CurrentEmblemHealthPolicy AHS-G2060

Fecal Analysis in the Diagnosis of Intestinal Dysbiosis and Fecal Microbiota Transplant Testing - Lab Benefit Program (LBM)

Reimbursement policy governing laboratory fecal analysis for diagnosis of intestinal dysbiosis and testing of fecal microbiota transplant (FMT) donors for EmblemHealth Lab Benefit Program; defines covered and non-covered fecal tests and donor screening requirements.

Policy Summary

PayerEmblemHealth

PolicyFecal Analysis in the Diagnosis of Intestinal Dysbiosis and Fecal Microbiota Transplant Testing - Lab Benefit Program (LBM)

Policy CodePolicy AHS-G2060

Change TypeClarifications and operational expansion (LBM expansion effective 10/1/2024)

Effective DateMar 1, 2023

Next Review DateN/A

Key ActionPrior to FMT donation, perform required bacterial culture and NAAT pathogen testing and exclude donors with positive MDRO results; use bookend testing ≤60 days with stool quarantine until cleared.

SourceLink

POLICY UPDATE CHANGES

Lab Benefit Program (LBM) expanded to include EmblemHealth HMO/ PPO (Non-City) Commercial, Medicare and Medicaid plans effective 10/1/2024.

Updated for clarity; no changes to coding or coverage criteria.

Transferred policy content to individual company-branded template. No changes to policy title or policy number.

Reformatted and reorganized policy, transferred content to new template with new Reimbursement Policy Number.

3NAAT-covered pathogen categories

7Bacterial culture pathogens covered

14+Fecal biomarkers/tests NOT covered

Trek Health ingests and normalizes Transparency in Coverage data and payer policy updates to give provider organizations a clear view of how commercial reimbursement behaves across markets, payers, and services. Our platform transforms raw payer disclosures into structured intelligence that supports contract evaluation, payer negotiations, and service line strategy. By combining market benchmarks with ongoing policy visibility, Trek helps teams identify variability, risk, and opportunity in commercial reimbursement. The result is faster insight, stronger negotiating positions, and more informed financial decisions.

≥4Minimum MDRO tests required

Coverage Criteria for Fecal Analysis and FMT Donor Testing

inv-01: Coverage criteria for fecal analysis and FMT donor testing

Coverage decisions for fecal testing and fecal microbiota transplant (FMT) donor screening:

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

ALL of the following

Clostridium difficile
Campylobacter
Salmonella
Shigella
Shiga toxin-producing Escherichia coli
Norovirus
Rotavirus

Not covered by NAAT for MDROs: NAAT testing of donor fecal samples for ESBL, VRE, CRE, MRSA and any other microorganisms not listed above does not meet coverage criteria.

Fecal biomarkers not covered for dysbiosis evaluation: As diagnostic tests for intestinal dysbiosis, irritable bowel syndrome, malabsorption, or small intestinal bacterial overgrowth, fecal analysis of the following components does not meet coverage criteria: triglycerides; chymotrypsin; iso-butyrate, iso-valerate, and n-valerate; meat and vegetable fibers; long chain fatty acids; cholesterol; total short chain fatty acids; quantification of Lactobacilli, bifidobacteria, E. coli and other potential pathogens (including Aeromonas, Bacillus cereus, Campylobacter, Citrobacter, Klebsiella, Proteus, Pseudomonas, Salmonella, Shigella, S. aureus, Vibrio); identification/quantitation of fecal yeast (including C. albicans, C. tropicalis, Rhodotorula and Geotrichum); N-butyrate; beta-glucuronidase; pH; short chain fatty acid distribution; and fecal secretory IgA.

Operational note

Application of coverage criteria depends on the individual's benefit coverage at the time of request; Medicare/Medicaid specifications referenced in State and Federal Regulations.

inv-02: Guideline-based criteria and operational notes

Guideline-based indications, cautions, and donor screening requirements referenced in the policy:

Indications — consider fecal microbiota-based therapies for prevention after second recurrence (third episode) of Clostridioides difficile infection (CDI) and select high-risk patients; RBL demonstrated benefit in trials.

Use in IBD and other GI conditions — FMT is investigational for inflammatory bowel disease and not recommended for ulcerative colitis, Crohn’s disease, pouchitis, or irritable bowel syndrome outside of clinical trials; FMT may be considered for recurrent CDI in patients with IBD.

Donor screening requirements — donor screening should include testing for C. difficile toxin B, enteric pathogens, parasites, and MDROs; MDRO testing should at minimum include ESBL-producing Enterobacteriaceae, VRE, CRE, and MRSA; donors and/or stools positive for MDROs should not be used.

COVID-19 precautions — screen donors for SARS-CoV-2 diagnosis, symptoms, or exposures since Dec 1, 2019, and consider testing stool or respiratory/rectal specimens for SARS-CoV-2 per FDA guidance.

inv-03: Coverage information — no explicit criteria in provided chunks

This section contains reimbursement, regulatory context, literature references, and revision history; no additional explicit coverage criteria are provided in these chunks.

If there is a conflict between this policy and applicable government policy (e.g., Local Coverage Determinations or National Coverage Determinations for Medicare, or state Medicaid policies), the government policy will be used to make determinations.

Revision history and administrative updates are documented in the policy revision history.

Coding and Reimbursement Information

Coding guidancemixed

Policy follows CPT, CMS, NCCI and MUE edits; may deny or recoup claims if coding/billing guidelines not followed.

Reimbursement metadatamixed

Reimbursement Policy: Fecal Analysis in the Diagnosis of Intestinal Dysbiosis and Fecal Microbiota Transplant Testing - Lab Benefit Program (LBM).

Enumerated CPT/HCPCS codesmixed

82542	Column chromatography, includes mass spectrometry, non-drug analyte(s), each specimen
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
87045	Culture, bacterial; stool, aerobic, with isolation and preliminary examination
87046	Culture, bacterial; stool, aerobic, additional pathogens
87075	Culture, bacterial; any source, except blood, anaerobic with isolation and presumptive identification of isolates
87076	Culture, bacterial; anaerobic isolate, additional methods required for definitive identification, each isolate

1–10 of 20

1/2

Coding edit sources

Primary coding edit sourcesEdits are based on CPT guidelines from the American Medical Association, specialty organizations, and CMS (including NCCI and MUE).

Conflict resolution between sourcesWhen coding sources conflict, the plan will apply the edits it determines appropriate and may provide explanations upon request.

Claims editing toolsIndustry-standard claims editing software products are used for claim editing decisions.

Compliance actionsIf appropriate coding/billing guidelines or current reimbursement policies are not followed, claims may be denied and/or payments recouped.

MDRO testing bookend interval

Permissible bookend interval

Provider Actions, Donor Screening, and Operational Requirements

Prior Authorization

Prior testing requirements for FMT donors

Prior to donation for a fecal microbiota transplant (FMT), the donor fecal sample must be tested by bacterial culture for the following microorganisms. A negative result is required before donation is used: Extended spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae; Vancomycin-resistant Enterococci (VRE); Carbapenem-resistant Enterobacteriaceae (CRE); Methicillin-resistant Staphylococcus aureus (MRSA); Campylobacter; Shigella; Salmonella.

Affected organisms: ESBL-producing Enterobacteriaceae, VRE, CRE, MRSA, Campylobacter, Shigella, Salmonella

Denial Risk

Donor stool MDRO testing and quarantine

Donor stool screening should include MDRO testing and donors and/or stools positive for MDROs should not be used for FMT. MDRO testing should at minimum include ESBL-producing Enterobacteriaceae, VRE, CRE, and MRSA. The FDA notes that culture of nasal or peri-rectal swabs is an acceptable alternative to stool testing for MRSA only. Bookend testing (no more than 60 days apart) before and after multiple stool donations is acceptable if stool samples are quarantined until post-donation MDRO tests are confirmed negative.

Definitions and Abbreviations

Intestinal dysbiosis

DefinitionIntestinal dysbiosis is a disruption or imbalance of the intestinal microbial ecology.

Associated conditionsDysbiosis has been associated with IBS, IBD, celiac disease, multiple sclerosis, Sjogren's Syndrome, obesity, allergy, and diabetes.

Context in policyTerm used to frame coverage for fecal analysis and to explain limited evidence for many fecal biomarkers.

Abbreviations

FMTFecal microbiota transplant.

NAATNucleic acid amplification testing.

MDROs

Policy Summary

PayerEmblemHealth

PolicyFecal Analysis in the Diagnosis of Intestinal Dysbiosis and Fecal Microbiota Transplant Testing - Lab Benefit Program (LBM)

Policy CodePolicy AHS-G2060

Change TypeClarifications and operational expansion (LBM expansion effective 10/1/2024)

Effective DateMar 1, 2023

Next Review DateN/A

SourceLink

On This Page

COVID-19 (SARS-CoV-2)

Bookend MDRO testing and quarantine — bookend MDRO testing (no more than 60 days apart) before and after multiple stool donations with quarantine of donations until post-donation MDRO tests are confirmed negative is acceptable.

Laboratory-developed tests (LDTs) — LDTs used for fecal analysis are regulated as CLIA high-complexity LDTs and are not FDA-cleared; laboratories must validate assays per CLIA requirements.

Pediatric acute gastroenteritis note: Routine microbiological investigation and fecal markers are generally not helpful for acute gastroenteritis in children except for severe/prolonged cases or underlying chronic conditions.

Bookend MDRO testing before and after multiple stool donations is acceptable if tests are no more than 60 days apart (≤60 days).

Quarantine requirementStool samples must be quarantined until post-donation MDRO test results are confirmed negative.

PurposeBookend testing facilitates use of multiple donations while ensuring negative post-donation MDRO results before release.

Procedure code list completeness note

Reference nature of code listProcedure/CPT/HCPCS codes listed are provided as general reference in the Medical Policy document and may not be all-inclusive.

Provider responsibilityProviders should confirm coding completeness and applicability to the specific service rendered before billing.

Policy scopeCodes included illustrate commonly associated fecal analysis and culture procedures but do not constitute an exhaustive coding table.

Minimum MDRO panel: ESBL-producing Enterobacteriaceae, VRE, CRE, MRSA
MRSA alternative testing: nasal or peri-rectal swab culture acceptable
Quarantine: stool donations must be quarantined until post-donation MDRO tests are confirmed negative; bookend testing may be used (≤60 days apart)

Note

Government policy precedence

When there is a conflict between this policy and any applicable government policy (for example, Local Coverage Determinations or National Coverage Determinations for Medicare, or state Medicaid policies), the government policy takes precedence and will be used to make coverage determinations. For up-to-date Medicare and Medicaid policy guidance, refer to the CMS Medicare Coverage Database and the applicable state Medicaid website.

Government policy precedence: LCDs, NCDs, and state Medicaid policies override this policy when applicable
Medicare CMS search site: https://www.cms.gov/medicare-coverage-database/search.aspx

Multidrug resistant organisms.

MRSAMethicillin-resistant Staphylococcus aureus.

VREVancomycin-resistant enterococci.

RBL / Rebyota

Term and productFecal microbiota, live-jslm (Rebyota; RBL).

Indication notedRBL is a standardized, donor stool-derived, rectally administered live biotherapeutic product approved by the FDA for prevention of recurrent C. difficile infection.

Clinical trial outcomePhase 3 trial estimated CDI cure rates: 80.6% with RBL versus 57.5% with placebo; sustained response >90% at six months among those cured at eight weeks.

MDRO testing

Minimum MDRO panelMDRO testing should at minimum include ESBL-producing Enterobacteriaceae, VRE, CRE, and MRSA.

Donor exclusionDonors and/or stools positive for MDROs must not be used for FMT.

Alternative for MRSACulture of nasal or peri-rectal swabs is an acceptable alternative to stool testing for MRSA only.

Laboratory-developed test (LDT)

DefinitionLaboratory-developed tests (LDTs) are tests developed and validated in-house by a laboratory and are regulated by CMS as high-complexity tests under CLIA '88.

FDA statusLDTs are not approved or cleared by the U.S. Food and Drug Administration; FDA clearance/approval is not currently required for clinical use.

Laboratory responsibilityLaboratories that develop LDTs must validate and perform these assays in-house in accordance with CLIA requirements.