The 14-Pathogen PCR STI Test: What It Detects and How to Read It

Testing for sexually transmitted infections doesn't have to be painful or embarrassing. These days, many infections can be detected from just a few millilitres of urine using PCR, which looks directly for the organism's genetic material. I use this kind of test very often, both at the clinic and with samples sent by post. But what I want everyone to understand before testing is "what the results mean", because the 14 organisms on the list don't all carry the same weight.

What is a multiplex PCR test?

PCR, or a nucleic acid amplification test (NAAT), copies an organism's genetic material until there's enough to detect. A multiplex test checks for many organisms at once in a single tube. It's highly accurate, picks up infections even without symptoms, and doesn't require culture. CDC and WHO guidelines now consider NAAT the standard method for testing for gonorrhoea and chlamydia.

The 14 organisms, in 3 groups

Group 1: Clear pathogens that need treatment (and partner treatment) if found

• Neisseria gonorrhoeae: gonorrhoea. Read more in gonorrhoea: symptoms, testing and treatment.
• Chlamydia trachomatis: chlamydia, common and often symptom-free.
• Mycoplasma genitalium: one cause of non-gonococcal urethritis that is becoming harder to treat because of antibiotic resistance.
• Trichomonas vaginalis: trichomoniasis; men can be infected too.

Group 2: Results that need to be read alongside symptoms

• Herpes simplex virus 1 and 2: herpes. The most accurate test is a swab taken directly from a sore or blister. A urine test when there are no sores may miss the virus even if you're infected. See more in herpes.
• Treponema pallidum: the syphilis bacterium. PCR works well on a swab from a sore, but it is often not detected in urine. Screening for syphilis always requires a blood test. Read syphilis: symptoms, stages and testing.
• Haemophilus ducreyi: the cause of chancroid, very rare nowadays.

Group 3: Organisms found in healthy people (usually no treatment needed without symptoms)

• Ureaplasma urealyticum, Ureaplasma parvum, Mycoplasma hominis are found in the reproductive tracts of many people without causing disease. European (IUSTI) and CDC guidelines don't recommend testing for or treating them when there are no symptoms.
• Gardnerella vaginalis is associated with bacterial vaginosis (an imbalance of vaginal bacteria), but finding the organism alone is not a diagnosis.
• Candida albicans is a yeast normally present in the body, treated only when there is itching or abnormal discharge.
• Streptococcus agalactiae (Group B Strep) is found in the gut and vagina and matters especially in late pregnancy.

Treat if found

and treat partners

• N. gonorrhoeae (gonorrhea)
• C. trachomatis (chlamydia)
• Mycoplasma genitalium
• Trichomonas vaginalis

Read with symptoms

• HSV-1, HSV-2 (best from a sore swab)
• T. pallidum (syphilis needs a blood test)
• H. ducreyi (chancroid, rare)

Found in healthy people

usually no treatment if no symptoms

• Ureaplasma (2 types), M. hominis
• Gardnerella vaginalis
• Candida albicans
• Group B Strep (matters in pregnancy)

IUSTI and CDC advise against testing or treating group 3 without symptoms. Have a doctor interpret results first.

How to collect urine for accurate results

The sample needed is first-catch urine, not the midstream urine used for routine urine tests.

1. Don't urinate for at least 1–2 hours before collecting. First thing in the morning is most convenient, but other times of day are fine.
2. Don't wash or wipe your genitals before collecting.
3. Collect only the first 10–20 ml of urine into the sterile container the clinic provides. You don't need to fill it.
4. Close the lid tightly, label it and send it promptly as the clinic instructs.
5. Women may use a self-collected vaginal swab, which is as accurate as or better than urine.

What urine can't test for

• Throat and rectum. If you have oral or anal sex, add throat and rectal swabs, because gonorrhoea and chlamydia at these sites usually cause no symptoms and won't show up in urine.
• HIV, syphilis, hepatitis B and C require a blood test. Read about testing times in HIV incubation and window periods.
• HPV. Women are screened through cervical screening, and some men who have sex with men may consider anal cancer screening.

Can I test too early?

PCR can detect gonorrhoea and chlamydia from about 1–2 weeks after exposure. Testing earlier than that can give a false negative. I usually advise testing about 2 weeks after a risk, or immediately if you have symptoms. After treatment, don't retest too soon, because PCR may still pick up genetic material from dead organisms for about 3–4 weeks.

1. < 1 week
   Too early

   May give a false negative; test now if you have symptoms

2. 1–2 weeks
   Can start to detect

   PCR can pick up infection from this point

3. ~2 weeks
   Recommended time to test

   After the exposure

4. 3–4 weeks
   After treatment, don't retest yet

   PCR may still detect dead bacteria

5. ~3 months
   Retest after treatment

   Because reinfection is common

If your result is positive, what next?

• Your doctor will explain which group the organism belongs to and whether it needs treatment.
• If treatment is needed, sexual partners from the past 60 days should also be tested and treated so you aren't reinfected. Read about talking to your partner in when your partner has an STI.
• Avoid sex during treatment until your doctor says it's safe.
• Retest at about 3 months, because reinfection is common.

Services at Dr. Kris Clinic

The clinic offers multi-pathogen PCR testing both in person and with samples sent by post (within Thailand), processed by a standard laboratory, with a doctor to interpret results and plan treatment. I'll help you choose which additional sites to test and which blood tests to add, so testing is worthwhile and doesn't miss important infections. English-speaking consultations are available. For an overview of common infections, see common sexually transmitted infections.