Table of ContentsView AllTable of ContentsHow NAATs WorkNAATs in STI TestingNAATs in Action
Table of ContentsView All
View All
Table of Contents
How NAATs Work
NAATs in STI Testing
NAATs in Action
Nucleic-acid amplification tests, also known as NAATs, can detect a variety of different sexually transmitted infections (STIs, formerly called sexually transmitted diseases, STDs). Manyurine testsfor STIs are performed using NAATs.NAAT tests work because they identify small amounts of DNA or RNA in test samples. They can, therefore, be used to identifybacteria,viruses, and otherpathogenseven when the material of interest is present in very small amounts.This article explains the use of nucleic-acid amplification tests to diagnose STIs, and how they work with various test samples.Andrew Brookes/Cultura/Getty ImagesHow Do Nucleic-Acid Amplification Tests Work?Though there are several kinds of NAATs, all are based on the same principles. For example, NAATs used to detect the COVID-19 virus can rely on methods that include:Reverse transcriptionpolymerasechain reaction (RT-PCR)Transcription mediated amplification (TMA)Clustered regularly interspaced short palindromic repeats (CRISPR)Strand displacement amplification (SDA)The NAAT uses a series of repeated chemical reactions to make numerous copies and amplify the amount of the DNA or RNA that healthcare providers are trying to detect.This offers some advantages. With PCR tests used to detect STIs, for example, the test doesn’t need a living sample (as is the case with a viral orbacterial culture) and can be done quickly.It often detects a more recent infection.How Accurate Is a NAAT test for STIs?NAAT tests can deliver highly accurate results. A 2021 review of studies looked at point-of-care tests (given during your healthcare visit) to diagnose chlamydia. The studies compared NAAT andantigendetection tests, along with the types of specimens (urine, swab, etc.) The NAAT tests were significantly more sensitive than the antigen detection tests, with excellent accuracy on urine samples.Polymerase Chain Reaction (PCR) for STI Detection and TestingNAATs in STI TestingThe process of amplifying bacterial or viral nucleic acids is not in itself anSTI test. Instead, once the amount of DNA or RNA has been increased in the sample using PCR orligasechain reaction (LCR), another step is used to detect and diagnose an infection.These tests usually involve some form of nucleic acid hybridization. In those tests, the sample is probed with an artificially produced complementary strand of DNA or RNA labeled in some way that makes it easy to detect. It may help to picture it as a glow-in-the-dark tag that only sticks to one very specific piece of identifying information.This process allows healthcare providers to detect an STI pathogen even when only a very small number of organisms are present. They also make someat-home testspossible.NAATs and Urine SamplesNAATs are incredibly useful for some STI tests, especially because they work with easy-to-collect urine samples. Keep in mind that not all STIs can be detected well with urine tests,trichomoniasisandhuman papillomavirus(HPV) among them. Even for chlamydia, the CDC still considers a vaginal swab to provide the best samples for diagnosis in females.Can a Urine Test Detect STIs?Example of This Test in ActionHow well a NAAT test will work to diagnose STIs can be seen in the example of genitalherpes(usually herpes simplex virus type 2, orHSV-2). NAATs are sensitive at detecting a bacteria or virus without looking for anti-herpes antibodies, although the ELISA and otherHSV blood testscan add this information.Nucleic-acid amplification also allowed for easier and more widespread chlamydia and gonorrhea screening methods.Collecting urine requires no medical expertise and people may be more likely to pee into a cup than undergo a genital swab. Therefore, it has become easier for healthcare providers to test larger numbers of young people for these STIs.Researchers have also used NAATs to get more information about the extent of the problem ofasymptomatic(with no symptoms) STIs in the United States. Large-scale NAAT-based screening programs have been implemented in military service, for example.These tests in urban areas, or among men who have sex with men (MSM), allow for the detection of STIs in the small urine or blood samples that are often taken as part of large research studies on population health.NAATs and Testing for Oral and Anal InfectionIn 2019, the Food and Drug Administration approved NAAT testing for STIs with samples taken from the rectum orpharynx(throat). These infections are more common in MSM and other groups with anal and oral sexual practices. Researchers found NAAT test accuracy adequate (a pooled sensitivity of 93%) for rectal samples but less is known about throat samples and more study is needed.SummaryNucleic-acid amplification tests (NAATs) are a fast, easy option to test for STIs at the point of care, typically a healthcare provider’s office, as opposed to waiting for lab results. NAATs come in a range of types, but all rely on the same basic technique of amplifying DNA or RNA in a sample and then identifying the presence of an STI like chlamydia or HSV-2.Although at-home tests are available, talk with your healthcare provider about the optimal test options for your specific concern. Keep in mind that the type of sample used is important, and not all STIs are optimally detected with NAAT using a simple urine sample.A Guide to Regular STI Screenings
Nucleic-acid amplification tests, also known as NAATs, can detect a variety of different sexually transmitted infections (STIs, formerly called sexually transmitted diseases, STDs). Manyurine testsfor STIs are performed using NAATs.
NAAT tests work because they identify small amounts of DNA or RNA in test samples. They can, therefore, be used to identifybacteria,viruses, and otherpathogenseven when the material of interest is present in very small amounts.
This article explains the use of nucleic-acid amplification tests to diagnose STIs, and how they work with various test samples.
Andrew Brookes/Cultura/Getty Images
How Do Nucleic-Acid Amplification Tests Work?
Though there are several kinds of NAATs, all are based on the same principles. For example, NAATs used to detect the COVID-19 virus can rely on methods that include:
The NAAT uses a series of repeated chemical reactions to make numerous copies and amplify the amount of the DNA or RNA that healthcare providers are trying to detect.
This offers some advantages. With PCR tests used to detect STIs, for example, the test doesn’t need a living sample (as is the case with a viral orbacterial culture) and can be done quickly.It often detects a more recent infection.
How Accurate Is a NAAT test for STIs?NAAT tests can deliver highly accurate results. A 2021 review of studies looked at point-of-care tests (given during your healthcare visit) to diagnose chlamydia. The studies compared NAAT andantigendetection tests, along with the types of specimens (urine, swab, etc.) The NAAT tests were significantly more sensitive than the antigen detection tests, with excellent accuracy on urine samples.
How Accurate Is a NAAT test for STIs?
NAAT tests can deliver highly accurate results. A 2021 review of studies looked at point-of-care tests (given during your healthcare visit) to diagnose chlamydia. The studies compared NAAT andantigendetection tests, along with the types of specimens (urine, swab, etc.) The NAAT tests were significantly more sensitive than the antigen detection tests, with excellent accuracy on urine samples.
Polymerase Chain Reaction (PCR) for STI Detection and Testing
The process of amplifying bacterial or viral nucleic acids is not in itself anSTI test. Instead, once the amount of DNA or RNA has been increased in the sample using PCR orligasechain reaction (LCR), another step is used to detect and diagnose an infection.
These tests usually involve some form of nucleic acid hybridization. In those tests, the sample is probed with an artificially produced complementary strand of DNA or RNA labeled in some way that makes it easy to detect. It may help to picture it as a glow-in-the-dark tag that only sticks to one very specific piece of identifying information.
This process allows healthcare providers to detect an STI pathogen even when only a very small number of organisms are present. They also make someat-home testspossible.
NAATs and Urine SamplesNAATs are incredibly useful for some STI tests, especially because they work with easy-to-collect urine samples. Keep in mind that not all STIs can be detected well with urine tests,trichomoniasisandhuman papillomavirus(HPV) among them. Even for chlamydia, the CDC still considers a vaginal swab to provide the best samples for diagnosis in females.
NAATs and Urine Samples
NAATs are incredibly useful for some STI tests, especially because they work with easy-to-collect urine samples. Keep in mind that not all STIs can be detected well with urine tests,trichomoniasisandhuman papillomavirus(HPV) among them. Even for chlamydia, the CDC still considers a vaginal swab to provide the best samples for diagnosis in females.
Can a Urine Test Detect STIs?
Example of This Test in Action
How well a NAAT test will work to diagnose STIs can be seen in the example of genitalherpes(usually herpes simplex virus type 2, orHSV-2). NAATs are sensitive at detecting a bacteria or virus without looking for anti-herpes antibodies, although the ELISA and otherHSV blood testscan add this information.
Nucleic-acid amplification also allowed for easier and more widespread chlamydia and gonorrhea screening methods.Collecting urine requires no medical expertise and people may be more likely to pee into a cup than undergo a genital swab. Therefore, it has become easier for healthcare providers to test larger numbers of young people for these STIs.
Researchers have also used NAATs to get more information about the extent of the problem ofasymptomatic(with no symptoms) STIs in the United States. Large-scale NAAT-based screening programs have been implemented in military service, for example.
These tests in urban areas, or among men who have sex with men (MSM), allow for the detection of STIs in the small urine or blood samples that are often taken as part of large research studies on population health.
NAATs and Testing for Oral and Anal InfectionIn 2019, the Food and Drug Administration approved NAAT testing for STIs with samples taken from the rectum orpharynx(throat). These infections are more common in MSM and other groups with anal and oral sexual practices. Researchers found NAAT test accuracy adequate (a pooled sensitivity of 93%) for rectal samples but less is known about throat samples and more study is needed.
NAATs and Testing for Oral and Anal Infection
In 2019, the Food and Drug Administration approved NAAT testing for STIs with samples taken from the rectum orpharynx(throat). These infections are more common in MSM and other groups with anal and oral sexual practices. Researchers found NAAT test accuracy adequate (a pooled sensitivity of 93%) for rectal samples but less is known about throat samples and more study is needed.
Summary
Nucleic-acid amplification tests (NAATs) are a fast, easy option to test for STIs at the point of care, typically a healthcare provider’s office, as opposed to waiting for lab results. NAATs come in a range of types, but all rely on the same basic technique of amplifying DNA or RNA in a sample and then identifying the presence of an STI like chlamydia or HSV-2.
Although at-home tests are available, talk with your healthcare provider about the optimal test options for your specific concern. Keep in mind that the type of sample used is important, and not all STIs are optimally detected with NAAT using a simple urine sample.
A Guide to Regular STI Screenings
9 Sources
Verywell Health uses only high-quality sources, including peer-reviewed studies, to support the facts within our articles. Read oureditorial processto learn more about how we fact-check and keep our content accurate, reliable, and trustworthy.
Centers for Disease Control and Prevention.Nucleic acid amplification tests (NAATs).
National Institutes of Health, National Human Genome Research Institute.Polymerase chain reaction (PCR) fact sheet.
Zhou Y, Jiang TT, Li J, Yin YP, Chen XS.Performance of point-of-care tests for the detection of chlamydia trachomatis infections: A systematic review and meta-analysis.EClinicalMedicine. 2021 Jun 18;37:100961. doi:10.1016/j.eclinm.2021.100961
Avivi MY, Touitou N, Rohana H, et al.Nucleic acid hybridization-based detection of pathogenic RNA using microscale thermophoresis. Journal of Biological Chemistry. 2024;300(3):105676. doi:10.1016/j.jbc.2024.105676
Workowski KA, Bachmann LH, Chan PA, et al.Sexually transmitted infections treatment guidelines, 2021.MMWR Recomm Rep. 2021;70(4):1-187. doi:10.15585/mmwr.rr7004a1
Nath P, Kabir MA, Doust SK, Ray A.Diagnosis of herpes simplex virus: Laboratory and point-of-care techniques.Infect Dis Rep. 2021 Jun 2;13(2):518-539. doi:10.3390/idr13020049
Bernstein KT, Chow JM, Pathela P, Gift TL.Bacterial Sexually Transmitted Disease Screening Outside the Clinic–Implications for the Modern Sexually Transmitted Disease Program.Sex Transm Dis. 2016;43(2 Suppl 1):S42-S52. doi:10.1097/OLQ.0000000000000343
Tobin L, Guerra L, Ahouanvoeke L, Carpio JG, Irambona D, Nyarko EO,et al.Is it time to use nucleic acid amplification tests for identification of persons with sexually transmitted infections?: evidence from seroprevalence and behavioral epidemiology risk surveys in men with chlamydia and gonorrhea.Pan Afr Med J. 2020 Aug 18;36:299. doi:10.11604/pamj.2020.36.299.20777
Trembizki E, Costa A-MG, Tabrizi SN, Whiley DM, Twin J.Opportunities and pitfalls of molecular testing for detecting sexually transmitted pathogens.Pathology. 2015;47(3):219-226. doi:10.1097/PAT.0000000000000239
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