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    v1.0.30
    OpenPayerBilling CodesPhenotype and Genotype-Infectious AgentsCPT cpt-87999-unlisted-microbiology-procedure
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    CPT 87999: Unlisted Microbiology Procedure

    CPT code 87999 is an unlisted microbiology procedure code used to report microbiology testing or laboratory procedures that lack a specific CPT code, typically representing specialized or novel infectious disease assays. Service type: microbiology/laboratory services; typical site of service: clinical laboratory or hospital laboratory. Data not available in the input.

    For related coverage guidance, see recent payer policy updates: Biomarker Testing for Autoimmune Rheumatic Disease, Immunopharmacologic Monitoring of Therapeutic Serum Antibodies, Immune Cell Function Assay.

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    Table of contents

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    Clinical & Coding Specifications

    Clinical Context

    A 62-year-old hospitalized patient on broad-spectrum antibiotics develops worsening sepsis with persistent fevers and hypotension. Blood cultures remain negative after standard testing but the infectious disease team suspects an unusual or atypical organism (for example, a novel viral pathogen, rare fungus, or emergent bacterial strain) requiring an off‑protocol, laboratory‑developed microbiology assay. A specimen (blood, bronchoalveolar lavage, or tissue) is submitted to the clinical microbiology laboratory for a specialized molecular or biochemical test that has no specific CPT code. The laboratory documents the unique procedure, performs a validated test (such as an in‑house multiplex PCR for an uncommon pathogen, advanced sequencing for pathogen identification, or specialized antigen/antibody assay), and bills using 87999 to report the unlisted microbiology procedure. Typical workflow includes clinician order, specimen accessioning, method validation review by the laboratory director, performance of the procedure by a clinical laboratorian, result verification, and inclusion of interpretive comments in the final report. The service commonly occurs in hospital inpatient laboratories, reference laboratories, academic medical centers, or public health laboratories. For outpatient clinics, emergency departments, and ambulatory surgery centers, 87999 may be used when an off‑protocol or novel microbiology assay is required and no specific CPT exists.

    Related CPT Codes

    CPT CodeDescriptionRelationship to This Procedure
    87220Culture, bacteria; any source, by fluorescent or chromogenic media, initial isolation (includes identification)Performed when standard culture methods are applicable; may precede 87999 when initial cultures fail and unlisted molecular testing is needed.
    87471Infectious agent detection by nucleic acid (DNA or RNA), direct probe technique, each organismUsed for single-target molecular tests; 87999 may be used when a novel or multi-target assay has no specific code.
    87798Infectious agent antigen detection by immunoassay technique, multiple-step, (e.g., enzyme immunoassay), each organismUsed for antigen testing; 87999 applies when an atypical antigen assay lacks a specific CPT.
    87635Infectious agent detection by nucleic acid (DNA or RNA); severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), amplified probe techniqueCommon molecular respiratory pathogen test; 87999 is used for emergent, non‑standard sequencing or novel pathogen assays without specific codes.
    87449Infectious agent detection by nucleic acid (DNA or RNA); multiple organisms, any methodUsed for multiplex panels with established CPT codes; when an in‑house multiplex panel lacks a code, 87999 may be reported.
    88291Microbial identification by nucleic acid (e.g., sequencing), per organismUsed for sequencing-based identification when a specific sequencing code exists; 87999 is used when no specific sequencing CPT applies.

    Related Modifiers

    8 rows

    ModifierDescriptionWhen to Use
    22Modifier –22 (Increased Procedural Services) is used when a reported procedure is substantially more extensive than normally required. The CPT Manual and CMS state it may be appended only when the…- When to use: Append modifier -22 to a procedural CPT code when the service performed is substantially more extensive than the usual service described by that code — i.e., the procedure required…
    26Modifier 26 (Professional Component) identifies and bills only the professional portion of a split service — the physician’s interpretation, report, and medical judgment — when the technical…- Use CPT Modifier -26 when you are billing only the professional component (PC) of a split‑bill eligible service—i.e., you performed the physician interpretation, medical judgment and prepared a…
    52Modifier ‑52 (Reduced Services) indicates that a service or procedure was partially reduced or omitted at the provider’s discretion, allowing reporting of the basic procedure number with a qualifier…- Use modifier -52 when a physician or qualified health professional electively reduces or omits part of a procedure or service (for example, performing fewer required views or omitting a portion of…
    53Modifier 53 (Discontinued Procedure) signals that a surgical or diagnostic service was begun by the physician but terminated because of extenuating circumstances that threatened the patient’s…- Use modifier -53 when a physician/qualified healthcare professional has started a surgical or diagnostic procedure (e.g., anesthesia administered, incision or scope insertion) and then discontinues…
    59Modifier 59 indicates a distinct procedural service when two procedures that are not normally billed together are clinically and procedurally separate. The CPT definition (as reiterated by CMS)…- Use modifier -59 to report a distinct procedural service when documentation supports that the procedure reported is not normally billed together with another service on the same day because of a…
    62Modifier 62 indicates that two surgeons function as co‑surgeons, each performing distinct parts of the same primary surgical procedure. It is appended to the primary procedure code (and any…- Use modifier -62 when two surgeons act as co‑surgeons (both primary surgeons) on a single definitive primary procedure, each performing distinct parts of the same surgical procedure (append -62 to…
    90Modifier ‑90 (Reference/Outside Laboratory) indicates that a laboratory test was performed by an entity other than the treating or reporting provider. The American Medical Association defines…- Use CPT modifier -90 when a laboratory test is performed by an outside/reference laboratory (an entity other than the treating or reporting physician or qualified professional) and the claim needs…
    91Modifier 91 — “Repeat Clinical Diagnostic Laboratory Test” — is appended when the exact same CPT laboratory test is performed more than once for the same patient on the same day because serial,…- Use modifier 91 when the exact same CPT laboratory test is performed more than once on the same patient on the same date because serial or repeated testing is medically necessary to monitor…

    Related Provider Taxonomies

    8 rows

    Taxonomy Code
    207RH0000X
    207L00000X
    207LP2900X
    311ZA0620X
    163WR0400X
    207XS0106X
    221700000X
    251S00000X

    Related Payer Policy Updates

    Specialty: Immunology/Rheumatology1 / 3

    10 rows

    PolicyPayerEffective Date
    Biomarker Testing for Autoimmune Rheumatic DiseaseOscar Health2026-10-01
    Immunopharmacologic Monitoring of Therapeutic Serum AntibodiesOscar Health2026-10-01
    Immune Cell Function AssayOscar Health2026-10-01
    Biomarker Testing for Autoimmune Rheumatic DiseaseBlue Cross Blue Shield - New Mexico2026-09-04
    Inflammatory Conditions - Orencia Intravenous Preferred Specialty Management Policy for Legacy Prescription Drug ListsCigna2026-09-01
    Secukinumab (Cosentyx) — intravenous (Medicare Advantage)blue cross blue shield - louisiana2026-09-01
    Intravenous Immune Globulin (IVIG) — indications and authorization criteriaBlue Cross Blue Shield - Iowa2026-08-28
    Infliximab Intravenous Products Preferred Specialty Management PolicyCigna2026-08-15
    Kineret (anakinra) — Coverage CriteriaBlue Cross Blue Shield - Iowa2026-08-14
    Actimmune (interferon gamma-1b) — Prior Authorization and Coverage Criteriameridian_health_plan_of_michigan2026-08-01

    Related Codes

    CPT-87900-VIRAL-DRUG-SUSCEPTIBILITY-GENOTYPIC-PHENOTYPE-PREDICTION

    CPT 87900: Viral Drug Susceptibility and Phenotype Prediction

    CPT-87901-HIV-1-GENOTYPE-REVERSE-TRANSCRIPTASE-PROTEASE-ANALYSIS

    CPT 87901: HIV‑1 Genotype — Protease and Reverse Transcriptase Sequencing

    CPT-87902-HEPATITIS-C-GENOTYPE-NUCLEIC-ACID-TESTING-TECHNICAL

    CPT 87902: Hepatitis C Virus Genotype by Nucleic Acid Analysis

    CPT-87903-HIV-1-DRUG-RESISTANCE-NUCLEIC-ACID-ANALYSIS

    CPT 87903: HIV-1 Drug Resistance Testing, Culture-Based

    CPT-87904-HIV-1-DRUG-RESISTANCE-ADDITIONAL-DRUG-TESTING

    CPT 87904: HIV‑1 Drug Resistance Test, Additional Drug

    CPT-87905-ENZYMATIC-ACTIVITY-TESTING-INFECTIOUS-AGENT-TECHNICAL

    CPT 87905: Enzymatic Activity Test for Non-Viral Infectious Agents

    CPT-87906-HIV-1-GENOTYPE-NUCLEIC-ACID-NON-RT-PROTEASE-REGIONS

    CPT 87906: HIV‑1 Genotype by Nucleic Acid (non-RT/protease)

    CPT-87910-CMV-GENOTYPE-NUCLEIC-ACID-ANALYSIS

    CPT 87910: CMV Genotype Analysis by Nucleic Acid Testing

    CPT-87912-HEPATITIS-B-GENOTYPE-ANALYSIS-NUCLEIC-ACID

    CPT 87912: Hepatitis B Virus Genotype Analysis

    CPT-87913-SARS-COV-2-GENOTYPE-ANALYSIS-NEXT-GENERATION-SEQUENCING

    CPT 87913: SARS–CoV–2 Genotype Analysis by Next‑Generation Sequencing

    Frequently Asked Questions

    References

    1. 1.CPT® Codes and Descriptions. AAPC. Retrieved Aug 11, 2026.Maintains the CPT code set's official descriptions and guidelines, licensed from the American Medical Association, used as the definitional source for CPT codes on this page.
    2. 2.HCPCS Quarterly Update. Centers for Medicare & Medicaid Services (CMS). Retrieved Aug 11, 2026.CMS's quarterly release of HCPCS Level II codes and short/long descriptors, the source for HCPCS code definitions and update history.
    3. 3.ICD-10-CM Full Code List. Centers for Medicare & Medicaid Services (CMS). Retrieved Aug 11, 2026.CMS's complete ICD-10-CM diagnosis code list, used to cross-reference diagnosis codes associated with this procedure or service.
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