Mycoplasma genitalium

You can get tested for chlamydia and gonorrhea, get a clean result, and still be carrying a sexually transmitted infection that was never checked. Mycoplasma genitalium is that infection, and in many clinics it is simply not part of the routine panel.

This matters because the organism is a leading cause of urethritis in men and is linked to inflammation of the reproductive tract in women. Knowing whether you carry it, and whether it is drug resistant, changes how it should be treated.

What This Test Actually Detects

MG (Mycoplasma genitalium) is one of the smallest known bacteria, first identified in men with urethral inflammation in 1981. It is not something your body produces. It is a germ passed through sexual contact that settles in the lower genital and urinary tract.

Because this bacterium grows extremely slowly and is very hard to culture in a lab, the test does not try to grow it. Instead it looks for the organism's genetic material in your urine using a technique that copies and detects tiny amounts of bacterial DNA or RNA (called a nucleic acid amplification test, or NAAT). A result is essentially yes or no: the organism is detected, or it is not.

That framing matters. This is not a test where a number goes up or down. There is no healthy range and no target level. The meaningful finding is presence, especially when it comes alongside symptoms or a drug-resistance marker.

Urethritis in Men

The clearest link is to nongonococcal urethritis, the irritation and discharge that comes from the urethra without gonorrhea being the cause. The CDC estimates MG accounts for 15% to 25% of nongonococcal urethritis cases in the US, and in one large US clinical study men diagnosed with urethritis were about three times as likely to carry MG (odds ratio 2.97). Among men attending sexual health clinics, surveillance found the organism in over a quarter of urethritis cases (26.8%).

Urine works well for detecting the organism in men, and the amount of bacteria tends to be higher in men with urethral symptoms than in men without them. If you have unexplained urethral irritation and standard tests came back negative, this is a specific answer worth having.

That said, most infected men have no symptoms. In one British population survey, 94.4% of men carrying MG reported no sexually transmitted infection symptoms at all. A positive result does not mean you will feel sick, and feeling fine does not mean you are clear.

Reproductive Risks in Women

In women, the organism is tied to inflammation deeper in the reproductive tract. A 2015 meta-analysis found that MG infection was associated with cervicitis (inflammation of the cervix, about 66% higher odds, pooled odds ratio 1.66) and pelvic inflammatory disease (pooled odds ratio 2.14). A more recent 2024 meta-analysis found a somewhat lower pooled odds ratio for pelvic inflammatory disease of 1.67, so the size of that link is still being refined.

The most consistently replicated pregnancy signal is preterm birth, with pooled estimates landing near 1.8 to 2.3 times the odds. Evidence for miscarriage is genuinely mixed: one meta-analysis found increased risk while others found no clear link, so this remains uncertain. Estimates for infertility vary widely, from roughly 2.4 to 13 times the odds, with wide uncertainty around those figures.

These female associations come from observational studies, many of which did not fully account for other risk factors, so causation is less settled than the male urethritis link. The direction of the evidence still points toward real reproductive tract harm.

Why Drug Resistance Is Part of the Picture

The single most practical reason to know your MG status is that this organism is frequently resistant to the antibiotic most often used to treat it. Resistance comes from changes in a specific bacterial gene (the 23S rRNA gene) that blunt azithromycin, a common first-line macrolide antibiotic.

Across many settings, resistance in urine-detected infections is common, reported at 56% in one Danish region, 63.6% in Saskatchewan, and higher still in some groups. In the US, macrolide resistance ranges from about 44% to 90%. In men with urethritis, those carrying a resistant strain were far more likely to stay symptomatic after standard treatment: about 40% saw no improvement, versus 14% with a drug-susceptible strain.

This is why some tests report both the organism and its resistance mutations from the same urine sample. Knowing resistance up front lets treatment be chosen correctly the first time instead of guessing and failing. Because of this resistance, the CDC no longer recommends single-dose azithromycin and instead favors resistance-guided treatment.

A Negative Urine Result Does Not Cover Every Site

Urine samples the urethra. It does not sample the rectum, and in men who have sex with men, rectal infection is often more common than urethral infection. In a Swedish study, positivity was 3.9% in urine versus 7.6% in rectal samples. Similar gaps appeared in Melbourne (2.7% urine vs 7.0% rectal) and across European sites.

In women, urine is a workable specimen but less sensitive than a vaginal swab. A clean urine result is reassuring, but it reflects that one specimen, not every possible site of infection.

Why One Reading Is Not the Whole Story

Unlike a cholesterol number you trend over years, MG testing answers a point-in-time question: is the organism here right now. A single negative is a genuine snapshot, not something you track quarterly. The value in retesting is tied to specific events, not a routine calendar.

Retest when circumstances change: after a new or untreated partner, after possible exposure, or after treatment to confirm the infection actually cleared. A follow-up test after therapy (a test of cure) is especially useful given how often resistant strains persist. In studies, patients who stayed positive after azithromycin were consistently infected with resistant strains.

Major guidelines, including the CDC, do not recommend routine screening of people without symptoms. Testing is generally driven by symptoms, a partner's diagnosis, or a possible exposure rather than a fixed interval for its own sake. If you are actively managing sexual health with multiple partners, testing alongside your other STI checks after an exposure is reasonable.

What to Do With an Unexpected Result

A positive urine test means the organism was detected in your genitourinary tract. The next step is not to panic but to get treatment guided by resistance information, because empiric azithromycin frequently fails. If your test did not already include resistance mutation testing, that is the first thing to add before choosing an antibiotic.

Pair the result with the rest of the picture. Because symptoms of MG, chlamydia, gonorrhea, and trichomonas overlap and cannot be told apart without testing, a full STI panel helps confirm whether you have coinfection. Coinfection is not rare: in one Danish study, 17% of chlamydia-positive urine samples also carried MG. If you are a man who has sex with men, discuss rectal sampling with a clinician, since urine alone can miss infection there.

A licensed clinician should interpret a positive result in the context of your symptoms, exposure sites, pregnancy status, coinfections, and local resistance patterns, and should also address partner treatment to prevent reinfection.

When a Result Can Mislead You

A few situations make a single urine reading less reliable:

• Wrong site sampled: urine checks the urethra only. Rectal and cervical infections can be missed, so a negative urine test does not rule out infection elsewhere.
• Lower sensitivity in women: female urine catches fewer infections than a vaginal swab. In one large US study using the same assay, urine sensitivity in women was 77.8% versus 98.9% for a self-collected vaginal swab, so a negative female urine result is weaker evidence than a negative male urine result.
• Very low organism amounts: when bacterial levels are low, both detection and resistance testing become less certain, which can produce borderline or missed results.
• Assay differences: not all lab methods perform equally. Some older PCR-based tests detected far fewer infections than newer methods, so results can vary by which test a lab uses.

None of these change whether you truly carry the organism. They change whether a single urine sample reliably captures it.