Double-blinded Randomized Placebo Controlled Study: Fecal Microbiota Transplantation in the Treatment of Chronic Pouchitis
Phase: PHASE2
Conditions: Pouchitis, Ulcerative Colitis
Sponsor: Helsinki University Central Hospital

Study Protocol and Statistical Analysis Plan 
 
 
 
Title of the project 
 
FECAL MICROBIOTA TRANSPLANTATION IN CHRONIC POUCHITIS: A RANDOMIZED, 
PARALLEL, DOUBLE-BLINDED CLINICAL TRIAL 
 
ClinicalTrials.gov identifier: NCT03378921 
 
Protocol last updated: 12.9.2018 
 
Published article:  
https://academic.oup.com/ibdjournal/advance-article/doi/10.1093/ibd/izab001/6121233 
 
Study group: 
Essi Karjalainen, M.D. Department of GI surgery, Helsinki University Hospital 
Laura Renkonen-Sinisalo, Ph.D. M.D. Department of GI surgery, Helsinki University Hospital 
Reetta Satokari, PhD. Helsinki University 
Harri Mustonen, DSc Department of GI surgery, Helsinki University Hospital 
Ari Ristimäki, MD. PhD. Department of Pathology, Medicum, Faculty of Medicine, University of 
Helsinki, Helsinki, Finland 
Anna Lepistö, M.D. PhD. Department of GI surgery, Helsinki University Hospital 
Perttu Arkkila, M.D. PhD. Department of Gastroenterology, Helsinki University Hospital 
 
 
 
Personal and contact Information  
Name  
 
Essi Karjalainen 
Current Work  
Colorectal surgeon  
Address  
 
PL 340, 00290 Helsinki, Finland 
Phone Nr.  
 
+358 504621853 
E-mail 
 
essi.karjalainen@hus.fi 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

Background 
 
Pouchitis is the most common complication among patients with ulcerative colitis (UC) who have 
undergone restorative proctocolectomy (Figure 1) with ileal pouch-anal anastomosis. The most 
common long term complication is pouchitis, which accounts for 10% of pouch failures. It is an 
idiopathic inflammatory condition that may occur in up to 50% of patients after an ileal-pouch anal 
anastomosis for UC (Landy 2012).  
 
Figure 1. Ileal pouch anal anastomosis (IPAA) 
 
 
The etiology of pouchitis remains unclear. There is significant clinical evidence implicating bacteria 
in the pathogenesis of pouchitis. Studies using culture and molecular methods demonstrate a 
dysbiosis of the pouch microbiota in pouchitis. The study of ileal pouch mucosal biopsies and fecal 
samples analyzed with a 16S rDNA-based terminal restriction fragment length polymorphism 
(TRFLP) approach have revealed statistically significant differences in the mucosal and fecal 
microbiota between UC and FAP (Familiar adenomatous polyposis) patients who had IPAA (Zella 
2011). UC pouches included significantly more TRFLP peaks matching Clostridium and 
Eubacterium genera compared to FAP pouches and fewer peaks matching Lactobacillus and 
Streptococcus genera compared to FAP. DNA Sanger sequencing of a subset of luminal samples 
revealed UC pouches having more identifiable sequences of Firmicutes (51.2% versus 21.2%) and 
Verrucomicrobia (20.2% versus 3.2%), and fewer Bacteroidetes (17.9% versus 60.5%) and 
Proteobacteria (9.8% versus 14.7%) compared to FAP. Risk factors, genetic associations, and 
serological markers of pouchitis suggest that the interactions between the host immune responses 
and the pouch microbiota underlie the etiology of this idiopathic inflammatory condition. Many 
factors contribute to the course of refractory pouchitis, such as the use of non-steroidal anti-
inflammatory drugs, infection with Clostridium difficile, pouch ischemia, or concurrent immune-
mediated disorders 
 
Initial acute episodes typically respond to antibiotic therapy such as metronidazole, patients can 
become dependent on antibiotics or develop refractory disease. Different treatments for the refrac-

tory pouchitis have been tested including different treatments used in the treatment of UC (mesala-
zine, immunosuppressive or immunomodulative), but long term remission is seldom achieved. 
Probiotics, especially products containing many strains of probiotics such as VSL3# have been 
been effective in some studies (Gionchetti 2003). Otherwise a single-strain probiotic bacterium 
supplement of Lactobacillus GG has been shown to be ineffective (Kuisma 2003). 
 
Treatment of recurrent Clostridium difficile-infection (CDI) with antibiotics leads to recurrences in 
up to 50% of patients. It has been shown that fecal microbiota transplantation (FMT) through 
colonoscopy is an effective treatment for recurrent CDI in over 90% of CDI patients. 
Transplantation was done for 70 patients and no significant complications occurred for the 
transplantation procedure (Mattila 2012). Case reports have also shown promising results of FMT 
in IBD patients (Anderson 2012). Only one case report about FMT in the treatment of Clostridium 
difficile-associated pouchitis is available (Patel 2013), where a patient with chronic antibiotic-
dependent pouchitis contracted refractory CDI. FMT lead to the eradication of CDI, but the 
baseline chronic pouchitis remained. There are three prospective uncontrolled cohort studies and 
one case report about FMT in the treatment of chronic pouchitis, reporting on 23 patients in total. 
Two of the cohort studies used a single FMT infusion with 25% (2/8) achieving clinical response in 
one study (Landy 2015) and 71% (5/7) in the other study (El-Nachef 2016), but no patients 
achieved clinical remission. In the third cohort study was used multiple FMT infusions and 4 of 5 
patients achieved clinical remission and the other patient achieved clinical response (Stallmach 
2016). The only case report used single infusion and the patient achieved clinical remission (Fang 
2016). 
 
Currently there is no established effective treatment for chronic antibiotic dependent or refractory 
pouchitis. The aim of our study is to investigate the efficacy and safety of fecal transplantation in 
treatment of chronic pouchitis instead of antibiotic therapy. Another aim is to evaluate phylogenetic 
analysis of the fecal microbiota trying to find microorganisms contributing to good results in fecal 
transplantation in IPAA patients.  
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

STUDY DESIGN  
 
STUDY POPULATION  
 
Inclusion criteria for study  
 
Status post of restorative proctocolectomy with ileal pouch-anal anastomosis (IPAA) for 
ulcerative colitis 
 
Pouchitis diagnosed by the symptoms and by endoscopy including histology within 6 
months prior to FMT. 
 
Need of frequent or continuous use of antibiotics or probiotics because of the chronic 
pouchitis 
 
Availability of consecutive fecal samples during one year  
 
Compliance to attend FMT and control pouchscopy after 52 weeks 
 
18-75 years  
 
 
Exclusion criteria for study  
 
Unable to provide informed consent  
 
Use of immunosuppressive or biological medication 
 
Pregnancy 
 
 
METHODS 
26 consecutive patients with pouchitis diagnosed by the symptoms and endoscopy. Patients are 
collected from the Helsinki University Central Hospital. Use of antibiotics or probiotics is not contin-
ued during the study. Fecal microbiota transplantation (FMT) is performed by experienced endos-
copists using frozen and thawed stool through flexible sigmoideoscopy into the afferent limb. The 
second FMT is installed via catheter into the pouch 3 weeks after the first FMT. Antibiotic treatment 
has been stopped 36 hours before the FMT. 13 pouchitis patients receive a fecal transplantation 
from the healthy tested donor and 13 patients in the control group receive their own feces donated 
and prepared at the same day. The endoscopists and personnel performing the FMT are blinded 
for the type of feces. The randomization is done by a doctor not attending the study. Pouchscopy is 
assessed at 52 weeks to evaluate the endoscopic and mucosal healing. Clinical Pouchitis Disease 
Activity Index, see table 1 (Sandborn 1994) is assessed at week 4, 12, 26 and 52 and in addition to 
the endoscopy and histological index at weeks 0 and 52. 

Table 1 Pouchitis Disease Activity Index (Sandborn 1994). 
 
 
Donors are excluded if they have taken antibiotics within the preceding 3 months; are on 
immunosuppressive or chemotherapeutic agents; have known or recent exposure to HIV; hepatitis 
B or C; have a current communicable disease; are morbidly obese; have IBD, IBS, atopy, chronic 
diarrhea or constipation; GI malignancy or polyposis; participate in high-risk sexual behaviors; use 
illicit drugs; have a history of recent incarceration or travel to areas with endemic diarrhea. Donor 

blood testing includes tests for HIV, hepatitis A, B and C; donor stool testing includes culture, C. 
difficile toxin, ova and parasites, and Helicobacter pylori. 
 
Follow up of the patients include a telephone call after 12 and 26 weeks after the FMT, and a 
clinical control visit 52 weeks after the transplantation. The clinical part of the Pouchitis Disease 
Activity Index score is assessed during each call and clinical visit.  
A general quality of life measurement (15D-questionnaire, www.15d-instrument.net) is done at the 
day of stool transplantation and 6 months after the transplantation. Any adverse events are 
recorded. Changes in the use of medication is recorded. 
Fecal stool samples for phylogenetic analysis are collected before FMT and on weeks 4, 12, 26, 
and 52. Fecal calprotectin indicating level of inflammation is measured before FMT and on weeks 
4, 12, 26 and 52. 
 
Endpoint of the study is the remission defined as Pouchitis Disease Activity Index <7 and no 
need for antibiotic treatment of pouchitis during the 52-week follow-up. Secondary objective for this 
study include an evaluation of the changes in gut microbiota within the 52 weeks. 
 
STATISTICAL ANALYSIS 
The sample size is calculated in according to the estimation that the difference in remaining in re-
mission is 55% (80 vs 25%) over 52 weeks. The calculated sample size is 26 patients and there-
fore 13 patients are selected for both groups (donor vs own feces). This difference is considered to 
be clinically meaningful. Confidence interval was selected to be 95% (α=0.05 and β=0.1). 
 
DATE 
Patient collection will be made from September 2017 until June 2018. The follow up of the patients 
will end one year after the last patient included the study. Data analysis and reporting of the results 
will be during the year 2019. 
 
 
 
 
 
ETHICAL ASPECTS 
The possible ethical risks for this study include the possible transmission of harmful microbiota to 
the patients causing some infection or other diseases. The risk is most likely minimal, because the 
feces and the donors are widely tested for many known pathogens and diseases. Risk for the acti-
vation of pouchitis is also possible, although this is unlikely according to previous case reports 
about FMT in IBD. All the patients are informed about the experimental nature of this treatment 
procedure and about the available results in other previously published reports and possible risks 
of the procedure. All of the patients are asked for informed consent. The permission for this study 
will be appealed from the Institutional Review Board of Helsinki University Central Hospital. 
 
 
WHAT MAKES THIS RESEARCH INNOVATIVE 
This is the first placebo controlled study of fecal transplantation in pouchitis patients. The study of 
microbiota by the repeated fecal samples during the one year follow-up makes it possible to study 
if the change in the gut microbiota is permanent after the fecal transplantation. 
 
 
 
 

 
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