CurrentBlue Cross Blue Shield - TennesseePolicy N/A

Identification of Microorganisms using Nucleic Acid Probes

Policy governing coverage of nucleic acid probe-based tests (direct probe, amplified probe, quantification) for identification of microorganisms; applies to providers submitting claims to Blue Cross Blue Shield of Tennessee and is dependent on member benefit coverage and applicable state/federal rules.

Policy Summary

PayerBlue Cross Blue Shield - Tennessee

PolicyIdentification of Microorganisms using Nucleic Acid Probes

Policy CodePolicy N/A

Change TypeNo material change

Effective DateN/A

Next Review DateN/A

Key ActionVerify coverage for the specific CPT code prior to ordering and ensure appropriate coding and any payer-specific prior authorization rules are met.

SourceLink

POLICY UPDATE CHANGES

No material clinical or coverage changes in this revision.

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Related Billing Codes

CPT-87582-MYCOPLASMA-PNEUMONIAE-NUCLEIC-ACID-PROBE-QUANTITATIVE

CPT 87582: Mycoplasma pneumoniae Quantitative Nucleic Acid Probe Test

CPT-87493-CLOSTRIDIUM-DIFFICILE-TOXIN-GENE-AMPLIFIED-NUCLEIC-ACID-PROBE

CPT 87493: Clostridium difficile Toxin Gene Detection, Amplified Probe

CPT-87593-ORTHOPOXVIRUS-NUCLEIC-ACID-PROBE-TEST

CPT 87593: Orthopoxvirus Nucleic Acid Probe Test

CPT-87480-CANDIDA-DIRECT-NUCLEIC-ACID-PROBE-TEST

CPT 87480: Direct Nucleic Acid Probe Test for Candida Species

CPT-87541-LEGIONELLA-PNEUMOPHILA-AMPLIFIED-NUCLEIC-ACID-PROBE

CPT 87541: Legionella pneumophila Detection by Amplified Nucleic Acid Probe

CPT-87485-CHLAMYDIA-PNEUMONIAE-NUCLEIC-ACID-PROBE-TEST

CPT 87485: Chlamydia pneumoniae Direct Nucleic Acid Probe Test

CPT-87542-LEGIONELLA-PNEUMOPHILA-NUCLEIC-ACID-QUANTIFICATION

CPT 87542: Quantitative Legionella pneumophila Nucleic Acid Probe Test

CPT-87471-BARTONELLA-NUCLEIC-ACID-AMPLIFICATION-TEST

CPT 87471: Nucleic Acid Amplification Test for Bartonella spp.

CPT-87498-MENINGITIS-AMPLIFIED-PROBE-DIAGNOSTIC

CPT 87498: Meningitis Diagnostic by Amplified Probe Technique

CPT-87481-CANDIDA-SPECIES-AMPLIFIED-NUCLEIC-ACID-PROBE

CPT 87481: Detection of Candida Species by Amplified Nucleic Acid Probe

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procedure codes enumerated in policy

Prohibitedsimultaneous testing rule

CDC/WHO/IDSA/AAPguideline sources cited

CLIA '88LDT regulatory status

Coverage Criteria for Nucleic Acid Probe-Based Tests

Organism-specific coverage and simultaneous testing rule

Coverage determinations provided by organism and test type; MCC = meets coverage criteria, DNMCC = does not meet coverage criteria.

Organism/test-specific coverage: Each organism/test code listed in the policy table is assigned a coverage status (MCC or DNMCC); refer to the table entries for the exact designation.

See policy table entries in chunks 2 and 4 for full list

Simultaneous testing prohibition: Simultaneous ordering of any combination of direct probe, amplified probe, and/or quantification for the same organism in a single encounter does not meet coverage criteria.

This is a standalone denial rule

Coverage considerations informed by guidance

Coverage is informed by public health and clinical guidance and by regulatory status of tests.

Public health-recommended organism testing: Testing recommendations follow CDC, ECDC, and UKHSA guidance for specific organisms (for example: PCR/NAAT for Legionella spp., Mycoplasma spp., orthopoxvirus/monkeypox, and organism-specific NAATs recommended by CDC).

See cited public health guidance for specimen and testing details

Clinical diagnosis vs molecular testing: Some conditions (e.g., mucocutaneous candidiasis/thrush) can often be diagnosed clinically without molecular testing; molecular assays (FISH or PCR) are described as options for rapid detection from positive blood cultures.

Clinical judgment and referenced guidelines inform when molecular testing is appropriate

Regulatory and laboratory-developed tests (LDTs): Laboratory-developed tests must be validated and are regulated under CLIA '88; FDA clearance is not required for clinical use, though FDA-cleared/approved nucleic acid tests exist and are listed by the FDA.

LDT validation and regulatory status may affect laboratory operations and payer considerations

Simultaneous ordering of any combination of direct probe, amplified probe, and/or quantification for the same organism in a single patient encounter does not meet coverage criteria and may be denied. Providers should avoid submitting more than one of these test types for the same organism on the same date of service.

When there is a conflict between this policy and any applicable government policy (for example, Medicare Local Coverage Determinations or National Coverage Determinations, or state Medicaid rules), the government policy governs and will be used to make the coverage determination. Providers should verify and follow the most current Medicare or state Medicaid guidance when applicable.

Tests listed in the policy table with the label DNMCC (Does Not Meet Coverage Criteria) are considered not covered for the specified organism and test type. Refer to the table entries for the exact CPT/HCPCS code and organism pairing when confirming coverage status.

Mucocutaneous candidiasis (thrush) is often a presumptive clinical diagnosis; the American Academy of Pediatrics notes that it "usually can be made clinically." Molecular testing for Candida from non-blood mucocutaneous sites is generally not required in typical presentations, although rapid detection methods such as FISH or PCR may be used to identify Candida species from positive blood cultures when clinically indicated.

Indications Where Testing Is Covered

Organism-specific testing consistent with clinical guidelines

Organism-specific testing is covered when consistent with relevant clinical guidance and the clinical presentation described by public health or specialty society recommendations.

CDC/Clinical guideline concordant indications: Perform organism-specific molecular testing (e.g., PCR/NAAT) when recommended by CDC, IDSA, AAP, or other disease-specific guidance — examples include PCR-based identification of Candida auris, RT-PCR as preferred method for Chlamydia pneumoniae, and NAAT for Mycoplasma genitalium when indicated (symptomatic or recurrent NGU/PID as per CDC).

Follow the cited disease-specific guidance for specimen type and testing indications

Suspected monkeypox (mpox) infection — specimen and testing guidance

Testing for suspected mpox (monkeypox) should follow public health specimen collection and PCR testing guidance.

Specimen collection for suspected mpox: Collect lesion swab(s) in viral transport or culture medium from vesicles or ulcers for MPXV PCR; if pharyngeal lesions are present, collect a throat swab as well.

Tests and Indications Not Covered

Tests and test types explicitly labeled DNMCC in the policy table (for example, many non-vaginal Candida probe codes, Hepatitis G probes, and certain quantification codes) are considered not medically necessary for coverage and will not be paid under this policy. Always confirm the specific code designation in the policy table prior to ordering or billing.

Any test or indication that is specifically excluded by an applicable government policy (e.g., an LCD or NCD for Medicare, or a state Medicaid policy) will not be covered; the government policy supersedes this policy in the event of a conflict. Verify member coverage against current government guidance before ordering.

Procedure Codes and Coverage Designations

Organism-specific CPT codes and coverage designationsCPT

87471	Bartonella henselae or quintana, Amplified Probe (MCC)
87472	Bartonella henselae or quintana, Quantification (DNMCC)
87480	Non-vaginal Candida species, Direct Probe (DNMCC)
87481	Non-vaginal Candida species, Amplified Probe (DNMCC)
87482	Non-vaginal Candida species, Quantification (DNMCC)
87485	Chlamydia pneumoniae, Direct Probe (MCC)
87486	Chlamydia pneumoniae, Amplified Probe (MCC)
87487	Chlamydia pneumoniae, Quantification (DNMCC)
87493	Clostridium difficile, Amplified Probe (MCC)
87495	Cytomegalovirus, Direct Probe (MCC)

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Covered CPT Codes (partial list)CPT

87471	Infectious agent detection by nucleic acid (DNA or RNA); Bartonella henselae and Bartonella quintana, amplified probe technique.
87472	Infectious agent detection by nucleic acid (DNA or RNA); Bartonella henselae and Bartonella quintana, quantification.
87480	Infectious agent detection by nucleic acid (DNA or RNA); Candida species, direct probe technique.
87481	Infectious agent detection by nucleic acid (DNA or RNA); Candida species, amplified probe technique.
87482	Infectious agent detection by nucleic acid (DNA or RNA); Candida species, quantification.
87485	Infectious agent detection by nucleic acid (DNA or RNA); Chlamydia pneumoniae, direct probe technique.
87486	Infectious agent detection by nucleic acid (DNA or RNA); Chlamydia pneumoniae, amplified probe technique.
87487	Infectious agent detection by nucleic acid (DNA or RNA); Chlamydia pneumoniae, quantification.
87493	Infectious agent detection by nucleic acid (DNA or RNA); Clostridium difficile, toxin gene(s), amplified probe technique.
87495	Infectious agent detection by nucleic acid (DNA or RNA); cytomegalovirus, direct probe technique.

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Covered CPT Codes (continued)CPT

87500	Infectious agent detection by nucleic acid (DNA or RNA); vancomycin resistance (eg, enterococcus species van A, van B), amplified probe technique.
87525	Infectious agent detection by nucleic acid (DNA or RNA); hepatitis G, direct probe technique.
87526	Infectious agent detection by nucleic acid (DNA or RNA); hepatitis G, amplified probe technique.
87527	Infectious agent detection by nucleic acid (DNA or RNA); hepatitis G, quantification.
87531	Infectious agent detection by nucleic acid (DNA or RNA); Herpes virus-6, direct probe technique.
87532	Infectious agent detection by nucleic acid (DNA or RNA); Herpes virus-6, amplified probe technique.
87533	Infectious agent detection by nucleic acid (DNA or RNA); Herpes virus-6, quantification.
87540	Infectious agent detection by nucleic acid (DNA or RNA); Legionella pneumophila, direct probe technique.
87541	Infectious agent detection by nucleic acid (DNA or RNA); Legionella pneumophila, amplified probe technique.
87542	Infectious agent detection by nucleic acid (DNA or RNA); Legionella pneumophila, quantification.

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Provider Billing, Ordering, and Documentation Actions

Denial Risk

Government Policy Supersedes

If there is a conflict between this policy and any relevant government policy (for example Local Coverage Determinations (LCDs), National Coverage Determinations (NCDs), or state Medicaid rules), the government policy will govern the coverage determination. Providers should verify applicable federal or state directives prior to ordering or billing to avoid claim denials.

Conflict with government policy may trigger denial — follow LCD/NCD/state rules

Documentation Required

Benefit-Dependent Coverage and Documentation

Coverage of nucleic acid tests is benefit-dependent. Providers must confirm the member's benefit plan and coverage at the time of the request. Medical record documentation must support medical necessity for the specific molecular test ordered, including clinical findings, relevant history, and prior testing when applicable.

Benefit-dependent coverage — verify member benefits prior to ordering
Documentation expectations: clinical indication, signs/symptoms, prior relevant tests

Ordering and Specimen Requirements

Note

Verify member benefit and Medicare/Medicaid specifications before ordering

Verify member benefit coverage and any Medicare/Medicaid specifications at the time of the request before ordering nucleic acid identification tests; coverage is dependent on individual benefit design.

Application of coverage criteria is dependent upon an individual's benefit coverage at the time of the request.
Providers must verify coverage prior to ordering.

Note

Follow specimen collection guidance and laboratory validation/regulatory requirements

Follow specimen collection guidance from public health agencies and ensure laboratory validation and regulatory requirements (e.g., CLIA/CAP, LDT validation) are met before ordering; labs performing LDTs must validate tests as high-complexity under CLIA '88.

UKHSA specimen instructions for mpox (lesion swab in viral transport medium; throat/blood/urine for follow-up) should be followed where applicable.
LDTs are regulated by CMS as high-complexity tests under CLIA '88 and must be validated and performed in-house.

Testing Frequency Notes and Limits

Giardia molecular testing specimen frequency recommendation

Recommended specimen frequencyCDC recommends collecting three stool specimens from patients over the course of a few days to improve accuracy for Giardia testing.

Purpose of multiple specimensCollecting multiple stools increases diagnostic sensitivity compared with a single specimen.

Test types referencedMolecular assays (e.g., DNA sequencing) can identify Giardia strains; DFA and immunoassays are alternative methods per CDC guidance.

Orthopoxvirus/monkeypox PCR and follow-up testing frequency/context

Primary diagnostic specimenMpox is diagnosed by PCR on a viral swab taken from one or more vesicles or ulcers (lesion swab).

Additional specimen for contacts or throat involvement

Definitions and Test Types

Nucleic acid amplification tests (NAATs) definition and examples

DefinitionNucleic acid amplification tests (NAATs) — assays that amplify target pathogen nucleic acids (includes PCR and related technologies).

Included technologiesExamples include polymerase chain reaction (PCR), reverse transcriptase-PCR (RT-PCR/rRT-PCR), and quantitative PCR (qPCR).

Common useUsed to detect DNA or RNA of infectious agents for rapid and sensitive identification in clinical specimens.

Culture-independent diagnostic test (CIDT) definition

DefinitionCulture-independent diagnostic test (CIDT) — a diagnostic method that detects pathogens without requiring traditional culture techniques.

Context in policyCIDT is listed in the policy terminology table and informs use of molecular testing approaches.

Background and Technology Overview

Nucleic acid hybridization and amplification technologies (including PCR and related NAAT methods) are highly sensitive and specific approaches for detecting pathogen nucleic acid and can reduce time to result compared with culture. These methods include direct probe, amplified probe, and quantification techniques and may be performed as either FDA-cleared assays or as laboratory-developed tests which must be validated and operated under CLIA requirements. Limitations of these technologies include contamination risk, variable validation of LDTs, interpretation complexity, and greater cost; therefore, their use should follow clinical and public health guidance as well as the coverage designations in this policy.

Policy Summary

PayerBlue Cross Blue Shield - Tennessee

PolicyIdentification of Microorganisms using Nucleic Acid Probes

Policy CodePolicy N/A

Change TypeNo material change

Effective DateN/A

Next Review DateN/A

Key ActionVerify coverage for the specific CPT code prior to ordering and ensure appropriate coding and any payer-specific prior authorization rules are met.

SourceLink

On This Page

UKHSA recommends swabbing one or more vesicles/ulcers and placing swab in viral transport medium

When to collect additional specimens: For high-risk contacts without rash but with systemic symptoms, a throat swab may be obtained; for follow-up or clinical deterioration, additional samples (lesion swab, throat swab, blood in EDTA, and urine) are recommended.

See UKHSA and ECDC rapid risk assessment for testing indications

Respiratory pathogens (Legionella pneumophila, Mycoplasma pneumoniae)

Respiratory pathogen testing using nucleic acid methods is acceptable when aligned with public health and clinical guidance.

Legionella pneumophila testing: PCR/NAAT may be performed for Legionella pneumophila; guidance does not indicate a requirement to perform quantification for Legionella.

CDC indicates PCR can be performed and does not mention the need to quantify

Mycoplasma pneumoniae testing: PCR/NAAT may be performed for Mycoplasma pneumoniae; quantification is not required per CDC guidance.

Refer to code descriptions (87580-87582) and CDC guidance for method preference

Candida species from positive blood cultures — rapid detection options

Rapid identification of Candida species from positive blood cultures may be clinically appropriate.

Candida identification from positive blood cultures: FISH probes or PCR assays may be used to rapidly detect and identify Candida species from positive blood culture samples.

AAP cites FISH and PCR as rapid detection options

Clinical diagnosis of mucocutaneous candidiasis: Presumptive diagnosis of mucocutaneous candidiasis (thrush) is usually clinical and molecular testing may not be necessary in typical presentations.

Clinical judgment should guide use of molecular tests for noninvasive mucocutaneous disease

Documentation Required

Specimen Collection and Documentation

Specimen collection must follow recognized guidance to ensure diagnostic accuracy. For mpox (orthopoxvirus) and other vesicular lesion pathogens, collect lesion swabs in viral transport or viral culture medium (for example, Virocult®); if pharyngeal lesions are present also collect a throat swab. When follow-up testing is required, consider additional specimens such as blood (EDTA) and urine as clinically indicated. Document specimen source, collection method, transport medium, and timing in the medical record.

Specimen collection and documentation expectations — record specimen source, collection method, transport medium, and collection date/time
Mpox/orthopoxvirus: lesion swab in viral transport medium; consider throat swab, blood (EDTA), and urine for follow-up

Note

Clinical Guidance — When Testing May Not Be Required

Some diagnoses (for example mucocutaneous candidiasis/thrush in pediatrics) can be made clinically and may not require molecular testing. Review clinical guidelines (e.g., AAP Red Book) to determine when testing is indicated versus when a presumptive clinical diagnosis is appropriate. Document the clinical rationale when choosing not to perform molecular testing.

Clinical guidance: certain conditions (eg, mucocutaneous candidiasis) may not require PCR/NAAT for diagnosis
If opting for clinical diagnosis, document rationale and findings in the medical record

Denial Risk

Simultaneous Testing Exclusion

Do not order more than one of direct probe, amplified probe, or quantification for the same organism during a single encounter; simultaneous ordering of multiple modalities for the same organism is not covered and may be denied.

Simultaneous testing denial trigger — simultaneous ordering exclusion applies to direct probe, amplified probe, and quantification for the same organism in one encounter

Billing Rule

Coding and Coverage Verification

Verify CPT/organism mapping and any coding-specific coverage rules before billing. Some procedure codes listed in the CPT code section meet coverage criteria (MCC) while others do not (DNMCC); providers should confirm which CPT codes are covered under the member's benefits and ensure documentation supports the chosen code.

Verify code-specific coverage and correct CPT-to-organism mapping
Coding and potential prior authorization may be required for listed nucleic acid tests

A throat swab may be taken for high-risk contacts with systemic symptoms but no rash; a negative throat swab does not exclude infection and monitoring continues.

Follow-up testing specimensIf follow-up testing is required (clinical deterioration or to inform discharge), additional samples should include lesion swab + throat swab in viral transport medium, blood in EDTA tube, and urine in a sterile container.

ImplicationCIDTs include molecular methods such as NAATs that can provide faster results than culture-based methods.

Laboratory-developed test (LDT) definition and regulatory note

DefinitionLaboratory-developed test (LDT) — a test developed and validated by a laboratory and performed in-house (not FDA-cleared/approved).

Regulatory statusLDTs are regulated by CMS as high-complexity tests under CLIA '88.

FDA noteLDTs are not approved or cleared by the U.S. Food and Drug Administration; FDA clearance is not currently required for clinical use.