethral discharge strongly suggests sexually transmitted urethritis rather than simple urinary tract infection 2
- The absence of urgency and abdominal pain makes bacterial cystitis less likely 2
Step 3: Test for additional pathogens if initial testing is negative
- If chlamydia and gonorrhea testing is negative but symptoms persist, consider testing for Mycoplasma genitalium and Trichomonas vaginalis, which also cause urethritis 4
Critical Pitfalls to Avoid
Do not rely on older testing methods such as enzyme immunoassay (EIA) or direct fluorescent antibody (DFA) tests, which have only 70-80% sensitivity compared to 90%+ for NAATs. 1
Do not use point-of-care tests for chlamydia screening, as these demonstrate unacceptably low sensitivity of only 12-62.9%. 1
Do not dismiss the possibility of STI simply because the patient denies recent sexual activity—urethral discharge with discolored urine is highly suggestive of sexually transmitted urethritis, and infections may have been acquired weeks to months prior. 2
Avoid collecting midstream urine for STI testing, as first-void urine contains higher concentrations of urethral organisms and is the validated specimen type for NAAT testing in men. 1, 3
Follow-Up Testing Considerations
If the patient tests positive, retest at 3 months regardless of treatment, as reinfection rates are highest during this period. 1
Delay any post-treatment testing for at least 3 weeks after completing antimicrobial therapy to avoid false-positive results from residual nucleic acid. 1
Why Not a Urethral Swab?
The 1993 CDC guidelines noted that urethral swabs in men were uncomfortable and had relatively low yield, particularly in asymptomatic cases 2. With the advent of highly sensitive NAAT technology, modern guidelines have definitively shifted away from urethral swabs in favor of first-void urine, which provides equivalent or superior diagnostic accuracy without patient discomfort. 1 Research confirms that first-void urine is the optimal specimen for detecting both C. trachomatis and M. genitalium by PCR in men 4.