Department of Medicine

Gastroenterology Hepatology

Fecal Microbiota Transplant Program

Fecal Microbiota Transplant for Recurrent Clostridium difficile Infection


Microbiota transplantation, also known as stool transplantation, is a procedure used to treat recurrent Clostridium difficile infection.   Stool is taken from a healthy donor and placed into the infected colon through a colonoscope.  The healthy bacteria repopulate the colon and fight off the C. difficile infection.


This procedure is very successful.  There are more than 500 cases reported worldwide with a cure rate over 90% with a single stool infusion.  Currently, the use of fecal microbiota transplant to treat C. difficile is considered investigational by the FDA and is only being performed at highly selected centers. The Indiana University fecal microbiota transplant program was established in May of 2012.  To date, over 80 transplantations have been done at University Hospital with a 94% cure rate without a single significant adverse event noted.


Why does fecal transplantation work?

Fecal microbiota transplantation theoretically works by replacing the protective natural colonic flora that has been disrupted by antibiotics and/or other environmental or iatrogenic factors. Clostridium difficile infection usually occurs after use of a powerful, broad spectrum antibiotic that is designed to kill off most of the bacteria in the body.  The antibiotic kills many of bacteria in the colon except for C. difficile.  Without any competition for food or space, C. difficile grows quickly and infects the colon leading to severe diarrhea.   To treat this infection, first another powerful antibiotic is given to kill of the infection but it also suppresses the healthy bacteria from recolonizing and protecting the colon.  A cure occurs only when antibiotics are stopped and healthy bacteria can return in great numbers to the colon.  The infection reoccurs when the C. difficile is able to return in great numbers before the beneficial bacterial communities are reestablished.  Fecal transplantation works as a sort of “mega probiotic” instantly repopulating the colon with trillions of healthy bacteria that effectively prevents  C. difficile from returning. 


Who qualifies for fecal transplantation?

Patients with at least 3 episodes of documented C. difficile infection or who have already failed a vancomycin taper are eligible for fecal transplant. There are no contraindications to this procedure as long as the patient is deemed to be fit to undergo a colonoscopy and sedation. Even patients with prolonged immunosuppression have successfully undergone transplantation without adverse reactions. Fecal microbiota transplantation has been successfully performed in children.


The procedure

The person who is receiving the stool transplant has a standard colonoscopy bowel preparation.   The donor, who is screened for infections, brings a fresh stool sample which is made into a thick liquid and injected through the colonoscope into the highest part of the colon. 


The recipient is asked stop taking vancomycin or other antibiotics 48 hours prior to the colonoscopy and to follow the prep instructions completely.  After the colonoscopy is done, the patient is observed in our endoscopy unit for a few ours and given Imodium to allow the stool to stay in the colon longer. Some patients report bloating and diarrhea for a few days after the transplantation.  Regular bowel movements usually recur after 3-5 days. Stool is tested for C. difficile at 1 week and 4 weeks after the stool transplantation. A clinic follow-up at 6 months after the stool transplant is recommended to monitor for long-term success and potential adverse reactions. If the first transplant is not successful, it can be repeated using the same stool donor or a different one. 


Risks of the procedure

Risks associated with colonoscopy – perforation, bleeding, adverse reaction to sedation among others are rare and may occur in less than 0.5% of patient. Significant risk from the fecal transplant are believed to be very rare, however, there is a possibility of infectious or autoimmune complications, such as fever, diarrhea, abdominal pain, allergic reactions, hepatitis, or other infections or complications.


The stool donor

The stool donor is may be selected by the patient and he/she is usually a close family member or friend.  If the patient is unable to find a suitable stool donor, we are able to provide stool from a properly screened healthy individual.  The donor is required to undergo testing specified by the physician within 2 weeks of the fecal transplant for communicable diseases.  The required tests are:

  • Stool:             Enteric pathogens, Clostridium difficile, parasites and their eggs, Giardia, Cryptosporidium, H. pylori
  • Blood:    Syphilis, HIV, Hepatitis A, B and C. 


The donor has to verify that he/she has no known immunodeficiency virus (HIV), no hepatitis B or C infections, no known exposure to HIV or viral hepatitis within the previous 12 months, no high-risk sexual behaviors (examples: sexual contact with anyone with HIV/acquired immune syndrome or hepatitis, men who have sex with men, sex for drugs or money), no use of illicit drugs, no tattoo or body piercing within 6 months, no current or recent diarrheal illness, no active hepatitis B & C or HIV infection, no incarceration or history of incarceration, no known current communicable disease (e.g. upper respiratory tract infection), no known risk factors for variant Creutzfeldt-Jakob disease, no travel to areas of the world within the last 6 months where diarrheal illnesses, hepatitis, or HIV are endemic or risk of traveler’s diarrhea is high (Asia, Middle East, Africa, Mexico, and central and South America), no history of inflammatory bowel disease, no history of irritable bowel syndrome, no  history of constipation of unknown cause or chronic diarrhea, no history of gastrointestinal tract cancer or known polyposis (presence of numerous internal polyps). The donor has to verify that he/she has not received antibiotics in the last 3 months, does not use immunosuppressive or chemotherapeutic medications, has no history of major gastrointestinal surgery (e.g. gastric bypass), no known metabolic syndrome, no known systemic autoimmunity (lupus, multiple sclerosis, etc.), no chronic pain syndrome, and no atopic diseases including asthma, eczema, and eosinophilic disorders of the gastrointestinal tract. The donor has to verify that he/she has not recently ingested a potential allergen (e.g. nuts) that the recipient (patient) has a known allergy to this agent.


Preparation of the donor

He or she will take 60 cc of Milk of Magnesia the night before, will bring fresh AM stool on ice. The donor is expected to notify the physician’s office if developing an acute illness (fever, diarrhea, vomiting) before donating.


If you are interested in setting up an appointment for fecal transplantation or receiving an information packet, please contact Dr. Monika Fischer’s office Marsha Johnston, Administrative Assistant at 317-948-6234 or fax to 317-944-0975.