Mycoplasma genitalium (MG) often has no symptoms but can cause pelvic inflammatory disease, which can leave some women infertile.
MG can be missed - and if it is not treated correctly, it can develop resistance to antibiotics.
The British Association of Sexual Health and HIV is launching new advice.
Its draft guidelines detail how best to spot and treat MG.
What is MG?
Mycoplasma genitalium is a bacterium that can cause inflammation of the urethra in men, causing discharge from the penis and making it painful to urinate.
In women, it can cause inflammation of the reproductive organs (womb and fallopian tubes) too, causing pain and possibly a fever and some bleeding.
You can get it by having unprotected sex with someone who has it. Condoms can prevent this spread.
It was first identified in the UK in the 1980s and is thought to affect 1-2% of the general population.
MG does not always cause symptoms and will not always need treatment, but it can be missed or mistaken for a different sexually transmitted infection, such as Chlamydia.
The BASHH says this is concerning.
Tests for MG have recently been developed but are not available in all clinics yet although doctors can send samples to Public Health England's laboratory to get a diagnostic result.
It can be treated with antibiotics - but the infection is developing resistance to some of these drugs.
'I tested positive for MG'
John - not his real name - contacted the BBC to tell of his experience of having the infection.
"I was diagnosed with MG last year after meeting my new partner.
"We both sensibly got tested and declared clean at the start of the relationship but GUM [genitourinary medicine] clinics don't test for MG, unless you have symptoms.
"So about a month into the relationship I developed the male symptoms - a sharp burning pain while urinating and a pus-like dishcharge from my urethra - but I had no idea what was wrong.
"After a few weeks I tested positive, while my partner was negative, which didn't make sense. She then got tested again and was positive.
"We were put on antibiotics for two weeks but had no sexual contact for five, to make sure we were clean. After further tests we both tested negative but I still had some small amount of leakage which I was told would go away. It eventually cleared.
"Then out of the blue I got a UTI and symptoms were exactly like MG.
"I am now certain it has returned and I am awaiting further test results.
"The GUM clinic refused to retest my partner as she hasn't shown any symptoms.
"I think clinics should test for MG as part of their sexual health screening process, as this would have been picked up at the start for me."
Eradication rates of MG following treatment with one family of antibiotics, called macrolides, are decreasing globally. Macrolide resistance in the UK is estimated at about 40%, say the guidelines.
One particular macrolide antibiotic, azithromycin, still works in most cases however.
Dr Peter Greenhouse, a sexual consultant in Bristol and BASHH member, urged people to take precautions.
"It's about time the public learned about Mycoplasma genitalium," he said.
"It's yet another good reason to pack the condoms for the summer holidays - and actually use them."
'Out of control'
Paddy Horner, who co-wrote the guidelines, said: "These new guidelines have been developed, because we can't afford to continue with the approach we have followed for the past 15 years as this will undoubtedly lead to a public health emergency with the emergence of MG as a superbug.
"Our guidelines recommend that patients with symptoms are correctly diagnosed using an accurate MG test, treated correctly then followed up to make sure they are cured.
"Resources are urgently needed to ensure that diagnostic and antimicrobial resistance testing is available for women with the condition who are at high risk of infertility.
"We are asking the government directly to make this funding available to prevent a public health emergency waiting to happen and which is already spiralling out of control."
Public Health England says testing is available to diagnose MG and any signs of drug resistance, if necessary.
Dr Helen Fifer, consultant microbiologist at Public Health England, welcomed the guidelines, adding: "If you have symptoms of an STI, we recommend you get tested at your local sexual health clinic.
"Everyone can protect themselves from STIs by consistently and correctly using condoms with new and casual partners."