Hidden infections and urethritis: why urine PCR-testing (NAAT) is the key diagnostic method

Hidden infections and urethritis: why urine PCR-testing (NAAT) is the key diagnostic method

December 22, 2025

Many patients believe that if urethral discharge is not purulent, the infection is not serious. However, the symptoms of urethritis can be highly misleading. The clinical syndromes of gonococcal and nongonococcal urethritis often overlap and cannot be reliably distinguished based on patient complaints alone. The greatest danger is that the infection may proceed as a hidden infection.

Relying only on urethritis symptoms is insufficient because:

  1. High risk of asymptomatic course: Up to 42% of men with laboratory-confirmed nongonococcal urethritis (NGU) and 5–10% of men with gonococcal urethritis may be asymptomatic. Therefore, the absence of dysuria in men or visible discharge does not exclude the presence of infection
  2. Nonspecificity of signs: Although an acute onset with purulent discharge may suggest gonorrhea, and dysuria in men without discharge may suggest chlamydia, these signs are not definitive

The diagnosis of urethritis requires detection of objective signs of inflammation. The diagnosis is confirmed if, in a symptomatic patient, at least one of the following is found:
• Presence of mucoid, mucopurulent, or purulent urethral discharge on examination
• A positive leukocyte esterase test or detection of ≥10 white blood cells (WBCs) on microscopy of the sediment from the first-void urine sample

To accurately identify the causative agent of urethritis in men, additional microbiological testing is required to rule out hidden infections.

The most sensitive and specific method for identifying pathogens (such as N. gonorrhoeae and C. trachomatis) is nucleic acid amplification testing (NAAT). **This method, often known to patients as a urine PCR test, is preferred because it is less invasive than obtaining a urethral swab. **The analysis uses the first-void urine sample (the first 10–20 mL), collected without prior cleansing of the urethral meatus, ideally at least one hour after the previous urination. Some specialists also recommend including testing for Mycoplasma genitalium (using NAAT) at the initial visit, as it is one of the key causative agents of nongonococcal urethritis.

External symptoms of urethritis cannot be relied upon due to their nonspecificity and the risk of hidden infections. Only accurate diagnosis using urine PCR testing (NAAT) allows identification of specific pathogens such as N. gonorrhoeae and C. trachomatis.

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