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Fecal microbiota transplantation (FMT) treats clostridium difficile (C. diff.) infection. C. diff. is often caused by antibiotics that change the bacteria in the colon. Antibiotics kill off good bacteria and this allows the C. diff. bacteria to thrive. This causes severe diarrhea and may cause death if not treated. FMT transfers healthy stool and bacteria into your colon to help treat the infection.
No antibiotics 2 days before FMT (vancomycin, metronidazole, or Flagyl®)
Clean bathrooms with bleach the morning of the FMT. This reduces risk of reinfection.
You will need a responsible adult to drive you home if your FMT is by colonoscopy, endoscopy, or sigmoidoscopy due to sedation medicines that are used. If you are not able to arrange this, we can reschedule your FMT.
If you are getting capsules or enemas, you do not need a driver.
A few days before the FMT buy your supplies. Only refer to instructions your doctor has chosen for you.
FMT by Enema Instructions
Supplies: 1-Sodium phosphate enema (can be purchased at local drugstore)
Diet: No special diet
How do I give myself the enema?
Lay a towel on your bed to protect it. Lie on your bed on your left side, knees bent. Gently insert lubricated enema tip into your anal canal. It may go in easier if you bear down, like you are having a bowel movement. This helps relax the muscles. Squeeze the enema bottle to get the liquid into your rectum. Gently remove enema tip from your body. Hold the liquid in for 3-5 minutes. Use the bathroom. It is normal to have mild cramping or burning, it will go away with rest.
Day of FMT: Complete the bowel prep. Give yourself the enema 1-2 hours before you leave home.
Your Visit: 2-3 hours. You may resume your normal routine and diet afterwards.
FMT by Capsule Instructions
Supplies: Stomach acid blocker medicine will be prescribed by your doctor. You will pick up at the pharmacy and take as directed for 2 days before your FMT.
Please Note: The FMT capsules are the size of a large vitamin. Let us know if you have problems swallowing.
Diet: The day before your FMT, no solid foods after midnight. You may have clear liquids only.
Day of FMT: Stop drinking liquids 2 hours before scheduled time to arrive.
Your Visit: 30-90 minutes. You will not be able to eat or drink anything for one hour after your FMT. You may resume your normal routine.
FMT by Colonoscopy, Endoscopy or Sigmoidoscopy
Supplies: Bowel prep-as directed by your doctor (you will pick up from pharmacy).
Going Home: You will need to arrange for a responsible adult to take you to and from the Digestive Health Center because of sedation medicines used.
Bowel Prep: Follow pharmacy mixing directions. Start drinking bowel prep at 6:00 pm the evening before your FMT. Prep will take 3-4 hours. Drink one 8-ounce glass every 15-20 minutes. Finish drinking the entire bottle of bowel prep before you go to sleep.
Diet: After you start your bowel prep eat no solid foods. You may have clear liquids.
Day of FMT: Stop drinking liquids 4 hours before scheduled arrival.
Your Visit: 3 hours. Diet and activity are restricted for 24 hours if you get sedation medicine.
Recovery of fecal microbiota in your gut may cause symptoms such as (but not limited to) diarrhea, abdominal pain, bloating, cramping and an urge to have a bowel movement. (These symptoms are very common in the first several weeks after treatment and slowly resolve over 1-2 months.)
No antibiotics, unless ordered by your doctor.
We will call you to follow-up and see how you are feeling. Please contact us if you are having problems or have questions prior to hearing from us. Diet – Bland diet (avoid dairy besides probiotic yogurt or kefir) at first and slowly begin your normal diet as you feel better.
When to Call
Fever over 100.4, for 2 readings 4 hours apart
New or worse abdominal pain or cramping
New weakness or fatigue
Extreme bowel movement urgency and/or loose bowel movements
Who to Call
Less than 2 days after FMT:
UW Health Digestive Health Center
750 University Row
Madison, WI 53792
(608) 890-5010 or (855) 342-9900
More than 2 days after FMT:
UW Health Infectious Disease Clinic
600 Highland Ave.
Madison, WI 53792
(608) 263-0946 or (800) 323-8942
If you are a patient receiving care at UnityPoint – Meriter, Swedish American or a health system outside of UW Health, please use the phone numbers provided in your discharge instructions for any questions or concerns.