STIs
Mycoplasma genitalium PCR (urine)
PCR test for Mycoplasma genitalium in the first part of the urine; most informative with long-lasting urethral symptoms or a treated partner.
Everything about this testWhat it measures
Mycoplasma genitalium is a small bacterium that is transmitted through sex. In men, it can cause inflammation of the urethra; for other symptoms or complications there is no good evidence. More than 90 in 100 infections cause no symptoms, and some clear up on their own. The PCR looks for genetic material of the bacterium in the first part of the urine; that is why you only collect the first part of the stream and, according to the kit instructions, do not urinate for at least 1 hour beforehand.
- An infection with Mycoplasma genitalium of the urethra
- A possible cause of urethritis in men that lasts longer than 4 weeks while chlamydia and gonorrhea have been ruled out or already treated
Positive
A positive result means that the bacterium is present. According to Thuisarts and Soa Aids Nederland, treatment is not medically needed without symptoms: the infection is not dangerous, probably has no effect on fertility and often clears up on its own. Treatment is useful in men with symptoms that have lasted longer than 4 weeks, and if a sexual partner is being treated. The bacterium is often insensitive (resistant) to antibiotics: in Dutch research, 66 percent of the bacteria found had features of resistance to the first-choice drug and 9 percent to the second-choice drug. Unnecessary treatment increases that resistance.
Negative
A negative result means that the bacterium was not found in the urine. How long it takes after infection before the test becomes positive is not known; the LCI guideline (RIVM) calls the incubation period unclear. If you keep having urethral symptoms, the doctor looks for another cause.
Preparation
- Collect the urine when you have not passed urine for at least 1 hour.
- Collect only the first part of the stream, not the middle part.
If your result is abnormal
With a positive result and symptoms, the GP has a separate test for macrolide resistance done if needed, because this PCR does not determine resistance, and usually prescribes a course of antibiotics matched to it; if the symptoms persist, a different antibiotic or referral to a urologist follows. The current sexual partner is informed so they can get tested. Mycoplasma genitalium is not notifiable.
Reliability
The real-time PCR (NAAT) on first-void urine or a genital swab is the way to detect Mycoplasma genitalium. In people without symptoms, a positive result has no proven health benefit, and treatment without symptoms makes resistance increase. This test only shows whether the bacterium is present and does not determine resistance to antibiotics. With a positive result, the guideline often advises a separate test for macrolide resistance (insensitivity to the first-choice drug); the treating doctor requests this separately if needed.
Limitations
- The incubation period is unknown; shortly after a risk contact, the test can miss an infection.
- A positive result does not say whether the bacterium is the cause of symptoms; most people with the bacterium have no symptoms.
- If you urinated less than 1 hour before collecting the sample, or collect more than the first part of the stream, the sample is diluted and the test can miss an infection.
- Urine only tests the urethra. In men who have sex with men, the bacterium is often in the anus, usually without symptoms; that infection is missed with urine.
How common is this
Because Mycoplasma genitalium is not routinely tested for, there are no current national figures. In general practice, the bacterium is found in about 4.5 percent of people tested. In a study at two large Centers for Sexual Health, this was 13.6 percent of women, 8.2 percent of heterosexual men and 20.1 percent of men who have sex with men, usually without symptoms.
Who is this useful for
The result is most informative in men with pain when urinating or discharge from the penis that lasts longer than 4 weeks, when chlamydia and gonorrhea have been ruled out or already treated without success, and in men whose sexual partner is being treated for Mycoplasma genitalium. In people without symptoms, a positive result has no proven health benefit. Urethral symptoms are more often caused by chlamydia or gonorrhea.
Downsides and risks
- A positive result without symptoms can lead to treatment that is not medically needed and that increases the bacterium's resistance to antibiotics.
- A positive result can cause unnecessary worry or tension in a relationship, while the bacterium usually does no harm.
Sources
- RIVM-LCI-richtlijn Mycoplasma genitalium-infectie (2024)
- Multidisciplinaire Richtlijn Seksueel overdraagbare aandoeningen (2024), module C7 Mycoplasma genitalium-infectie
- Thuisarts.nl: Ik heb mycoplasma
- RIVM: Mycoplasma genitalium
- Soa Aids Nederland (professionals): Testen op mycoplasma (bijgewerkt 9 juli 2026)
- Medlab Stein, leistungsverzeichnis: Mycoplasma-genitalium-DNA
Always discuss an abnormal result with your GP. If a result is strongly abnormal, we try to reach you as soon as possible. Read your result yourself as well and contact your GP if in doubt. A test does not make a diagnosis. Read more about risks and results

