Fecal Analysis in the Diagnosis of Intestinal Dysbiosis and Fecal Microbiota Transplant Testing
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This policy governs coverage for fecal testing used to diagnose intestinal dysbiosis and required stool testing prior to fecal microbiota transplant (FMT) donation, affecting Capital Bluecross members and providers submitting claims for these services.
No material clinical or coverage changes in this revision.
Coverage Criteria
Coverage criteria for fecal testing
Coverage determinations are itemized below; application depends on member benefits and applicable regulations.
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
- COVID-19 (SARS-CoV-2)
ALL of the following
- 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 above
ALL of the following
- 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 specified bacterial taxa (including 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-glucuronidase
- pH
- Short chain fatty acid distribution
- Fecal secretory IgA
Guideline and regulatory stance
Guideline-based indications, limitations, and donor screening expectations extracted from cited societies and FDA.
Guideline indications and limitations
- World Gastroenterology Organization (WGO): routine fecal examinations and cultures to eliminate bacterial, viral, or parasitic causes of diarrhea; test for C. difficile (consider even without antecedent antibiotics) and perform tests to detect inflammation (e.g., calprotectin) when IBD is possible.
- American Gastroenterological Association (AGA): suggests fecal microbiota–based therapies be considered for recurrent CDI after standard antibiotics (conditional, low certainty); recommends rigorous donor screening and generally advises against FMT for ulcerative colitis, Crohn's disease, pouchitis, and IBS outside clinical trials.
- American College of Gastroenterology (ACG): in patients with suspected active Crohn's or UC, stool testing should include fecal pathogens and C. difficile; notes FMT requires more study for UC and variability in procedures limits interpretation; ACG recommends FMT for recurrent or severe CDI in specified circumstances.
- British Society of Gastroenterology (BSG): stool cultures and C. difficile assay should always be performed in suspected UC or acute colitis; considers FMT investigational in IBD outside clinical trials.
- FDA regulatory stance: exercises enforcement discretion for FMT but requires MDRO testing of donors (at minimum ESBL, VRE, CRE, MRSA), accepts nasal or peri-rectal swab as alternative for MRSA, and permits bookend MDRO testing no more than 60 days apart with quarantining of donations until postdonation tests are negative.
Evidence and guidance references
Guidelines and safety communications relevant to clinical indications and donor screening for FMT are cited; no explicit payer coverage rules appear in this excerpt.
ALL of the following
- AGA Clinical Practice Guideline on Fecal Microbiota–Based Therapies (2024) — recommendations on use for recurrent CDI and cautions for other indications.
- ACG Clinical Guidelines — management of Crohn's disease, ulcerative colitis, IBS, and C. difficile infection; provides guidance on stool testing and FMT use in CDI.
- WGO Global Guidelines — recommendations for stool testing to rule out infectious causes and use of fecal tests (e.g., calprotectin) when IBD is suspected.
- BSG guidance — recommends stool cultures and C. difficile testing in acute flares and treats FMT as investigational for IBD outside trials.
- Pediatric joint position papers (NASPGHAN/ESPGHAN) — address FMT for recurrent CDI and related considerations in children.
- FDA safety communications and updates (multiple alerts) — emphasize risk of MDRO transmission with FMT and additional protections for SARS-CoV-2 screening and testing; provide recommended minimum MDRO panel and bookend testing approach.
Covered Indications
Donor stool screening prior to fecal microbiota transplantation
Specific donor screening organisms listed below meet coverage criteria for culture or NAAT as indicated; MDRO testing and bookend testing expectations follow FDA recommendations.
ALL of the following
- 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
- SARS-CoV-2 (COVID-19)
ALL of the following
- NAAT for ESBL-producing Enterobacteriaceae
- NAAT for VRE
- NAAT for CRE
- NAAT for MRSA
- NAAT for any other microorganisms not listed as covered above
Stool testing to exclude infectious causes and assess for C. difficile
Stool testing is indicated when infection must be excluded and to assess for C. difficile or inflammation in patients with suspected IBD, acute flares, or recurrent CDI.
Indications for stool testing to exclude infectious causes
- Patients presenting with suspected IBD or acute flares should have stool testing to exclude bacterial, viral, or parasitic causes of diarrhea (WGO, BSG, ACG).
- Perform C. difficile testing in patients with suspected IBD or acute flares; consider C. difficile testing even in absence of antecedent antibiotics (WGO, ACG).
- Stool cultures for enteroinvasive bacterial infections and assays for ova and parasites should be used per guideline recommendations to exclude infectious causes (WGO, BSG).
Recurrent C. difficile infection and select GI diseases where FMT is considered
Clinical practice guidelines identify recurrent C. difficile infection as the primary established indication for FMT; other GI conditions are considered investigational or limited to clinical trials per societies.
Select GI diseases and limitations
- Ulcerative colitis and Crohn's disease: AGA and ACG note FMT requires further study and generally recommend against routine use for UC/Crohn's outside clinical trials; some guidance allows FMT in clinical trials or for CDI complicating IBD.
- Irritable bowel syndrome (IBS) and pouchitis: AGA and ACG recommend against use of conventional FMT for global IBS symptoms; evidence is limited and of very low quality, and FMT remains investigational for these indications.
Coding and Procedure Codes
| No codes listed |
| 82542 | Fat or lipids, feces; qualitative or quantitative (example in list) |
| 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; anaerobic with isolation and presumptive identification |
| 87493 | Infectious agent detection by nucleic acid; C. difficile, toxin |
| No codes listed |
Provider Actions and Regulatory Notes
Donor stool testing required prior to FMT
Prior to donation for a fecal microbiota transplant (FMT), perform the specific donor stool testing listed in the policy: bacterial culture for ESBL-producing Enterobacteriaceae, VRE, CRE, MRSA, Campylobacter, Shigella, and Salmonella; and NAAT for Clostridium difficile, Campylobacter, Salmonella, Shigella, Shiga-toxin–producing E. coli, Norovirus, Rotavirus, and SARS‑CoV‑2. Coverage of these tests is subject to the individual member’s benefit plan and applicable Medicare/Medicaid specifications referenced in the policy.
- Perform culture-based screening for: ESBL-producing Enterobacteriaceae; Vancomycin-resistant Enterococci (VRE); Carbapenem-resistant Enterobacteriaceae (CRE); Methicillin-resistant Staphylococcus aureus (MRSA); Campylobacter; Shigella; Salmonella.
- Perform NAAT-based screening for: Clostridium difficile; Campylobacter; Salmonella; Shigella; Shiga toxin–producing Escherichia coli; Norovirus; Rotavirus; COVID-19 (SARS‑CoV‑2).
- Do not rely on NAAT for MDROs listed (ESBL, VRE, CRE, MRSA) for donor screening, as NAAT for these organisms does not meet coverage criteria per policy.
Government coverage governs when in conflict
When this policy conflicts with an applicable government coverage determination (for example, a Medicare LCD or NCD, or state Medicaid coverage), the government policy takes precedence and will be used to make the coverage determination.
- Check Local Coverage Determinations (LCDs), National Coverage Determinations (NCDs), and state Medicaid policies for the member before finalizing coverage decisions.
Follow FDA safety communications on FMT donor screening
Follow FDA safety communications related to FMT donor screening and testing: the policy cites FDA alerts regarding risk of transmission of multi‑drug resistant organisms and additional protections/testing for SARS‑CoV‑2; these communications inform donor safety expectations and testing considerations.
- Refer to FDA Safety Communication: Risk of Serious Adverse Reactions Due to Transmission of Multi‑Drug Resistant Organisms.
- Refer to FDA updates on additional protections for screening donors for COVID‑19 and testing for SARS‑CoV‑2, and the April 7, 2020 Safety Alert on risk of serious adverse events from transmitted pathogenic organisms.
Definitions
Frequency Limits
Ordering Requirements
Confirm individual benefit coverage; donor pathogen lists may vary
Application of the coverage criteria for donor screening and diagnostic stool testing depends on the member’s individual benefits; donor pathogen screening panels may vary by institution and should be confirmed for each case.
- Confirm member coverage and Medicare/Medicaid specifications before ordering.
- Donor screening organism lists in the policy represent required/covered targets but local donor programs may have different panels.
Order stool testing to exclude infectious causes in suspected IBD/acute flares
Society guidelines recommend stool testing to exclude infectious causes when patients present with suspected IBD, acute flares, or when infection should be ruled out; order stool cultures, C. difficile testing, and tests for enteric pathogens as clinically indicated.
- WGO: routine fecal exams and cultures to eliminate bacterial, viral, or parasitic causes of diarrhea and rapid C. difficile testing.
- ACG: stool testing for fecal pathogens, C. difficile, and fecal calprotectin in active Crohn’s disease.
Follow society and FDA donor screening/testing recommendations; permitted orderers not specified here
Donor screening/testing recommendations referenced include professional society guidance and FDA communications; the policy notes these recommendations but does not restrict who may order tests in this excerpt.
- Professional society guidance and FDA safety information are cited for donor screening practices.
- Specific permitted orderers (e.g., specialist vs primary care) are not specified in this excerpt—order by the treating clinician as clinically indicated.
Not Covered
The following fecal component analyses do not meet coverage criteria for the diagnosis of intestinal dysbiosis, irritable bowel syndrome, malabsorption, or small intestinal bacterial overgrowth due to insufficient published evidence of clinical benefit: 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 and quantitation of fecal yeast (including Candida spp., Rhodotorula, Geotrichum); N-butyrate; beta-glucuronidase; pH; short chain fatty acid distribution; and fecal secretory IgA.
Professional guidance cited in the policy supports limited roles for many specialized fecal markers and broad microbiome panels in routine diagnosis. NICE recommends standard laboratory testing to exclude alternative diagnoses in patients who meet IBS criteria and explicitly lists several tests that are not necessary to confirm IBS, while the British Society of Gastroenterology notes that fecal tests for malabsorption and small bowel bacterial overgrowth have not established a role in routine practice outside specialist centers and that faecal tests have limited support; BSG also states that FMT remains investigational for IBD outside of C. difficile infection or clinical trials. These guideline positions inform the policy decision that many fecal biomarkers and broad panels are not supported for routine diagnostic coverage.
The policy references commercial and consumer microbiome products and informational sites (for example, Viome, BioHM, DNATestingChoice and commercial ‘GI Effects’ style panels) in the evidence section but does not equate these offerings with covered, evidence-based diagnostic testing. Promotional materials and commercial microbiome reports are cited for context in the scientific background; the policy does not support routine coverage of commercial/consumer microbiome products or promotional microbiome testing panels as diagnostic tools for dysbiosis.
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