Mycoplasma Genitalium in South Africa: The STI Most Clinics Miss | Epicentre
⚠ Emerging STI · Often Missed
Mycoplasma Genitalium: The STI Most Clinics Miss
Discovered in 1981. Still not included in standard STI screens. Only PCR can detect it. If you have been treated for chlamydia or gonorrhoea but your symptoms persist, M. genitalium may be the cause. Curable, but antibiotic resistance is rising fast.
✓ Curable with targeted treatment⚠ Rising antibiotic resistance🧬 PCR only (not in standard screens)🏥 No referral needed
MB ChB, FCP (SA) · Medical Director, Epicentre Laboratories
Published: 2 August 2025 · Last reviewed: 1 March 2026
Key facts
What is Mycoplasma genitalium and why does it matter?
1-6%
of sexually active adults carry it
Ona et al., 2016
24%
of HIV+ pregnant women in Cape Town
Smullin et al., 2020
PCR
only way to detect it
Culture and rapid tests fail
⚠
High antibiotic resistance
Resistance-guided therapy now standard
✓
Curable with targeted treatment
From your doctor, guided by PCR
1,400+
Mgen detections at Epicentre in 2025
Across JHB, CPT & DBN labs
Does this sound familiar?
Could Mycoplasma genitalium be causing your symptoms?
M. genitalium is the leading suspect when standard STI treatment fails. These are the patients Epicentre sees most often for Mgen testing.
"I was treated for chlamydia but the discharge and burning won't go away."
This is the most common scenario. Your standard screen tested negative for chlamydia and gonorrhoea, or you completed treatment, but symptoms persist. M. genitalium is the most common cause of non-gonococcal, non-chlamydial urethritis and is only detectable by PCR.
"My partner keeps getting BV or cervicitis and we don't know why."
Recurrent cervicitis and unexplained pelvic pain in women, especially when standard STI tests come back negative, may be caused by M. genitalium. Both partners need PCR testing to break the cycle.
"I tested negative for everything but I still have symptoms."
"Everything" at most clinics means chlamydia, gonorrhoea, and maybe syphilis. Most standard STI panels do not include M. genitalium, Ureaplasma, or Mycoplasma hominis. Epicentre's Medium PCR package covers all three.
"
"M. genitalium is the infection I wish more GPs would test for. I see patients who have been on two or three rounds of antibiotics for 'chlamydia' that was never there. When we run our Medium PCR panel, Mgen lights up. The right diagnosis means the right treatment first time."
Dr. Samantha Naidoo, MB ChB, FCP (SA), Medical Director, Epicentre
Why it gets missed
Why do most clinics not test for Mycoplasma genitalium?
Three reasons combine to make M. genitalium one of the most under-diagnosed STIs in South Africa.
1. Cannot be cultured. Unlike gonorrhoea, M. genitalium does not grow in standard laboratory culture. It is one of the smallest known bacteria and grows extremely slowly. The only reliable detection method is PCR (polymerase chain reaction), which requires specialised equipment.
2. Not in standard STI panels. Most public clinics and many private GPs use syndromic management (treating based on symptoms without testing) or test only for chlamydia and gonorrhoea. M. genitalium is simply not on their radar.
3. Symptoms mimic other infections. M. genitalium causes the same symptoms as chlamydia: discharge, burning, pelvic pain. When a standard chlamydia test comes back positive, the doctor treats for chlamydia. But if M. genitalium is also present, it persists after treatment and the symptoms return.
Epicentre includes M. genitalium in all Medium, Large, and XL PCR panels. This means every patient who orders a Medium package or above is automatically tested for Mgen alongside chlamydia, gonorrhoea, herpes, trichomoniasis, ureaplasma, and more.
Symptoms
What are the symptoms of Mycoplasma genitalium?
Many carriers have no symptoms at all. When symptoms do appear, they closely resemble chlamydia, making clinical diagnosis almost impossible without PCR.
Most women are asymptomatic. When symptoms appear, they often get attributed to chlamydia, BV, or thrush.
💧Abnormal vaginal discharge
🔥Pain or burning when urinating
😖Pain during sex
⚠️Pelvic pain (if ascending to uterus/tubes)
🩸Bleeding between periods or after sex
M. genitalium is the most common cause of persistent urethritis in men when chlamydia and gonorrhoea have been ruled out or treated.
💧Clear or cloudy urethral discharge
🔥Burning or stinging when urinating
🔴Irritation at the tip of the penis
⚠️Symptoms that persist after chlamydia/gonorrhoea treatment
🔍 Could M. genitalium Be Your Missing Diagnosis?
Answer honestly. Confidential. No data stored.
If untreated
What happens if Mycoplasma genitalium goes undetected?
M. genitalium can persist in the body for months or years without symptoms. When it does cause damage, the consequences mirror those of chlamydia.
1
Weeks 1-4: Silent colonisation
The bacteria establish in the urethra, cervix, or endometrium. No symptoms in most people. You are infectious from this point.
2
Months 1-6: Persistent symptoms or chronic carrier state
Some people develop discharge, burning, or pelvic discomfort. Others remain completely asymptomatic but continue to transmit the bacteria to partners. M. genitalium can persist for months to years without treatment.
3
In women: PID and infertility
Ascending infection causes pelvic inflammatory disease (PID), which can lead to tubal scarring, infertility, ectopic pregnancy, and chronic pelvic pain. The same consequences as untreated chlamydia.
4
In men: persistent urethritis and epididymitis
Chronic urethral inflammation that does not respond to standard treatment. Can spread to the epididymis, causing pain and swelling. May affect fertility.
5
HIV risk increased
M. genitalium causes genital inflammation that increases HIV susceptibility and shedding, similar to other STIs.
Get tested
Where can I test for Mycoplasma genitalium in South Africa?
M. genitalium requires PCR testing. It is not included in Epicentre's Small PCR package (4 pathogens) or Express STI (blood). You need the Medium package or above.
Medium PCR (9 pathogens) ⭐ Includes Mgen
R1,508🎓 R1,357
M. genitalium + chlamydia + gonorrhoea + HSV-1 + HSV-2 + M. hominis + Ureaplasma + Trichomoniasis + E. coli. Most popular.
Important: The Small PCR (R1,235) and Express STI (R1,076) do not include M. genitalium. If you specifically want Mgen testing, choose Medium (R1,508) or above.
FAQ
Mycoplasma Genitalium: Your Questions Answered
Why have I never heard of Mycoplasma genitalium?
M. genitalium was only discovered in 1981 and has only recently been recognised as a significant STI. Most public health messaging still focuses on chlamydia, gonorrhoea, and HIV. Many GPs are not yet routinely testing for it. Awareness is growing, but testing infrastructure is lagging behind.
Can standard STI tests detect M. genitalium?
No. M. genitalium cannot be grown in culture and is not detected by rapid tests or standard STI screens. Only PCR testing can identify it. Epicentre includes it in all Medium, Large, and XL packages.
I tested negative for chlamydia and gonorrhoea but still have symptoms. Could this be Mgen?
Yes, this is the most common scenario. M. genitalium is the leading cause of non-gonococcal, non-chlamydial urethritis in men and a significant cause of persistent cervicitis in women. A Medium PCR package at Epicentre will tell you definitively.
Is M. genitalium curable?
Yes, but treatment requires the right antibiotics. M. genitalium has high rates of resistance to common first-line treatments. Your doctor needs the PCR result to choose the correct antibiotics. This is why testing matters.
Why is antibiotic resistance a concern with Mgen?
M. genitalium develops resistance rapidly, partly because it is often treated with the wrong antibiotics (intended for chlamydia or gonorrhoea). PCR-guided treatment, where the right antibiotic is chosen based on the specific diagnosis, is now the standard of care.
Does M. genitalium affect pregnancy?
Yes. Studies in Cape Town found M. genitalium in 24% of HIV-positive pregnant women and 12% of HIV-negative pregnant women. It is associated with preterm birth and may contribute to fertility problems.
How much does M. genitalium testing cost?
Medium PCR (includes Mgen): R1,508. Large: R1,925. XL: R3,305. Students 10% off. Payflex 4× interest-free. Note: Small PCR (R1,235) does not include Mgen. View all packages →
