CurrentPremera BluecrossPolicy N/A

Fecal microbiota testing and donor screening for fecal microbiota transplantation (FMT) and fecal analysis for intestinal dysbiosis

Defines reimbursable donor stool testing and which fecal analyses are not reimbursable for evaluation of dysbiosis, IBS, malabsorption, or SIBO; specifies donor screening and MDRO testing requirements for FMT.

Policy Summary

PayerPremera Bluecross

PolicyFecal microbiota testing and donor screening for fecal microbiota transplantation (FMT) and fecal analysis for intestinal dysbiosis

Policy CodePolicy N/A

Change TypeNew policycoding update

Effective DateFeb 6, 2026

Next Review DateN/A

Key ActionDocument donor screening for FMT by recording which reimbursable culture and NAAT assays were performed, note any non-reimbursable tests not performed, and confirm member benefit limits and prior authorization requirements as needed.

SourceLink

POLICY UPDATE CHANGES

New policy created and approved October 14, 2025; effective for dates of service on or after February 6, 2026 following 90-day provider notification.

Coding update on February 6, 2026 removed several CPT codes from the policy.

8microorganisms for which culture prior to FMT donation is reimbursable

8microorganisms for which NAAT prior to FMT donation is reimbursable

4MDROs for which NAAT is NOT reimbursable prior to donation

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Reimbursable and Non-reimbursable Fecal Tests and Donor Screening

Reimbursable donor stool testing prior to FMT (by culture)

Prior to donation for a fecal microbiota transplant (FMT), bacterial culture analysis of the donor fecal sample is considered reimbursable when ALL of the following organisms are tested:

ALL of the following

Extended spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae
Vancomycin-resistant Enterococci (VRE)
Carbapenem-resistant Enterobacteriaceae (CRE)
Methicillin-resistant Staphylococcus aureus (MRSA)
Campylobacter
Shigella
Salmonella

Reimbursable donor stool testing prior to FMT (by NAAT)

Prior to donation for an FMT, nucleic acid amplification testing (NAAT) of the donor fecal sample is considered reimbursable when ANY of the following microorganisms are tested:

ANY of the following

Clostridium difficile
Campylobacter
Salmonella
Shigella
Shiga toxin-producing Escherichia coli

Not reimbursable donor stool testing by NAAT

Prior to donation for an FMT, NAAT of the donor fecal sample for the following microorganisms is NOT reimbursable:

ANY of the following (not reimbursable)

Extended spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae
Vancomycin-resistant Enterococci (VRE)
Carbapenem-resistant Enterobacteriaceae (CRE)
Methicillin-resistant Staphylococcus aureus (MRSA)
Any other microorganisms not listed as reimbursable by NAAT

Not reimbursable fecal analyses for evaluation of intestinal dysbiosis/IBS/malabsorption/SIBO

As diagnostic tests for the evaluation of intestinal dysbiosis, irritable bowel syndrome, malabsorption, or small intestinal bacterial overgrowth, the following fecal analyses are NOT reimbursable:

ANY of the following (not reimbursable)

Triglycerides
Chymotrypsin
Iso-butyrate, iso-valerate, and n-valerate
Meat and vegetable fibers
Long chain fatty acids

Reimbursable donor fecal sample analysis

Analysis of the donor fecal sample for the microorganisms listed in this policy via the means indicated may be considered reimbursable when ALL of the following operational conditions are met:

ALL of the following operational conditions

Test is performed prior to donation for a fecal microbiota transplant (FMT)
The analysis targets microorganisms listed in this policy (see code/groups and referenced methods)
Coverage and reimbursement are subject to applicable member benefit plan limits and conditions

Relevant CPT Codes and Coding Updates

Listed CPT codes mentioned in documentCPT

82705	Fat or lipids, feces; qualitative
82710	Fat or lipids, feces; quantitative
82715	Fat differential, feces, quantitative
83986	pH; body fluid, not otherwise specified
84311	Spectrophotometry, analyte not elsewhere specified
87076	Culture, bacterial; anaerobic isolate, additional methods required for definitive identification, each isolate
87077	Culture, bacterial; aerobic isolate, additional methods required for definitive identification, each isolate
87102	Culture, fungi (mold or yeast) isolation, with presumptive identification of isolates; other source (except blood)
87106	Culture, fungi, definitive identification, each organism; yeast
89160	Meat fibers, feces

Removed CPT codes (no longer included)CPTNot Covered

87045
87046
87075
87081
87493
87500
87641
87798

Operational Requirements, Documentation, and Authorization

Documentation Required

Donor screening scope and documentation

Document which reimbursable culture and NAAT assays were performed as part of donor screening and explicitly note any assays not performed because they are non‑reimbursable. Follow relevant society and FDA donor‑screening guidance, including testing for multidrug‑resistant organisms (MDROs) and enteric pathogens when screening donors for FMT.

Record that donor stool testing included reimbursable bacterial culture for ESBL-producing Enterobacteriaceae, VRE, CRE, MRSA, Campylobacter, Shigella, and Salmonella.
Record that donor stool testing included reimbursable NAATs for C. difficile, Campylobacter, Salmonella, Shigella, STEC, norovirus, rotavirus, and SARS-CoV-2 where performed.
If NAATs for MDROs (ESBL, VRE, CRE, MRSA) were not performed, document that these NAATs are not reimbursable per policy and note the alternative culture‑based MDRO testing performed if applicable.

Prior Authorization

Quarantine and bookend testing practice (operational guidance cited)

Clinical and Policy Context

Alterations in the gut microbial community—often termed dysbiosis—have been associated with a wide range of conditions including irritable bowel syndrome, inflammatory bowel disease, celiac disease, obesity, diabetes, certain autoimmune disorders, and other systemic illnesses. The intestinal microbiome is complex and individualized, and while many tests and biomarkers (for example, sequencing of microbial DNA or measurement of fecal metabolites) have been proposed for assessing microbiome composition and function, there is limited standardization across laboratories and a lack of well‑established normal ranges for many analytes, which constrains their routine clinical utility.

Fecal microbiota transplantation (FMT)—the infusion of stool from a healthy donor to a recipient to restore microbiome balance—has proven clinical benefit for recurrent Clostridioides difficile infection and is an FDA‑approved approach in specific settings; however, FMT remains investigational for most other gastrointestinal and systemic conditions, and available trials show mixed results outside of CDI.

Because FMT involves transfer of biologic material, rigorous donor screening is essential. National and international guidance and FDA communications emphasize testing to identify enteric pathogens and, critically, screening for multidrug‑resistant organisms (MDROs) such as extended‑spectrum beta‑lactamase (ESBL)–producing Enterobacteriaceae, vancomycin‑resistant Enterococci (VRE), carbapenem‑resistant Enterobacteriaceae (CRE), and methicillin‑resistant Staphylococcus aureus (MRSA) to minimize the risk of transmitting infectious agents to recipients. Practices such as quarantining donations and performing bookend MDRO testing for multiple donations are recommended to reduce transmission risk.

Defined Terms

Definitions

FMTFecal microbiota transplant; infusion of stool from a healthy donor to a patient to restore gut microbiome.

NAATNucleic acid amplification testing.

ESBLExtended spectrum beta-lactamase.

VREVancomycin-resistant enterococci.

CRECarbapenem-resistant Enterobacteriaceae.

MRSAMethicillin-resistant Staphylococcus aureus.

FMT (duplicate entry)Fecal Microbiota Transplantation — transfer of stool from a healthy donor to a recipient to restore healthy gut microbiota.

Policy Changes and Coding Updates

2025-10-14policy added (material)

New policy created and approved establishing routine test management guidance that analysis of donor fecal samples for the microorganisms listed may be considered reimbursable when criteria are met; effective for dates of service on or after 2026-02-06 following 90-day provider notification.

2026-02-06coding update (material)Latest

Coding update removed CPT codes 87045, 87046, 87075, 87081, 87493, 87500, 87641, and 87798 from the policy.

Policy Summary

PayerPremera Bluecross

PolicyFecal microbiota testing and donor screening for fecal microbiota transplantation (FMT) and fecal analysis for intestinal dysbiosis

Policy CodePolicy N/A

Change TypeNew policycoding update

Effective DateFeb 6, 2026

Next Review DateN/A

SourceLink

On This Page

Denial Risk

Reimbursement denial risk for listed non-reimbursable fecal analytes and NAATs

Claims for the fecal analytes and NAATs listed as not reimbursable in this policy will be denied, because available published literature does not confirm these tests are required or beneficial for diagnosis or treatment.

Non‑reimbursable fecal analytes include triglycerides, chymotrypsin, iso‑butyrate/iso‑valerate/n‑valerate, meat/vegetable fibers, long chain fatty acids, cholesterol, total short chain fatty acids, fecal yeast identification/quantitation, n‑butyrate, beta‑glucuronidase, pH, and fecal secretory IgA.
NAAT‑based testing for MDROs (ESBL, VRE, CRE, MRSA) is listed as not reimbursable.

Documentation Required

Confirm indication and benefit coverage

Document that testing was performed prior to FMT donation and verify coverage by checking the member's benefit plan limits and conditions prior to submitting claims.

Include in the medical record that the analyses were performed as part of pre‑donation FMT screening.
Confirm any benefit limitations or conditions that may affect coverage for donor fecal sample analysis.