Chlamydia testing: types, accuracy, timing, and necessity

In this chapter, we will talk about chlamydia testing.

Testing is ultimately necessary to establish or rule out a diagnosis of chlamydia. All the other things we covered in earlier chapters, such as:

Symptoms (what you feel)
Signs (what you see)
Statistics (the odds of getting chlamydia), help us go in the right direction with testing and early treatment while we’re waiting for the test results, but they don’t establish the diagnosis

Unlike other infections, chlamydia, if contracted, stays at the point of initial contact, so a negative test of one area of the body doesn’t rule out the possibility of having chlamydia in another area. This means that all “susceptible” areas that came into contact with the partner’s potentially affected areas during sex should be tested.

This section will summarize the different chlamydia tests, when they should be done, and their accuracy. As in previous chapters, tables with statistics will be followed by frequently asked questions from real patients and algorithms for the most common case scenarios.

So, let’s move on!

Timing and accuracy of chlamydia tests

The table below summarizes what is known about timing (how soon the test can be done) and the accuracy of chlamydia tests in various anatomic areas for asymptomatic people.

Please note: If you have symptoms, the test can be done any time, irrespective of the amount of time that has passed since the sexual encounter that you believe may have given you chlamydia.

The table is separated into three columns:

Test area. The area being tested (remember, each area that came with your partner’s potentially infected area during sex need to be tested)
Earliest time. The earliest time after exposure when the test for that area can be performed
Ideal time. The ideal time after exposure for the test for that area to be performed

Please note: the percentages given below are averages and will vary from case to case (various factors, including the testing technique, may affect the results.

	Earliest testing time (after exposure)	Ideal testing time (after exposure)
Genital Swab	2–7 days Likely to detect (no stats on sensitivity)	2 weeks post exposure: 98.3% accuracy
Rectal swab	2–7 days Likely to detect (no stats on sensitivity)	2 weeks post exposure: 94.7% accuracy
Oral swab	2–7 days Likely to detect (no stats on sensitivity)	2 weeks post exposure: 80% accuracy
Urine test	2–7 days Likely to detect (no stats on sensitivity)	2 weeks post exposure: 94.3% accuracy

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Frequently Asked Questions

Here we summarize real patients’ questions, grouped by topic, and Dr. Fuzayloff’s answers to them. “Dr. F” (his patients’ name for him) has been an STD doctor for over two decades in Midtown Manhattan, NYC.

Who should be tested for chlamydia?

Chlamydia is an extremely common condition and it often has no noticeable signs or symptoms. That is why chlamydia testing is recommended for both symptomatic and asymptomatic people who fall into any of the following categories:

Asymptomatic people
	Characteristics	Schedule
Preventive testing for general population	Sexually active females who are younger than 25	Once a year
	People who have had unprotected sex with a new partner	2–3 weeks after unprotected sex
	People who have a chlamydia- ositive partner	2–3 weeks after unprotected sex

Testing for high-risk individuals	People with multiple sex partners	Once a year
	Sexually active MSM	Once a year (for those who use drugs and/or have multiple sex partners, screening is recommended once every 3–6 months)
	Pregnant females engaging in high- risk behavior (having a partner with an STD, having multiple partners, using drugs, etc.) or living in a chlamydia-prevalent area	First trimester, and also during the last trimester for females engaging in high-risk behavior or living in a chlamydia -prevalent area

Symptomatic
Sexually active people who have chlamydia-related signs and symptoms (swollen, red pharynx; fever; pus-filled patches on the throat, etc.) can be tested at any time, irrespective of the time that has passed since the exposure. The test is reliable if chlamydia is detected. If the test is negative and it was performed earlier than generally advised time (2 weeks after contact), it should be repeated to rule out chlamydia.

How are chlamydia test results interpreted?
We will talk about three different scenarios for chlamydia test results and what they mean.
1. Positive chlamydia test
If a chlamydia test (swab or urine) is positive, you are considered positive and need to be treated, and your partner needs to be notified.
2. Negative chlamydia test
If a chlamydia test is performed and is negative, that generally means you do not have chlamydia.
But two things need to be considered:
- Timing of the test. Has enough time passed after a sexual encounter for the test to be most accurate? Two to three weeks post exposure is the ideal time to get tested.
- The overall accuracy of the particular test performed: 98.3% accuracy for the urine test versus 94.3% accuracy for the swab test.
3. Inconclusive or equivocal chlamydia test
If the test results are not conclusive, the test needs to be repeated.

For all inconclusive tests:
- the ideal test needs to be performed (swab)
- after the ideal incubation period (2–3 weeks)
- both an alternative test and the test that had inconclusive results should be performed
Should I have a urethral swab test or urine test?
A chlamydia test is point-of-contact test. Here, we are comparing the swab test and the urine test for urethral chlamydia only. The oral and rectal areas can be tested only with a swab test. Both the swab test and urinalysis are widely used in the diagnosis of urethral chlamydia.

Below we summarize the key points to consider when comparing the two test types and choosing between them.
Accuracy
Urethral chlamydia swab tests are more accurate than urine tests (99% versus 79%).
Pain and discomfort
The urine test is simpler to perform since it is not invasive, and it doesn’t cause any pain.
Things to consider regarding the swab test
- Males: mildly painful test; privacy issue (must expose the genitals)
- Females: privacy issue (must expose genitals)
How to choose
The urine test is simpler to perform since it is not invasive, and it doesn’t cause any pain.
Screening only
- Male: urine test
- Female: urine or swab
Partner is positive for chlamydia
- Male: urine or swab
- Female: swab and urine
Since the swab test is more accurate, why is the urine test still being offered?
Though swab tests are more accurate in the detection of genital chlamydia (especially for females), sometimes people choose to take the urine test for one or more of the following reasons:
1. The urine test is noninvasive
Urine chlamydia tests are noninvasive and totally free of any discomfort. By contrast, the swab test may cause mild pain for males and (rarely) vaginal bleeding during the procedure for females.
2. Cost
Swab tests are more expensive than urine tests.
3. Availability and simplicity
Urine tests are easier to perform and more widely available than swab tests (you can get a urine test at almost any health facility).
How reliable (accurate) are chlamydia tests?
Chlamydia tests are considered reliable for establishing a diagnosis. The reliability (accuracy) of the chlamydia test is based on three main factors:
1. 1. The type of test performed (urine vs. swab)
2. 2. The time that has passed from the possible chlamydia exposure (2–3 weeks after exposure is ideal)
3. 3. Preparation before the test (avoid douching or using vaginal creams for 24 hours, and avoid urinating for 2 hours before a urine test)
4. 4. The test technique—it should be properly collected.
Assuming ideal circumstances in compliance with the points above, the urine and swab tests will have 94.3% and 98.3% accuracy, respectively.
How is the swab test done in females?
The test is performed by a doctor. It takes two minutes to perform the test. A sample of fluid from the vagina and/or the cervix will be collected by a sterile thin cotton swab (the procedure is illustrated below). The procedure might cause very mild discomfort. If the area is infected and the mucosa is fragile, swabbing might cause minor spotting afterward (this is not common). Remember: you should not use vaginal creams or practice douching 24 hours before being tested.
Image source:
Chlamydia / N. Gonorrhoeae RNA, TMA - Unisex Collection | Diagnostic Laboratory of Oklahoma. https://www.dlolab.com/chlamydia-n-gonorrhoeae-rna-tma-unisex-collection
How is the swab test done in males?
A thin sterile cotton swab is inserted into the tip of the penis, three fourths of an inch into the urethra, to collect urethral fluid. The test is very quick—about 15 to 30 seconds long—and performed by a doctor. Mild discomfort at the time of the procedure is possible.
Image source:
Chlamydia / N. Gonorrhoeae RNA, TMA - Unisex Collection | Diagnostic Laboratory of Oklahoma. https://www.dlolab.com/chlamydia-n-gonorrhoeae-rna-tma-unisex-collection
What is the swab test called?
The chlamydia swab test has several names that are used interchangeably by different labs:
- Chlamydia NAAT test
- Chlamydia Nucleic Acid Amplification Test
- Chlamydia DNA probe test
- CT TMA
- CT Aptima
What is the urine test called?
The chlamydia urine test has a couple of interchangeable names:
- Chlamydia NAAT test
- Chlamydia Nucleic Acid Amplification Test
Where can I get tested for chlamydia?
Where you can get tested depends on the type of test you choose:
Urine test
- Can be done in any health facility, including urgent care clinics, STD clinics , and the offices of primary care physicians, urologists, and gynecologists.
Swab test
- Not every health care facility carries swab kits and has a healthcare professional who performs the swab test. Swabs are mostly performed at STD clinics, Planned Parenthood offices, city sexual health clinics, and urology and gynecology clinics.
Is chlamydia testing covered by health insurance?
Chlamydia testing is considered medically necessary and usually covered by health insurance. It can be done as many times as necessary.

If you want to be sure, call your insurance company and inquire about the following:
- The preferred lab for your plan
- If a copay, coinsurance, or deductible applies
Who should get tested for oral or rectal chlamydia?
Oral (pharyngeal) chlamydia is a common condition that affects up to 1.4% of MSMs (homosexual males) and 3%–4% of heterosexual males and females. According to international guidelines, the pharyngeal (oral) swab test for chlamydia is recommended to all persons who:
- Have oral chlamydia signs and symptoms (swollen, red pharynx; fever; pus-filled patches on the throat, etc.), and
- Engaged in a risky behavior (oral sex)
According to the CDC, the oral chlamydia screening test is recommended to the following:
- MSMs who have practiced oral sex in the preceding year. Moreover, a screening test every 3–6 months is recommended to MSMs who use methamphetamine, have sex with multiple partners, and/or have a partner who does either
- People with HIV
Remember: chlamydia bacteria are stored locally (in mucosal cells of the area of exposure), and by getting a genital swab, urine, or blood test you cannot identify oral (pharyngeal) chlamydia.
Is retesting for genital chlamydia recommended after treatment?
No retesting after treatment is recommended. Patients with genital chlamydia who have completed the prescribed treatment and have no symptoms of infection do not need to get a test to find out if they are cured.
If you choose to get retested after the treatment
- The kind of test used to diagnose you with chlamydia initially (urine or swab) can be done to confirm recovery. The test can be performed not earlier than 3 weeks and not later than 3 months after treatment. It is your choice to get retested for genital chlamydia recovery.
In general, people who have tested positive for chlamydia need to be tested more frequently because they are considered at higher risk to get it again. Retesting is advised every 3 months.
What type of tests are used for resistant cases?
The NAAT test is considered the gold standard for resistant chlamydia cases. This test has over 99% and 97% specificity and sensitivity, respectively, and should tell you which antibiotic is best for the chlamydia you have.

The NAAT test detects 20%–50% more chlamydial infection than a chlamydial culture test.
A strict protocol should be followed before chlamydia is considered resistant:
1. 1. Received the gold-standard treatment of azithromycin 1 gm once — 5.7% of chlamydia cases are resistant* to the gold-standard treatment.
2. 2. Waited a week after treatment before being sexually active again.
3. 3. Avoided sex with a partner until the partner was tested and treated. The partner should be tested 2–3 weeks after the last exposure, in case infection was passed then.
*Usually, treatment failure is associated with reinfection, not antibiotic resistance.