CurrentBlue KCPolicy POL-PP-278

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

Defines coverage and noncoverage for fecal laboratory testing used to evaluate intestinal dysbiosis and for screening FMT donors; applies to professional and facility providers submitting claims to Blue KC across commercial and Medicare Advantage lines.

Policy Summary

PayerBlue KC

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

Policy CodePolicy POL-PP-278

Change TypeMinor — no material coverage changes

Effective DateOct 1, 2025

Next Review DateOct 1, 2026

Key ActionDocument indication (diagnostic vs donor‑screening) and ensure tests billed match covered donor‑screening targets when submitting claims.

SourceLink

POLICY UPDATE CHANGES

No material clinical or coverage changes in this revision.

listedcovered donor-screening tests

listeddiagnostic fecal tests not covered

commercial + MAlines of business impacted

yescoding included

Covered FMT donor screening tests

Reimbursable testing prior to FMT donation

Bacterial culture targets: Culture of donor fecal sample for Extended spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae; Vancomycin-resistant Enterococci (VRE); Carbapenem-resistant Enterobacteriaceae (CRE); Methicillin-resistant Staphylococcus aureus (MRSA); Campylobacter; Shigella; Salmonella may be reimbursed.

NAAT targets (reimbursable): Nucleic acid amplification testing (NAAT) of donor fecal sample for Clostridioides (Clostridium) difficile; Campylobacter; Salmonella; Shigella; Shiga toxin-producing Escherichia coli; Norovirus; Rotavirus; COVID-19 (SARS-CoV-2) may be reimbursed.

Non-reimbursable NAAT targets for donor screening

Not reimbursed when performed by NAAT on donor fecal sample

NAAT targets (not reimbursable): NAAT of donor fecal sample for Extended spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae; Vancomycin-resistant Enterococci (VRE); Carbapenem-resistant Enterobacteriaceae (CRE); Methicillin-resistant Staphylococcus aureus (MRSA); or any other microorganisms not listed as reimbursable are not reimbursed.

Not medically necessary — diagnostic fecal analyses for dysbiosis

Fecal analyses that do not meet coverage criteria due to lack of supportive literature

Not covered fecal analytes: 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 albicans, C. tropicalis, Rhodotorula, Geotrichum); N-butyrate; beta-glucuronidase; pH; short chain fatty acid distribution; fecal secretory IgA are not reimbursed for evaluation of intestinal dysbiosis, IBS, malabsorption, or small intestinal bacterial overgrowth.

This policy applies to fecal laboratory testing used either to evaluate intestinal dysbiosis or to screen stool donors prior to fecal microbiota transplant (FMT). Coverage is determined by the member's benefits at the date of service and by the documented indication for testing (diagnostic evaluation versus donor screening). Specific bacterial culture and NAAT tests listed in the policy may be reimbursed when performed on donor stool prior to donation; conversely, a separate set of fecal biochemical and microbiologic assays are identified as not meeting coverage criteria for diagnosis of dysbiosis, irritable bowel syndrome, malabsorption, or small intestinal bacterial overgrowth.

Fecal analysis of the enumerated components in the policy (see Not covered fecal analytes) is considered not medically necessary for evaluation of intestinal dysbiosis, IBS, malabsorption, or small intestinal bacterial overgrowth and therefore is not reimbursed when performed for these diagnostic purposes.

Covered Indications

Donor screening prior to fecal microbiota transplant (FMT)

Specific bacterial cultures and NAATs listed below may be reimbursed when performed on donor stool prior to donation for FMT

Reimbursable bacterial cultures for donor screening: Culture of donor fecal sample for ESBL-producing Enterobacteriaceae; VRE; CRE; MRSA; Campylobacter; Shigella; Salmonella may be reimbursed when performed prior to donation.

Specimen must be the donor fecal sample and testing performed prior to donation.

Reimbursable NAATs for donor screening: NAAT of donor fecal sample for C. difficile; Campylobacter; Salmonella; Shigella; Shiga toxin-producing E. coli; Norovirus; Rotavirus; COVID-19 (SARS-CoV-2) may be reimbursed when performed prior to donation.

Specimen must be the donor fecal sample and testing performed prior to donation.

Coding

Listed CPT/HCPCS codes referencedmixed

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 (eg, 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
87076	Culture, bacterial; anaerobic isolate, additional methods required for definitive identification, each isolate

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Provider Actions / Billing Guidance

Prior Authorization

Prior Authorization Required / Coverage Determined by Date of Service

Prior to donation for a fecal microbiota transplant (FMT), specified bacterial culture and NAAT tests performed on donor fecal samples may be eligible for reimbursement when documented as donor screening. Prior authorization is required for FMT donor screening. Coverage is determined by the date of service and the member's eligibility and benefit limits at the time of service. Document whether testing is performed for donor screening (pre-donation) versus diagnostic evaluation of a recipient. Fecal analyses performed as diagnostic tests for evaluation of intestinal dysbiosis, irritable bowel syndrome, malabsorption, or small intestinal bacterial overgrowth do not meet coverage criteria.

Prior authorization required for FMT donor screening before donation.
Reimbursable donor-screening bacterial cultures (when prior authorized and documented): ESBL-producing Enterobacteriaceae; VRE; CRE; MRSA; Campylobacter; Shigella; Salmonella.
Reimbursable donor-screening NAATs (when prior authorized and documented): C. difficile; Campylobacter; Salmonella; Shigella; Shiga toxin-producing E. coli; Norovirus; Rotavirus; COVID-19 (SARS-CoV-2).
NAATs not reimbursed for donor screening: ESBL-producing Enterobacteriaceae; VRE; CRE; MRSA; any other microorganisms not listed as reimbursable above.
Coverage is determined by date of service and member benefits/eligibility at the time of the request; verify benefits prior to performing testing.
Always document the indication: donor screening (pre-donation) versus recipient diagnostic testing. Tests billed as diagnostic for intestinal dysbiosis, IBS, malabsorption, or small intestinal bacterial overgrowth do not meet coverage criteria and may be denied.

Not Covered

The following tests and analytes are explicitly not covered for diagnostic evaluation of dysbiosis and related conditions: triglycerides; chymotrypsin; iso-butyrate, iso-valerate, and n-valerate; meat and vegetable fibers; long chain fatty acids; cholesterol; total short chain fatty acids; N-butyrate; beta-glucuronidase; pH; short chain fatty acid distribution; fecal secretory IgA; quantitative assays for Lactobacilli, bifidobacteria, E. coli and other potential pathogens (including Aeromonas, Bacillus cereus, Campylobacter, Citrobacter, Klebsiella, Proteus, Pseudomonas, Salmonella, Shigella, S. aureus, Vibrio); and identification/quantitation of fecal yeast (including C. albicans, C. tropicalis, Rhodotorula, Geotrichum).

Background

Intestinal dysbiosis is a disruption or imbalance of the intestinal microbial ecology that has been associated with conditions such as irritable bowel syndrome, inflammatory bowel disease, celiac disease, and other systemic disorders. Although research explores fecal biochemical markers and microbial profiling as potential indicators of microbiome status, the fecal analyses listed in this policy lack sufficient evidence to support routine reimbursement for diagnosis of dysbiosis; testing for donor qualification prior to FMT is addressed separately with specific culture and NAAT targets identified as reimbursable when documented.

OpenPayer

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

Coverage Criteria

Covered Indications

Coding

Provider Actions / Billing Guidance

Ordering Requirements

Not Covered

Definitions

Frequency Limits

Background