Mycoplasma Genitalium: Symptoms, Testing & Treatment
It's one of the most common bacterial STIs in the country, it causes real symptoms, and it's not on the standard STI panel — which is why so many people bounce between clinics with "mystery" urethritis before anyone names it. If that's you, this page is the map.
The short version
- Mycoplasma genitalium (MGen) is a sexually transmitted bacterium that causes persistent urethritis in men and cervicitis — sometimes pelvic inflammatory disease — in women.
- Standard gonorrhea/chlamydia panels don't detect it; diagnosis needs a specific NAAT test you usually have to ask for by name.
- Doxycycline alone cures it only about a third of the time. Current CDC guidance is resistance-guided two-step therapy — which antibiotic comes second depends on resistance testing.
Symptoms — and the classic "everything's negative" story
In men, MGen typically shows up as urethritis: burning with urination, discharge, or penile discomfort that lingers. In women: unusual discharge, bleeding between periods or after sex, pelvic pain — and untreated, it can ascend into pelvic inflammatory disease with its fertility risks. The classic story goes like this: symptoms appear, the standard STI panel comes back negative, symptoms persist or return. When that's happened to you more than once, MGen is the test to request.
Testing: you have to ask for it
MGen can't be cultured in a routine lab — diagnosis requires a nucleic acid amplification test (NAAT), and FDA-cleared versions exist but aren't included in default STI panels. That means two things. First, a "full panel" that came back clean did not rule out MGen. Second, when you ask, ask specifically: a Mycoplasma genitalium NAAT, ideally with macrolide-resistance testing. The resistance result matters because it dictates treatment. (Note the similar-but-different ureaplasma — same testing limbo, different bacteria, different rules about when to treat.)
Treatment: why the two-step approach exists
MGen shrugs off antibiotics at rates that would alarm most prescribers. Single-dose azithromycin — the old default — fails so often against resistant strains that guidance moved on. Doxycycline alone clears only about 30–40% of infections. The current CDC-recommended approach is resistance-guided sequential therapy:
| Resistance result | Regimen |
|---|---|
| Macrolide-sensitive | Doxycycline 100 mg twice daily × 7 days, then azithromycin |
| Macrolide-resistant (or unknown) | Doxycycline 100 mg twice daily × 7 days, then moxifloxacin 400 mg daily × 7 days |
The lead-in week of doxycycline lowers the bacterial load so the second drug can finish the job. Partners need treatment too, sex pauses until both are done, and a test of cure (about three weeks after finishing) is genuinely recommended here — unlike most STIs — because failure is common enough to check for.
MGen and DoxyPEP: an honest gap
If you're on DoxyPEP, here's the candid picture: single 200 mg doses of doxycycline after sex are not a reliable MGen strategy, and MGen's doxycycline resistance is part of why researchers watch DoxyPEP's resistance footprint so carefully. DoxyPEP remains strongly protective against syphilis and chlamydia; MGen is simply not one of its wins. What protects you here is testing when symptoms appear and insisting on the right test.
When to get seen
Persistent urinary or genital symptoms with negative standard panels; symptoms that returned after a treatment course; a partner diagnosed with MGen; or pelvic pain in women — all four warrant a visit and a specific MGen NAAT request. Our telehealth team orders the right test and manages the sequential treatment, including partner strategy — start a consult here.