CPT® Code 87046 is used to report stool culture testing for additional aerobic bacterial pathogens, including identification of each organism beyond the primary culture. This code is typically used in conjunction with 87045, which represents the initial stool culture.
This service supports the diagnosis of infectious gastrointestinal conditions by identifying less common or additional bacterial pathogens contributing to patient symptoms.
Key Facts About CPT® 87046
- Service type: Laboratory test (microbiology)
- Test: Stool culture for additional aerobic bacterial pathogens
- Reporting: Add-on code (reported per additional pathogen identified)
- Specimen type: Stool
- Provider type: Laboratories, physicians, and qualified healthcare professionals
Common clinical indications:
- Persistent or severe diarrhea
- Suspected bacterial gastrointestinal infection
- Travel-related gastrointestinal illness
- Foodborne illness investigations
- Immunocompromised patients with GI symptoms
When to Use CPT® 87046
CPT 87046 is appropriate when:
- A stool culture identifies additional aerobic bacterial pathogens beyond the primary test
- The laboratory performs separate identification of each additional organism
- The test is performed alongside 87045 (initial stool culture)
- Clinical presentation supports expanded microbiological evaluation
Examples:
- Identifying multiple bacterial pathogens in a patient with severe infectious diarrhea
- Additional organism identification following an initial positive stool culture
- Expanded stool testing in a patient with prolonged GI symptoms
- Detecting co-infections in high-risk or immunocompromised patients
Documentation Requirements
To support CPT 87046 billing, documentation should include:
- Patient identifiers and date of service
- Clinical indication for stool culture testing
- Specimen source (stool)
- Initial culture results (linked to CPT 87045)
- Identification of each additional pathogen
- Laboratory report with organism details
- Ordering provider information
Clear documentation ensures accurate reporting of each additional organism identified.
Reimbursement and Coding Considerations
- CPT 87046 is an add-on code and must be billed with 87045
- Reported per additional pathogen identified
- Medical necessity must support expanded testing
- Diagnosis coding should reflect infectious or gastrointestinal conditions
- Payer policies may limit the number of reportable organisms
- Often used in conjunction with other stool studies (e.g., ova and parasites, C. difficile testing)
Always verify payer-specific microbiology billing guidelines.
How OptiMantra Supports Microbiology Testing
OptiMantra’s integrated EMR and practice management platform streamlines documentation and billing for CPT 87046:
With OptiMantra, providers can:
- Order stool cultures and related tests within the patient chart
- Track lab results, including multiple identified organisms
- Link microbiology findings to diagnoses and treatment plans
- Maintain detailed laboratory documentation that supports compliance and audit preparedness
- Integrate lab workflows for efficient infectious disease management
- Simplify coding and billing workflows to help support accurate billing for add-on laboratory services
By centralizing lab and microbiology workflows, OptiMantra helps practices improve efficiency, ensure compliance, and optimize reimbursement.
Try OptiMantra for free here!
Disclaimer: CPT® codes are maintained by the American Medical Association. This guide is for informational purposes only and does not replace official coding guidelines or payer policies.
.png)
