How to test for chlamydia

Chlamydia (Chlamydia trachomatis) is the most common sexually transmitted disease (STD) that can infect both men and women in the United States, with 1,708,569 cases reported in 2017 ¹. Chlamydia can also be easily cured. Chlamydia can cause serious, permanent damage to a woman’s reproductive system if left untreated. If you are a woman, untreated chlamydia can spread to your uterus and fallopian tubes (tubes that carry fertilized eggs from the ovaries to the uterus). This can cause pelvic inflammatory disease (PID). Pelvic inflammatory disease often has no symptoms, however some women may have abdominal and pelvic pain. Even if it doesn’t cause symptoms initially, pelvic inflammatory disease can cause permanent damage to your reproductive system. Pelvic inflammatory disease can lead to long-term pelvic pain, inability to get pregnant, and potentially deadly ectopic pregnancy (pregnancy outside the uterus). Men rarely have health problems linked to chlamydia. Infection sometimes spreads to the tube that carries sperm from the testicles, causing pain and fever. Rarely, chlamydia can prevent a man from being able to have children.

Chlamydia can also cause a potentially fatal ectopic pregnancy (pregnancy that occurs outside the womb). Untreated chlamydia may also increase your chances of getting or giving HIV – the virus that causes AIDS.

Laboratory tests can diagnose chlamydia. Your health care provider may ask you to provide a urine sample or may use (or ask you to use) a cotton swab to get a sample from your vagina to test for chlamydia. A list of U.S. Food and Drug Administration (FDA)-cleared specimen types and transport and storage requirements is provided (see Table 1) (for all the latest FDA approved tests go here https://www.fda.gov/MedicalDevices/ProductsandMedicalProcedures/InVitroDiagnostics/ucm330711.htm). Chlamydia trachomatis nucleic acid amplification tests (NAATs) are FDA-cleared for use on urine specimens from men and women, urethral swabs in men, and endocervical swabs in women; some tests are cleared for vaginal swabs ². The use of C. trachomatis NAAT for pharyngeal and rectal specimens is not FDA approved; however, laboratories can perform certain validation procedures, such as Clinical Laboratory Improvement Amendment (CLIA)-defined performance specifications, to enable them to test specimens for clinical purposes. In men, nucleic acid amplification tests (NAATs) are the most sensitive and recommended test for detecting C. trachomatis from a urethral swab or first-catch urine specimen ². For chlamydia screening in women, vaginal swabs are preferred over urine samples and several studies have shown that self-collected vaginal swabs are preferred by women and perform equal to or better than clinician-collected vaginal swabs ³. In addition, in men and women, self-collected rectal swabs for NAAT have also performed well ⁴. There is currently insufficient evidence to support the use of self-collected oropharyngeal or penile meatal swabs for the diagnosis of chlamydia ². Multiple NAATs are commercially available for the detection of Chlamydia trachomatis (see Table 1 below).

Laws and regulations in all states require that persons diagnosed with chlamydia be reported to public health authorities by clinicians, laboratories, or both.

Chlamydia test key facts

• Nucleic acid amplification tests (NAATs) that are cleared by the Food and Drug Administration (FDA) are recommended for detection of genital tract infections caused by Chlamydia trachomatis and Neisseria gonorrhoeae infections in men and women with and without symptoms. For detecting these infections of the genital tract, optimal specimen types for NAATs are vaginal swabs from women and first catch urine from men. Older nonculture tests and non-NAATs have inferior sensitivity and specificity characteristics and no longer are recommended.
• Nucleic acid amplification tests (NAATs) have not been cleared by FDA for the detection of rectal and oropharyngeal infections caused by Chlamydia trachomatis and Neisseria gonorrhoeae. CDC is recommending NAATs to test for these extragenital infections based on increased sensitivity, ease of specimen transport and processing. Because these specimen types have not been cleared by FDA for use with NAATs, laboratories must establish performance specifications when using these specimens to meet Clinical Laboratory Improvement Amendments (CLIA) regulatory requirements and local or state regulations as applicable prior to reporting results for patient management. Positive reactions with nongonococcal Neisseria species have been reported with some NAATs, particularly with oropharyngeal specimens. Alternate target testing using NAATs without reported crossreactivity might be needed to avoid false positive gonorrhea results when using these tests with these specimens.
• Routine repeat testing of NAAT-positive genital tract specimens is not recommended because the practice does not improve the positive predictive value of the test.
• Laboratory interpretation of test results should be consistent with product inserts for FDA-cleared tests or have met all federal and state regulations for a modified procedure if the laboratory has changed the cutoff values or testing algorithm. This approach provides the most appropriate information to the clinicians and users, who is ultimately responsible for assessing test results to guide patient and partner management.
• Neisseria gonorrhoeae culture capacity is still needed for evaluating suspected cases of treatment failure and monitoring antimicrobial susceptibility.
• Chlamydia trachomatis and Neisseria gonorrhoeae culture capacity might still be needed in instances of child sexual assault in boys and extragenital infections in girls.
• Women or men treated for chlamydia should be retested three months after their treatment.

Table 1. Food and Drug Administration–cleared* specimen types and requirements for the transport and storage of specimens for the detection of Chlamydia trachomatis and Neisseria gonorrhoeae by nucleic acid amplification test (NAAT) type

FDA-cleared NAAT	FDA-cleared specimen types	Specimen transport and storage conditions
Abbott RealTime CT/NG (Abbott Molecular Inc., Des Plaines, IL)	Asymptomatic women: clinician-collected vaginal swab, patient-collected vaginal swab in a clinical setting, and urine. Asymptomatic men: urine. Symptomatic women: endocervical swab, clinician-collected vaginal swab, patient-collected vaginal swab in a clinical setting, and urine. Symptomatic men: urethral swab and urine.	14 days at 2°–30°C 90 days at -10°C or lower Thaw frozen specimens at 2°–30°C Specimens must not undergo more than four freeze/ thaw cycles
Aptima COMBO 2 assay Aptima CT assay Aptima GC assay (Hologic/Gen-Probe Inc., San Diego, CA)	Asymptomatic women: endocervical swab, clinician-collected vaginal swab, patient-collected vaginal swab in a clinical setting, gynecologic specimens collected in PreservCyt solution and urine. Asymptomatic men: urethral swab and urine. Symptomatic women: endocervical swab, clinician-collected vaginal swab, patient-collected vaginal swab in a clinical setting, gynecologic specimens collected in PreservCyt solution and urine. Symptomatic men: urethral swab and urine.	24 hours at 2°–30°C (urine specimen in primary cup) 30 days at 2°–30°C (urine specimen in Aptima urine transport tube) 60 days at 2°–30°C (swab in Aptima swab transport tube) 12 months at -20° to -70°C (urine specimen and swab specimens in respective Aptima transport tubes)
BD ProbeTec ET CT/GC Amplified DNA assay (Becton Dickinson and Company, Sparks, MD)	Asymptomatic women: endocervical swab and urine. Asymptomatic men: urethral swab and urine. Symptomatic women: endocervical swab and urine. Symptomatic men: urethral swab and urine.	30 hours at 2°–30°C (urine specimen in primary cup) 7 days at 2°–8°C (urine specimen in primary cup) 30 days at 2°–30°C (urine specimen in urine processing tube) 60 days at -20°C or lower (neat urine specimen or urine in urine processing tube) 6 days at 2°–27°C (swab specimens) 30 days at 2°–8°C (swab specimens)
BD ProbeTec QX CT Amplified DNA assay BD ProbeTec QX GC Amplified DNA assay (Becton Dickinson and Company, Sparks, MD)	Asymptomatic women: endocervical swab, patient-collected vaginal swab in a clinical setting, gynecologic specimens collected in BDSurePath or PreservCyt solution and urine. Asymptomatic men: urethral swab and urine. Symptomatic women: endocervical swab, patient-collected vaginal swab in a clinical setting, gynecologic specimens collected in BDSurePath or PreservCyt solution and urine. Symptomatic men: urethral swab and urine.	30 hours at 2°–30°C (urine specimen in primary cup). 7 days at 2°–8°C (urine specimen in primary cup) 30 days at 2°–30°C (urine specimen in urine processing tube) 180 days at -20°C or lower (neat urine specimen or urine in urine processing tube) 30 days at 2°–30°C (endocervical and urethral swab specimens) 180 days at -20°C or lower (endocervical and urethral swab specimens) 14 days at 2°–30°C (dry vaginal swab specimens) 30 days at 2°–30°C (expressed vaginal swab specimens) 180 days at -20°C or lower (dry or expressed vaginal swab specimens)
Xpert CT/NG assay (Cepheid, Sunnyvale, CA)	Asymptomatic women: endocervical swab, patient-collected vaginal swab in a clinical setting, and urine. Asymptomatic men: urine. Symptomatic women: endocervical swab, patient-collected vaginal swab in a clinical setting, and urine. Symptomatic men: urine.	24 hours at room temperature (female urine specimen in primary cup) 3 days at room temperature (male urine specimen in primary cup) 8 days at 4°C (female and male urine specimen in primary cup) 3 days at 15°–30°C (female urine specimen in Xpert CT/NG Urine Transport Reagent tube) 45 days at 2°–15°C (female urine specimen in Xpert CT/NG Urine Transport Reagent tube) 45 days at 2°–30°C (male urine specimen in Xpert CT/NG Urine Transport Reagent tube) 45 days at 2°–30°C (swab in Xpert CT/NG Swab Transport Reagent tube)
cobas CT/NG test (Roche Diagnostics, Indianapolis, IN)	Asymptomatic women: endocervical swab, patient-collected vaginal swab in a clinical setting, clinician-collected vaginal swab, gynecologic specimens collected in PreservCyt solution and urine. Asymptomatic men: urine. Symptomatic women: endocervical swab, patient-collected vaginal swab in a clinical setting, clinician-collected vaginal swab, gynecologic specimens collected in PreservCyt solution and urine. Symptomatic men: urine.	≤1 yr at 2°– 30°C (swab or urine specimen in cobas PCR media) 24 hrs at 2°–30°C (Neat male urine specimen prior to addition to cobas PCR media) Cervical specimens collected in PreservCyt Solution may be stored at 2°–30°C for up to 12 months. Aliquots (≥1mL) of cervical specimens collected in PreservCyt Solution may be stored in 13 mL round-based Sarstedt tubes for up to 4 weeks at 2°–30°C.

Footnote: FDA-cleared NAATs and specimen types as of January 1, 2014.

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Table 2. Chlamydia trachomatis and Neisseria gonorrhoeae Nucleic Acid Amplification Test (NAAT) target sequences and possible false reactions, by test type

FDA-cleared NAAT	Nucleic acid target for C. trachomatis	Nucleic acid target for N. gonorrhoeae
Abbott RealTime CT/NG (Abbott Laboratories, Abbott Park, IL)	Two distinct specific sequence regions within the 7,500 base pair C. trachomatis cryptic plasmid DNA. The test does not detect plasmid free C. trachomatis. No false-positive tests based on analytical specificity testing.	48 base pair sequence within the Opa gene of N. gonorrhoeae. No false-positive tests based on analytical specificity testing.
Aptima COMBO 2 assay Aptima CT assay Aptima GC assay (Hologic/Gen-Probe Inc., San Diego, CA)	Specific region within the 23S rRNA from C. trachomatis (Aptima Combo 2 assay). Specific region with the 16S rRNA from C. trachomatis (Aptima CT assay). Both the Aptima Combo 2 assay and APTIMA CT assay detects nvCT. The test does not detect plasmid-free C. trachomatis. No false-positive tests based on analytical specificity testing.	Specific region within the 16S rRNA from N.gonorrhoeae (Aptima Combo 2 assay). Specific region with the 16S rRNA from N. gonorrhoeae that is distinct from the Aptima Combo 2 assay target (Aptima GC assay). No false-positive tests based on analytical specificity testing.
BD ProbeTec ET CT/GC Amplified DNA assay (Becton Dickinson and Company, Sparks, MD)	One distinct sequence within the 7,500 base pair C. trachomatis cryptic plasmid DNA. The test does not detect plasmid-free C. trachomatis. No false-positive tests based on analytical specificity testing.	Chromosomal pilin gene-inverting protein homologue. Neisseria cinerea, Neisseria subflava and Neisseria lactamica might result in false-positive test results based on analytical specificity testing.
BD ProbeTec QX CT Amplified DNA Assay BD ProbeTec QX GC Amplified DNA Assay (Becton Dickinson and Company, Sparks, MD)	One distinct sequence within the 7,500 base pair C. trachomatis cryptic plasmid DNA. The test does not detect plasmid-free C. trachomatis. No false-positive tests based on analytical specificity testing.	Chromosomal pilin gene-inverting protein homologue. N. cinerea and N. lactamica might result in false-positive test results based on analytical specificity testing.
Xpert CT/NG Assay (Cepheid, Sunnyvale, CA)	One distinct C. trachomatis chromosomal DNA sequence. No false-positive tests based on analytical specificity testing. The test detects plasmid-free C. trachomatis.	Two distinct chromosomal sequences each with a different reporter. Both sequences have to be detected to obtain a positive N. gonorrhoeae result. No false-positives based on analytical specificity testing
cobasCT/NG test (Roche Diagnostics, Indianapolis, IN)	CT primers CP102 and CP103 to define a sequence of approximately 206 nucleotides within the cryptic plasmid DNA of C. trachomatis. CT primers CTMP101 and CTMP102 to define a sequence of approximately 182 nucleotides within the chromosomal DNA of C. trachomatis. No false-positive tests based on analytical specificity testing. The test detects plasmid-free C. trachomatis.	NG primers NG514 and NG519 to define a sequence of approximately 190 nucleotides (DR-9A) from the DR-9 region. NG primers, NG552 and NG579, to define a second sequence of approximately 215 nucleotides (DR-9B) from the DR-9 region. No false-positive tests based on analytical specificity testing.

Footnote: FDA-cleared NAATs and specimen types as of January 1, 2014.

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How do I know if I have chlamydia?

Most people who have chlamydia have no symptoms. If you do have symptoms, they may not appear until several weeks after you have sex with an infected partner. Even when chlamydia causes no symptoms, it can damage your reproductive system.

Women with symptoms may notice:

• An abnormal vaginal discharge
• A burning sensation when urinating
• Bleeding between menstrual periods and after sexual intercourse
• Abdominal pain
• Painful intercourse
• Painful and/or frequent urination

Symptoms in men can include:

• A discharge from their penis
• Pus or milky discharge from the penis
• A burning sensation when urinating
• Painful and/or frequent urination
• Pain and swelling in one or both testicles (although this is less common).

Men and women can also get infected with chlamydia in their rectum. This happens either by having receptive anal sex, or by spread from another infected site (such as the vagina). While these infections often cause no symptoms, they can cause:

• Rectal pain;
• Discharge;
• Bleeding.

You should be examined by your doctor if you notice any of these symptoms or if your partner has an sexually transmitted disease (STD) or symptoms of an STD. STD symptoms can include an unusual sore, a smelly discharge, burning when urinating, or bleeding between periods.

How is chlamydia spread?

You can get chlamydia by having vaginal, anal, or oral sex with someone who has chlamydia.

If your sex partner is male you can still get chlamydia even if he does not ejaculate (cum).

If you’ve had chlamydia and were treated in the past, you can still get infected again. This can happen if you have unprotected sex with someone who has chlamydia.

If you are pregnant, you can give chlamydia to your baby during childbirth.

How can I reduce my risk of getting chlamydia?

The only way to avoid sexually transmitted diseases (STDs) is to not have vaginal, anal, or oral sex.

If you are sexually active, you can do the following things to lower your chances of getting chlamydia:

• Be in a long-term mutually monogamous relationship with a partner who has been tested and has negative sexually transmitted disease (STD) test results;
• Use latex condoms the right way every time you have sex.

Am I at risk for chlamydia?

Anyone who has sex can get chlamydia through unprotected vaginal, anal, or oral sex. However, sexually active young people are at a higher risk of getting chlamydia. This is due to behaviors and biological factors common among young people. Gay, bisexual, and other men who have sex with men are also at risk since chlamydia can spread through oral and anal sex.

Have an honest and open talk with your health care provider. Ask whether you should be tested for chlamydia or other sexually transmitted diseases (STDs). If you are a sexually active woman younger than 25 years, you should get a test for chlamydia every year. If you are an older woman with risk factors such as new or multiple sex partners, or a sex partner who has an sexually transmitted disease (STD), you should get a test for chlamydia every year. Gay, bisexual, and other men who have sex with men; as well as pregnant women should also get tested for chlamydia.

How is chlamydia treated?

Treating persons infected with Chlamydia trachomatis prevents adverse reproductive health complications and continued sexual transmission, and treating their sex partners can prevent reinfection and infection of other partners. Treating pregnant women usually prevents transmission of Chlamydia trachomatis to babies during birth. Chlamydia treatment should be provided promptly for all persons testing positive for infection; treatment delays have been associated with complications (e.g., pelvic inflammatory disease) in a limited proportion of women ⁶.

Recommended Regimens ⁷:

• Azithromycin 1 g orally in a single dose
  OR
• Doxycycline 100 mg orally twice a day for 7 days

Alternative Regimens ⁷:

• Erythromycin base 500 mg orally four times a day for 7 days
• OR
• Erythromycin ethylsuccinate 800 mg orally four times a day for 7 days
• OR
• Levofloxacin 500 mg orally once daily for 7 days
• OR
• Ofloxacin 300 mg orally twice a day for 7 days

Treatment of Chlamydial Infections During Pregnancy

The recommended regimen for treatment of chlamydial infections in pregnant women is azithromycin 1 g orally in a single dose ⁷. Doxycycline is pregnancy category D because of potential toxicity for fetal bone development and possible discoloration of teeth in the unborn baby; doxycycline is not recommended to treat chlamydial infections in pregnancy. Erythromycin estolate is contraindicated during pregnancy because of hepatotoxicity risk. The alternative regimens in pregnancy are amoxicillin, erythromycin base, or erythromycin ethylsuccinate. Pregnant women should have a test-of-cure performed 3 weeks after completion of therapy. Women younger than 25 years of age and those at increased risk for chlamydial infection also should be retested during the third trimester.

Alternative for treatment of Chlamydial Infections During Pregnancy:

• Amoxicillin 500 mg orally three times a day for 7 days
• OR
• Erythromycin base 500 mg orally four times a day for 7 days
• OR
• Erythromycin base 250 mg orally four times a day for 14 days
• OR
• Erythromycin ethylsuccinate 800 mg orally four times a day for 7 days
• OR
• Erythromycin ethylsuccinate 400 mg orally four times a day for 14 days

Resumption of Sexual Activity

Patients should be instructed to abstain from sexual intercourse for seven days after a single dose of azithromycin or until completion of a seven-day regimen of doxycycline; in addition, they should not resume sexual activity until all symptoms related to the chlamydial infection have resolved and their sex partners have received treatment for chlamydia ².

Post-Treatment Follow-Up

Test-of-cure to detect therapeutic failure (i.e., repeat testing 3–4 weeks after completing therapy) is not advised for persons treated with the recommended or alterative regimens, unless therapeutic adherence is in question, symptoms persist, or reinfection is suspected. Moreover, the use of chlamydial mucleic acid amplification tests (NAATs) at <3 weeks after completion of therapy is not recommended because the continued presence of nonviable organisms can lead to false-positive results ⁸.

A high prevalence of chlamydia and gonorrhea infection has been observed in women and men who were treated for chlamydial infection during the preceding several months ⁹. Most post-treatment infections do not result from treatment failure, but rather from reinfection caused by failure of sex partners to receive treatment or the initiation of sexual activity with a new infected partner, indicating a need for improved education and treatment of sex partners. Repeat infections confer an elevated risk for pelvic inflammatory disease and other complications in women. Men and women who have been treated for chlamydia should be retested approximately 3 months after treatment, regardless of whether they believe that their sex partners were treated ⁹. If retesting at 3 months is not possible, clinicians should retest whenever persons next present for medical care in the 12-month period following initial treatment.

Management of Sex Partners

Sex partners should be referred for evaluation, testing, and presumptive treatment if they had sexual contact with the partner during the 60 days preceding the patient’s onset of symptoms or chlamydia diagnosis. Although the exposure intervals defined for the identification of at-risk sex partners are based on limited data, the most recent sex partner should be evaluated and treated, even if the time of the last sexual contact was >60 days before symptom onset or diagnosis.

Among heterosexual patients, if health department partner management strategies (e.g., disease intervention specialists) are impractical or not available for persons with chlamydia and a healthcare provider is concerned that sex partners are unable to promptly access evaluation and treatment services, expedited partner therapy (EPT) should be considered as permitted by law ¹⁰. Expedited Partner Therapy (EPT) is the clinical practice of treating the sex partners of patients diagnosed with chlamydia or gonorrhea by providing prescriptions or medications to the patient to take to his/her partner without the health care provider first examining the partner. The Centers for Disease Control and Prevention (CDC) has concluded that expedited partner therapy (EPT) is a useful option to facilitate partner management, particularly for treatment of male partners of women with chlamydial infection or gonorrhea.

How to read chlamydia test results?

A positive test indicates an active chlamydia infection that requires treatment with a course of antibiotics.

A negative test means only that there is no evidence of infection at the time of the test. It is important for those who are at increased risk to have screening tests performed on an annual basis to check for possible infection, especially since re-infection is common, particularly among teenagers.

If you are infected, your sexual partner(s) should be tested and treated as well.

How long does it take to get results?

This will depend on where the lab testing is done and the method used to diagnose the infection. Nucleic acid amplification (NAAT) methods can give results in one to a few days. Cultures take longer and results are typically reported in 5 to 7 days.

Over the counter chlamydia test or at home chlamydia test

Nucleic acid amplification tests (NAATs) that are cleared by the Food and Drug Administration (FDA) ¹¹ are recommended for detection of genital tract infections, as screening or diagnostic tests, caused by Chlamydia trachomatis and Neisseria gonorrhoeae infections in men and women with and without symptoms. For detecting these infections of the genital tract, optimal specimen types for nucleic acid amplification tests (NAATs) are vaginal swabs from women and first catch urine from men.

Nucleic acid amplification tests (NAATs) are designed to amplify and detect nucleic acid sequences (either DNA or RNA) that are specific for the organism being detected. Similar to other nonculture tests, NAATs do not require viable organisms, NAATs can detect live or non-viable organisms. The increased sensitivity of NAATs is attributable to their theoretic ability to produce a positive signal from as little as a single copy of the target DNA or RNA. This high sensitivity has allowed the use of less invasively collected specimens such as first catch urines and vaginal swabs to detect shed organisms. Use of such specimens greatly facilitates screening.

Commercial tests differ in their amplification methods and their target nucleic acid sequences (see Table 1 above). The two Roche tests and the Abbott RealTime CT/NG use polymerase chain reaction (PCR) and both Becton Dickinson tests use strand displacement amplification (SDA) to amplify Chlamydia trachomatis DNA sequences in the cryptic plasmid that is found in >99% of strains of Chlamydia trachomatis. The Hologic/Gen-Probe Aptima Combo 2 assay for Chlamydia trachomatis uses transcription-mediated amplification (TMA) to detect a specific 23S ribosomal RNA target. The Roche cobas CT/NG test, Abbott, Becton Dickinson, and Hologic/Gen-Probe tests detect the new variant of Chlamydia trachomatis (nvCT) strain. These nucleic acid amplification methods also are used to detect Neisseria gonorrhoeae, and each manufacturer has marketed a duplex assay that allows for simultaneous detection of both organisms. The nucleic acid primers used by commercial NAATs for Chlamydia trachomatis are not known to detect DNA from other bacteria found in humans. However, the primers employed by the Becton Dickinson Neisseria gonorrhoeae NAATs might detect nongonococcal Neisseria species ¹² (see Table 2 above). Most commercial NAATs have been cleared by FDA to detect Chlamydia trachomatis and Neisseria gonorrhoeae in vaginal and endocervical swabs from women, urethral swabs from men, and first catch urine from both men and women (see Table 1 above).

Because NAATs are so sensitive, efforts are warranted to prevent contamination of specimens in the clinic or spread of environmental amplicon in the laboratory.

Specimen Collection Method

Chlamydia trachomatis and Neisseria gonorrhoeae testing in men

• Nucleic acid amplification tests (NAATs) are the recommended test method.
• A first catch urine is the recommended sample type and is equivalent to a urethral swab in detecting infection.
• A urethral swab specimen for Neisseria gonorrhoeae culture should be obtained and evaluated for antibiotic susceptibility in patients who have received Centers for Disease Control and Prevention (CDC)-recommended an antimicrobial regimen as treatment, and subsequently had a positive Neisseria gonorrhoeae test result (positive NAAT ≥7 days after treatment), and did not engage in sexual activity after treatment.

Chlamydia trachomatis and Neisseria gonorrhoeae testing in women

• Nucleic acid amplification tests (NAATs) are the recommended test method.
• A self- or clinician-collected vaginal swab is the recommended sample type. Self-collected vaginal swab specimens are an option for screening women when a pelvic exam is not otherwise indicated.
• An endocervical swab is acceptable when a pelvic examination is indicated.
• A first catch urine specimen is acceptable but might detect up to 10% fewer infections when compared with vaginal and endocervical swab samples.
• An endocervical swab specimen for Neisseria gonorrhoeae culture should be obtained and evaluated for antibiotic susceptibility in patients that have received
• Centers for Disease Control and Prevention (CDC)-recommended antimicrobial regimen as treatment, and subsequently had a positive Neisseria gonorrhoeae test result (positive NAAT ≥7 days after treatment), and did not engage in sexual activity after treatment.

Detection of Chlamydia trachomatis and Neisseria gonorrhoeae infections in the rectum and oropharynx

• Nucleic acid amplification tests (NAATs) are the recommended test method for rectal and oropharyngeal specimens.
• Laboratories must be in compliance with Clinical Laboratory Improvement Amendments (CLIA) for test modifications since these tests have not been cleared by the FDA for these specimen types.
• Commensal Neisseria species commonly found in the oropharynx might cause false positive reactions in some NAATs, and further testing might be required for accuracy.
• A rectal or oropharyngeal swab specimen for Neisseria gonorrhoeae culture should be obtained and evaluated for antibiotic susceptibility in patients who have received Centers for Disease Control and Prevention (CDC)-recommended antimicrobial regimen as treatment, had a subsequent positive Neisseria gonorrhoeae test result (positive NAAT ≥7 days after treatment), and did not engage in sexual activity after treatment.

Chlamydia test limitations

All diagnostic tests including nucleic acid amplification tests (NAATs) can generate inaccurate results, and it is important for patients and clinicians to understand test limitations. Certain false positives and false negatives can occur as a consequence of specimen collection, test operation, and laboratory environment. However, NAATs are far superior in overall performance compared with other Chlamydia trachomatis and Neisseria gonorrhoeae culture and nonculture diagnostic methods. NAATs offer greatly expanded sensitivities of detection, usually well above 90%, while maintaining very high specificity, usually ≥99%. Nucleic acid amplification tests (NAATs) typically detect 20%–50% more chlamydial infections than could be detected by culture or earlier nonculture tests (see below). The increment for detection of gonococcal infections is somewhat less.

Screening for genitourinary chlamydia and gonorrhoeae infections in Men

Chlamydia trachomatis and Neisseria gonorrhoeae control efforts in men differ substantially from those recommended for women. Although chlamydia prevalence data have provided a basis for setting age guidelines for routine annual screening and behavioral guidelines for targeted screening in women ¹³, no such consensus has been reached regarding control program definitions in men who have sex with women ¹⁴. Although there are no recommendations to screen heterosexual men, the US Preventive Services Task Force suggests testing to test sexually active heterosexual men in clinical settings with a high prevalence of Chlamydia trachomatis (e.g., STD clinics, adolescent clinics, and detention and correctional facilities) and among persons entering the Armed Forces or the National Job Training Program ¹⁵.

The prevalence of Neisseria gonorrhoeae varies widely among communities and populations; health-care providers should consider the local gonorrhea epidemiology when making screening recommendations. There is insufficient evidence for or against routine screening for gonorrhea in sexually active heterosexual men at increased risk for infection ¹⁵. However, it is not recommended to screen for gonorrhea infections in men at low risk for infection ¹⁵.

Overwhelming evidence described the performance of male first catch urine samples as equivalent to, and in some situations superior to, urethral swabs ¹⁶. Use of urine samples is highly acceptable and might improve the likelihood of uptake of routine screening in men.

Screening for genitourinary chlamydia and gonorrhoeae infections in Women

Screening programs have been demonstrated to reduce both the prevalence of Chlamydia trachomatis infection and rates of pelvic inflammatory disease (PID) in women ¹⁷. Sexually active women aged ≤25 years and women aged >25 years with risk factors (e.g., those who have a new sex partner or multiple partners) should be screened annually for chlamydial infections ¹⁵.

The prevalence of gonorrhea varies widely among communities and populations; health-care providers should consider local gonorrhea epidemiology when making screening decisions. Although widespread screening is not recommended, targeted screening of young women (i.e., those aged ≤25 years) at increased risk for infection is a primary component of gonorrhea control in the United States because gonococcal infections among women are frequently asymptomatic. For sexually active women, including those who are pregnant, the U.S. Preventive Services Task Force (USPSTF) recommends that clinicians provide gonorrhea screening only to those at increased risk for infection (e.g., women with previous gonorrhea infection, other STDs, new or multiple sex partners, and inconsistent condom use; those who engage in commercial sex work and drug use; women in certain demographic groups; and those living in communities with a high prevalence of disease). The U.S. Preventive Services Task Force does not recommend screening for gonorrhea in women who are at low risk for infection ¹⁵.

For female screening, specimens obtained with a vaginal swab are the preferred specimen type. Vaginal swab specimens are as sensitive as cervical swab specimens, and there is no difference in specificity ¹⁸. Self-collected vaginal swabs are equivalent in sensitivity and specificity to those collected by a clinician ¹⁸. Cervical samples are acceptable when pelvic examinations are done, but vaginal swab specimens are an appropriate sample type, even when a full pelvic exam is being performed. Cervical specimens collected into a liquid cytology medium for Pap screening are acceptable for NAATs that have been cleared by FDA for such specimen types (see Table 1 above). However, following Pap screening, there should be a clinical indication for reflex additional testing of liquid cytology specimens for chlamydia and gonorrhea since these specimen types are more widely used in older populations at low risk for infection. First catch urine from women, while acceptable for screening, might detect up to 10% fewer infections when compared with vaginal and endocervical swab samples ¹⁹.

Chlamydia blood test

Serologic testing is rarely used to diagnose uncomplicated genital infections caused by Chlamydia trachomatis because chlamydia serologic tests do not reliably distinguish current from prior infection ²⁰. Two main types of serologic tests are used for diagnosis ⁵:

1. Chlamydia complement fixation test, which measures antibody against group specific lipopolysaccharide antigen, and
2. Micro-immunofluorescence.

Serology may be of value in the diagnosis of anogenital infections (lymphogranuloma venereum) because many clinicians do not have access to OmpA serotyping or genotyping. Complement fixation titers of 1:64 or greater can support the diagnosis of LGV in the appropriate clinical context ²¹. The more sensitive and species-specific micro-immunofluorescence has replaced the chlamydia complement fixation test. High background prevalence and infrequent rises and falls in IgG and IgM make serology less practical to use as a diagnostic test for uncomplicated genital chlamydial infection. Serology may be useful in evaluation of inguinal anogenital infections (lymphogranuloma venereum) and selected chlamydia complications (e.g., perihepatitis and infertility) ²⁰.

Chlamydia trachomatis cell culture

Historically, cell culture to detect Chlamydia trachomatis was the most sensitive and specific method available to detect chlamydial infection. Cell culture, however, is technically complex, expensive, difficult to standardize, and has a lower sensitivity than nucleic acid amplification tests (NAATs) (50% versus 80%). In addition, performing Chlamydia trachomatis cell culture requires collection of columnar cells from relevant anatomical site(s) and use of stringent transport requirements. The excellent sensitivity and specificity of the nucleic acid amplification test (NAAT) has led to its use in place of culture for most clinical situations; the use of culture for Chlamydia trachomatis is limited to evaluation of suspected cases of sexual assault in children ²⁰.

Nucleic acid amplification tests (NAATs) can be used for vaginal and urine specimens, although data are insufficient to recommend the use of nucleic acid amplification test (NAAT) in boys. Chlamydial culture remains the preferred technique for evaluation of Chlamydia trachomatis infection from all sites in boys and extragenital sites in girls as part of any sexual assault evaluation ²⁰. If sexual abuse is suspected, specimens for chlamydia cultures should be collected from the anus (for boys and girls) and from the vagina of girls ⁵. All specimens should be retained for additional confirmatory testing. Other nonculture tests, such as direct fluorescent antibody tests (DFA), are not recommended in this setting because of poor specificity. Insufficient data are available regarding the use of nucleic acid amplification tests (NAATs) for extragenital specimens in boys or girls; thus, in this setting, culture remains the preferred method for detecting chlamydia from extragenital sites.

Detection of Extragenital chlamydia and gonorrhoeae infections in Men and Women

Infections with Chlamydia trachomatis and Neisseria gonorrhoeae are common in extragenital sites in certain populations such as men who have sex with men. Because extragenital infections are common in men who have sex with men, and most infections are asymptomatic ²², routine annual screening of extragenital sites in men who have sex with men is recommended. No recommendations exist regarding routine extragenital screening in women because studies have focused on genitourinary screening, but rectal and oropharyngeal infections are not uncommon.

A 2003 study that assessed NAATs for diagnosing Chlamydia and gonorrhoeae infections in multiple anatomic sites in men who have sex with men ²² used Becton Dickinson’s ProbeTec NAAT, which had been validated previously for such use. Among 6,434 men who have sex with men attending an STD clinic or a gay men’s clinic, the study found that the prevalence by site for Chlamydia was 7.9% for the rectum, 5.2% urethral, and 1.4% pharyngeal; and prevalence by site for gonorrhoeae was 6.9% for the rectum, 6% urethral, and 9.2% pharyngeal. The great majority (84%) of the gonococcal and chlamydial rectal infections were asymptomatic. More than half (53%) of Chlamydia and 64% of gonorrhoeae infections were at nonurethral sites and would have been missed if the traditional approach to screening of men by testing only urethral specimens had been used.

The scope of the problem of extragenital infection in men who have sex with men is not known at the national level. In 2007, CDC coordinated an evaluation of men who have sex with men attending several community-based organizations and public or STD clinics and found that of approximately 30,000 tests performed, 353 (5.4%) men who have sex with men were positive for rectal infection with gonorrhoeae, and 468 (8.9%) were positive for rectal Chlamydia. Pharyngeal gonorrhoeae tests were positive for 759 men who have sex with men (5.3%), and 54 (1.6%) were positive for Chlamydia ²³.

In the United Kingdom, some studies on screening men who have sex with men have been performed using NAATs ²⁴, and in one study of 3,076 men who have sex with men attending an STD clinic, there was an 8.2% prevalence of infection with Chlamydia in the rectum and 5.4% in the urethra. The majority (69%) of the men with Chlamydia were asymptomatic, stressing the need for screening ²⁴.

A study that compared culture to two NAATs (Hologic/Gen-Probe’s Aptima Combo2 [AC2]) and Becton Dickinson’s ProbeTec) for the detection of Chlamydia and gonorrhoeae in pharyngeal and rectal specimens collected from 1,110 men who have sex with men being seen in an STD clinic confirmed all NAAT positive results when either the original test or a test using alternate primers was positive (95). For oropharyngeal gonorrhoeae, sensitivities were 41% for culture, 72% for strand displacement amplification (Becton Dickinson test), and 84% for Hologic/Gen-Probe’s Aptima Combo2 [AC2]; and for rectal gonorrhoeae, sensitivities were 43% for culture, 78% for strand displacement amplification (Becton Dickinson test), and 93% for Hologic/Gen-Probe’s Aptima Combo2 [AC2]. For oropharyngeal infections with Chlamydia (for which only nine infections were detected), sensitivities were 44% for culture, 67% for strand displacement amplification (Becton Dickinson test), and 100% for Hologic/Gen-Probe’s Aptima Combo2 [AC2]; for rectal Chlamydia, sensitivities were 27% for culture, 63% for strand displacement amplification (Becton Dickinson test), and 93% for Hologic/Gen-Probe’s Aptima Combo2 [AC2]. Specificities were >99.4% for all specimens, tests, and anatomic sites. The number of infections detected was more than doubled when a more sensitive NAAT was used as compared with the use of standard culture. Other researchers also have demonstrated the superiority of NAATs as compared with culture for diagnosing Chlamydia and gonorrhoeae in rectal and oropharyngeal sites ¹².

Although commercially available NAATs are recommended for testing genital tract specimens, they have not been cleared by FDA for the detection of Chlamydia and gonorrhoeae infections of the rectum and oropharynx ²⁵. Results from commercially available NAATs can be used for patient management if the laboratory has established specifications for the performance characteristics according to Clinical Laboratory Improvement Amendments (CLIA) regulations ²⁶. If a moderate complexity test such as the GeneXpert is modified in any manner, the test defaults to high complexity and the laboratory must meet all high complexity Clinical Laboratory Improvement Amendments (CLIA) requirements, including those for personnel. Certain NAATs that have been demonstrated to detect commensal Neisseria species in urogenital specimens might have comparable low specificity when testing oropharyngeal specimens for gonorrhoeae. Thus, a gonorrhoeae NAAT that does not react with nongonococcal commensal Neisseria species is recommended when testing oropharyngeal specimens (see Table 2 above).

Screening for Chlamydial Infection

Screening for chlamydia in asymptomatic persons has been found to significantly reduce the incidence of chlamydia–associated pelvic inflammatory disease (PID) ²⁷.

In general, routine screening for chlamydia should utilize NAAT as the diagnostic test; the United States FDA has cleared NAATs for chlamydia testings on:

1. Male and female urine samples,
2. Clinician-collected endocervical, vaginal, and male urethral samples, and
3. Self-collected vaginal swabs if obtained in a clinical setting.

Routine oropharyngeal screening for Chlamydia trachomatis infection is not recommended, primarily because of the low prevalence of oropharyngeal Chlamydia trachomatis infection. Although chlamydia NAATs for chlamydia are not FDA cleared for rectal samples, the CDC and U.S. Preventive Services Task Force (USPSTF) note that chlamydia NAAT can be used on rectal swabs in persons who engage in receptive anal intercourse. The following summarizes the CDC and USPSTF recommendations for routine chlamydia screening ², ²⁸.

• Women Who Have Sex with Men: The high frequency of asymptomatic infection among young women combined with greater risk for morbidity led to the recommendation by the CDC and the USPSTF that all sexually active females younger than 25 years of age undergo annual screening for chlamydial infection ². More frequent screenings may be appropriate for sexually active adolescents and women with recent Chlamydia trachomatis infections. In addition, women 25 and older should undergo routine screening if they are considered to have increased risk for chlamydial infection, such as a new sex partner, more than one sex partner, a sex partner with concurrent (overlapping) partners, or a sex partner who has been diagnosed with an sexually transmitted infection (STI or STD). Women diagnosed with chlamydia should have repeat testing approximately 3 months after completing treatment.

• Women Who Have Sex with Women: The CDC recommends that chlamydia screening for sexually active women who have sex with women should be based on the same recommendations as for sexually active women who have sex with men ²⁹.

• Pregnancy: At the first prenatal visit, screen all pregnant women younger than 25 and those older than 25 who have increased risk of acquiring chlamydial infection ²⁹. Identified factors associated with increased risk for chlamydial infection include a new sex partner, more than one sex partner, a sex partner with concurrent (overlapping) partners, or a sex partner who has been diagnosed with an sexually transmitted disease (STD). Retest for chlamydial infection during the third trimester in women younger than 25 and in women older than 25 who have increased risk of acquiring chlamydial infection. Pregnant women diagnosed with chlamydia should have a test-of-cure 3-4 weeks after completing treatment and they should have repeat testing for chlamydia approximately 3 months after completing treatment.

• Men Who Have Sex Only with Women: Routine screening for chlamydial infection is not recommended by either the CDC or the USPSTF for sexually active men who have sex only with women ². The CDC recommends considering screening for chlamydia in sexually active young men who only have sex with women in populations with a high prevalence of chlamydia, including those seen at adolescent clinics, correctional facilities, and STD clinics ².

• Men Who Have Sex with Men: The CDC recommends routine chlamydia screening in sexually active men who have sex with men at least annually; the screening should consist of testing genital and rectal sites exposed during sexual activity, regardless of a history of condom use during sexual exposure ²⁹. Routine testing of oropharyngeal testing for chlamydia infection is not recommended. More frequent screening at 3- to 6-month intervals is indicated for men who have sex, including those with HIV infection, if risk behaviors persist or their sexual partners have multiple partners. The USPSTF does not recommend routine screening for chlamydia in men who have sex with men ³⁰.

• Transgender Men and Women: The CDC recommends that screening for chlamydia in transgender men (“trans-men”) and transgender women (“trans-women”) should be based on age, current anatomy, and sexual practices ²⁹.

• Persons with HIV Infection: The CDC recommends performing routine screening for chlamydia for persons with HIV infection who are sexually active; testing for chlamydia should be performed at the initial evaluation and at least annually thereafter (more frequent screening may be indicated based on risk) ³¹. The testing should consist of obtaining samples from the anatomic sites of sexual exposure, with the exception that routine screening for oropharyngeal chlamydia infection is not recommended.

• Correctional Facilities: The CDC recommends performing routine screening for chlamydial infection at the initial intake in a correctional facility for all women 35 and younger and men younger than 30 ²⁹.

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