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Chlamydia and Gonorrhea NAAT Screening Method Endorsed by CDC

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May 22, 2014

People who think they may have chlamydia or gonorrhea or who have a high risk of infection with one of these two sexually transmitted diseases (STDs) have improved options for getting screened. The Centers for Disease Control and Prevention (CDC) now promotes nucleic acid amplification testing, also known as NAAT, as the preferred method to detect these STDs in men and women in its latest recommendations to clinical laboratories.

The NAAT method detects the genetic material (nucleic acid) of the bacteria causing the infection. It does this in part by amplifying or making numerous copies of the genetic material so that the detection system can identify the presence of the bacteria. NAAT is now considered the test of choice by the CDC because it is very sensitive; it is theoretically able to detect as little as a single copy of bacterial nucleic acid in a sample taken from the individual tested.

The method is also favored because the preferred samples are relatively easy to obtain. Men can submit a first morning urine sample and women can submit a vaginal swab collected themselves or by a healthcare practitioner. Generally, NAAT can also provide results faster than culturing the bacteria. It can take a few days for the bacteria to multiply to sufficient numbers to be identified by culture.

Easier sample collection, improved detection, and faster results might encourage those with possible infections to get tested and treated, helping to limit the spread of these STDs. Chlamydia and gonorrhea often cause no symptoms, or vague ones, so people at risk are encouraged to get regular screening. If untreated, these infections can have serious consequences, such as pelvic inflammatory disease, increased risk of ectopic pregnancy and infertility in women and sterility in men.

Currently, NAATs available from commercial manufacturers are only approved by the U.S. Food and Drug Administration for genital and urine samples. However, the CDC recommends expanding the use of NAAT to other samples, such as throat and rectal swabs. Since the rectal and oral samples have not been validated by the test's manufacturers, they would require validation by any laboratory using swabs from these sites.

One drawback of the method is that because NAAT only detects the genetic material, it cannot determine whether the bacteria causing infection are living or resistant to antibiotics. Thus, the test cannot be used to determine whether treatment is effective and an antibiotic is killing the bacteria.

For this reason, laboratories must still maintain the ability to perform cultures for chlamydia and gonorrhea, says the CDC. Drug-resistant gonorrhea is becoming increasingly common. If bacteria are suspected to be resistant to the most commonly prescribed medicines or an individual is not responding to treatment, then culture is still needed and sensitivity testing is performed to find the most appropriate antibiotic to treat the STD. Furthermore, data are insufficient at this time for use of NAAT in cases of sexual assault in boys and for samples other than genital in girls. Culture remains the required test in these cases.

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NOTE: This article is based on research that utilizes the sources cited here as well as the collective experience of the Lab Tests Online Editorial Review Board. This article is periodically reviewed by the Editorial Board and may be updated as a result of the review. Any new sources cited will be added to the list and distinguished from the original sources used. To access online sources, copy and paste the URL into your browser.

Papp JR et al. Recommendations for the laboratory-based detection of Chlamydia trachomatis and Neisseria gonorrhoeae — 2014. Morbidity and Mortality Weekly Report, 2014 Mar 14; 63:1. Available online at through Accessed May 2014.

Zuger, A. New Recommendations for Lab-Based Sexually Transmitted Disease Diagnosis. JournalWatch. April 10, 2014. Available online at through Accessed May 2014.