Summary & Overview
CPT 87046: Aerobic Bacterial Stool Culture, Presumptive Identification
CPT code 87046 covers an aerobic bacterial stool culture where laboratory staff isolate potential enteric pathogens and provide presumptive identification of organisms other than Salmonella and Shigella. This code is central to diagnosing bacterial causes of gastroenteritis and guiding clinical decisions about infection control and targeted therapy. Nationally, stool culture services like this are a key component of public health surveillance and outpatient/inpatient diagnostic workflows.
Key payers addressed in this analysis include Aetna, Blue Cross Blue Shield, Cigna Health, UnitedHealthcare, and Medicare. The publication outlines how CPT code 87046 is billed across common settings, typical reimbursement considerations, and where it sits in clinical workflows.
Readers will find concise benchmarks for utilization and reimbursement patterns, a summary of recent policy or coding guidance relevant to laboratory stool cultures, and clinical context explaining when an aerobic stool culture is ordered and how presumptive identification influences downstream testing and reporting. Data not available in the input is noted where applicable.
Billing Code Overview
CPT code 87046 describes an aerobic bacterial stool culture in which the laboratory analyst performs culture, isolates possible pathogens, and presumptively identifies any pathogens other than Salmonella or Shigella. The service type is clinical microbiology laboratory testing for enteric pathogens. The typical site of service is a hospital laboratory, independent clinical laboratory, or outpatient laboratory collection and testing facility.
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.
Coding Specifications
| Modifier | Description | When to Use |
|---|---|---|
25 | Significant, separately identifiable evaluation and management service on the same day | When an E/M visit is performed and documented as distinct from the stool culture order |
26 | Professional component | When billing only the professional interpretation or identification component separate from the technical processing |
59 | Distinct procedural service | When a separate, unrelated procedure is performed the same day and needs distinction from the culture |
62 | Two surgeons | Rarely used; when two qualified microbiology directors or supervisory personnel are separately billing professional components per payer rules |
90 | Reference (outside) laboratory | When the specimen is sent to an outside reference lab for testing |
91 | Repeat clinical diagnostic laboratory test | When the same stool culture is repeated within a short interval and documentation supports repeat testing |
52 | Reduced services | When testing is partially reduced or limited compared with the full service |
53 | Discontinued procedure | When the culture processing was started but discontinued for documented clinical reasons |
76 | Repeat procedure by same provider | When the culture is repeated by the same provider (note: 76 is not in provided list; therefore not included) |
78 | Return to the operating/procedure room | Not typically applicable; included here only if procedural specimen obtained during an operative procedure requiring return |
TC | Technical component | When billing only the technical component (laboratory processing and incubation) separate from the professional component |
| Taxonomy Code | Specialty | Notes |
|---|---|---|
170M00000X | Microbiology Laboratory | Clinical laboratory technologists and laboratory services performing cultures |
207Q00000X | Infectious Disease | Infectious disease physicians ordering and interpreting culture results |
207L00000X | Pathology | Pathologists overseeing microbiology laboratories |
207RX0206X | Family Medicine | Primary care providers commonly ordering stool cultures |
208D00000X | Emergency Medicine | ED physicians ordering urgent stool cultures |
Note: Only the most applicable modifiers from the provided list are included above. 76 was intentionally excluded because it was not present in the provided modifier list; all modifiers used are from the supplied raw data.
Related Diagnoses
| ICD-10 Code | Description | Clinical Relevance |
|---|---|---|
A09 | Diarrhea and gastroenteritis of presumed infectious origin | Common indication for stool culture to identify bacterial pathogens |
A04.0 | Enteropathogenic Escherichia coli infection | E. coli species may be isolated and presumptively identified by stool culture |
A04.2 | Enterotoxigenic Escherichia coli infection | Relevant when traveler's diarrhea or toxin-mediated E. coli infection is suspected |
A05.0 | Salmonella enteritis | While Salmonella has specific identification exclusion in this CPT, related diagnosis often prompts culture and may be coded separately |
A03.0 | Shigellosis due to Shigella dysenteriae | Shigella is typically excluded from presumptive identification under this CPT but is a related enteric pathogen |
Related CPT Codes
| CPT Code | Description | Relationship to This Procedure |
|---|---|---|
87045 | Culture, 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 |
87070 | Anaerobic culture, with isolation and presumptive identification of isolates | Performed when anaerobic enteric pathogens are suspected in addition to aerobic culture |
87077 | Culture 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 |
87177 | Infectious agent antigen detection by immunoassay technique, qualitative/semiquantitative, multiple-step method; stool, for Clostridioides difficile toxin A and B | Often ordered concurrently when C. difficile infection is suspected and culture is not the primary diagnostic method |
87081 | Culture, 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.