Blue Cross Blue Shield Iowa FMT Coverage Update

Coverage Criteria for Fecal Microbiota Transplantation (FMT)

Coverage conclusions by indication

Coverage conclusions by indication — summarized coverage determinations based on the evidence reviewed.

ALL of the following

Clostridioides difficile infection (recurrent CDI refractory to antibiotic therapy): Evidence from systematic reviews, meta-analyses, RCTs, and observational studies demonstrates that FMT using a non-commercially prepared (conventionally compounded) product is effective for recurrent CDI and durable in long-term follow-up. Coverage conclusion: MEDICALLY NECESSARY when criteria for recurrent CDI and prior antibiotic treatment failure are met (see Medical Necessity criteria).
Inflammatory bowel disease (Ulcerative colitis and Crohn disease): The evidence includes systematic reviews and RCTs with mixed results — some trials and reviews show signals of benefit for UC but findings are inconsistent and limited by heterogeneity, small sample sizes, and uncertain durability. Two RCTs in Crohn disease failed to show superiority of FMT versus placebo. Coverage conclusion: NOT SUFFICIENT EVIDENCE to support routine use; FMT for IBD (UC, CD, pouchitis) should be considered investigational or limited to clinical trials or specialty settings following guideline recommendations.
Irritable bowel syndrome (IBS): Systematic reviews and RCTs are inconsistent, with heterogeneity in populations, delivery routes, and outcomes; overall evidence is insufficient and does not reliably demonstrate benefit. Coverage conclusion: NOT SUFFICIENT EVIDENCE — investigational / not medically necessary for IBS.
Pouchitis, Idiopathic constipation, Multi-drug-resistant organism (MDRO) colonization/infection, and Metabolic syndrome/obesity: Available systematic reviews, RCTs, and cohort studies are inadequate to support durable clinical benefit. RCTs in MDROs and pouchitis have not consistently demonstrated efficacy; metabolic changes observed were not durable. Coverage conclusion: NOT SUFFICIENT EVIDENCE — investigational / not medically necessary for these indications.
Use of commercially prepared FDA‑approved fecal microbiota products: This evidence review focused on non-commercially prepared (compounded) products. Commercial FDA‑approved fecal microbiota–based therapies are addressed separately (see Drug Authorization List). Coverage conclusion: follow Drug Authorization List and applicable formulary/prior authorization policies for commercially approved products.
Stool bank–distributed material and regulatory considerations: Per FDA draft guidance, use of stool bank–distributed FMT product may require IND compliance; enforcement discretion for non–stool bank use of physician‑directed donor stool remains limited. Coverage conclusion: Regardless of coverage determination above, use of material obtained from a stool bank may have regulatory pathways that affect availability and require compliance; prior authorization and documentation should reflect FDA guidance and payer coding rules.

Prior Authorization, Documentation, and Operational Requirements

Prior Authorization

Medical necessity / Prior authorization

Prior authorization not applicable; however, medical necessity for FMT in Clostridioides difficile infection (CDI) requires documentation that the member has had two or more recurrences after the initial episode (i.e., ≥3 CDI episodes) and that episodes are refractory to appropriate standard antibiotic therapy.

Medical necessity: require documentation of ≥2 recurrences after the initial episode (3 episodes total).
Require evidence episodes were refractory to standard antibiotic treatments (vancomycin, vancomycin→rifaximin, fidaxomicin, metronidazole) or documented contraindication/intolerance.
Prior authorization: recommended to evaluate medical necessity due to limited/inconsistent evidence outside recurrent CDI.

Prior Authorization

Prior authorization / Regulatory verification

Providers should verify regulatory status of the FMT product. FMT obtained from a stool bank typically requires IND compliance per FDA draft guidance; use of non-stool-bank (clinician-directed, non-commercial) products may be allowed under FDA enforcement discretion when informed consent, donor screening/testing, and safety procedures are followed.

Verify whether FMT product is sourced from a stool bank (stool-bank = centralized collection/preparation/distribution) — stool-bank products generally require IND compliance per FDA draft guidance.
If product is prepared under direction of licensed health care providers solely to treat their patients (not a stool bank), ensure documentation of informed consent, donor screening and testing, and safety procedures per FDA recommendations.

Documentation Required

Require documentation of recurrent/refractory CDI

Coverage decisions should require documentation confirming recurrent or refractory CDI with both clinical and laboratory evidence, consistent with guideline definitions of recurrence.

Document clinical evidence of CDI recurrence (clinically significant diarrhea) and a positive C. difficile laboratory test within the guideline-specified timeframe (commonly within 2–8 or 8 weeks of prior therapy completion).
Document timing of episodes to demonstrate recurrence count and relation to prior antibiotic therapy.

Documentation Required

Prior authorization — clinical documentation required

Prior authorization requests should include detailed clinical documentation used to determine medical necessity and rationale for FMT.

Baseline and current disease activity assessments (e.g., frequency of diarrheal episodes, severity measures) and pertinent lab results (C. difficile toxin or PCR).
History of prior FMT courses and response timing if applicable.
Prior antibiotic regimens tried, including dosing and duration, and documentation of failure, intolerance, or contraindication.
Rationale for FMT use when requested for indications other than recurrent CDI (note: many non-CDI uses are investigational).

Prior Authorization

Prior authorization: rationale and documentation

When FMT is requested for non-CDI indications or as maintenance/induction for IBD/IBS, require a clear rationale and documentation of prior therapies attempted; evidence for efficacy is inconsistent and generally insufficient for routine coverage.

For investigational indications (e.g., IBD, IBS, pouchitis, constipation, MDRO decolonization, metabolic syndrome) include detailed prior treatment history and rationale — these indications are generally considered investigational by the policy.
Documentation should explain why standard-of-care therapies were inadequate and why FMT is being considered despite limited evidence.

Step Therapy

Prior treatment requirement

Prior to FMT for recurrent CDI, the member must have completed appropriate antibiotic therapy trials consistent with society guidance; document antibiotic type, course, and response.

Acceptable prior therapies include vancomycin (including tapered/pulsed regimens), fidaxomicin, vancomycin followed by rifaximin, or metronidazole where appropriate.
Society guidance generally recommends attempting appropriate antibiotic regimens for at least 2 recurrences (i.e., 3 CDI episodes) before offering FMT.

Billing Rule

Report using listed codes

Report FMT provider services using the listed CPT/HCPCS and revenue codes.

CPT codes: 44705 (preparation of fecal microbiota for instillation), 44799 (unlisted small intestine procedure when applicable), and 0780T (instillation via rectal enema).
HCPCS: G0455 (preparation with instillation of fecal microbiota by any method).
Specify appropriate place and type of service (inpatient/outpatient, Medicine).

Denial Risk

Denial triggers

Requests for FMT for investigational indications or lacking required documentation may be denied.

Denial triggers include: lack of documented ≥2 recurrences after initial episode, absence of documented failure of appropriate antibiotic therapy, and requests for indications considered investigational (e.g., IBD, IBS, pouchitis, MDRO decolonization, metabolic syndrome).
Claims may also be denied if providers fail to use the appropriate CPT/HCPCS/revenue codes.

Denial Risk

Regulatory and safety-related denial risks

Regulatory and safety-related risks that can lead to noncoverage or enforcement action should be addressed in submissions.

Donor and stool testing for MDROs is required; donor screening should assess MDRO colonization risk and exclude high-risk donors.
Be aware of FDA safety alerts (MDRO transmission, SARS-CoV-2, monkeypox) — ensure documentation of compliance with recommended screening/testing.
Use of stool-bank sourced products without IND compliance may be subject to FDA enforcement; verify IND status and include documentation.

Note

Evidence selection influences coverage

Evidence selection and study limitations affect coverage determinations; reviewers should consider trial populations, follow-up duration, and applicability when assessing requests.

Study selection favored RCTs and comparative prospective studies; single-arm and long-term observational studies were used for harms and durability.
Limitations such as short follow-up for harms, heterogeneous populations, variable delivery routes, and small sample sizes may reduce applicability to individual members.

Note

Study follow-up often insufficient to assess harms

Many trials have limited follow-up for safety outcomes; submitters should provide longer-term follow-up data when available to support safety claims.

Insufficient duration of follow-up in some RCTs limits assessment of long-term harms — provide observational or registry data if available.
Documented long-term outcomes (when available) may support durability claims for CDI but are limited for non-CDI indications.

Denial Risk

Evidence limitations may prompt denial

Insufficient or conflicting evidence for many non-CDI indications may prompt denial of coverage.

Evidence limitations include inconsistent efficacy findings, small trials, heterogeneity in delivery methods and donor characteristics, and insufficient long-term safety data.
Requests for FMT for indications without convincing evidence should include a strong rationale and comprehensive supporting data; otherwise, denial is likely.

Documentation Required

Eligibility for FMT in CDI per IDSA/SHEA

Eligibility for FMT in CDI should follow guideline recommendations (IDSA/SHEA, ASCRS, ACG): multiple recurrences with failure of appropriate antibiotic treatments and both clinical and laboratory confirmation of recurrence.

Guidelines generally recommend considering FMT after at least 2 recurrences (i.e., 3 CDI episodes) that failed conventional antibiotics.
Recurrent CDI generally requires clinical symptoms (significant diarrhea) plus laboratory confirmation within the guideline-specified timeframe (commonly within 8 weeks).

Documentation Required

Required documentation and safety measures

Required documentation and safety measures must be provided with FMT requests to meet FDA-recommended protections.

Obtain and include informed consent that describes FMT risks (including MDRO transmission and other infectious risks).
Provide evidence of donor screening and specific MDRO testing of donor stool; quarantine of stored products until testing complete if applicable.
Describe procedures followed to mitigate safety concerns (testing for SARS-CoV-2, monkeypox considerations, and adherence to FDA recommendations).

Documentation Required

Required documentation and consent

Obtain informed consent and document donor and stool testing, including MDRO and emerging pathogen considerations.

Informed consent must describe potential risks including MDRO transmission and the measures implemented to reduce risk.
Donor screening questionnaires addressing MDRO colonization risk and laboratory testing for ESBL, VRE, CRE, MRSA at a minimum.
Document additional screening/testing implemented for SARS-CoV-2 and other FDA alerts as applicable.

Documentation Required

Documentation of CDI recurrence and lab confirmation

Document both clinical and laboratory confirmation of CDI recurrence when submitting for FMT; align with trial and guideline definitions.

Clinical documentation: description of diarrhea (frequency, duration) and timing relative to prior therapy.
Laboratory confirmation: positive C. difficile toxin or PCR assay within the recurrence window specified by guidelines.

Documentation Required

Expected clinical documentation

Expected clinical documentation parallels what is commonly required in trials and prior authorization: baseline disease scores, prior therapy history, and relevant lab tests.

For IBD/IBS requests include baseline disease activity scores (e.g., Mayo score, SES-CD, IBS-SSS) and fecal calprotectin when relevant.
Provide prior treatment histories, concomitant medications, and objective measures used to define remission or relapse.

Documentation Required

Required clinical documentation

For certain non-CDI indications (e.g., IBS, IBD) the policy specifies required clinical documentation such as disease subtype, baseline scores, and prior therapies tried.

IBD: document subtype (UC vs CD), baseline Mayo score or SES-CD, endoscopic findings, fecal calprotectin, and prior biologic or immunomodulator use.
IBS: document IBS subtype, baseline IBS-SSS score, prior conventional therapies tried and response.

Note

No explicit additional documentation requirements stated

No additional explicit documentation requirements beyond those above are stated in this document, but reviewers may request supplementary data when evidence is limited.

When evidence or study applicability is limited, the payer may request longer-term follow-up, registries, or additional safety data to support coverage decisions.

Billing Rule

Coding and documentation

Coding and billing must use the appropriate CPT/HCPCS/revenue and ICD diagnosis codes when reporting provider services related to FMT.

Use CPT 44705, 44799 (as appropriate), 0780T, and HCPCS G0455 as applicable; include appropriate ICD-10 diagnosis codes for CDI or other conditions being treated.
Claims may be denied or miscoded if the listed codes are not used.

Step Therapy

Step therapy context

Step-therapy context: FMT is considered when individuals have recurrent CDI refractory to antibiotic therapy; standard antibiotic regimens are the expected comparator and should be documented as tried and failed.

Standard-of-care antibiotic regimens (vancomycin, fidaxomicin, metronidazole, vancomycin→rifaximin) should be attempted prior to FMT for recurrent CDI.
Trials frequently used continuation of concomitant therapies; document prior therapy stability and timing relative to FMT request.

Step Therapy

Prior antibiotic therapy expected

Prior antibiotic therapy is expected before considering FMT for recurrent CDI; document the specific agents, dosing, duration, and outcome.

Acceptable prior antibiotic regimens include vancomycin (including tapered/pulsed regimens), fidaxomicin, vancomycin followed by rifaximin, or metronidazole where appropriate.
If antibiotics were contraindicated or not tolerated, provide supporting documentation.

Step Therapy

Step therapy considerations

Step therapy considerations: given uncertainty of added benefit in some indications, policy may require standard therapies attempted prior to FMT and justification for deviating from sequencing.

Policy preference is to consider FMT after standard therapies have been addressed, particularly for CDI where guidelines recommend antibiotic trials before FMT.
When requesting FMT earlier in the treatment course, provide justification and supporting evidence.

Note

No step-therapy rules or sequencing required beyond guidelines

No explicit step-therapy rules or rigid sequencing beyond guideline-recommended prior antibiotic trials are imposed; reviewers will evaluate on a case-by-case basis.

Guidelines recommend attempting appropriate antibiotics for at least 2 recurrences before FMT, but individual clinical circumstances may alter sequencing with adequate documentation.

Step Therapy

Antibiotic step therapy

Antibiotic step therapy: guidelines recommend completing appropriate antibiotic regimens (e.g., vancomycin tapered/pulsed or fidaxomicin) prior to FMT for recurrent CDI.

Document completion and failure of recommended antibiotic regimens including taper/pulse vancomycin or fidaxomicin before FMT is authorized.

Definitions and Scoring Systems

inv-76: Recurrent CDI definition and clinical criteria used in document

DefinitionRecurrent CDI: complete abatement of CDI symptoms while on therapy followed by reappearance of symptoms within 2–8 weeks after treatment stopped (policy guideline)

Policy coverage contextPolicy applies to individuals with two or more recurrences following the initial episode (i.e., three CDI episodes) before considering FMT

Trial-aligned criteriaRCTs and guidelines define recurrence and use clinical/laboratory confirmation to document recurrent CDI for eligibility

inv-77: Fecal Microbiota Transplantation (FMT) — definition and delivery methods

DefinitionFecal microbiota transplantation (FMT): transfer of stool from a healthy donor into a recipient to restore intestinal microbiota

Delivery methodsDelivered via upper GI infusion (nasogastric tube, gastroscopy), lower GI instillation (colonoscopy, rectal catheter/enema), or oral capsules

Preparation sourcesMaterial prepared within hospital facilities or obtained from stool banks (fresh, frozen, or lyophilized preparations referenced)

inv-78: Recurrent Clostridioides difficile infection (CDI) — definition summary

Concise definitionRecurrent Clostridioides difficile infection (CDI): CDI that returns after initial treatment, with recurrence rates up to ~35% after first episode and higher with subsequent recurrences

Policy threshold for considerationPolicy considers FMT for recurrent CDI refractory to antibiotic therapy, typically after ≥2 recurrences (i.e., 3 CDI episodes)

Clinical significanceRecurrent CDI can lead to chronic recurrent patterns and serious complications such as toxic megacolon and colonic perforation

inv-79: Definite CDI recurrence — clinical/lab criteria (≥3 loose stools/day etc.)

Clinical/lab criteria (definite recurrence)≥3 loose stools per day for 2 consecutive days with a positive C. difficile toxin test

Possible recurrenceSame clinical criteria (≥3 loose stools/day for 2 days) without laboratory confirmation

Severe manifestationsSevere gastrointestinal manifestations with toxin confirmation also meet definite recurrence criteria

inv-80: Mucosal healing — endoscopic definition and scoring references

Endoscopic definitionMucosal healing defined as absence of ulceration on endoscopy

Scoring referenceSimple Endoscopic Score for Crohn's Disease (SES-CD) used to quantify degree of ulceration and endoscopic activity

Clinical relevanceMucosal healing is an important target in assessing efficacy of therapies for IBD (used alongside clinical and histologic outcomes)

inv-81: Clinical remission examples used in trials (HBI, Mayo, fecal calprotectin thresholds)

Crohn disease (example)Clinical remission often defined by Harvey-Bradshaw Index <5 in CD trials (Kao et al 2024)

Ulcerative colitis (examples)Trials used clinical Mayo score thresholds and fecal calprotectin levels (e.g., calprotectin <100 μg/g for entry; sustained remission <200 μg/g) to define remission

Trial endpointsCombined endpoints frequently include both clinical remission measures and endoscopic scores (e.g., HBI <5 plus SES-CD <5)

inv-82: IBD — definition used in document (UC and CD)

DefinitionInflammatory bowel disease (IBD): includes ulcerative colitis (UC) and Crohn disease (CD) evaluated for response to FMT

Trial considerationsOutcomes include induction/maintenance of remission, endoscopic remission, and corticosteroid-free remission; mucosal healing is a key outcome

Evidence summarySystematic reviews and RCTs provide mixed results; current evidence insufficient to conclude consistent benefit for IBD

inv-83: IBS — definition used in document

DefinitionIrritable bowel syndrome (IBS): chronic abdominal pain with altered bowel patterns without identified structural pathology

Clinical measurementSeverity assessed via patient-reported scales (IBS-SSS) and functional indices; IBS subtypes and symptom patterns are relevant to trial eligibility

Trial contextEvidence for FMT in IBS is mixed; trials heterogeneous in route, controls, and outcomes

inv-84: IBS-SSS — severity scoring ranges and categories

Scale rangeIBS-SSS provides scores 0–500 assessing symptoms over 10 days

Mild75–175

Moderate175–300

Severe>300

inv-85: Functional Bowel Disorder Severity Index — severity categories

Index purposeFunctional Bowel Disorder Severity Index assesses pain behaviors and healthcare utilization to categorize IBS severity

Mild categoryScore ≤36

Moderate categoryScore 37–110

Severe categoryScore >110

inv-88: Clinical remission (constipation) — pooled CSBM definition

Pooled CSBM definitionClinical remission for constipation defined as achieving ≥3 spontaneous complete bowel movements (CSBMs) per week

Evidence sourceDefinition used across constipation systematic reviews and pooled analyses (Wang et al 2025)

Clinical relevanceUsed as the primary pooled clinical remission outcome in constipation studies of FMT

inv-89: Pouchitis Disease Activity Index (PDAI) remission example (PDAI <7 at 4 weeks)

PDAI remission examplePouchitis Disease Activity Index (PDAI) remission example: PDAI <7 at 4-week follow-up used in pooled pouchitis studies

Evidence contextPooled clinical remission and response rates reported in systematic reviews of chronic pouchitis using PDAI thresholds

LimitationsStudies heterogeneous in route, frequency, and donor; high-quality RCTs lacking

inv-90: Severe and fulminant CDI definitions and thresholds (leukocytosis, creatinine, fulminant signs)

Severe CDI criteriaSevere CDI may include leukocytosis ≥15 x 10^9 cells/L or creatinine ≥1.5 mg/dL (as used in guideline definitions)

Fulminant CDI featuresFulminant CDI includes severe disease with shock, ileus, or megacolon

Guideline contextAGA and other society recommendations reference these thresholds when considering escalation of therapy including FMT in specific settings

inv-91: FMT evidence base — references include RCTs, systematic reviews, guidelines cited

Evidence typesEvidence base includes randomized clinical trials, systematic reviews, meta-analyses, and clinical guidelines (ACG, AGA, ASCRS, IDSA/SHEA)

Representative referencesLong-term cohort studies (Lee et al 2019), multiple systematic reviews and RCTs summarized in policy references, and society guideline statements cited

Clinical implicationRCTs and meta-analyses support FMT for recurrent CDI; evidence for other indications is inconsistent or insufficient

OpenPayer

Fecal Microbiota Transplantation

Coverage Criteria for Fecal Microbiota Transplantation (FMT)

Coding and Procedure Codes

Prior Authorization, Documentation, and Operational Requirements

Definitions and Scoring Systems

Background and Evidence Summary

Policy Revision History

44705	Preparation of fecal microbiota for instillation, including assessment of donor specimen.
44799	Unlisted procedure, small intestine (when specified for instillation of the specimen by nasogastric tube).
0780T	Instillation of fecal microbiota suspension via rectal enema into lower gastrointestinal tract.
G0455	Preparation with instillation of fecal microbiota by any method, including assessment of donor specimen.