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    OpenPayerBilling CodesMicrobiology Culture and Typing ProceduresCPT cpt-87046-aerobic-bacterial-stool-culture-presumptive-id-non-salmonella-shigella
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    CPT 87046: Aerobic Bacterial Stool Culture, Presumptive ID (non-Salmonella/Shigella)

    CPT code 87046 describes an aerobic bacterial stool culture in which the laboratory analyst isolates potential enteric pathogens and performs presumptive identification of organisms other than Salmonella or Shigella; this service is a microbiology laboratory diagnostic test typically performed in a clinical laboratory or hospital microbiology lab and categorized as a bacteriology culture of stool specimens to evaluate infectious gastrointestinal illness.

    For related coverage guidance, see recent payer policy updates: Long-Acting Injectable Antiretroviral Agents for HIV, B-Hemolytic Streptococcus Testing, Human Immunodeficiency Virus (HIV) — Coverage Criteria for Testing and Resistance Assays.

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    Clinical & Coding Specifications

    Clinical Context

    A typical patient is an adult or pediatric outpatient presenting with acute gastroenteritis characterized by diarrhea, abdominal cramps, fever, or suspected bacterial enteric infection. A clinician collects a stool specimen in the clinic, emergency department, or inpatient unit and sends it to the microbiology laboratory for aerobic bacterial stool culture. In the laboratory workflow, a technologist inoculates selective and nonselective media, incubates aerobically, inspects growth, isolates colonies that appear pathogenic, and performs presumptive biochemical or rapid identification tests for organisms other than Salmonella or Shigella. Results are reported to the ordering provider to guide antimicrobial therapy and infection control. Typical sites of service include outpatient clinics, emergency departments, hospital inpatient laboratories, and independent clinical laboratories performing routine microbiology culture services.

    Related CPT Codes

    CPT CodeDescriptionRelationship to This Procedure
    87045Culture, bacterial; each source, aerobic, with isolation and presumptive identification of isolates (except urine)Alternative/additional culture CPT for other specimen sources; used when multiple sources are cultured
    87070Anaerobic culture, with isolation and presumptive identification of isolatesPerformed when anaerobic enteric pathogens are suspected in addition to aerobic culture
    87077Culture for pathogenic organisms; fecal leukocyte or fecal occult blood testing (separate rapid tests)Adjunct rapid stool tests that may be ordered alongside culture to assess inflammation or bleeding
    87177Infectious agent antigen detection by immunoassay technique, qualitative/semiquantitative, multiple-step method; stool, for Clostridioides difficile toxin A and BOften ordered concurrently when C. difficile infection is suspected and culture is not the primary diagnostic method
    87081Culture, bacterial, smear, each source (with direct smear)Direct smears or gram stains may be performed alongside culture as preliminary diagnostic information

    If additional related CPT codes are needed for payer-specific bundling rules, providers reference payer guidance from Aetna, Blue Cross Blue Shield, Cigna Health, UnitedHealthcare, BUCA, and Medicare.

    Related Modifiers

    10 rows

    ModifierDescriptionWhen to Use
    25CPT modifier 25 indicates that on the same day as another procedure or service, the same physician or other qualified health care professional provided a significant, separately identifiable…- When to apply: Use modifier 25 only on an E/M code to indicate the same provider delivered a significant, separately identifiable E/M service on the same day as another procedure or service — i.e.,…
    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…
    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…
    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…
    76Modifier -76, Repeat Procedure or Service by Same Physician or Other Qualified Health Care Professional, is appended when the same provider performs an identical, medically necessary procedure or…- Use modifier -76 when the same physician or other qualified health care professional performs an identical procedure or service a second (or subsequent) time on the same date of service and the…
    78CPT modifier -78 indicates an unplanned, related return to the operating or procedure room by the same provider during the global postoperative period. It is appended when treatment for a…- Use modifier -78 when an unplanned, related complication during the original procedure’s global postoperative period requires the patient to return to a formal operating or procedure room and the…

    Related Provider Taxonomies

    8 rows

    Taxonomy Code
    207Q00000X
    207L00000X
    208D00000X
    367500000X
    174N00000X
    225400000X
    174V00000X
    173F00000X

    Related ICD-10-CM Codes

    24 rows

    ICD-10-CM CodeDescription
    A02.0Salmonella enteritis
    A02.1Salmonella sepsis
    A03.9Shigellosis, unspecified
    A04.0Enteropathogenic Escherichia coli infection
    A04.2Enteroinvasive Escherichia coli infection
    A04.3Enterohemorrhagic Escherichia coli infection
    A04.5Campylobacter enteritis
    A04.6Enteritis due to Yersinia enterocolitica
    A04.8Other specified bacterial intestinal infections
    A05.1Botulism food poisoning

    Showing 1–10 of 24

    Related Payer Policy Updates

    Specialty: Infectious Disease1 / 3

    10 rows

    PolicyPayerEffective Date
    Long-Acting Injectable Antiretroviral Agents for HIVColorado Rocky Mountain Health Plans2026-10-01
    B-Hemolytic Streptococcus TestingOscar Health2026-10-01
    Human Immunodeficiency Virus (HIV) — Coverage Criteria for Testing and Resistance AssaysOscar Health2026-10-01
    Hepatitis Testing (A, B, C, D) Coverage CriteriaOscar Health2026-10-01
    Lyme Disease Testing Coverage CriteriaOscar Health2026-10-01
    Pathogen Panel TestingOscar Health2026-10-01
    Diagnostic Testing of Common Sexually Transmitted InfectionsOscar Health2026-10-01
    Coronavirus Testing in the Outpatient SettingOscar Health2026-10-01
    Testing for Vector-Borne InfectionsOscar Health2026-10-01
    Testing for Diagnosis of Active or Latent TuberculosisOscar Health2026-10-01

    Related Codes

    87086-CULTURE-BACTERIAL-QUANTITATIVE-COLONY-COUNT

    CPT 87086: Urine Culture with Quantitative Colony Count

    CPT-87040-BLOOD-CULTURE-ISOLATION-PRESUMPTIVE-IDENTIFICATION

    CPT 87040: Blood Bacterial Culture with Isolation and Presumptive ID

    CPT-87045-AEROBIC-BACTERIAL-STOOL-CULTURE-SALMONELLA-SHIGELLA

    CPT 87045: Aerobic Bacterial Stool Culture for Salmonella/Shigella

    CPT-87070-AEROBIC-CULTURE-ISOLATION-PRESUMPTIVE-IDENTIFICATION

    CPT 87070: Aerobic Culture with Isolation and Presumptive Identification

    CPT-87071-AEROBIC-QUANTITATIVE-BACTERIAL-CULTURE-NON-URINE-BLOOD-STOOL

    CPT 87071: Quantitative Aerobic Bacterial Culture, Non-urine/blood/stool

    CPT-87073-ANAEROBIC-CULTURE-NONBLOOD-NONURINE-NONSTOOL

    CPT 87073: Anaerobic Culture, Non-Urine/Blood/Stool

    CPT-87075-ANAEROBIC-CULTURE-IDENTIFICATION-NON-BLOOD-SPECIMEN

    CPT 87075: Anaerobic Culture and Bacterial Identification (Nonblood)

    CPT-87076-ANAEROBIC-ISOLATE-DEFINITIVE-IDENTIFICATION

    CPT 87076: Anaerobic Isolate Identification to Species Level

    CPT-87077-DEFINITIVE-IDENTIFICATION-AEROBIC-ISOLATE

    CPT 87077: Definitive Identification of Aerobic Isolate

    CPT-87081-TARGETED-SINGLE-ORGANISM-CULTURE

    CPT 87081: Selective Culture for Specific Pathogen

    Showing 1–10 of 30

    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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