False Postive and Negatives 

The Number One Reason STI Tests Go Wrong

Here is something very few people understand.

Most false negatives in sexual health happen not because the lab made a mistake and not because the test itself malfunctioned.

They happen because people are being tested in the wrong anatomical location.

Bacterial STIs do not magically migrate through the body. They infect the place they are exposed to.

If the exposure happened through oral sex, the infection will be in the throat.

If the exposure happened through receptive anal sex, the infection will be in the rectum.

If the exposure happened through genital sex, the infection will be in the genitals.

Three different locations.

Three different ecosystems.

Three different results.

If a provider uses only urine or a genital swab, they will miss oral and rectal infections every single time. This is not speculation. Large clinical studies confirm it.

For example, research shows that if you only test urine in sexually active men, up to 80 percent of gonorrhea or chlamydia infections are missed because they are in the throat or rectum, not the genitals.

This is exactly what happened to me. Before founding Shameless Care, I used a very well-known online service. They tested my urine and told me I was negative for everything. But I actually had oral gonorrhea. They had simply never tested the site where my infection lived. In fact, because that company did not offer throat swabs at the time, they had functionally never diagnosed oral gonorrhea in the history of their organization.

That is a false negative.

It is the most common false negative in sexual health.

And almost everybody who uses a genital only test experiences it without knowing.

The same logic applies to infections like Mycoplasma genitalium and Trichomonas. If a panel simply does not include them, a person can have the infection and still be told they are “negative.” That is another kind of false negative. You can only diagnose what you actually test for.

But even when the right sites are swabbed and the right infections are included, there are still reasons a test might not match someone’s true infection status.

That brings us to sensitivity and specificity.

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Sensitivity and Specificity

These are the two concepts that determine how good any medical test is.

Sensitivity answers the question:

If the person actually has the infection, how often will the test detect it?

Specificity answers:

If the person does not have the infection, how often will the test correctly be negative?

A test with lower sensitivity will miss infections.

A test with lower specificity will falsely label people as positive.

Modern PCR based STI tests have extremely high specificity. That means false positives are rare. Sensitivity varies more, especially at certain body sites.

For example:

• Pharyngeal (throat) chlamydia NAAT sensitivity ranges from about 70 to 95 percent, depending on the study, the brand of test, and organism load.
• Pharyngeal gonorrhea NAAT sensitivity is usually 85 to 95 percent, but published ranges run from 74 to 100 percent.
• Rectal gonorrhea and chlamydia NAATs generally show sensitivity in the mid-80s to mid-90s.

These results are excellent, but not perfect.

Mycoplasma genitalium tests are also very good, but sensitivity varies by sample type. For example, in women, a vaginal swab detects Mgen at roughly 90 percent sensitivity, while urine is significantly lower and can miss more cases.

Trichomonas testing historically had poor sensitivity with wet mounts and cultures. Modern NAAT testing solves most of that, bringing sensitivity into the mid-90 percent range, but many providers still use older methods.

All of this means one thing:

Modern STI testing is extremely accurate, but not infallible.

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How People and Providers Accidentally Create False Negatives

Even with excellent laboratory technology, human behavior can reduce accuracy.

Here are the most common real-world causes.

Urinating too soon before a urine test

Almost every guideline recommends waiting at least one hour after your last urination before collecting a sample. That’s because you need enough time for organisms to accumulate in the urethra.

Urinating right before a test can flush out or dilute the bacteria and produce a false negative.

Poor sample collection

This matters a lot, especially for throat swabs.

Some clinicians barely touch the swab to the throat for half a second. Others avoid the tonsils because they don’t want to trigger a gag reflex. That swab is unlikely to pick up enough DNA for a high-sensitivity test to work properly.

Proper technique touches both tonsillar pillars and the posterior throat for several seconds.

The difference in accuracy between a good swab and a superficial swab is substantial.

At-home collection works extremely well when done correctly. But rushing the process or barely touching the swab to the site can cause a false negative. The PCR machine does not know whether the patient followed instructions. It only knows whether the organism’s DNA is present.

Testing the wrong site

A urine test cannot detect throat gonorrhea.

A genital swab cannot detect rectal infection.

A blood test cannot detect oral chlamydia.

This is the most preventable cause of false negatives.

Recent antibiotic use

Even a single dose of an antibiotic taken for an unrelated issue can temporarily suppress bacteria enough to produce a negative result, even if the infection is not fully cleared.

Very early infection

If someone tests very soon after an exposure, the organism may not have multiplied to detectable levels. Gonorrhea and chlamydia NAATs generally detect most infections by about a week after exposure and almost all by two weeks. Testing earlier can produce a false negative.

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The Truth

False positives and false negatives exist in every corner of medicine.

The goal is not perfection. The goal is accuracy with the lowest possible risk of error.

Modern PCR based STI testing in a high complexity CLIA certified lab is the best technology we have today. It is extremely accurate.

But the most important ways to reduce the risk of false results are simple.

• Test every site where an infection could be.
• Take your time with sample collection.
• Avoid urinating right before a urine test.
• Retest if your symptoms do not match your results.
• Use a panel that actually includes the infections you care about.

This is the entire philosophy behind Shameless Care.

We want your negative result to mean something.

We want your positive result to be real.

And we want you to understand how these tests work, so you never again mistake a partial test for a complete one.