Medical Policy: 08.01.23 

Original Effective Date: February 2015 

Reviewed: January 2018 

Revised: January 2018 


Benefit Application:

Benefit determinations are based on the applicable contract language in effect at the time the services were rendered. Exclusions, limitations or exceptions may apply. Benefits may vary based on contract, and individual member benefits must be verified. Wellmark determines medical necessity only if the benefit exists and no contract exclusions are applicable. This medical policy may not apply to FEP. Benefits are determined by the Federal Employee Program.


This Medical Policy document describes the status of medical technology at the time the document was developed. Since that time, new technology may have emerged or new medical literature may have been published. This Medical Policy will be reviewed regularly and be updated as scientific and medical literature becomes available.



Fecal Bacteriotherapy, also called fecal microbiota transplantation (FMT) involves the infusion of intestinal microorganisms via transfer of stool from a healthy individual into a diseased individual, with the intent of restoring normal intestinal flora. Fecal transplant is proposed for the treatment of treatment-refractory Clostridium difficile infection (CDI).


The US Food and Drug Administration (FDA) has classified human stool as a biological agent and determined that its use in fecal microbiota transplantation (FMT) therapy and other research should be regulated to ensure patient safety.


Fecal transplantation is usually performed by colonoscopy and less commonly by nasoduodenal tube. During colonoscopy the colonoscope is advanced through the entire colon. As the colonoscope is withdrawn, the donor stool is delivered through the colonoscopy into the colon.


The goal of FMT is to replace damaged and/or disordered native microbiota with a stable community of donor microorganisms. The treatment is based on the premise that an imbalance in the community of microorganisms residing in the gastrointestinal tract (i.e., dysbiosis) is associated with specific disease states, including susceptibility to infection.


In July 2013, the U.S. Food and Drug Administration (FDA) issued guidance regarding investigational new drug requirements for use of fecal microbiota transplant to treat CDI not responsive to medication therapy. The document states that FDA is continuing to consider how to regulate fecal microbiota transplant and that, during this interim period, the agency will use enforcement discretion regarding use of fecal transplant to treat treatment-resistant CDI infections. FDA requires that physicians obtain adequate informed consent from patients or their legal representative before performing the intervention. The document also states that selective enforcement does not apply to use of fecal transplant for treating conditions other than treatment resistant CDI.  There is a new draft guidance (2016) awaiting final recommendation.


The American College of Gastroenterology recommends that FMT should be considered second-line therapy for a third recurrence of CDI.


Prior Approval:


Not applicable.



Fecal microbiota transplantation/fecal bacteriotherapy may be considered medically necessary when ALL of the following have been met:

  • Infection confirmed by a positive stool test for Clostridium difficile toxin
  • There have been at least 3 episodes of recurrent Clostridium difficile infection and associated diarrhea refractory to antibiotic therapy including at least one regimen of pulsed vancomycin (unless allergic to vancomycin).
  • Patient is not immunocompromised, including:
    • Patients on major immunosuppressive agents including high-dose corticosteroids, calcineurin inhibitors, mammalian target of rapamycin (mTOR) inhibitors, lymphocyte-depleting biological agents, anti-tumor necrosis factor agents, and others; chemotherapeutic antineoplastic agents.
    • Patients with decompensated liver cirrhosis, advanced HIV/acquired immune deficiency syndrome, recent bone marrow transplant, or other cause of severe immunodeficiency

Fecal microbiota transplantation/fecal bacteriotherapy is considered investigational for, but not limited to, the following conditions:

  • Alopecia Areata
  • Autism
  • Crohn’s disease
  • Colon Cancer
  • Diabetes
  • Graft versus Host Disease
  • Irritable Bowel Syndrome
  • Inflammatory Bowel Disease
  • Obesity
  • Pouchitis
  • Ulcerative Colitis
  • Constipation
  • Multiple Sclerosis
  • Insulin resistance
  • Metabolic Syndrome
  • Neurologic disorders
  • Mental Health Disorders (e.g. anxiety, OCD, autism)
  • Autoimmune Disorders

The current studies fail to address and show success with repeated fecal transplants. Therefore, the use of repeat fecal transplant for any indication is considered not medically necessary.


Fecal bacteriotherapy is considered not medically necessary for the first or second episode of clostridium difficile.


Procedure Codes and Billing Guidelines:

To report provider services, use appropriate CPT* codes, Alpha Numeric (HCPCS level 2) codes, Revenue codes, and/or diagnosis codes.

  • 44705  Preparation of fecal microbiota for instillation, including assessment of donor specimen.
  • G0455 Preparation with instillation of fecal microbiota by any method, including assessment of donor specimen.
  • 44799 Unlisted procedure, small intestine


Selected References:

  • American College of Gastroenterology (ACG). Guidelines for diagnosis, treatment, and prevention of Clostridium difficile infections
  • Food and Drug Administration (FDA). Enforcement Policy Regarding Investigational New Drug Requirements for Use of Fecal Microbiota for Transplantation to Treat Clostridium difficile  infection Not Responsive to Standard Therapies. July 2013
  • Van Nood E, Vrieze A, Nieuwdorp M, Fuentes S, Zoetendal EG, de Vos WM, Visser CE, Kuijper EJ, Bartelsman JF, Tijssen JG, Speelman P, Dijkgraaf MG, Keller JJ (2013). Duodenal Infusion of Donor Feces for Recurrent Clostridium difficile. N Engl J Med 20 Jan 16.
  • NICE guideline: Faecal microbiota transplant for recurrent clostridium difficile infection March 2014
  • ECRI Institute, emerging technology reports. Fecal microbiota transplantation for treating recurrent clostridium difficile infection. Updated Aug 2014
  • Austin M, Mellow M, Tierney WM. Fecal microbiota transplantation in the treatment of clostridium difficile infections. Am J Med. 2014 Jun;127(6):479-83. doi: 10.1016/j.amjmed.2014.02.017. Epub 2014 Feb 26
  • Kelly CR, de Leon L, Jasutkar N. Fecal microbiota transplantation for relapsing Clostridium difficile infection in 26 patients: methodology and results. J Clin Gastroenterol. 2012;46:145–149
  • Kelly CP. Fecal microbiota transplantation--an old therapy comes of age. N Engl J Med. 2013;368:474–475
  • Vyas D, L’esperance HE, Vyas A. Stool therapy may become a preferred treatment of recurrent Clostridium difficile? World J Gastroenterol. 2013;19:4635–4637
  • Brandt LJ, Aroniadis OC. An overview of fecal microbiota transplantation: techniques, indications, and outcomes. Gastrointest Endosc. 2013;78:240–249
  • Moore T, Rodriquez A, Bakken JS. Fecal microbiota transplantation: a practical update for the infectious disease specialist. Clin Infect. Dis. 2014:58(4):541-545
  • Surawicz CM1, Brandt LJ, Binion DG, Ananthakrishnan AN, Curry SR, Gilligan PH, McFarland LV, Mellow M, Zuckerbraun BS. Guidelines for diagnosis, treatment, and prevention of clostridium difficile infections. Am J Gastroenterolo. 2013 Apr;108(4):478-98;  doi: 10.1038/ajg.2013.4
  • Borody TJ, Leis S, Pang G, et al. Fecal microbiota transplantation in the treatment of recurrent clostridium difficile infection
  • Brandt LJ, Aroniadis OC, Mellow M, et al.: Long-Term Follow-Up of Colonoscopic Fecal Microbiota Transplant for Recurrent Clostridium difficile Infection. Am J Gastroenterol 2012; 107: 1079–87
  • Mattila E, Uusitalo-Seppala R, Wuorela M, et al.: Fecal transplantation, through colonoscopy, is effective therapy for recurrent Clostridium difficile infection. Gastroenterology 2012; 142: 490–6
  • Allen-Vercoe E, Reid G, Viner N, Gloor GB, Hota S, Kim P, Lee C, O’Doherty K, Vanner SJ, Weese JS, et al. A Canadian Working Group report on fecal microbial therapy: microbial ecosystems therapeutics. Can J Gastroenterol. 2012;26:457–462.
  • Kelly CR, et al. Update on fecal microbiota transplantation 2015: indications, methodologies, mechanisms and outlook. Gastroenterol 2015 May 15 [Epub ahead of print].
  • Kelly CR, et al. Fecal microbiota transplant for treatment of Clostridium difficile infection in immunocompromised patients. Am J Gastroenterol 2014 Jul;109(7):1065-71.
  • Aroniadis OC, Brandt LJ, Greenberg A et al. Long-term Follow-up Study of Fecal Microbiota Transplantation for Severe and/or Complicated Clostridium difficile Infection: A Multicenter Experience. J Clin Gastroenterol. 2015 Jun 23.
  • Borody TJ, Leis S, Pang G, Wettstein AR. Fecal microbiota transplantation in the treatment of recurrent Clostridium difficile infection. UptoDate Inc., Waltham, MA
  • Varier RU, et al. Cost-effectiveness analysis of fecal microbiota transplantation for recurrent Clostridium difficile infection. Infect Control Hosp Epidemiol 2015 Apr;36(4):438-44.
  • Rossen NG, et al. Findings from a randomized controlled trial of fecal transplantation for patients with ulcerative colitis. Gastroenterol 2015 Mar 30 [Epub ahead of print].
  • Drekonja D, et al. Fecal microbiota transplantation for Clostridium difficile infection: A systematic review. Ann Intern Med 2015 May 5;162(9):630-8.
  • Malani PN, Rao K. Expanded evidence for frozen fecal microbiota transplantation for clostridium difficile infection: A fresh take. JAMA. 2016;315(2):137-138.
  • Almeida R, Gerbaba T, Petrof EO, et al. Recurrent Clostridium difficile infection and the microbiome. J Gastroenterol. 2016;51(1):1-10.
  • Lee CH, Steiner T, Petrof EO, et al. Frozen vs fresh fecal microbiota transplantation and clinical resolution of diarrhea in patients with recurrent clostridium difficile infection: A randomized clinical trial. JAMA. 2016;315(2):142-149.
  • Kakihana K, Fujioka Y, Suda W, et al. Fecal microbiota transplantation for patients with steroid-resistant/dependent acute graft-versus-host disease of the gut. Blood. 2016 Jul 26 [Epub ahead of print]
  • Fecal Microbiota Transplantation, FDA Emerging Clinical Issues (2016).
  • Quraishi MN, Widlak M, Bhala N, et al. Systematic review with meta-analysis: the efficacy of faecal microbiota transplantation for the treatment of recurrent and refractory Clostridium difficile infection. Aliment Pharmacol Ther. Sep 2017;46(5):479-493. PMID 28707337


Policy History:

  • January 2018 - Annual Review, Policy Revised
  • January 2017 - Annual Revew, Policy Revised
  • January 2016 - Annual review, Policy revised
  • February 2015 - New policy

Wellmark medical policies address the complex issue of technology assessment of new and emerging treatments, devices, drugs, etc.   They are developed to assist in administering plan benefits and constitute neither offers of coverage nor medical advice. Wellmark medical policies contain only a partial, general description of plan or program benefits and do not constitute a contract. Wellmark does not provide health care services and, therefore, cannot guarantee any results or outcomes. Participating providers are independent contractors in private practice and are neither employees nor agents of Wellmark or its affiliates. Treating providers are solely responsible for medical advice and treatment of members. Our medical policies may be updated and therefore are subject to change without notice.


*CPT® is a registered trademark of the American Medical Association.