Currentmedical mutual - ohioPolicy AHS - G2060

Fecal Analysis in the Diagnosis of Intestinal Dysbiosis and Fecal Microbiota Transplant Testing

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Defines coverage criteria for stool testing prior to fecal microbiota transplantation and states which fecal analyses for intestinal dysbiosis are considered not medically necessary; applies to Medical Mutual - Ohio members and providers submitting claims.

Policy Summary

Payermedical mutual - ohio

PolicyFecal Analysis in the Diagnosis of Intestinal Dysbiosis and Fecal Microbiota Transplant Testing

Policy CodePolicy AHS - G2060

Change TypeNo material change

Effective DateFeb 1, 2026

Last ReviewSep 4, 2025

Next Review DateSep 4, 2025

Key ActionDocument donor screening method, organisms tested, and verify prior authorization per member benefit.

SourceLink

OpenPayer is powered by Trek Health's payer performance platform. Trek continuously ingests, validates, and normalizes Transparency in Coverage data alongside payer policies and other commercial payer data to create a structured payer intelligence foundation. OpenPayer uses this foundation to deliver personalized search results, dynamically generated policy pages, and tailored policy monitoring based on each user's payers, specialties, billing codes, and areas of interest. The same intelligence powers broader payer performance workflows, including reimbursement benchmarking, contract evaluation, payer negotiations, and financial decision-making.

Currentmedical mutual - ohioPolicy AHS - G2060

Fecal Analysis in the Diagnosis of Intestinal Dysbiosis and Fecal Microbiota Transplant Testing

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Policy Summary

Payermedical mutual - ohio

PolicyFecal Analysis in the Diagnosis of Intestinal Dysbiosis and Fecal Microbiota Transplant Testing

Policy CodePolicy AHS - G2060

Change TypeNo material change

Effective DateFeb 1, 2026

Last ReviewSep 4, 2025

Next Review DateSep 4, 2025

Key ActionDocument donor screening method, organisms tested, and verify prior authorization per member benefit.

SourceLink

8Enteric pathogens covered by culture

8Microorganisms covered by NAAT

13Fecal analytes not meeting coverage

MDRO testing requiredFDA-required MDRO tests

AHS-G2056, AHS-G2121Related payer policies

Coverage Criteria for Donor Stool Testing and Fecal Analyses

Donor stool culture testing — Covered

Covered when performed prior to donation for FMT to detect specified organisms by bacterial culture:

Organisms required by culture: Extended spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae; Vancomycin-resistant Enterococci (VRE); Carbapenem-resistant Enterobacteriaceae (CRE); Methicillin-resistant Staphylococcus aureus (MRSA); Campylobacter; Shigella; Salmonella.

These culture tests MEET COVERAGE CRITERIA when used for donor screening prior to FMT.

Donor stool NAAT testing — Covered

Covered when performed prior to donation for FMT to detect specified organisms by NAAT:

Organisms required by NAAT: Clostridium difficile; Campylobacter; Salmonella; Shigella; Shiga toxin-producing Escherichia coli; Norovirus; Rotavirus; COVID-19 (SARS-CoV-2).

These NAAT tests MEET COVERAGE CRITERIA when used for donor screening prior to FMT.

Donor stool NAAT testing — Not covered

The following NAATs do not meet coverage criteria for donor screening prior to FMT:

NAAT organisms not covered: 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 covered by NAAT.

These NAATs are explicitly listed as DOES NOT MEET COVERAGE CRITERIA for FMT donor screening.

Fecal analyses for intestinal dysbiosis — Not covered

As diagnostic tests for evaluation of intestinal dysbiosis, IBS, malabsorption, or small intestinal bacterial overgrowth, the following fecal analyses do NOT meet coverage criteria:

Fecal analytes not covered: 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 (Aeromonas, Bacillus cereus, Campylobacter, Citrobacter, Klebsiella, Proteus, Pseudomonas, Salmonella, Shigella, S. aureus, Vibrio); Identification and quantitation of fecal yeast (including C. albicans, C. tropicalis, Rhodotorula and Geotrichum); N-butyrate; Beta-glucoronidase; pH; Short chain fatty acid distribution; Fecal secretory IgA.

Lack of published literature confirming clinical utility is cited as reason for not meeting coverage.

Covered Indications and Required Donor Testing

Coverage considerations follow guideline-supported indications and FDA donor-screening requirements:

FMT for recurrent CDI: Consider fecal microbiota–based therapies (including conventional FMT and approved live biotherapeutic products) after completion of standard-of-care antibiotics for recurrent Clostridioides difficile infection, particularly after a second recurrence or in select high-risk patients; repeat FMT can be considered for recurrence within 8 weeks of initial FMT.clinical decision per guideline

AGA and ACG guidance support use for recurrent CDI; ACG recommends FMT for severe/fulminant refractory CDI in poor surgical candidates and for second or further recurrence; repeat within 8 weeks may be suggested.

Donor screening and testing: Donor screening must include assays for C. difficile toxin B and culture for enteric pathogens; MDRO testing (at minimum ESBL, VRE, CRE, MRSA) is required per FDA guidance with bookend testing no more than 60 days apart when multiple donations are quarantined until post-donation MDRO tests are negative.FDA and society guidance

Multiple professional societies list additional fecal and serum infectious agents to screen for prior to donor use.

Not Routinely Covered Indications

Indications where FMT or fecal analysis is generally not recommended outside trials or is conditional:

IBD and functional GI disorders: Use of FMT for ulcerative colitis, Crohn's disease, pouchitis, and irritable bowel syndrome is not recommended routinely; societies suggest use only in clinical trials or with caution due to variable evidence and procedural heterogeneity.guideline-based

AGA/ACG/BSG statements advise against routine FMT for these indications and recommend trials or caution.

A broad list of fecal biomarkers and microbial quantifications are excluded from coverage when requested as diagnostic tests for evaluation of intestinal dysbiosis, irritable bowel syndrome (IBS), malabsorption, or small intestinal bacterial overgrowth (SIBO). Examples of analyses that DO NOT MEET COVERAGE CRITERIA include, but are not limited to: triglycerides, chymotrypsin, iso-butyrate/iso-valerate/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, identification/quantitation of fecal yeast, N‑butyrate, beta‑glucuronidase, pH, short chain fatty acid distribution, and fecal secretory IgA.

Donor stools or donors who test positive for multidrug‑resistant organisms (MDROs) should not be used for fecal microbiota transplantation (FMT). Per guidance, MDRO testing should at minimum include extended‑spectrum beta‑lactamase (ESBL)‑producing Enterobacteriaceae, vancomycin‑resistant Enterococci (VRE), carbapenem‑resistant Enterobacteriaceae (CRE), and methicillin‑resistant Staphylococcus aureus (MRSA), and donors or stools positive for these organisms must be excluded from use.

Laboratory‑developed tests (LDTs) referenced in this document are tests that are validated and performed in‑house and are regulated by CMS under CLIA '88 as high‑complexity tests. LDTs are not FDA‑approved or FDA‑cleared, although current practice does not require FDA clearance or approval for clinical use.

Use of the fecal analyses specifically listed in this policy as diagnostic tests for intestinal dysbiosis, IBS, malabsorption, or SIBO is considered to NOT MEET COVERAGE CRITERIA and claims for these tests may be denied when submitted for those indications.

Fecal microbiota transplantation (FMT) is not routinely covered for treatment of global IBS symptoms, ulcerative colitis, Crohn's disease, pouchitis, or other functional gastrointestinal symptoms outside of clinical trials. Professional society guidance characterizes FMT for these indications as investigational or recommends use only within research settings because evidence is limited and results are heterogeneous.

Procedure Codes and Coding Guidance

Applicable CPT/HCPCS Procedure Codesmixed

No codes listed

Applicable CPT Codes (excerpt)CPT

82542	Column chromatography, includes mass spectrometry, non-drug analyte(s) not elsewhere specified, qualitative or quantitative, 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 (e.g., KIA, LIA), Salmonella and Shigella species
87046	Culture, bacterial; stool, aerobic, additional pathogens, isolation and presumptive identification of isolates, each plate
87075	Culture, bacterial; any source, except blood, anaerobic with isolation and presumptive identification of isolates
87077	Culture, presumptive, pathogenic organisms, screening only

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Applicable CPT/HCPCS Procedure Codesmixed

82542	LC/MS, LC/MS-MS, GC, GC/MS-MS, GC/MS, HPLC/MS (column chromatography with mass spectrometry), non-drug analyte(s) not elsewhere specified, qualitative or quantitative, 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, isolation and presumptive identification of isolates, each plate
87075	Culture, bacterial; any source, except blood, anaerobic with isolation and presumptive identification of isolates
87077	Culture, bacterial; anaerobic isolate, additional methods required for definitive identification, each isolate

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Provider Actions, Documentation, and Billing Notes

Prior Authorization

Prior authorization depends on member benefit and listed coverage

Prior authorization is determined by the member’s benefit coverage; tests explicitly listed as MEET COVERAGE CRITERIA for FMT donor screening (by culture or NAAT) are covered under this policy, while tests listed as DOES NOT MEET COVERAGE CRITERIA are not covered. Verify benefit-specific prior authorization requirements at time of request.

Covered donor culture organisms: ESBL-producing Enterobacteriaceae, VRE, CRE, MRSA, Campylobacter, Shigella, Salmonella.
Covered NAAT organisms: C. difficile, Campylobacter, Salmonella, Shigella, Shiga toxin–producing E. coli, Norovirus, Rotavirus, SARS‑CoV‑2.

Note

Government policy supersedes conflicting policy

If there is any conflict between this medical policy and applicable government policy (for example, Medicare LCDs or NCDs), the government policy will govern the determination for that member.

Background and Context

Intestinal dysbiosis refers to a disruption or imbalance of the gut microbial ecosystem that has been associated with a range of conditions including irritable bowel syndrome (IBS), inflammatory bowel disease (IBD), celiac disease, metabolic disorders, and autoimmune diseases. Fecal microbiota transplantation (FMT) aims to restore microbial balance and has established efficacy for recurrent Clostridioides difficile infection (CDI), but donor selection and laboratory screening (donor health questionnaire, serum and stool assays) are required to minimize infectious risks. Many proposed fecal biomarkers and organism quantifications lack consistent evidence of clinical utility and therefore are not supported as diagnostic tests for dysbiosis.

Definitions

Intestinal dysbiosis definition and associated conditions

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

Associated conditionsIrritable bowel syndrome (IBS), inflammatory bowel disease (IBD), celiac disease, multiple sclerosis, Sjogren's syndrome, obesity, allergy, diabetes.

Clinical contextDysbiosis is cited as linked to a wide range of immune, metabolic, and gastrointestinal disorders and is the rationale for microbiome-directed interventions such as FMT.

FMT — definition of fecal microbiota transplant

DefinitionFecal microbiota transplant (FMT): infusion of stool from a healthy donor to a patient to restore microbiome balance.

PurposeUsed to restore microbial balance; established efficacy for recurrent Clostridioides difficile infection when donor screening and product handling are performed.

Policy Summary

Payermedical mutual - ohio

PolicyFecal Analysis in the Diagnosis of Intestinal Dysbiosis and Fecal Microbiota Transplant Testing

Policy CodePolicy AHS - G2060

Change TypeNo material change

Effective DateFeb 1, 2026

Last ReviewSep 4, 2025

Next Review DateSep 4, 2025

Key ActionDocument donor screening method, organisms tested, and verify prior authorization per member benefit.

SourceLink

On This Page

Billing Rule

Verify applicable CPT/HCPCS procedure codes before authorization

Procedure codes listed in section VIII are the CPT/HCPCS codes referenced by this policy; providers must verify the most current and payer-appropriate codes when requesting authorization or submitting claims.

Example codes included in section VIII: 82542, 82705, 82710, 82715, 83986, 84311, 87045, 87046, 87075, 87077, 87081, 87102, 87106, 87493, 87500, 87641, 87798, S3708.
Procedure codes in the policy are a general reference and may not be all‑inclusive; confirm payer-specific billing rules before submission.

Step Therapy

FMT use follows completion of standard therapies per clinical practice

FMT clinical use typically follows completion of standard therapies; for recurrent C. difficile infection, fecal microbiota–based therapies are considered after standard-of-care antibiotics have been completed.

Standard practice: perform anti‑C. difficile antibiotic course prior to FMT or RBL administration as in trials and guidelines.

Step Therapy

Sequence fecal microbiota therapies after standard‑of‑care antibiotics for recurrent CDI

For recurrent C. difficile infection, consider fecal microbiota–based therapies (including conventional FMT and approved LBPs) only after completion of standard-of-care antibiotics, typically after the second recurrence or in select high‑risk patients; repeat FMT may be considered for recurrence within 8 weeks of initial FMT per guidelines.

AGA: consider after completion of standard antibiotics; prevention may be considered after second recurrence or in select high‑risk patients.
ACG: suggests FMT for second or further recurrence and allows repeat FMT for recurrence within 8 weeks.

Note

Provider action placeholder

(Reserved) Provider-impact statements or additional provider actions related to this section are noted elsewhere in the policy.

Documentation Required

Document donor screening method and organisms tested

Document the indication for donor screening and explicitly record which screening methods were used (bacterial culture versus NAAT) and which organisms were tested, since coverage differs by method and organism.

If culture performed, document testing for ESBL-producing Enterobacteriaceae, VRE, CRE, MRSA, Campylobacter, Shigella, Salmonella.
If NAAT performed, document testing for C. difficile, Campylobacter, Salmonella, Shigella, Shiga toxin–producing E. coli, Norovirus, Rotavirus, SARS‑CoV‑2.

Documentation Required

Ensure complete donor screening documentation (questionnaire and lab assays)

Donors must complete a donor health questionnaire and have laboratory screening assays performed before donation and after donation when applicable; professional society recommendations list additional fecal and serum assays to include in documentation.

Recommended elements: donor health questionnaire, pre‑donation stool assays (e.g., C. difficile toxin B, enteric pathogen culture), and post‑donation MDRO testing when multiple donations are quarantined.
Follow society workgroup recommendations (Fecal Microbiota Transplantation Workgroup) for specific analytes to screen and document.

Documentation Required

Validate and document LDTs per CLIA requirements

Laboratory‑developed tests (LDTs) used for donor screening must be validated and performed in‑house and are regulated by CMS as high‑complexity tests under CLIA ’88.

Denial Risk

Risk of denial for tests listed as not meeting coverage criteria

Claims for fecal analyses listed in this policy as DOES NOT MEET COVERAGE CRITERIA (including many fecal biomarkers and certain NAATs) should be denied as not meeting coverage criteria.

Examples of NOT COVERED diagnostic fecal analytes: triglycerides; chymotrypsin; short‑chain fatty acid measures; quantification of specific bacteria or fecal yeast; fecal secretory IgA.
NAATs listed as DOES NOT MEET COVERAGE CRITERIA for donor screening include ESBL, VRE, CRE, MRSA and any organisms not listed as covered by NAAT.

Denial Risk

Exclude donors/stool positive for MDROs (ESBL, VRE, CRE, MRSA)

Do not use donor stool or donors that test positive for multidrug‑resistant organisms (MDROs); MDRO testing must at minimum include ESBL‑producing Enterobacteriaceae, VRE, CRE, and MRSA, and positive results exclude donor use for FMT.

FDA requires MDRO testing at minimum for ESBL, VRE, CRE, and MRSA; nasal or peri‑rectal swab culture is an acceptable alternative to stool testing for MRSA only.
If multiple donations are quarantined, bookend testing no more than 60 days apart is acceptable with negative post‑donation MDRO results before use.

Billing Rule

Procedure codes in policy are reference only — verify payer billing rules

Procedure codes listed in the Medical Policy are provided as a general reference and may not be all‑inclusive; verify payer‑specific billing and code sets before submission.

Policy lists multiple CPT/HCPCS codes in section VIII (examples: 87045, 87493, 87500, 87641, 87798, S3708).
Confirm current codes and payer requirements when seeking authorization or billing.

Components of donor screeningDonor health questionnaire plus laboratory stool and serum assays to minimize infectious risk prior to transplantation.

Fecal microbiota, live-jslm (RBL) — definition and trial context

Product definitionFecal microbiota, live-jslm (RBL; formerly RBX2660): a standardized, donor stool–derived, microbiota-based, rectally administered live biotherapeutic product (LBP) approved by the FDA for prevention of recurrent CDI.

Clinical trial contextPhase 3 trial in patients with ≥2 recurrent CDI episodes showed estimated cure rates of 80.6% with RBL vs 57.5% with placebo (Bayesian analysis).

DurabilityAmong those cured at 8 weeks, >90% had a sustained clinical response through 6 months.

MDRO — definition and FDA minimum testing requirements

DefinitionMDRO = multidrug-resistant organisms.

FDA minimum MDRO testsAt minimum include testing for extended spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae, vancomycin-resistant enterococci (VRE), carbapenem-resistant Enterobacteriaceae (CRE), and methicillin-resistant Staphylococcus aureus (MRSA).

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

Bookend testing intervalWhen multiple donations are quarantined, bookend testing before and after donations is acceptable if no more than 60 days apart and post-donation MDRO tests are negative.

LDT — laboratory-developed test definition and CLIA regulation note

DefinitionLaboratory-developed test (LDT): a test developed and performed in‑house by a laboratory.

RegulationLDTs are regulated by the Centers for Medicare and Medicaid Services (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.