CPT 87491: Chlamydia trachomatis Test by Amplified Nucleic Acid Probe
CPT code 87491 represents a laboratory diagnostic assay for Chlamydia trachomatis using an amplified nucleic acid probe technique. This molecular test is widely used for accurate detection of a common sexually transmitted infection and informs clinical management, public health screening, and reporting. Its use has national relevance due to the prevalence of Chlamydia infections and the role of nucleic acid amplification tests in recommended screening strategies.
Key payers in this analysis include Aetna, Blue Cross Blue Shield, Cigna Health, UnitedHealthcare, and Medicare. Readers will find a concise overview of clinical context, common service settings, and the types of benchmarks and policy considerations typically associated with molecular diagnostic billing for sexually transmitted infections. The publication covers reimbursement benchmarks, applicable coding guidance, and payer policy highlights that affect coverage and payment for amplified nucleic acid probe testing.
The piece provides practical reference material for billing staff, laboratory managers, and policy analysts seeking to understand where this code fits within laboratory service lines, how major payers approach coverage, and what operational considerations—such as typical settings and test purpose—are relevant for compliance and claims processing. Data not available in the input is explicitly noted where applicable.
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Billing Code Overview
CPT code 87491 describes a laboratory test performed by a lab analyst to detect Chlamydia trachomatis using an amplified nucleic acid probe technique. This is a molecular diagnostic assay that identifies genetic material specific to the pathogen.
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Service type: Laboratory diagnostic test (amplified nucleic acid probe)
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Typical site of service: Clinical laboratory or hospital laboratory setting where molecular testing is performed
Clinical & Coding Specifications
Clinical Context
A sexually active 24-year-old female presents to a community sexual health clinic for routine sexually transmitted infection (STI) screening after reporting new sexual partners. She denies symptoms but requests testing. A urine nucleic acid amplification test (NAAT) is ordered for Chlamydia trachomatis. The clinic collects a first-catch urine specimen and sends it to the on-site or reference laboratory. The laboratory analyst performs the amplified nucleic acid probe technique to detect C. trachomatis RNA/DNA. Results are reported back to the ordering clinician; positive results prompt partner notification and treatment per local public health guidance. Typical workflow roles include: clinician/patient encounter and specimen collection in an ambulatory clinic or urgent care setting, courier transport (if performed off-site), and laboratory processing and reporting in a clinical microbiology or molecular diagnostics lab. Typical site of service: ambulatory clinic, urgent care center, or clinical laboratory performing diagnostic testing.
Coding Specifications
| Modifier | Description | When to Use |
|---|---|---|
26 | Professional component | Use when billing only the professional (interpretive) portion of a lab test if separated from technical component. |
TC | Technical component | Use when billing only the technical portion (laboratory processing, equipment, supplies) of the test. |
91 | Repeat clinical diagnostic laboratory test | Use when the same test is repeated on the same day to obtain subsequent (confirmatory) result. |
59 | Distinct procedural service | Use when an unrelated service or procedure is performed on the same day and needs to be distinguished from this lab test in bundling determinations. |
90 | Reference lab | Use to indicate service performed by a reference laboratory (outside the billing laboratory) when required by payer. |
95 | Synchronous telemedicine service rendered via real-time interactive audio and video | Rarely used for lab billing but applicable when ordering/consultation occurs via live telemedicine and payer requires modifier. |
QW | CLIA waived test | Use when the test performed is CLIA-waived and the payer requires indication of waived status. |
QK | Medicare demonstration project | Use only if the test is part of a CMS demonstration project requiring this modifier. |
GE* | (Not in provided list; placeholder omitted) | Data not available in the input. |
59 | (Listed above) | (Duplicate entries are not included.) |
| Taxonomy Code | Specialty | Notes |
|---|---|---|
| Data not available in the input. | Data not available in the input. | Data not available in the input. |
Related Diagnoses
| ICD-10 Code | Description | Clinical Relevance |
|---|---|---|
A56.01 | Chlamydia trachomatis infection of lower genitourinary tract | Direct diagnosis targeted by this test for symptomatic or screening evaluation. |
Z11.3 | Encounter for screening for infections with a predominantly sexual mode of transmission | Common screening indication prompting C. trachomatis NAAT in asymptomatic patients. |
N76.0 | Acute vaginitis | Vaginal symptoms that may prompt STI testing including chlamydia NAAT. |
N34.1 | Urethritis, unspecified | Urethral symptoms in males or females leading to chlamydia testing. |
A56.9 | Chlamydial infection, unspecified | General coding when chlamydial infection is confirmed or suspected and site unspecified. |
Related CPT Codes
| CPT Code | Description | Relationship to This Procedure |
|---|---|---|
87491 | The lab analyst performs a test for Chlamydia trachomatis using amplified nucleic acid probe technique. | Primary molecular diagnostic code describing the NAAT for C. trachomatis. |
87880 | Infectious agent detection by nucleic acid (DNA or RNA); multiple organisms, amplified probe technique | May be used when multiplex panels that include Chlamydia are performed instead of single-organism assay. |
87492 | The lab analyst performs a test for Chlamydia trachomatis using amplified nucleic acid probe technique; with simultaneous detection of Neisseria gonorrhoeae (when paired) | Used when a combined Chlamydia and Gonorrhea NAAT is performed in the same assay. |
87070 | Culture, bacterial; any other source except urine, blood or stool, aerobic with isolation and presumptive identification of isolates | May be performed if organism culture is indicated in atypical cases or treatment failures. |
87899 | Unlisted microbiology procedure | Used when a novel or unlisted molecular diagnostic method for C. trachomatis is performed and no specific CPT exists. |