A Phase II Randomized, Double-blind Placebo-controlled Trial to Determine if Fecal Microbiota Transplantation is Efficacious for Hospitalized Patients With C. Difficile Infection History During Antibiotic Treatment
Phase: PHASE2
Conditions: Clostridium Difficile Infection, C.Difficile Diarrhea, CDI
Sponsor: University of Wisconsin, Madison

GRAFT Study Protocol 
 
           Nasia Safdar 
 
 
 
 
 
 
 
 
Project Title: A PHASE II RANDOMIZED, DOUBLE-BLIND PLACEBO-CONTROLLED TRIAL TO 
DETERMINE IF FECAL MICROBIOTA TRANSPLANTATION IS EFFICATIOUS FOR HOSPITALIZED 
PATIENTS WITH C. DIFFICILE INFECTION HISTORY DURING ANTIBIOTIC TREATMENT 
 
Principal Investigator: Nasia Safdar, MD, PhD 
Department of Medicine 
Division of Infectious Disease 
University of Wisconsin-Madison 
MFCB 5138 
1685 Highland Ave. 
Madison, WI 53705 
(608) 213-4075 
ns2@medicine.wisc.edu  
 
      Project Coordinator:  Ashley Kates, PhD 
Department of Medicine 
Division of Infectious Disease 
University of Wisconsin-Madison 
akates@medicine.wisc.edu 
 
Funding Source: AHRQ 
(Finch Therapeutics and OpenBiome will manufacture and provide 
study drug capsules and placebos free of charge) 
 
This document is confidential. No part of it may be transmitted, reproduced, published, or used by other 
persons without prior written authorization from the Sponsor or Principal Investigator. 
 
 
 
PROTOCOL REVISIONS AND AMENDMENTS 
 
Protocol Version 
Date 
Change 
Initiated 
by (initials) 
Brief 
description 
of 
protocol 
modifications/ 
actions 
requested, if any 
Template 
9/5/17 
TNK, AK 
Input from IRB, OCT, MARCH, IND/IDE services, PIs 
Draft 1 
4/10/17  
AK, NS 
First draft of the protocol from the template 
Draft 2 
4/13/17 
TNK 
Comments up to consent portion of the protocol 
Draft 3 
6/17/17 
AK 
Addressing TNK comments, formatting 
Draft 4 
6/25/17 
AK 
Responding to IRB comments 
Draft 5 
8/3/17 
TO, AES, AR (ICTR)
ICTR DMC and SMS comments, formatting 
Draft 6 
8/7/2017 
AK 
Addressing DMC and SMS comments 
Draft 7 
8/25/2017 
AK 
Finalizing protocol 
Draft 8 
9/12/17 
AK 
Minor updates 
Draft 9 
3/23/18 
AK 
Updates to FMT product  
Draft 10 
5/22/18 
AK 
Minor editorial updates 
Draft 11 
7/31/2018 
AK 
Responses to FDA comments 

GRAFT Study Protocol 
 
           Nasia Safdar 
 
 
Draft 12 
9/14/18 
AK 
Changes requested by IRB 
Draft 13 
11/26/18 
SZ 
Changes requested by IRB 
Draft 14 
12/5/18 
AK, IG 
Updates to protocol 
 Inserted protocol number and clinicaltrials.gov number 
 Corrected typos 
 Clarified stool collection during intervention period regardless 
of hospitalization, for all groups 
 Updated contact information as needed 
 Clarified CRU nurse is considered a study nurse for the 
purpose of this study 
 Clarified fasting allows for clear liquids (not strict NPO) 
 Updated inclusion for new antibiotic to be started within 72 
hours rather than three doses 
 Clarified 30-minute post-dose observation need only be done 
for first dose 
 Study test capsule and pregnancy test (when applicable) will 
be taken at intervention visit 
 Defined timeline for exclusion of bowel obstruction or gut 
motility issues 
 Clarified exclusion for neutropenia and how/when to evaluate 
 Further explained recruitment 
 Change from 19 days to 14 days for cutoff of antibiotic regimen 
concurrence 
 Explained withdrawal and early termination visit 
 Explained accountability recording (med diary) and potential 
drug return 
 Clarified concomitant medications, including certain long-term 
antibiotics 
 Removed Charlson's Comorbidity Index 
 Added option to collect perirectal swabs at baseline if needed 
 Removed phrase "safety assessment" - defined as AE 
evaluation, which is already listed 
 Clarified calls during treatment period will be once  per week 
 
 
 

GRAFT Study Protocol 
 
           Nasia Safdar 
 
 
STATEMENT OF COMPLIANCE 
 
The study will be carried out in accordance with Good Clinical Practices (GCP) as required by the following: 
 
 
United States Code of Federal Regulations (CFR) applicable to clinical studies (45 CFR Part 46; 21 
CFR Part 50, 21 CFR Part 54, 21 CFR Part 56, and 21 CFR Part 312); 
 
International Conference on Harmonization (ICH) E6; 62 Federal Register 25691 (1997); 
 
Compliance with these standards provides public assurance that the rights, safety and well-being of study 
subjects are protected, consistent with the principles that have their origin in the Declaration of Helsinki. 
All key personnel (all individuals responsible for the design and conduct of this study) have completed Human 
Subjects Protection Training. 
 
 

GRAFT Study Protocol 
 
           Nasia Safdar 
 
 
SIGNATURE PAGE 
 
The signature below constitutes the approval of this protocol and the attachments and provides the necessary 
assurances that this trial will be conducted according to all stipulations of the protocol, including all statements 
regarding confidentiality, and according to local legal and regulatory requirements and applicable US federal 
regulations and ICH guidelines. 
 
Lead Principal Investigator: 
 
Signed: 
 
Date: 
 
 
 
Name, Title 
 
 
 
 
 

GRAFT Study Protocol 
 
           Nasia Safdar 
Version #: 14 
Page 5 of 48 
TABLE OF CONTENTS 
1. 
LIST OF ABBREVIATIONS .................................................................................................................................... 8 
2. 
STUDY SUMMARY .............................................................................................................................................. 9 
3. 
SCHEMATIC OF STUDY DESIGN ......................................................................................................................... 11 
4. 
KEY ROLES ........................................................................................................................................................ 12 
5. 
BACKGROUND AND INTRODUCTION ................................................................................................................ 13 
5.1. 
BACKGROUND AND RATIONALE ..................................................................................................................................... 13 
5.2. 
HYPOTHESIS ............................................................................................................................................................... 13 
5.3. 
STUDY AGENT ............................................................................................................................................................ 13 
5.4. 
SUMMARY OF CLINICAL DATA ....................................................................................................................................... 14 
5.5. 
DOSE RATIONALE, CAPSULE PREPARATION, AND ADMINISTRATION OF STUDY PRODUCT ......................................................... 14 
5.6. 
POTENTIAL RISKS AND BENEFITS TO SUBJECTS .................................................................................................................. 15 
5.6.1. 
Known Potential Risks ..................................................................................................................................... 15 
5.6.2. 
Protection Against Risks .................................................................................................................................. 15 
5.6.3. 
Potential Benefits to the Subjects.................................................................................................................... 15 
5.6.4. 
Risk Minimization ............................................................................................................................................ 16 
6. 
STUDY OBJECTIVES AND PURPOSE ................................................................................................................... 16 
7. 
STUDY DESIGN AND ENDPOINTS ...................................................................................................................... 16 
7.1. 
GENERAL DESIGN ........................................................................................................................................................ 16 
7.2. 
STUDY OUTCOME MEASURES ....................................................................................................................................... 17 
7.2.1. 
Primary Study Outcome Measures .................................................................................................................. 17 
7.2.2. 
Secondary Study Outcome Measures .............................................................................................................. 17 
7.2.3. 
Primary Safety Outcome Measures ................................................................................................................. 17 
8. 
STUDY SUBJECTS – ENROLLMENT AND WITHDRAWAL ..................................................................................... 17 
8.1. 
SUBJECT POPULATION .................................................................................................................................................. 17 
8.2. 
INCLUSION CRITERIA .................................................................................................................................................... 18 
8.3. 
EXCLUSION CRITERIA ................................................................................................................................................... 18 
8.4. 
SUBJECT SCREENING AND RETENTION ............................................................................................................................. 19 
8.4.1. 
Subject Identification ....................................................................................................................................... 19 
8.4.2. 
Recruitment and Retention ............................................................................................................................. 19 
8.5. 
INFORMED CONSENT .................................................................................................................................................... 21 
8.5.1. 
Process of Consent........................................................................................................................................... 21 
8.5.2. 
Consent Form .................................................................................................................................................. 22 
8.5.3. 
Future Use of Stored Specimens ...................................................................................................................... 22 
8.5.4. 
HIPAA ............................................................................................................................................................... 22 
8.5.5. 
Revoking Consent ............................................................................................................................................ 23 
8.5.6. 
Costs to the Subject ......................................................................................................................................... 23 
8.5.7. 
Payment to the Subjects .................................................................................................................................. 23 
8.5.8. 
Exclusion of Women, Minorities, and Children (Special Populations) ............................................................. 23 
8.6. 
EARLY WITHDRAWALS OF SUBJECTS ............................................................................................................................... 23 
8.6.1. 
Premature Termination of the Study ............................................................................................................... 23 
8.6.2. 
When and How to Withdraw Subjects ............................................................................................................ 23 
8.7. 
PARTICIPANT CONFIDENTIALITY ..................................................................................................................................... 24 
9. 
STUDY AGENT .................................................................................................................................................. 24 
9.1. 
DESCRIPTION AND FORMULATION .................................................................................................................................. 24 

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9.2. 
PACKAGING AND DISSEMINATION .................................................................................................................................. 25 
9.3. 
PREPARATION, ADMINISTRATION AND STORAGE OF STUDY DRUG ....................................................................................... 25 
9.4. 
ROUTE OF ADMINISTRATION ......................................................................................................................................... 25 
9.5. 
PRIOR AND CONCOMITANT THERAPY/ STANDARD OF CARE ................................................................................................ 25 
9.6. 
RANDOMIZATION AND BLINDING OF STUDY DRUG ............................................................................................................ 26 
9.7. 
ACCOUNTABILITY PROCEDURES FOR THE STUDY INTERVENTION/INVESTIGATIONAL PRODUCT .................................................. 26 
9.8. 
MODIFICATION OF STUDY INTERVENTION/INVESTIGATIONAL PRODUCT FOR A PARTICIPANT .................................................... 26 
9.9. 
CONCOMITANT MEDICATIONS/TREATMENTS ................................................................................................................... 26 
10. 
LABS ................................................................................................................................................................ 27 
11. 
STUDY VISITS ................................................................................................................................................... 27 
11.1. 
SCREENING/ENROLLMENT, AND BASELINE VISIT ........................................................................................................... 27 
11.2. 
FOLLOW‐UP ............................................................................................................................................................ 29 
11.3. 
UNSCHEDULED VISITS: WILL TAKE PLACE IN A CLINICAL SETTING. ..................................................................................... 30 
11.4. 
STUDY END ............................................................................................................................................................ 31 
12. 
STUDY ANALYSIS .............................................................................................................................................. 31 
12.1. 
SAMPLE SIZE ........................................................................................................................................................... 31 
12.2. 
SUBJECT POPULATION FOR ANALYSIS .......................................................................................................................... 31 
12.3. 
FINAL ANALYTIC PLAN .............................................................................................................................................. 31 
12.4. 
SOURCE DOCUMENTS AND ACCESS TO SOURCE DATA/DOCUMENTS ................................................................................ 32 
12.5. 
QUALITY MANAGEMENT SYSTEM ............................................................................................................................... 32 
12.5.1. 
Study Team Training .................................................................................................................................... 32 
12.5.2. 
Standardized Procedures ............................................................................................................................. 33 
12.5.3. 
Internal Quality Monitoring ......................................................................................................................... 33 
12.5.4. 
External Quality Monitoring ........................................................................................................................ 33 
12.5.5. 
Database Quality Control (QC) .................................................................................................................... 33 
12.6. 
DATA CAPTURE ....................................................................................................................................................... 33 
12.6.1. 
Case Report Forms ....................................................................................................................................... 33 
12.6.2. 
Data Collection Tools ................................................................................................................................... 33 
12.7. 
RECORDS RETENTION ............................................................................................................................................... 33 
13. 
ASSESSMENT OF SAFETY .................................................................................................................................. 34 
13.1. 
SPECIFICATIONS OF SAFETY PARAMETERS .................................................................................................................... 34 
13.1.1. 
Definition of Adverse Events (AE) ................................................................................................................ 34 
13.1.2. 
Definition of Serious Adverse Events (SAE) .................................................................................................. 34 
13.1.3. 
Definition of Unanticipated Problems (UP) ................................................................................................. 35 
13.2. 
CLASSIFICATION OF AN ADVERSE EVENT ...................................................................................................................... 35 
13.2.1. 
NIH Grading of Severity of Events ................................................................................................................ 35 
13.2.2. 
Relationship to Study Agent ........................................................................................................................ 35 
13.2.3. 
Solicited Adverse Events after FMT.............................................................................................................. 36 
13.3. 
ADVERSE EVENT DOCUMENTATION AND REPORTING PROCEDURES .................................................................................. 37 
13.3.1. 
Procedures to Document AEs ....................................................................................................................... 37 
13.3.2. 
Procedures to Report AEs ............................................................................................................................ 37 
13.4. 
FOLLOW‐UP AFTER ADVERSE EVENTS .......................................................................................................................... 38 
13.5. 
STUDY HALTING RULES ............................................................................................................................................. 38 
13.5.1. 
Study Halting Rules ...................................................................................................................................... 38 
13.5.2. 
Individual’s Halting Rights ........................................................................................................................... 39 
13.6. 
SAFETY OVERSIGHT – DATA MONITORING COMMITTEE (DMC) ...................................................................................... 39 

GRAFT Study Protocol 
 
           Nasia Safdar 
Version #: 14 
Page 7 of 48 
14. 
PROTOCOL DEVIATIONS ................................................................................................................................... 39 
15. 
REFERENCES ..................................................................................................................................................... 41 
16. 
APPENDIX I ...................................................................................................................................................... 41 
16.1. 
OSMAN ET AL. ID WEEK 2016 .................................................................................................................................. 41 
16.2. 
DUBOIS ET AL. ID WEEK 2015 .................................................................................................................................. 43 
17. 
APPENDIX II ..................................................................................................................................................... 45 
17.1. 
STUDY SCHEMATIC .................................................................................................................................................. 45 
17.2. 
STUDY CALENDAR .................................................................................................................................................... 46 
17.3. 
NIH COMMON TERMINOLOGY CRITERIA FOR ADVERSE EVENTS (CTCAE) ......................................................................... 47 
17.4. 
ADVERSE EVENT ASSESSMENT FLOW CHART ................................................................................................................ 48 
 
 
 

GRAFT Study Protocol 
 
           Nasia Safdar 
Version #: 14 
Page 8 of 48 
1. LIST OF ABBREVIATIONS 
ADL 
Activities of Daily Living 
AE 
Adverse event 
ANCOVA Analysis of covariance 
CAP 
Community acquired pneumonia 
CDI 
C. difficile Infection 
CFR 
Code of Federal Regulations 
CLIA 
Clinical Laboratory Improvement Amendments 
CRF 
Case Report Form 
CRO 
Contract Research Organization 
CRU 
Clinical Research Unit 
DCC 
Data Coordinating Center 
DHHS 
Department of Health and Human Services 
DMC 
Data Monitoring Committee 
eCRF 
Electronic Case Report Forms 
FDA 
Food and Drug Administration 
FFR 
Federal Financial Report 
FMT 
Fecal Microbiome Transplant 
GCP 
Good Clinical Practice 
GLP 
Good Laboratory Practices 
GMP 
Good Manufacturing Practices 
GWAS 
Genome-Wide Association Studies 
HIPAA 
Health Insurance Portability and Accountability Act 
IB 
Investigator’s Brochure 
ICH E6 
International Conference on Harmonisation Guidance for Industry, Good Clinical Practice: 
Consolidated Guidance 
ICMJE 
International Committee of Medical Journal Editors  
ICU 
Intensive Care Unit 
IDE 
Investigational Device Exemption 
IND 
Investigational New Drug Application 
IRB 
Investigational Review Board 
ISO 
International Organization for Standardization 
MDRO 
Multidrug Resistant Organism 
MOP 
Manual of Procedures 
MRSA 
Methicillin-resistant Staphylococcus aureus 
MSDS 
Material Safety Data Sheet 
NIH IC 
NIH Institute & Center 
NSAID 
Non-steroidal Anti-inflammatory Drug  
OHRP 
Office for Human Research Protections 
PCR 
Polymerase Chain Reaction 
PI 
Principal Investigator 
PRC 
Pharmaceutical Research Center 
QA 
Quality Assurance 
QC 
Quality Control 
SAE 
Serious Adverse Event 
SAP 
Statistical Analysis Plan 
SMC 
Safety Monitoring Committee 
SMS 
Study Monitoring Service 
TNF 
Tumor necrosis factor 
UTI 
Urinary Tract Infection 
UW-ICTR University of Wisconsin Institute for Clinical and Translational Research 

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Page 9 of 48 
VRE 
Vancomycin-resistant Enterococcus 
2. STUDY SUMMARY 
Title 
A phase II randomized, double-blind placebo-controlled trial to determine if 
fecal microbiota transplantation is efficacious for hospitalized patients with C. 
difficile infection history during antibiotic treatment 
 
Short Title and Precis 
The GRAFT study 
Protocol Number 
2017-0789 
ClinicalTrials.gov number 
NCT03621657 
Funding Sponsor 
Agency for Healthcare Research and Quality (AHRQ) 
5600 Fishers Ln, Rockville, MD 20857 
301-427-1364 
 
Study Product 
OpenBiome fecal microbiota preparation capsule [FMT Capsule DE] 
 
Phase 
Phase II study 
 
Methodology 
Randomized, double-blind, placebo-controlled trial 
 
Study Duration 
1 year 
 
Study Center(s) 
Single-center, University of Wisconsin Hospitals and Clinics 
 
Objectives 
The primary objective of this study is to compare the gut microbiota and clinical 
outcomes of oral FMT during antibiotic treatment, immediately following 
antibiotic treatment, and placebo. The second objective is to assess the safety 
and feasibility of daily oral Fecal Microbiome Transplant (FMT) as a treatment 
option. 
 
Number of Subjects 
30 (1:1:1 randomization), 10 subjects per group 
 
Diagnosis  
Changes in the gut microbiota and C. difficile infection (CDI) 
 
Main Inclusion Criteria 
Receiving antibiotics for reasons other than CDI following a recent CDI 
episode (within last 90 days)  
 
Main Exclusion Criteria 
Bowel obstruction or gut motility issues, severely immunocompromised, or 
admitted to the ICU.   
 
Study Product, Dose, 
Route, Regimen 
FMT will be delivered through oral capsules prepared by OpenBiome. It will be 
administered in one of two ways depending on the arm of the trial. 1) A low 
dose of 5 capsules per day during antibiotic treatment and for seven days 
following conclusion of antibiotics. 2) A single dose of 30 capsules (22.5g) of 
oral FMT will be given 48-72 hours after antibiotic treatment conclusion.   
 
FDA status of product 
Encapsulated fecal microbiota preparation (FMT Capsule DE). Please 
refer to Finch Therapeutics BBMF # 17194. 
 
Sourced from human-derived microbes. Please refer to OpenBiome BBMF # 
15543, Section F. 
 
IND: 18262 

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           Nasia Safdar 
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Page 10 of 48 
Duration of administration 
Group 1: 5 capsules of oral FMT per day undergoing antibiotic treatment and 
for 7 days following conclusion of antibiotic treatment. 
 
Group 2: 30 capsules taken 48-72 hours following conclusion of antibiotic 
treatment 
 
Reference therapy 
Placebo: 5 capsules of oral placebo per day undergoing antibiotic treatment 
and for 7 days following conclusion of antibiotic treatment. 
 
Statistical Methodology 
All data will be analyzed using SAS and R. Patient characteristics will be 
summarized using descriptive statistics. To assess changes in the gut 
microbiota, ANCOVA and linear mixed models will be used for longitudinal 
measurements. Safety and adverse events will be summarized using 
descriptive statistics.  
 
 

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           Nasia Safdar 
Version #: 14 
Page 11 of 48 
3. SCHEMATIC OF STUDY DESIGN 
 
 
Baseline/ Day 0 
Recruitment/Consent 
 
 
 
Day 1 
Randomization into trial 
 
 
 
 
 
 
 
 
 
Days 2-60 
Intervention 
 
 
 
 
 
 
 
 
 
 
 
Intervention End 
 
 
 
 
Study End (6 months  
post FMT completion) 
 
 
 
 
 
 
 
 
 
 
 
Obtain informed consent. Screen potential subjects by inclusion and exclusion 
criteria; obtain history, document (n=30). 
Randomize 30 patients
Daily FMT 
dose 
(n=10) 
Collect stool samples every 3 days during intervention period and once per week 
following conclusion of FMT treatment. Detection of incident CDI and C. difficile 
colonization.  
 
For daily FMT: deliver 5 capsules of oral FMT every day for duration of antibiotic 
treatment + 7 days 
For single dose FMT: deliver oral FMT dose (30 capsules) 48-72 hours post 
completion of antibiotic treatment. 
For placebo: deliver 5 capsules of placebo capsules every day for duration of 
antibiotic treatment + 7 days 
 
Phone call assessing any new medical conditions or adverse events occurring 
since the last visit. 
Single 
FMT dose 
(n=10)
Placebo 
(n=10)  
Occurs when patient completes intervention 
Patient will continue to provide stool samples weekly for 4 weeks  
 

GRAFT Study Protocol 
 
           Nasia Safdar 
Version #: 14 
Page 12 of 48 
4. KEY ROLES 
 
Principal Investigator:  
Nasia Safdar MD, PhD  
University of Wisconsin-Madison, Division of Infectious Diseases  
UW Medicine Foundation Centennial Building 
1685 Highland Ave, Madison, WI, 53705 
Email: ns2@medicine.wisc.edu   
 
Researchers:  
Garret Suen, PhD 
University of Wisconsin-Madison, Department of Bacteriology 
5159 MSB, 1550 Linden Dr, Madison, WI 53706 
Email: gsuen@wisc.edu 
 
Ashley Kates, PhD 
University of Wisconsin-Madison, Division of Infectious Diseases  
5th Floor UW Medicine Foundation Centennial Building 
1685 Highland Ave, Madison, WI, 53705 
Email: akates@medicine.wisc.edu 
 
Project Coordinator 
Ilsa Gaulke 
University of Wisconsin-Madison, Division of Infectious Diseases  
H6/581 CSC 
600 Highland Ave, Madison, WI 53792 
Email: iagaulke@medicine.wisc.edu  
 
Medical Monitor: 
Nasia Safdar MD, PhD  
University of Wisconsin-Madison, Division of Infectious Diseases  
UW Medicine Foundation Centennial Building 
1685 Highland Ave, Madison, WI, 53705 
Email: ns2@medicine.wisc.edu   
 
Biostatistician/Informatics: KyungMann Kim, PhD 
University of Wisconsin-Madison, Department of Biostatistics and Medical 
Informatics 
600 Highland Ave, BX4675 CSC, Madison, WI 53705 
Email: kmkim@biostat.wisc.edu 
 
Data Monitoring Committee:  Contact: Amy Siedschlag 
Data Monitoring Committee Protocol Manager 
University of Wisconsin-Madison, UW Institute for Clinical & Translational 
Research 
750 Highland Ave. 2112 Health Sciences Learning Center, Madison, WI 53705 
Email: asiedschlag@wisc.edu  
 
Study Monitoring Service: 
Contact: Tracy Ohrt 
Administrative Director, FDA Regulated Research Oversight Program 
University of Wisconsin-Madison, UW Institute for Clinical & Translational 
Research 
750 Highland Ave. 2112 Health Sciences Learning Center, Madison, WI 53705 
Email: tracy.ohrt@wisc.edu  
 
 
 
 

GRAFT Study Protocol 
 
           Nasia Safdar 
Version #: 14 
Page 13 of 48 
5. BACKGROUND AND INTRODUCTION 
This document is a protocol for a human research study. This study is to be conducted according to US and 
international standards of Good Clinical Practice (FDA Title 21 part 312 and International Conference on 
Harmonization guidelines), applicable government regulations and Institutional research policies and 
procedures.  
5.1. 
Background and Rationale 
Antibiotics have been the leading treatment for bacterial infections over several decades. Unfortunately, 
antibiotic use in healthcare has led to microbial adaptation, resulting in increasing rates of antibiotic resistant 
organisms. Clostridium difficile is resistant to many antibiotics used to treat infections and therefore 
proliferates in the intestine of the host during antibiotic treatment. Recent data suggests that C. difficile has 
replaced other antibiotic resistant organisms, such as methicillin-resistant Staphylococcus aureus, as the 
most common etiologic agent for infections in acute care facilities. Of the 2-million people in the U.S. that 
acquire serious healthcare-acquired infections each year, half a million were due to C. difficile infection (CDI), 
claiming nearly 29,000 lives within 30 days of diagnosis. Additional analyses by the National Hospital 
Discharge Survey, Annual Files, found that rates of CDI among hospitalized patients aged ≥65 years 
increased 200%. 
 
Gut microbiota disruption is fundamental to CDI pathogenesis. The gut microbiota is a symbiotic community 
of microorganisms that play an integral role in preventing pathogen colonization and infection, a feature 
termed colonization resistance. The pressures of antibiotic use in healthcare settings lead to alterations in 
native gut microbiota, resulting in loss of colonization resistance. This is especially relevant for acute care 
hospitals, where susceptible patients are exposed to heavy antibiotic pressure, diet changes, invasive 
procedures and C. difficile. The mitigation and prevention of CDI is a major challenge. Despite treatment with 
antibiotics metronidazole and vancomycin, recurrence occurs in 24 to 65% of patients. Approximately 12% 
of patients will experience an additional recurrence and 6% will experience more than two. Concurrent 
antibiotic use serves as a trigger for recurrent CDI. 
5.2. 
Hypothesis 
Specific aim 1: To demonstrate the effects of fecal microbiota transplantation (FMT) compared to placebo on 
the composition and function of the gut microbiota of hospitalized patients with recent history of CDI and who 
are currently receiving antibiotic treatment or just completed antibiotic treatment.  
 
Hypothesis: Daily or at completion oral FMT will maintain the diversity and function of the gut microbiome 
in patients receiving antibiotic treatment.  
 
Specific aim 2: To evaluate the feasibility and safety of concurrent oral FMT and antibiotic treatment in 
hospitalized patients at high risk for CDI recurrence in a phase II, randomized, controlled trial.   
 
Hypothesis: Patients will be willing to take oral FMT daily or at the completion of antibiotic treatment and 
oral FMT will be safe for these patients.  
5.3. 
Study Agent 
The oral FMT formulation DE capsules will be provided by OpenBiome. These oral FMT capsules are 
considered an IND by the FDA (IND number: PENDING). These are encapsulated fecal microbiota. Refer to 
Finch Therapeutics BBMF #17192. The fecal microbiota are human-derived microbes. The human source 
generating the fecal microbes has been extensively screened for infectious pathogens and microbiome 
mediated diseases using a standardized process (refer to OpenBiome’s BBMF#15542, Section F). 
Additionally, the capsule delivery vehicle enables targeted deposition of the investigational active 
pharmaceutical ingredient into the colon. 

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Version #: 14 
Page 14 of 48 
5.4. 
Summary of Clinical Data 
FMT-instillation of stool from a healthy donor into the intestine of a CDI patient has been shown to be an 
effective approach for the treatment of recurrent CDI. A recent randomized controlled trial of FMT in patients 
with recurrent CDI found a 90% success rate. Its efficacy is thought to be due to restoration of gut microbial 
diversity and colonization resistance. In mouse models of CDI recurrence, FMT has been shown to be highly 
effective at reestablishing colonization resistance to C. difficile by restoring bacterial community structure in 
the gut. Current guidelines recommend that FMT be reserved for patients who have had several episodes of 
recurrent CDI and have exhausted other treatment options. Because of the high risk of recurrence with 
antibiotic use and lack of effective therapies available, novel and innovative approaches to prevent CDI 
recurrence in hospitalized patients receiving antibiotics would be a major advance in the field. This is a critical 
gap that our research group strives to fill. 
 
Restoration of gut microbiota and prevention of antibiotic-associated diarrhea and CDI has been studied in 
several clinical trials using concurrent probiotics with antibiotic therapy with conflicting, although largely 
positive results. Given that FMT is comprised of entire bacterial communities rather than isolated taxa, FMT 
offers an ecological advantage. FMT, has been shown to be a highly effective and safe intervention for 
treatment of recurrent CDI. A recent systematic review and pooled analysis reports FMT was 83% effective 
in the treatment of recurrent CDI, with few reported adverse events.13 Although not fully elucidated, the 
hypothesized mechanism of FMT for CDI is that normal colonic microbiota outcompete and competitively 
exclude C. difficile.14  
 
Recently, Osman et al presented effectiveness and safety data from a 2,050 patient cohort among 
OpenBiome recipients. The data suggests that among the 42 suspected adverse events, 0 were definitely 
related to FMT material based on NIH criteria after a comprehensive investigation (Appendix 16.1).  
5.5. 
Dose Rationale, Capsule Preparation, and Administration of Study Product 
Thirty (30) DE capsules will be administered to the single dose FMT group. This dosing has been used in the 
past to successfully clear CDI. Five DE capsules or placebo will be administered to the daily groups every 
day of antibiotic treatment plus seven days post antibiotics. This dose was chosen to determine if lower doses 
of FMT treatment are effective at CDI prevention during antibiotic treatment and if they are well tolerated by 
the patient. Participants will undergo capsule administration in the following manner: 
 
1. Document review: Confirmation/review of inclusion and exclusion criteria and contraindications 
2. Safety capsules: Direct observed capsule test. Participants will ingest one inert, size 00 “safety” capsule 
under direct supervision of the study physician/nurse.  In the CRU, for the purpose of this study, the CRU 
nurse will be considered a study nurse. 
3. Dietary instructions: Patients in the one-time administration of 30 capsules group should maintain a clear 
liquid diet 8 hours prior to capsule ingestion and one hour post administration. Patients receiving the daily 
dosing should fast (clear liquids allowed) for a minimum of 2 hours prior to administration and one hour 
following administration (clear liquids allowed). 
4. Capsule administration: 
a. One-time group: Patients should ingest 30 DE capsules under the direct observation of the study 
physician/nurse. 
Daily groups: Patients should ingest 5 DE capsules under the direct observation of the study 
physician/nurse while admitted to the hospital. Following discharge, patients will take 5 DE 
capsules daily at home. Outpatients will return to the clinic for their first dose of FMT and will 
ingest the first dose (five capsules) under direct observation of a study nurse/physician. There is 
currently no published data on home administration of DE capsules; however, this method of 
administration is currently being used in several studies being conducted by OpenBiome with 
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b. Patients should ingest the capsules within 90 minutes of extraction from the freezer. Patients 
receiving FMT at home will be provided a cooler and freezer packs, a method which has been 
used in prior studies by OpenBiome, to keep the capsules in good condition. Patients in the daily 
arms of the trial should ingest the capsules upon removal from the cooler or within 90 minutes. 
These patients will be asked to record when the capsules are consumed in a monitoring chart.  
c. All patients should remain fasting (clear liquids allowed) for 1 hour following capsule ingestion 
after which they can return to a normal diet.  
5.6. 
Potential Risks and Benefits to Subjects 
There are risks associated with conducting this study; however, OpenBiome and its clinical affiliates possess 
a unique set of resources and expertise to mitigate these risks. To clarify, the risks described below are 
generalized to FMT therapies that are delivered endoscopically. There is no data available that is specific to 
FMT therapies that are delivered orally, which is the case for DE. It is expected that the risks of oral FMT 
therapy will be significantly reduced because many of the risks of FMT therapy delivered via endoscope are 
due to the procedure itself, not the drug that is delivered. 
5.6.1. 
Known Potential Risks 
In the first randomized controlled trial on FMT, mild diarrhea (94%), abdominal cramping (31%) and 
belching (19%) were observed on the day of colonoscopic infusion; however, these symptoms resolved 
within 3 hours. Of note, in follow-up, three patients who were treated with donor feces (19%) had 
constipation. No other adverse events related to the study treatment were reported. 
 
There is a paucity of data on long term follow-up related to FMT. Brandt et al. conducted a retrospective 
multi-center study (n=77) with a follow up varying between 3 to 68 months and reported 7 deaths. 
However, none were related to FMT.37 A recent systematic review on the safety of FMT suggests there 
are risks including: infection (fever, bacteremia), autoimmune disease (peripheral neuropathy, Sjogren’s 
syndrome, idiopathic thrombocytopenic purpura and rheumatoid arthritis, inflammatory bowel disease 
flare among patients with ulcerative colitis) and other studies have suggested a link to metabolic 
syndrome. However, comprehensive screening of donors should decrease any potential future risk. 
OpenBiome donors are highly selected with only 2.8% of candidate donors qualifying to donate after 
screening both infectious disease and microbiome-mediated disease (Appendix 16.3). 
 
While there is the potential for additional risks associated with FMT treatment due to the nature of 
capsules, OpenBiome donors are highly screened before selection to ensure safety. OpenBiome donors 
undergo a rigorous clinical evaluation with an internal medicine specialist as well as a wide range of 
screenings for infectious pathogens.  
5.6.2. 
Protection Against Risks 
To minimize risks, we will monitor all patients for fever and other signs of infection. All patients will have 
the phone number for the medical monitor to report any side effects. Subjects will be instructed to seek 
medical care emergency care if severe illness develops. If it is determined that a subject has a clinical 
infection due to the FMT, as determined by culture and strain-typing, standard medical care will be 
provided to the subject. 
5.6.3. 
Potential Benefits to the Subjects 
The potential benefit to the subjects is prevention of recurrent CDI. This benefit will only apply to the 
subjects receiving the FMT. If this study is able to demonstrate oral FMT is able to prevent recurrent CDI 
in patients at risk for CDI due to current antibiotic treatment, the community at large will benefit by gaining 
a preventative treatment for C. difficile. Additionally, the identification of a non-antibiotic treatment for 
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Additionally, a number of case reports have reported decolonization of antibiotic resistant bacteria 
following FMT, including carbapenem-resistant Enterobacteraciae (CRE), extended spectrum beta-
lactamase (ESBL)-producing Escherichia coli and methicillin-resistant Staphylococcus aureus (MRSA) 
enteritis.23-29 Participants enrolled in this study who have received an FMT may benefit from close health 
surveillance at follow up consultations in comparison to non-participants. 
5.6.4. 
Risk Minimization 
As stated in section 5.6.2, we will ensure patients know the signs of infection and know who to contact if 
they develop an illness during the study period. Additionally, we will administer the capsules under direct 
supervision while the patient is in the hospital. Subjects’ tolerance for consuming capsules will be 
established at enrollment visit by giving them an inert size 00 capsule. 
6. STUDY OBJECTIVES AND PURPOSE 
The goal of this study is to assess the effect of daily oral FMT and a single dose FMT on the gut microbiota in 
patients currently undergoing antibiotic treatment.  
 
Primary Objective: To assess the efficacy of oral FMT on the composition and function of the gut 
microbiota compared to the placebo groups. 
 
Secondary Objective: To assess the safety and feasibility of both oral FMT regimens versus placebo. 
 
Secondary Objective: To determine the rate of CDI during oral FMT versus placebo. 
 
Secondary Objective: To determine the rate of C. difficile colonization during oral FMT compared to 
placebo. 
 
Secondary Objective: To evaluate time to CDI and/or colonization with C. difficile. 
7. STUDY DESIGN AND ENDPOINTS 
7.1. 
General Design 
This is a phase II, double-blind, randomized, placebo controlled trial assessing the effects of either daily 
(group 1) or one-time (group 2) oral FMT on the composition and function of the gut microbiome compared 
to placebo (group 3) in a population of patients with a history of CDI currently on antibiotics for a reason other 
than current CDI. Participants will be 18 years of age or older, have 72 hours or less of an antibiotic and meet 
all inclusion criteria while having no exclusion criteria prior to randomization. Patients will be randomized at 
a 1:1:1 ratio using permuted blocks (block size=10). Randomization will be double-blinded. Each subject 
(n=30) will be followed for 6 months. Stool samples will be taken at baseline and every 3 days ± 1 day from 
all subjects regardless of treatment group while the patient is hospitalized. If/when a patient is discharged 
from the hospital, the patient will continue to provide stool samples every three days during FMT. Following 
completion of the FMT intervention, the patient will provide stool samples once weekly for the 1 month follow-
up period. All patients will be asked to complete a patient diary to report diarrhea history.  
 
Up to one gram of stool will be sent to Finch therapeutics for additional 16s rRNA sequencing.  
 
Intervention: There are 2 intervention groups for this study. Both groups will receive oral FMT capsules from 
OpenBiome for the prevention of CDI during antibiotic treatment. All patients will fast (clear liquids only) for 
a minimum of 2 hours prior to administration and 1-hour post-administration for the daily groups and be 
fasting for 8 hours prior and 1 hour post FMT consumption for the single dose group. The capsules will be 
administered in the patient’s room while admitted or in the ID clinic or CRU if the patient is an outpatient and 
the first dose will occur under direct observation. Patients admitted to the hospital as well as all patients in 
the single dose group will be observed for 30 minutes post-administration to ensure the capsules are safely 
consumed. Hospitalized patients need to be observed 30-minutes post-administration following only the first 
dose.  As mentioned above, the oral FMT capsules will be administered in two ways: 
 
Group 1: This group will receive daily oral FMT capsules. Five capsules will be administered each day of the 

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patient’s antibiotic treatment plus seven days post-antibiotic treatment.  
 
Group 2: This group will receive 30 oral FMT capsules one time 48-72 hours following completion of antibiotic 
treatment.  
 
Oral FMT capsules: Capsules contain fecal microbiota sourced from healthy donors and screened for 
pathogens.  
 
Control: The control is an oral placebo capsule identical to the FMT capsules given to the intervention groups 
and will be provided by OpenBiome. The placebo capsule consists of glycerol and saline and will be 
administered daily as five capsules per day during the duration of antibiotic treatment plus an additional 
seven days post-antibiotic treatment (group 3). Patients will be fasting (clear liquids allowed) for at least 2 
hours prior to administration and at a minimum of 1-hr post-administration (Appendix 17.1)  
7.2. 
Study Outcome Measures 
7.2.1. 
Primary Study Outcome Measures 
The primary outcome of the study is the microbial composition and function of the gut following oral FMT 
treatment during concurrent antibiotic treatment. Microbial composition of the stool will be assessed using 
16s rRNA targeted amplicon sequencing at baseline, every three days (1 day) during hospitalization 
and during the intervention, and weekly for one month following completion of the FMT intervention. At 
the same time points, function of the gut microbiome will be assessed using shotgun metagenomics. 
7.2.2. 
Secondary Study Outcome Measures 
1. Safety and feasibility. Safety endpoints are described in 7.2.3. For feasibility, are patients willing 
and able to take both daily oral FMT capsules or the one day FMT treatment? What are 
recruitment and retention rates for each group?  
2. Recurrence of CDI: Does the patient develop a CDI during the course of the study, assessed 
through clinical symptoms and PCR for the C. difficile toxin in the stool samples collected as 
described in 7.2.1? If the patient develops a CDI during the study period, what is the time (in days) 
from randomization into the study to the CDI? 
3. C. difficile colonization: Is the patient colonized or do they become colonized with C. difficile at 
any point during the study? C. difficile colonization will be detected by the presence of C. difficile 
via PCR. If the patient becomes colonized, what is the time (in days) from randomization into the 
study to colonization? 
7.2.3. 
Primary Safety Outcome Measures 
1. Proportion of participants with an adverse event (AE) occurring during any point of the study 
following randomization. 
2. Proportion of participants with a severe adverse event (SAE) occurring during any point of the 
study following randomization.   
3. Proportion of participants with newly acquired transmissible infectious diseases which are 
considered adverse events of special interest (AESI) after randomization. 
8. STUDY SUBJECTS – ENROLLMENT AND WITHDRAWAL 
8.1. 
Subject Population 
We plan to enroll 30 subjects, 10 subjects per group, with the goal of having eight analyzable subjects who 
complete trial in each group. Children under 18 years of age will not be included in this study due to the 
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meet inclusion criteria and have no exclusion criteria prior to randomization (described below). We expect 
the study population to be predominantly Caucasian due to the demographics of Dane County. We expect 
roughly 14% of the subjects to be minorities and half the subjects to be female. There are no study restrictions 
based on gender or race/ethnicity. Subjects will be patients at the University of Wisconsin Hospitals and 
Clinics (UWHC). Two groups of subjects from UWHC will be included in this study, inpatients and/or 
outpatients. Both study populations will have had a CDI within the last 90 days and are on an antibiotic for 
an unrelated reason and meeting all additional inclusion criteria listed in section 8.2. Both inpatients and 
outpatients will be identified through medical record review. Inpatients will always be contacted in a clinical 
setting while outpatients may be contacted by either mail/phone or in the clinic. Outpatients are included in 
this study as many infections treated with antibiotics are not severe enough to require hospitalization. 
8.2. 
Inclusion Criteria 
1. Cognitively intact and willing to provide informed consent. 
2. Willing and able to comply with all study procedures for the duration of the study. 
3. Able to take oral medications. 
4. Age 18 or over. 
5. Recent CDI episode occurring in the last 90 days with completion of therapy as confirmed by the 
electronic medical record (EMR) 
6. Receiving antibiotics at enrollment for reasons other than CDI and having taken the antibiotics for 
no longer than 72 hours. 
7. Women of childbearing potential in a sexual relationship with men must use an acceptable method 
of contraception (including, but not limited to, barriers with additional spermicidal foam or jelly, 
intrauterine devices, hormonal contraception started at least 30 days before enrollment into the 
study, or intercourse with men who underwent a vasectomy) for 4 weeks following completion of 
the study treatment.  
8. Males must agree to avoid impregnation of women during and for 4 weeks following completion 
of the study treatment.  
9. Able to take the test capsule successfully with no signs or symptoms of dysphagia.* 
*For patients not receiving treatment during the enrollment visit, the ability to successfully swallow 
the test capsule can be confirmed the day the intervention is administered. 
8.3. 
Exclusion Criteria 
1. Admitted to an intensive care unit (ICU). 
2. Females who are pregnant, lactating, or planning to become pregnant during the study. Female 
patients of childbearing potential will take a pregnancy test at the intervention visit and will be 
excluded if pregnant.  
3. Inability (e.g. dysphagia) to or unwilling to swallow capsules. 
4. Known or suspected toxic megacolon and/or known small bowel ileus.  
5. Bowel obstruction or other gut motility issues occurring in the last two weeks that are unresolved 
as noted by the patient or in the EMR. 
6. Major gastrointestinal surgery (e.g. significant bowel resection) within 3 months before enrollment 
not including appendectomy or cholecystectomy. 
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8. Concurrent intensive induction chemotherapy, radiation therapy, or biologic treatment for an 
active malignancy. Patients on maintenance chemotherapy may be enrolled after consultation 
with the medical monitor.  
9. Expected life expectancy <6 months. 
10. Patients with severe anaphylactic or anaphylactoid food allergy. 
11. Solid organ transplant recipients 90 days post-transplant or on active treatment for rejection. 
12. Neutropenia ( 500 neutrophils/mL) or other severe immunosuppression. Anti-TNF will be 
permitted. Patients on monoclonal antibodies to B and T cells, glucocorticoids, antimetabolites 
(azathioprine, 6-mercaptoputine, methotrexate), calcineurin inhibitors (tacrolimus, cyclosporine), 
and mycophenolate mofetil may only be enrolled after consultation with the medical monitor.*  
13. At risk of CMV/EBV associated disease, negative IgG testing for cytomegalovirus (CMV) or 
Epstein Barr Virus (EBV). 
14. Any other gastrointestinal illness including diarrhea. 
15. On oral vancomycin or metronidazole. 
16. Having been taking the currently prescribed antibiotic for over 72 hours. 
17. On an antibiotic treatment anticipated to exceed 19 days.  
18. Having received an FMT by any route in the 90 days prior to enrollment. 
19. Any condition that would jeopardize the safety or rights of the patient, would make it unlikely for 
the patient to complete the study, or would confound the results of the study. 
 
*Patients enrolled into the trial do not need to be checked for neutropenia.  When considering whether 
a patient meets inclusion/exclusion criteria, conditions commonly causing neutropenia should be only 
enrolled at the discretion of the medical monitor.  Such conditions include, but are not limited to, 
chemotherapy, chronic idiopathic neutropenia, Kostmann’s syndrome, leukemia, myelofibriosis, and 
sepsis. 
8.4. 
Subject Screening and Retention 
8.4.1. 
Subject Identification 
Potential subjects will be identified by the study team who has access to a list of patients admitted to 
UWHC for infectious diseases that is updated daily. The medical monitor will screen these patients’ EMR 
to determine eligibility. Once potential subjects meeting the eligibility criteria are identified, the treatment 
team’s physician or nurse will ask the patient if he/she is interested in hearing about the study and if so, 
will introduce the research team. The patient will be invited to hear about the study and, if interested and 
meeting all eligibility criteria, participate in the study. As patients with community acquired pneumonia 
(CAP) and urinary tract infections (UTIs) are likely to be on shorter antibiotic courses, initial recruitment 
will focus on these patients. We, however, do not plan to limit to just CAP and UTI patients and will 
consider patients admitted to other non-ICU acute care units or outpatients with anticipated short courses 
(2 weeks or fewer) of antibiotic treatment. 
8.4.2. 
Recruitment and Retention 
8.4.2.1. 
Recruitment 
Adult inpatients that are on infectious control list secondary to a recent (90 day) CDI diagnosis and 
potentially meet the inclusion criteria will be invited to join the study. If patients have been discharged 
before recruitment, we will utilize the ‘mailed letter option’ signed by the study PI with clear study 
descriptions to reach them and schedule a day/time for a phone screening. We will follow-up this 

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letter with up to three phone calls. If the subject does not respond to the letter or any calls, they will 
be considered not interested in the study.  
 
If the study team identifies an outpatient through screening that has not previously been contacted 
and appears to be potentially eligible a study team member will cold call them (using specific 
telephone script) to assess their interest in the study without mailing a letter first due to the 72-hour 
enrollment window.  If they are interested and meet inclusion criteria they will be invited to a clinic 
visit for further screening and possible study enrollment.  
 
Potentially eligible patients will also be recruited from ambulatory settings. Clinic providers will be 
given information on the study and eligibility criteria in order to assess the patient’s interest in the 
study.  Interested patients will be contacted by a study team member to further discuss the study and 
meet for the enrollment visit if indicated. Inpatients who have a diagnosis of CDI within the past 90 
days will be approached by the study team to introduce the study and provide contact information for 
the study should the patients be prescribed antibiotics not targeting CDI.  
 
The mailed letter option may also be utilized for those with known CDI within the past 90 days to alert 
them to the study with contact information should they be prescribed antibiotics and be interested in 
joining the study. One method research teams will use to identify potentially eligible patients from 
ambulatory settings is through viewing schedules of clinics that have a high percentage of potential 
subjects. These include Infectious Disease, Transplant and Primary Care clinics, and may expand as 
other focus areas are identified. Patients from these clinic lists will be prescreened for eligibility and 
approached as previously described. This prescreening process will help ensure only patients who 
are likely to meet eligibility criteria are approached. 
 
If available, software (ex: Clinithink) may be used as screening aids provided they meet standards 
for data confidentiality as outlined in the protocol and IRB approval is obtained. 
8.4.2.2. 
Retention 
Stool samples will be taken from all subjects at baseline and every 3 days ± 1 day regardless of 
treatment group while the patient is hospitalized. If/when a patient is discharged from the hospital, 
the patient will continue to provide stool samples every three days during FMT and once weekly for 
4 weeks following FMT. We will call or email the patient weekly  until they have completed FMT and 
once weekly during follow-up to remind him/her to mail us a stool sample and discuss the patient 
diary. If the patient is receiving either the daily FMT or placebo, we will also remind him/her to be 
taking his/her capsules as well as ask him/her to count how many pills he/she currently has left for 
us. If a patient in the one-time FMT group is discharged prior to the FMT consumption time point (48-
72 hours post antibiotic treatment completion), he/she will be asked to return to the ID clinic or CRU 
to receive his/her FMT capsules. Inpatients in the daily and placebo groups will have each dose of 5 
capsules observed by a nurse/physician during admission and will be discharged with a cooler 
containing their FMT capsules and instructed on use. Outpatients in the daily and placebo groups will 
be asked to come to the ID clinic or CRU to have their first dose observed by a nurse or physician 
and be given the remaining FMT doses to take home. After discharge, all patients will receive a study 
brochure tailored to their study arm describing all post-discharge study procedures.  
 
While we will target patients who are on antibiotic doses with a duration of less than 14 days, if a 
patient’s antibiotic regimen exceeds 14 days will be handled in the following manner: 
 
Group 1: Patients will be given the 30 capsule dose of FMT on day 16 or 17 (day 14 + 48 to 72 hours) 
of antibiotic treatment unless they meet one of the criteria for halting a patient’s participation in the 
study (13.5.2). Participants who are not withdrawn from the study will continue follow-up the same as 
other patients.  
 

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Groups 2 and 3: At 14 days of antibiotics, we will discontinue the daily FMT treatments and patients 
will move to the weekly follow-up phase of the study unless they meet one of the criteria in section 
13.5.2 in which case they will be withdrawn from the study.   
8.4.2.3. 
Subject Capacity 
We will ensure each subject’s comprehension by asking the subject to explain the basics of the study, 
including his/her role and the possible risks and benefits after we have walked through the informed 
consent with him/her. This study will not enroll patients with impaired decision-making abilities.  
8.5. 
Informed consent 
The PI will be responsible for ensuring that valid consent is obtained and documented for all subjects. 
Consent will be obtained in-person during the enrollment/baseline visit. A member of the treatment team will 
introduce the research team and obtain permission from the potential subjects to discuss the study and 
provide information. During the enrollment visit, the research team member will explain the relevant aspects 
of the study (purpose, relevance, disclosure of risks and benefits) and the subject’s role in the study.  
8.5.1. 
Process of Consent 
The written consent document will embody the elements of informed consent as described in the 
Declaration of Helsinki and will adhere to the ICH Harmonised Tripartite Guideline for Good Clinical 
Practice.  Informed consent will be conducted before any protocol-specified procedures or interventions 
are carried out. Informed consent will be obtained in accordance with 21 CFR 50.25 and 45 CFR 46. 
Information will be presented both orally and in written form. 
 
An investigator or designee will describe the protocol to potential participants in person. The Participant 
Information and Consent Form may be read to the participants, but, in any event, the investigator shall 
give the participants ample opportunity to inquire about details of the study and ask any questions before 
the signing and dating the consent form. 
 
Study staff must inform participants that the trial involves research, and explain the purpose of the trial, 
those aspects of the trial that are experimental, any expected benefits, all possible risks, the expected 
duration of the participant’s participation in the trial, the procedures of the research study, and the 
probability for random assignment to treatment groups. Participants will be informed they will be notified 
in a timely manner if information becomes available that may be relevant to their willingness to continue 
participation in the trial. They must also be informed of alternative procedures that may be available, and 
the important potential benefits and risks of these available alternative procedures. Participants and/or 
legal guardian must receive an explanation as to whether any compensation and any medical treatments 
are available if injury occurs, and, if so, what they consist of, or where further information may be 
obtained. Participants and/or substitute decision maker/proxy guardian must be informed of the 
anticipated financial expenses, if any, to the participant for participating in the trial, as well as any 
anticipated prorated payments, if any, to the participant for participating in the trial. They must be informed 
of whom to contact (e.g., the PI or study physician/nurse practitioner) for answers to any questions 
relating to the research project.  Information will also include the foreseeable circumstances and/or 
reasons under which the participant’s participation in the trial may be terminated. The participants and/or 
substitute decision maker/proxy must be informed that participation is voluntary and that they are free to 
withdraw from the study for any reason at any time without penalty or loss of benefits to which the 
participant is otherwise entitled. 
 
Neither the investigators, nor the trial staff, will coerce or unduly influence a participant to participate or 
continue to participate in the trial. The extent of the confidentiality of the participants’ records must be 
defined, and participants must be informed that applicable data protection legislation will be followed. 
Participants and/or substitute decision maker/proxy must be informed that the monitor(s), auditors(s), 
IRB and regulatory authority(ies) will be granted direct access to the participant’s medical records for 

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verification of clinical trial procedures and/or data without violating the confidentiality of the participant, to 
the extent permitted by the applicable laws and regulations, and that, by signing a written informed 
consent form, the participant is authorizing such access.  Participants and/or substitute decision 
maker/proxy must be informed that records identifying the participant will be kept confidential, and, to the 
extent permitted by the applicable laws and/or regulations, will not be made publicly available and, if the 
results of the trial are published, the participant’s identity will remain confidential. 
 
Consent forms are in a language fully comprehensible to the prospective participants. Informed consent 
will be documented by the use of a written consent form approved by the IRB and signed and dated by 
the participant or substitute decision maker/proxy and the person who conducted the informed consent 
discussion. The signature confirms that the consent is based on information that has been provided and 
all questions have been answered to the prospective participant’s satisfaction. Each participant’s signed 
informed consent form must be kept on file by the investigator for possible inspection by Regulatory 
Authorities and/or the sponsor and Regulatory Compliance persons. The participant should receive a 
copy of the signed and dated written informed consent form and any other written information provided 
to the participants, and should receive copies of any signed and dated consent form updates and any 
amendments to the written information provided to participants. 
8.5.2. 
Consent Form 
The consent form can be found in the supporting documents. 
8.5.3. 
Future Use of Stored Specimens 
Any leftover stool specimens will be stored and may be used for future research, under a future protocol, 
to learn more about DE. These specimens will be stored indefinitely after the study is completed. In the 
informed consent document, participants will be given an opportunity to choose whether or not their 
specimens are stored for future use. For participants who choose not to allow storage of their samples 
for future use, these samples will be destroyed at the end of the study. Data collected during the trial will 
be coded and stored on secure servers for future research as well. Stored specimens will be provided a 
unique coded identifier and only Dr. Safdar’s research team will be allowed access to the linking data. 
Any specimens shared with other researchers are to be coded and no linking information shared.  
 
There are no benefits to participants in the collection, storage and subsequent research use of 
specimens. Reports about future research done with participant’s samples will NOT be kept in their health 
records, but participant’s samples may be kept with the study records or in other secure areas. 
Participants can decide if they want their samples to be used for future research or have their samples 
destroyed at the end of the study. A participant’s decision can be changed at any time before the end of 
the study by notifying the study doctors or nurses in writing. However, if a participant consents to future 
use and some of their stool has already been used for research purposes, the information from that 
research may still be used. If a participant decides they no longer want their specimens stored following 
the completion of the study, the research team will identify their specimens and destroy them. Any 
specimens already used for other research purposed or shared with other researchers may still be used. 
 
Up to one gram of stool will be sent to Finch therapeutics for additional analysis. Samples will be de-
identified.  
 
8.5.4. 
HIPAA 
Information about study subjects will be kept confidential and managed according to the requirements of 
the Health Insurance Portability and Accountability Act of 1996 (HIPAA). As part of our consent form is a 
signed subject authorization form. 
 
The HIPAA identifiers that will be collected for this study include: 

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 
The subjects name 
 
Race 
 
Birthdate 
 
Medical record number 
8.5.5. 
Revoking Consent 
In the event a subject revokes authorization to collect or use PHI, the investigator, by regulation, retains 
the ability to use all information collected prior to the revocation of subject authorization.  For subjects 
that have revoked authorization to collect or use PHI, the research will ask permission to at least collect 
a final stool sample and/or ask final questions regarding the main outcomes of the study.  
8.5.6. 
Costs to the Subject 
The subject will incur no additional costs to their care by being in this study. 
8.5.7. 
Payment to the Subjects 
The subjects will be paid $50.00 upon completion of the study.  
8.5.8. 
Exclusion of Women, Minorities, and Children (Special Populations) 
Children are excluded for safety reasons.  
8.6. 
Early Withdrawals of Subjects 
8.6.1. 
Premature Termination of the Study 
In the unlikely event that significant safety concerns arise, the principal investigator can terminate or halt 
the study pending review by the DMC. In addition, this study may be halted early based on the DMC 
charter or FDA recommendations. If the study is prematurely terminated or suspended, the PI will 
promptly inform the IRB and will provide the reason(s) for the termination or suspension.  
 
Circumstances that may warrant termination or suspension include, but are not limited to:  
 
Determination of unexpected, significant, or unacceptable risk to participants  
 
Demonstration of efficacy that would warrant stopping  
 
Insufficient compliance to protocol requirements  
 
Data that are not sufficiently complete and/or evaluable  
 
Determination of futility  
 
Study may resume once concerns about safety, protocol compliance, or data quality are addressed and 
satisfy the sponsor, IRB, DMC, and/or FDA. 
8.6.2. 
When and How to Withdraw Subjects 
All subjects will be informed during consent that consent is voluntary and they may discontinue 
participation at any time. If a subject wishes to withdraw from the study, we will ask him/her to contact 
the study coordinator whose number will be in the enrollment materials.  
8.6.2.1. 
Data Collection and Follow-up for Withdrawn Subjects 
If the subject is willing, the coordinator will ask to schedule a close-out study visit to collect a final 
stool sample and follow-up safety evaluation. 
 
A subject may withdraw from the study at any time for any reason with no consequences. A participant  

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may be withdrawn from the study by the Investigator for the following reasons: 
 
Adverse event that may make it no longer in the best interest of the subject to continue to 
participate  
 
Recurrent C.diff infection 
 
Participant’s choice 
 
Protocol violation/ non-compliance 
 
Pregnancy 
 
Lost to follow-up  
 
Other (must be noted) 
 
The primary reason for withdrawal from the study will be recorded. Participants will be encouraged to 
complete the Early Termination Visit.  The Early Termination Visit procedures are listed in Section 
11.4.  Although participants are free to withdraw at any time, subjects will be encouraged to remain 
in the study for follow-up safety evaluation.  Every  attempt  should  be  made  to  follow  all  AEs  and  
SAEs  ongoing  at  the  time  of  early withdrawal  to  resolution  or  until  stabilized.  If  possible,  a  
final  stool  sample  will  be  collected  at the time of  Early Termination.  All subjects who are 
randomized will be included in the safety analysis.  
8.7. 
Participant Confidentiality 
Participant confidentiality is held strictly in trust by the PI, his/her staff, and his/her agents. This confidentiality 
is extended to cover testing of biological samples in addition to the clinical information relating to participating 
participants. 
 
The study protocol, documentation, data, and all other information generated will be held in strict confidence. 
No information concerning the study or the data will be released to any unauthorized third party without prior 
written approval from the PI. 
 
The PI or delegate and the FDA may inspect all documents and records required including, but not limited 
to, medical records (office, clinic, or hospital) and pharmacy records for the participants in this study. 
9. STUDY AGENT 
9.1. 
Description and Formulation 
DE is encapsulated fecal microbiota sourced from human-derived microbes. The human source generating 
the fecal microbes has been extensively screened for infectious pathogens and microbiome mediated 
diseases using a standardized process (found in OpenBiome’s BBMF # 15543, Section F). Additionally, the 
capsule delivery vehicle enables targeted deposition of the investigational active pharmaceutical ingredient 
into the colon.  
 
DE capsules: The OpenBiome FMT Capsule DE contains frozen human fecal microbiota filtered to 330 
microns, theobroma oil, glycerol, hide bovine gelatin, sodium lauryl sulfate, colorants FD&C, and titanium 
dioxide. The material is contained in a two capsule system: an interior gelatin capsule that houses the drug 
substance, and an exterior acid-resistant capsule for delivery of the drug substance past the stomach. The 
product should be stored at -20°C to -80°C. Product expires 6 months after freezing if stored at -20°C. 
 
Placebo capsules: Placebo capsules will be identical in appearance to DE capsules but will not have human 
feces, the active pharmaceutical ingredient. The placebo capsules are filled with Sodium Chloride (0.9%, 
USP), Glycerol (12.5%, USP) and deionized water to the previously stated volume specification. Capsules 
are stored frozen at -80°C before dispensing to local site storage. Placebo will be administered the same as 
the daily arm of the trial. 

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9.2. 
Packaging and Dissemination 
OpenBiome will package the placebo and FMT capsules at their facility. Packaging will be identical and 
consist of the same saline and glycerol buffer used in FMT processing without the addition of stool. The 
capsules will be sent to the UW Pharmaceutical Research Center (PRC) to be dispensed.  
 
An inventory will be performed and a drug receipt log filled out and signed by the person accepting the 
shipment.  The designated study staff will count and verify that the shipment contains all the items noted in 
the shipment inventory. Any damaged or unusable study drug in a given shipment (active drug or comparator) 
will be documented in the study files. 
 
The site principal investigator (PI) (or designee) will maintain an accurate record of the receipt of the 
investigational materials as shipped by OpenBiome, including the date received. One copy of this receipt will 
be returned to OpenBiome when the contents of the investigational materials shipment have been verified. 
In addition, the unblinded laboratory technician based at the PRC will maintain a log of all clinical trial 
materials (DE and placebo) dispensed. This clinical trial material accountability record will be available for 
inspection at any time. 
9.3. 
Preparation, Administration and Storage of Study Drug 
Produced material will be stored at -80°C and each unit will have a date of production printed on it for tracking 
purposes. Studies have been conducted to ensure long-term bacterial viability following the freezing process 
based on studies conducted by Hamilton et al. and Youngster et al.40,41 Local site storage at -20°C will be 
permitted for up to 6 months. Discharged patients will be provided with a kit and instructions on proper at-
home storage. 
9.4. 
Route of Administration 
Participants will undergo administration: 
1. Document Review: Confirmation/review of exclusion criteria/contraindications as previously 
described at baseline. 
2. Safety Capsules: Direct observed capsule test, where participants will ingest one inert, size 00 
‘safety’ capsule under direct supervision of the study physician/nurse. 
3. Dietary instructions: Patients should fast (clear liquids allowed) for a minimum of 2 hours prior to 
administration.  
4. Capsule administration:  
a. Patient should ingest the capsules of either FMT or placebo (5 capsules daily or a one-time 
dose of 30 capsules depending on treatment group) under the direct observation of a physician/ 
nurse while they are admitted.  
b. Patient should ingest capsules after extraction from freezer, and no longer than 90 minutes after 
removal. 
c. Patients should remain fasting (clear liquids allowed) for 1 hour following ingestion but may then 
return to a full diet. 
9.5. 
Prior and Concomitant Therapy/ Standard of Care 
We will collect the following information on the patients care during their stay: 
 
Current medication list 
 
Antibiotic they are on and dose 
 
Vital signs at baseline and discharge (taken from medical record): temperature, height, weight, 
heart rate, blood pressure, O2 saturation if on chronic oxygen therapy. 
 
Overall assessment of current health 

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9.6. 
Randomization and Blinding of Study Drug 
Participants meeting the eligibility criteria and willing to consent to the study procedures will be randomized 
on a 1:1:1 basis with block sizes of 10 to receive one of the following treatments: 
1. Daily FMT treatment with 5 capsules/day 
2. One-time FMT treatment of 30 capsules 
3. Daily placebo (5 capsules/day) 
Randomization will be carried out by the UW PRC so that the research team and treatment team remains 
blinded to whether the patient is receiving FMT or placebo. 
9.7. 
Accountability Procedures for the Study Intervention/Investigational Product 
The site principal investigator (PI) (or designee) will maintain an accurate record of the receipt of the 
investigational materials as shipped, including the date received. One copy of this receipt will be returned to 
OpenBiome when the contents of the investigational materials shipment have been verified. In addition, the 
unblinded laboratory technician based at OpenBiome will maintain a log of all clinical trial materials (DE and 
placebo) dispensed. This clinical trial material accountability record will be available for inspection at any 
time.  
 
Participants in the daily FMT or placebo groups will be given a diary to record when doses are taken and 
number of doses remaining.  This diary will be collected after participants complete the treatment portion of 
the study.  Study staff will attempt to collect any remaining study capsules from the participants in person or 
via mail as appropriate, and this accountability will be reviewed by the Infectious Disease Research Lab. 
 
9.8. 
Modification of Study Intervention/Investigational Product for a Participant 
If the participant is unable to complete the full dose of DE or placebo in one sitting the actual dose ingested 
will be recorded. Further study product administration, including the remainder of the incomplete dose and 
scheduled upcoming doses as applicable will be at the discretion of the treating physician. The remaining 
capsules scheduled to be administered may be offered to the participant on the same day they were 
scheduled. Intention-to-treat analysis will be utilized according to best practices in clinical trials. 
9.9. 
Concomitant Medications/Treatments 
Given our patient population is likely to have multiple comorbidities, all medications except those listed in the 
exclusion criteria will be accepted in this study, at the discretion of the treating physician. Though the 
exclusion criteria lists antibiotics used for more than 72 hours as an exclusionary medication, patients on 
long-term antibiotics – such as prophylactic Bactrim, azithromycin, or doxycycline – are eligible at the 
discretion of the study physician.  This includes, but is not limited to: 
1. Long-term antibiotics (one month or more, e.g. prophylactic Bactrim, azithromycin, or doxycycline) 
2. Anti-hypertensive therapies  
3. Heart failure medications 
4. Diuretics 
5. Laxatives 
6. Topical medications 
7. Anti-depressants 
8. Statins 
9. Diabetic medication 

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10. Non-steroidal Anti-inflammatory Drug (NSAID) 
11. Acid-blockers 
12. Anticoagulants 
13. Opioids 
14. Iron supplementation 
15. Anti-TNF will be permitted. Patients on monoclonal antibodies to B and T cells, glucocorticoids, 
antimetabolites 
(azathioprine, 
6-mercaptopurine, 
methotrexate), 
calcineurin 
inhibitors 
(tacrolimus, cyclosporine) and mycophenolate mofetil may be enrolled only after consultation with 
the medical monitor. 
10. LABS 
Tests will not be done in a CLIA-certified lab. Samples will be collected from the patient and brought to the lab 
while the subject is admitted. After discharge, the subject will mail the samples to the laboratory for processing. 
Samples will be labeled with only an ID number. We will not disclose any results to the patients. Data generated 
by the laboratory procedures will be used to determine the patient’s colonization status with MDROs and C. 
difficile at baseline and to determine if colonization status changes during the course of the trial.  
 
Laboratory procedures include: 
 
Bacterial DNA isolation from stool 
 
16s rRNA sequencing of the v4 region 
 
Culture to identify MDROs, including but not limited to: MRSA, Vancomycin-resistant enterococcus 
(VRE), and C. difficile 
 
Polymerase Chain Reaction (PCR) 
 
Data from laboratory procedures will also be used to determine if the FMT treatment has an impact on the 
patients gut microbiome. All stool remaining following the completion of laboratory procedures will be stored at -
80C and labeled with the sample ID and held for future analysis.  
 
Up to one gram of stool will be sent to Finch therapeutics for additional 16s rRNA sequencing.  
11. STUDY VISITS 
11.1. Screening/Enrollment, and Baseline Visit 
For some patients the screening, enrollment, and baseline visit should occur on the same day. However, the 
enrollment and baseline visit may be at a later time (though it must still be within the first 3 doses of the 
prescribed antibiotic window) if needed to meet the patient’s needs. 
 
Screening: Will take place in a clinical setting 
Active screening. Any inpatient admitted to a non-ICU unit or outpatient presenting to any UWHC clinic (with 
a focus on patients presenting with CAP and UTI) meeting the enrollment criteria will be contacted about the 
study. Patients may also be identified through letters mailed to patients with a history of CDI in the last 90 
days. 
 
Enrollment: Will take place in a clinical setting 
All patients with a history of CDI on anitbiotics for any reason other than CDI meeting the eligibility criteria 
will be eligible for enrollment. Eligibility will be confirmed during the enrollment visit.  Patients admitting with 
CAP and UTIs will be preferred. A detailed consent process will be administered by study staff who are 
trained in consenting procedures. Potential participants who fulfill the eligibility criteria will undergo a detailed 
clinical assessment by the research team which will include demographics, medical history, dietary 

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information and current medication. Data from this assessment may be from the participant/substitute 
decision maker, healthcare team and/or medical record.  
 
 
Data points at enrollment study visit: 
o 
General parameters: 
▪ Date of birth 
▪ Sex 
▪ Smoking status 
▪ Race  
▪ Ethnicity 
▪ Highest level of education 
o 
Past medical history and allergies  
▪ A focused collection of past medical history (including common infections) 
o 
Current medication list 
▪ Current antibiotic use, including dose 
o 
Dietary history 
o 
Social history 
▪ Alcohol, smoking history 
o 
Recent hospitalizations 
o 
Exposure to farm animals 
o 
Recent international travel history 
o 
Examination findings 
▪ Vital signs: temperature, height, weight, heart rate, blood pressure, O2 saturation if on chronic 
oxygen therapy.  (Vital signs measurements at all time points may be abstracted from medical 
records if available.) 
▪ Relevant review of symptoms 
o 
Overall assessment of current health 
o 
Stool consistency (Bristol Stool Scale) and frequency 
 
Sample collection 
o 
Stool sample collected using a stool collection kit/hat and provided with patient diary 
 
Formal aspects 
o 
Informed consent procedure 
o 
Verification of inclusion and exclusion criteria including administering ‘test’ capsule and documenting: 
▪ Safe to receive intervention (yes/no) 
▪ Able to swallow test capsule (yes/no) 
 
Immunocompromised patients at risk for CMV/EBV will have blood drawn for the EBV and CMV antibody test 
done by the UWHC lab. The blood draw will done by a UWHC phlebotomist or their local lab if this is preferred 
by the patient. All costs will be covered by the study. Results will be released to the patient and included in their 
medical record. 
 
Baseline (Day 0): Will take place in a clinical setting 
After the baseline clinical asssessment and stool sample have been collected, subjects in groups 1 and 3 
(daily FMT and daily placebo) are eligible to undergo adminstration of the intervention (DE or placebo) in 

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accordance with the randomization schedule. The intervention will be administered by the blinded treatment 
staff and the participant observed for 30 minutes following administration. Post-ingestion observation of 
inpatients will only occur after the first dosing; subsequent inpatient dosing will be administered by a study 
physician/nurse but do not require 30 minutes of observation. Pre-intervention vital signs (as previously 
described) will be collected or abstracted from the medical record prior to first dose. Participants will be 
provided with information regarding monitoring for minor and severe adverse event related to the intervention 
administration. Participants will be encouraged to report any concerning symptoms to staff. Oral nutrition 
may commence 1 hour post-capsules administration.  Study staff do not need to collect a blood sample to 
check for neutropenia prior to dosing. 
 
For all patients, a baseline stool sample will be collected and all patients should begin to fill out their patient 
diary starting on Day 0.  If a patient is unable to provide a stool sample, peri-rectal swabs may be collected. 
11.2. Follow-up 
Follow up will be different based on the group the patient is in.  
 
Group 1 (daily FMT) and Group 3 (daily placebo): Will occur in a clinical setting for inpatients. 
Capsules will be delivered to the patients every day by a blinded member of the treatment team during the 
time they are admitted. If the patient is discharged or an outpatient, he/she will be provided with enough 
capsules to complete the study and will be asked to consume 5 capsules per day while on antibiotics as well 
as for 7 days post-antibiotic treatment completion. Outpatients and patients discharged during the follow-up 
period will be called or emailed (depending on patient preference) weekly to remind them to take their 
capsules as well as to send in their stool samples every three days (+/- 1 day). The researcher calling the 
subject will also ask the subject to count the number of pills he or she has remaining (recorded in the patient 
diary) and ask about any adverse events or changes to medications and diet.  Study staff do not need to 
collect a blood sample to monitor for neutropenia. If the subject has any capsules remaining after completion 
of study intervention (e.g. missed doses, shortened antibiotic course after study intervention has been 
dispensed), the subject will be asked to return the remaining capsules to the Infectious Disease Research 
lab.   
 
Group 2 (single dose FMT): Visit will occur in a clinical setting 
Capsules will be delivered to the patient by a blinded member of the treatment team 48-72 hours following 
antibiotic treatment completion. If the patient is discharged he/she will be asked to return to the clinic 48-72 
hours following completion of his/her antibiotics to consume the 30 capsules under supervision of a nurse or 
physician. Study staff do not need to collect a blood sample to monitor for neutropenia.  During this visit the 
following will occur: 
 Vitals collection 
 Physical exam 
 Clinical symptoms assessment 
 Diet assessment 
 Concomitant medications 
 Stool sample 
 FMT dosing 
 Adverse events assessment  
 30 minute post-dose observation 
 
All subjects: 
All subjects will provide stool samples every three days after the baseline visit until their FMT intervention is 
complete and weekly for one month following conclusion of FMT treatment. Patients will also be asked to 
complete a patient diary daily from enrollment through the first month of follow-up. If a subject is discharged 
during the study period, he/she will be asked to complete the patient diary from home as well as provide stool 
samples to be mailed back to the lab for processing. A member of the study team will also call or email 
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as well as record any adverse events. If a patient is discharged, vital signs, general health status, and 
medications at discharge will be assessed through the medical record.  
 
At the end of the 1 month follow-up (last week of providing the weekly, post-FMT stool samples), patients will 
receive a call assessing the following: 
 
 
Clinical assessment by study nurse or physician, specifically evaluating adverse events related to the 
intervention. 
 
Data collection at visit: 
o 
Interim medical history with focus on infectious diseases  
o 
Concomitant medication 
o 
Significant changes in diet 
o 
Changes in stool consistency (Bristol Stool Scale) and frequency 
o 
General health status 
o 
Adverse events (NIH criteria)  
 
A table of all study events is provided in Appendix II, 17.2 (Study Calendar). 
11.3. Unscheduled Visits/Data Collection 
If a patient develops CDI or related serious adverse event, an unscheduled visit will take place and the patient 
will be treated with standard recurrent CDI care by the treatment team. The development of a CDI will also 
result in early termination of the patient’s study participation, and early termination procedures should be 
conducted.  Other serious adverse events will be evaluated on a case-by-case basis for continuation versus 
termination of participation. 
 
If a patient develops an infection (besides any he/she was admitted for) with a MDRO, the study team will 
track the duration of the infection. Any changes to the type of antibiotic, duration, and dosage will be noted 
as well.  
 
Data points for infectious episode: 
 
Date  
 
Preliminary diagnosis 
 
Physical exam and vital signs 
 
Changes to diet 
 
Clinical symptoms questionnaire 
 
Method of testing for pathogen and pathogen(s) identified 
 
Sites from which organism was isolated and whether clinical specimens were collected from infection site 
 
Antibiotic(s)  
o Name 
o Dosage 
o Prescribed duration 
o Final (actual) duration of antibiotics 
o Change in antibiotics regimen  
 
Concomitant medication (Name, dose, route of administration, duration) 
 
Hospital admission (yes/no) 
o Name of facility 
o Department where participant was admitted (ward / step down/ ICU) 

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o Relevant medical procedures 
 
Colonoscopy (including preparation) 
 
Intestinal surgery 
 
Dialysis 
 
Other 
 
Final diagnosis 
 
Data points collected at both the early termination and unscheduled visit only need to be recorded once to 
avoid duplication.  This may include vitals, changes to diet, etc.  
11.4. Early Termination 
In the case of an early termination, all study procedures will stop.  Study staff will attempt to collect patient 
diary and a final stool sample. The following will be assessed: 
 
Clinical assessment, including vital signs if visit is done in person 
 
Data collection 
o Changes to dietary history 
o Discharge diagnosis 
o Stool consistency and frequency 
o Changes to concomitant medications 
o Clinical symptoms 
 
Stool sample collection or peri-rectal swab (only if participant is unable to provide a stool sample at 
in-person visit) 
 
Early termination procedures may be done over the phone or in person if the early termination is occurring 
during an unscheduled visit. Participants will be asked if study staff may follow participants passively using 
the medical record if clinical follow-up and/or stool collection is not viable. 
11.5. Study End 
All subjects will be called 6 months following completion of FMT treatment. 
 
Data collected during the final study visit call: 
o 
Changes to medical history 
o 
Changes in stool consistency (Bristol Stool Scale) and frequency 
o 
Adverse events (including SAEs, NIH criteria)  
12. STUDY ANALYSIS 
12.1. Sample Size 
A total of 30 subjects – 10 per treatment group – will be recruited into this study. As this is a pilot study, 
sample size was not driven by a statistical test of hypotheses, instead it was driven by a pool of available 
patients eligible and willing to participate.   
12.2. Subject Population for Analysis 
We plan to enroll 10 patients per group with the goal of having 8 patients per group complete the treatment 
and be analyzed in the final analysis.  
12.3. Final Analytic Plan 
Categorical data will be described using descriptive statistics (proportions and percentages). Continuous 
data will be described using means and standard deviations (normally distributed data) or using medians 
and interquartile range (non-parametric data). Appropriate comparative statistical tests will be chosen based 

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in the variable types (categorical, dichotomous, continuous) and distribution (parametric, non-parametric) 
and will be used to describe significant differences between intervention and control groups. Where 
appropriate, point estimates and confidence intervals will be reported. The p-value will be two tailed with a 
significance level of 0.05. 
 
The microbiome will be assessed using 16s rRNA targeted amplicon sequencing. Sequences will be cleaned 
and binned into operational taxonomic units and assigned taxonomy. Differences within individuals will be 
assessed using the Inverse Simpsons Diversity index and comparisons between study groups will be done 
using the Bray Curtis dissimilarity matrix and visualized using principal coordinates analysis.  
12.4. Source Documents and Access to Source Data/Documents 
We will maintain appropriate medical and research records for this trial, in compliance with ICH E6 GCP, 
Section 4.9, and regulatory and institutional requirements for the protection of confidentiality of participants. 
Forms for use as source documents will be derived from the electronic CRFs. Additional source data include 
records of clinical findings, observations, or other activities in a clinical trial necessary for the reconstruction 
and evaluation of the trial. Examples of these documents and data records include, but are not limited to, 
hospital records, clinical and office charts, laboratory notes, memoranda, pharmacy dispensing records, 
recorded data from automated instruments, copies or transcriptions certified after verification as being 
accurate and complete, microfiches, photographic negatives, microfilm or magnetic media, imaging, and 
participant files and records kept at the pharmacy, laboratories, and medico-technical departments involved 
in the clinical trial. 
 
The study protocol, documentation, data, and all other information generated will be held in strict confidence. 
No information concerning the study or the data will be released to any unauthorized third party without prior 
written approval from the PI. 
 
The study monitor or other authorized representatives of the research team and FDA may inspect all 
documents and records required to be maintained by the Investigator, including, but not limited to, medical 
records (office, clinic, or hospital) and pharmacy records for the participants in this study. The clinical study 
site will permit access to such records. 
 
All samples and forms will be encoded (labeled) only with a barcode and a unique tracking number to protect 
participant’s confidentiality. 
 
Up to one gram of stool from each collected sample will be sent to Finch therapeutics for additional 16s rRNA 
sequencing. Samples sent to Finch will be de-identified.  
 
12.5. Quality Management System 
The monitoring of subjects enrolled in this study includes both internal and external activities governing the 
administration of the investigational product. Internal monitoring is performed by members of the study team 
and external monitoring by a team of staff not involved in the conduct of study procedures with the appropriate 
clinical and technical expertise. 
12.5.1. 
Study Team Training 
The PI will ensure that members of the study team are appropriately qualified and trained on the protocol, 
and/or on study procedures applicable to their delegated roles/responsibilities. When the protocol and/or 
methods to conduct study procedures are updated, staff are retrained prior to performing any study-
related activities described in the updated document. All training is documented and maintained in the 
study files. 
 

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Per University of Wisconsin-Madison policy, all personnel engaging in human subjects research must 
also complete Human Subjects Protection, Good Clinical Practice (GCP), and Health Insurance 
Portability and Accountability Act (HIPAA) training. 
12.5.2. 
Standardized Procedures 
A Manual of Procedures (MOP) has been created for this study to supplement the study protocol by 
providing additional details on the conduct of the study and study procedures. It is routinely updated to 
ensure consistent performance of study activities. 
12.5.3. 
Internal Quality Monitoring 
Members of the study team will conduct internal monitoring activities in real time when completing the 
study records and following each study visit. These activities will include, but are not limited to, periodic 
review of completed data collection forms, eligibility records, regulatory files and electronic data. Reviews 
will be performed by a different individual than those involved in data entry. 
12.5.4. 
External Quality Monitoring 
The purpose of external study monitoring is to ensure compliance with applicable regulations (21 CFR 
312 and GCP), which require monitors to verify that: 
 
The rights and well-being of human subjects are protected.  
 
Reported study data are accurate, complete, and verifiable from source documentation.  
 
The conduct of the trial is in compliance with the currently approved protocol and all applicable 
regulatory requirements. 
 
The sponsor-investigator has contracted with UW ICTR Study Monitoring Service. Refer to the ICTR 
SMS Monitoring Plan and Service Agreement for more information. The PI will provide direct access to 
all trial-related sites, source data/documents, and reports for the purpose of monitoring and auditing, and 
inspection by local and regulatory authorities. 
12.5.5. 
Database Quality Control (QC) 
QC procedures regarding data entry will be implemented. Regular data quality control checks will be run 
on the database. Any missing data or data anomalies will be assessed for clarification and resolution. 
12.6. Data Capture 
12.6.1. 
Case Report Forms 
The study case report form (CRF) is a data reporting instrument for the study.  All data requested on the 
CRF must be recorded. All missing data must be explained. All entries should be printed legibly in black 
ink. If any entry error has been made, to correct such an error, a single straight line is drawn through the 
incorrect entry and the correct data is entered above/near the correction. All such changes must be 
initialed and dated. 
12.6.2. 
Data Collection Tools 
Clinical data (including AEs, concomitant medications, and solicited events data) and clinical laboratory 
data will be entered into a secure, web-based Research Electronic Data Capture (REDCap) system. The 
data system includes password protection and internal quality checks, such as automatic range checks, 
to identify data that appear inconsistent, incomplete, or inaccurate. Clinical data will be entered directly 
from the source documents.  
12.7. Records Retention 
Study files (except for future use consent forms) must be maintained for a minimum of two years after the 

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last approval of a marketing application in an ICH region and until there are no pending or contemplated 
marketing applications in an ICH region or at least 2 years have elapsed since the formal discontinuation of 
clinical development of the investigational product. These documents should be retained for a longer period, 
however, if required by local regulations. No records will be destroyed without the written consent of the lead 
PI or designate, if applicable. It is the responsibility of the lead PI or designate to inform the site PIs when 
these documents no longer need to be retained. Consent forms for future use will be maintained as long as 
the sample exists. 
13. ASSESSMENT OF SAFETY 
Safety will be assessed by the frequency and severity of adverse events (AE).  
13.1. Specifications of Safety Parameters 
13.1.1. 
Definition of Adverse Events (AE) 
Adverse events (AEs) will be recorded at administration of the treatment and during phone calls once the 
patient is discharged, in the study patient record (source document) as well as on a specific AE case 
report form (CRF). 
 
An AE is any untoward medical occurrence in a study patient or clinical investigation participant 
administered a pharmaceutical product. An AE does not necessarily have a causal relationship with this 
treatment. An AE can therefore be any unfavorable and unintended sign, symptom, or disease temporally 
associated with the use of a medicinal product, whether or not related to the medicinal product, e.g.: 
 
any new clinical diagnosis 
 
any symptom that requires medical clarification or leads to in-patient admission (surgery or 
accident) 
 
any suspected adverse drug reaction (ADR) 
 
any symptom, such as fever, that appears on the study patient’s medical records 
 
any event related in time with the application of the study medication and affecting the health of 
the study patient (including laboratory value changes) 
 
For the purposes of this study, baseline symptoms will be collected prior to the administration of study 
intervention. Only those symptoms identified as new or worsened compared to the baseline assessment 
will be recorded as an AE. In addition, only those abnormal laboratory values or physical examination 
assessments that are considered clinically significant will be recorded in the study documents.  
 
If there is any doubt as to whether a clinical observation is an AE, the event will be recorded and assessed 
by the study medical monitor. AEs must be graded for severity and relationship to study product. Adverse 
events of special interest (AESI) will be defined as newly acquired transmissible infectious diseases. 
13.1.2. 
Definition of Serious Adverse Events (SAE) 
An adverse event or suspected adverse reaction is considered “serious” if, in the view of the PI, it results 
in any of the following outcomes: 
 
Death 
 
Life-threatening adverse event* 
 
Inpatient hospitalization or prolongation of existing hospitalization 
o Subjects might be admitted to an inpatient unit to be eligible for the study; in these cases 
the initial hospitalization will not be considered an SAE in and of itself, rather it will only be 
considered an SAE if the planned hospitalization is prolonged 
 
A congenital anomaly/birth defect 

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 
Persistent or significant disability or incapacity or substantial disruption of the ability to conduct 
normal life function 
 
Important medical events that may not result in death, be life-threatening, or require 
hospitalization may be considered when, based upon appropriate medical judgement, they may 
jeopardize the patient or subject and may require medical or surgical intervention to prevent one 
of the outcomes listed in this definition 
 
*Life-threatening adverse event.  An adverse event is considered “life-threatening” if, in the view of the 
PI, its occurrence places the patient or participant at immediate risk of death. It does not include an 
adverse event which, had it occurred in a more severe form, might have caused death. 
 
Any adverse event or suspected adverse reaction that meets the criteria for serious adverse event will 
be:  
 
recorded on the appropriate SAE CRF 
 
followed through resolution by a study clinician or up to 30 days post-treatment, whichever comes 
first 
 
reviewed and evaluated by a study clinician 
13.1.3. 
Definition of Unanticipated Problems (UP) 
On enrollment in the study, the study participants will be instructed to contact the medical monitor if an 
AE occurs. Patients will be given a patient diary with date, details and action taken to help with data 
collection. This diary will be taken to the site PI for evaluation if needed and patients instructed to seek 
immediate medical attention if indicated. 
13.2. Classification of an Adverse Event 
13.2.1. 
NIH Grading of Severity of Events 
AEs will be assessed by the clinician using the NIH Common Terminology Criteria for Adverse Events 
(CTCAE) defined grading system (Appendix 17.3). Briefly, the criteria for estimating adverse event 
severity grade:  
 
Grade 1, Mild: Asymptomatic or mild symptoms; clinical or diagnostic observations only; 
intervention not indicated. 
 
Grade 2, Moderate: Minimal, local or noninvasive intervention indicated; limiting age-appropriate 
instrumental activities of daily living (ADL). 
 
Grade 3, Severe: Severe or medically significant but not immediately life-threatening; 
hospitalization or prolongation of hospitalization indicated; disabling; limiting self-care ADL. 
 
Grade 4, Life threatening: Places the patient or subject at immediate risk of death. It does not 
include an adverse event that, had it occurred in a more severe form, might have caused death. 
 
Grade 5, Death  
13.2.2. 
Relationship to Study Agent 
All adverse events, regardless of relatedness, should be reported. All adverse events should be 
evaluated for relatedness when reporting and documenting on the CRF.  
 
The following guidelines of relatedness are used modified from the NIH guidelines: 
 
Related:  The adverse event is related to the FMT material – i.e. an event that follows a reasonable 
temporal sequence from administration of the FMT material, follows a known or expected response 
pattern to the FMT material, that is confirmed by improvement on stopping and reappearance of the event 

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on repeated exposure and that could not be reasonably explained by the known characteristics of the 
patient’s clinical state. 
 
Not Related:  The adverse event is not related to the FMT material -  i.e. another cause of the event is 
most plausible; and/or a clinically plausible temporal sequence is inconsistent with the onset of the event 
and the study intervention and/or a causal relationship is considered biologically implausible.  
13.2.3. 
Solicited Adverse Events after FMT 
In addition to open-ended questions on adverse events meeting the above definitions, specific potential 
adverse events will be inquired about during the follow up period (following intervention through to 6 
months after randomization): 
Symptom that 
is clinically 
more severe 
than 
participant’s 
baseline 
Severity 
Grade 1 
Grade 2 
Grade 3 
Grade 4 
Grade 5 
Fever* 
38.0 - 39.0 
degrees C  
(100.4 - 102.2 
degrees F) 
>39.0 - 40.0 
degrees C 
(102.3 - 104.0 
degrees F) 
>40.0 degrees 
C (>104.0 
degrees F) for 
<=24 hrs 
>40.0 degrees 
C (>104.0 
degrees F) for 
>24 hrs 
Death 
Diarrhea 
Increase of <4 
stools per day 
over baseline 
pre-FMT; mild 
increase in 
ostomy output 
compared to 
baseline 
Increase of 4 - 
6 stools per 
day over 
baseline; 
moderate 
increase in 
ostomy output 
compared to 
baseline; 
limiting 
instrumental 
ADL 
Increase of 
>=7 stools per 
day over 
baseline; 
incontinence; 
hospitalization 
indicated; 
severe 
increase in 
ostomy output 
compared to 
baseline; 
limiting self-
care ADL 
Life-
threatening 
consequences; 
urgent 
intervention 
indicated 
Death 
Vomiting 
1 - 2 episodes 
(separated by 
5 minutes) in 
24 hrs 
3 - 5 episodes 
(separated by 
5 minutes) in 
24 hrs 
>=6 episodes 
(separated by 
5 minutes) in 
24 hrs; tube 
feeding, TPN 
or 
hospitalization 
indicated 
Life-
threatening 
consequences; 
urgent 
intervention 
indicated 
Death 
Abdominal 
Pain 
 
Mild pain  
Moderate pain; 
limiting 
instrumental 
activities of 
daily life 
Severe pain; 
limiting self-
care activities 
of daily life 
n/a 
n/a 
Bloating 
 
No change in 
bowel function 
or oral intake 
Systemic, 
decreased oral 
intake; change 
in bowel 
function 
n/a 
n/a 
n/a 

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Symptom that 
is clinically 
more severe 
than 
participant’s 
baseline 
Severity 
Grade 1 
Grade 2 
Grade 3 
Grade 4 
Grade 5 
Constipation 
Occasional or 
intermittent  
symptoms; 
occasional  
use of stool 
softeners,  
laxatives, 
dietary  
modification, or 
enema  
Persistent 
symptoms with 
regular use of 
laxatives  
or enemas 
indicated; 
limiting 
instrumental 
activities of 
daily life 
Symptoms 
interfering  
with self-care 
activities of 
daily life; 
obstipation  
with manual 
evacuation  
indicated  
Life-
threatening 
consequences 
(e.g. 
obstruction, 
toxic 
megacolon); 
urgent 
intervention 
indicated 
Death 
13.3. Adverse Event Documentation and Reporting Procedures 
13.3.1. 
Procedures to Document AEs 
Study participants will be instructed to contact medical monitor if any serious or unexpected adverse 
event occurs. Study staff will inquire about AEs when treatment is administered and during the follow-up 
phone calls following the patients discharge. AE’s will be recorded and documented in detail in an AE 
CRF.  
 
AE information to be collected in the AE CRF: 
 
Nature of the event 
 
Date of onset 
 
Concomitant treatment: product (generic name), indication, dosage, dosage interval, 
presentation, mode of administration, administration regimen 
 
Duration of the AE 
 
Severity 
 
Seriousness 
 
Causality 
 
Outcome     
 
The course and outcome of the adverse event will be commented on as follows: 
 
Recovered without sequelae 
 
Not yet recovered 
 
Recovered with sequelae 
 
Fatal 
13.3.2. 
Procedures to Report AEs 
Any SAE (including death, irrespective of the cause) occurring during the study will be immediately 
reviewed by the PI/medical monitor, the DMC, and the Health Sciences IRB (the IRB of record for this 
study). 
 
If determined to be a SUSAR (suspected unexpected serious adverse reaction – SUSAR; Appendix II) 
by the PI/medical monitor, the event will be reviewed by the DMC. Regulatory filing to the FDA or local 

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IRB as per standard practices will occur. Any hospital related death due to a bowel obstruction or infection 
that could be related to FMT will be reviewed by the DMC to discuss a temporary suspension of the 
protocol until a full safety review is conducted.  
 
In case of a SAE (non-SUSAR), the site PI will report the event to the study medical monitor and lead PI 
for review and compilation. The DMC will review all SAEs every 6 months or ad hoc depending on the 
clinical case at the discretion of the PI/medical monitor. A specific SAE CRF will be provided similar to 
Appendix 17.3. The report must contain a detailed description of the symptoms observed and the 
concomitant treatment administered. Furthermore, the report must comment on a possible causative 
relationship between the AE and the trial medication. Each SAE must be followed until it is resolved or 
can be explained satisfactorily.  
 
For non-serious adverse reactions (definitely related, not related) the medical monitor/PI will complete a 
report. All non-serious adverse reactions will be reviewed by the DMC every 6 months or ad hoc 
depending on the clinical case at the discretion of the PI/medical monitor. 
 
In accordance with safety requirements, the PI will inform the local IRB and will make sure that the 
involved persons will obtain adequate information. The following instructions must be heeded: 
 
In the case of an intolerable SAE, the study patient must, at the decision of the PI, be withdrawn 
from further treatment/placebo, and symptomatic treatment must be administered. The participant 
may opt to voluntarily provide samples for duration of study. 
 
The measures taken must be recorded on the CRF. 
 
In accordance with local legislation, the PI will submit copies of the final SAE-report to the 
Regulatory Authorities concerned, if necessary. 
13.4. Follow-up after Adverse Events 
AEs will be followed until resolution or stability even if this extends beyond the study-reporting period. 
Resolution of an AE is defined as the return to pretreatment status or stabilization of the condition with the 
expectation that it will remain chronic. 
 
Follow-up procedures, evaluations, and outcomes will be recorded on the participant's case report forms.  
13.5. Study Halting Rules 
13.5.1. 
Study Halting Rules 
Enrollment and administration of study intervention will be suspended pending a safety review by the 
DSMB to determine whether the study will be terminated or re-initiated in the following situations: 
 
Three or more of the randomized participants in a study treatment group have a Grade 3 AE of 
the same organ system deemed related to the study intervention. 
 
Any serious adverse event of an enrolled participant related to the study intervention including 
transmission of a pathogen from donor to recipient. 
 
An overall pattern of symptomatic, clinical, or laboratory events that the Medical Monitor considers 
related to study product and that may appear minor in terms of individual events, but that may 
collectively represent a serious potential concern for safety. 
 
The FDA and AHRQ will be notified of any study halt that occurs as a result of any of the above halting 
criteria. 

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13.5.2. 
Individual’s Halting Rights 
Participants who meet any of the following criteria must be assessed by the site PI to determine if it is in 
the participant’s best interest to stop the study product(s): 
 
Participant choice (withdrawal of consent). 
 
Participant’s non-compliance.  
 
Development of a significant medical condition and/or participation in the study is no longer in the 
best interest of the participant. 
 
Development of a severe or serious AE related to the FMT product. 
13.6. Safety Oversight – Data Monitoring Committee (DMC)  
UW-ICTR has established a Data Monitoring Committee (DMC) to provide a key resource for UW-Madison 
investigators conducting clinical research.  This DMC will provide investigators services to ensure appropriate 
measures are in place to promote subject safety, research integrity and compliance with federal regulations 
and local policies for individual clinical research protocols in need of DMC review (as determined by the 
Principal Investigator (PI), the funding agency, the local Scientific Review Committee, or the local IRB, and 
for which no DMC exists). For these studies, the UW ICTR DMC will be the primary data and safety advisory 
group for the Principal Investigator.  
 
The DMC is supported in its mission of safety and compliance by experienced ICTR staff to provide 
administrative assistance, experienced members representing a diversity of backgrounds, skills and 
knowledge, and the use of the Research Electronic Data Capture (REDCap) tool which provides data 
management functionality by allowing the development of eCRFs and surveys to support data capture. In 
providing oversight for the conduct of this study, the ICTR DMC will meet every 6 months during the 1-year 
study. Additional meetings may be scheduled as determined by the DMC or as requested by the PI. The 
DMC members will review protocol-specific reports created by statisticians that serve a non-voting member 
role on the DMC using data pulled from REDCap. These standard reports will include an overview of study 
objectives, a review of actual and projected accrual rates, an evaluation of patient demographics for balance 
of randomization, and a summary of the number and seriousness of adverse events. An interim analysis of 
study results may be performed and source documents may be reviewed to allow the DMC to independently 
judge whether the overall integrity and conduct of the protocol remain acceptable based on data provided 
and reported by the Principal Investigator. Additionally, the DMC may conduct a safety interim analysis after 
50% of patients have enrolled in the daily treatment arm. The DMC will make recommendations to the 
Principal Investigator that could include actions of continuation, modification, suspension, or termination. 
14. PROTOCOL DEVIATIONS 
A protocol deviation is any noncompliance with the clinical trial protocol, GCP, or protocol-specific MOP 
requirements. The noncompliance may be either on the part of the participant, the PI, or the study staff. As a 
result of deviations, corrective actions are to be developed by the site and implemented promptly. 
 
These practices are consistent with ICH E6: 
 
4.5 
Compliance with Protocol, Sections 4.5.1, 4.5.2, and 4.5.3 
 
5.1 
Quality Assurance and Quality Control, Section 5.1.1 
 
5.20 
Noncompliance, Sections 5.20.1, and 5.20.2. 
 
It is the responsibility of the PI/study staff to use continuous vigilance to identify and report deviations within five 
working days of identification of the protocol deviation, or within five working days of the scheduled protocol-
required activity.  All deviations must be promptly reported to the PI or designated personnel. 
 
All protocol deviations, as defined above, must be addressed in study participant source documents. A 
completed copy of the Protocol Deviation Form must be maintained in the Regulatory File, as well as in the 

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participant's source document. Protocol deviations must be sent to the IRB/IEC per their guidelines.  The PI/study 
staff is responsible for knowing and adhering to their IRB requirements. 
 

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15. REFERENCES 
16. APPENDIX I 
16.1. Osman et al. ID Week 2016 
 
Osman et al. ID Week 2016, “Safety and efficacy of fecal microbiota transplantation for 
recurrent Clostridium difficile infection”  
 
Abstract #59497 
Title: Safety and efficacy of fecal microbiota transplantation for recurrent Clostridium difficile infection from 
an international public stool bank: Results from a 2,050 patient multi-center cohort 
Original Submission Date: May 17, 2016 
Last Edited Date: May 18, 2016 
Authors: Majdi Osman, MD MPH1, Kelsey O'Brien, MPH2, Zachery Stoltzner, BS2, Kelly Ling, BS1, Emily 
Koelsch, RN BSN1, Nancy Dubois, MSN MBA3, Adila Khoiri, MD4, Kanchana Amaratunga, MD, MPH5, Mark 
Smith, PhD1 and Zain Kassam, MD MPH1, (1) OpenBiome, Medford, MA, (2)Clinical Safety, OpenBiome, 
Medford, MA, (3)William F. Connell School of Nursing, Boston College, Chestnut Hill, MA, (4)Sydney 
Children's Hospital, Sydney, Australia, (5)Infectious Disease, The Ottawa Hospital, Ottawa, ON, Canada 
 
Background: Clostridium difficile infection (CDI) is a public health threat and fecal microbiota transplantation 
(FMT) appears to be an effective therapy. Recently, universal stool banks have emerged to enable safe and 
seamless access to FMT. However, there is a paucity of real-world safety and efficacy data from stool banks.  
 
Methods: Quality assurance data on CDI classification, FMT delivery modality and clinical efficacy was 
consecutively collected from 482 healthcare facilities across 50 U.S states and 7 countries between January 
16, 2014 and April 12, 2016. The primary outcome was physician-reported clinical cure as per standard of 
care follow-up. Safety data was assessed through mandatory adverse event (AE) reporting. Descriptive 
statistics and Chi-square analysis for binomial variables was conducted.   
 
Results: Among consecutively collected reports, complete safety and efficacy data was returned for 2,050 
patients, which were included in these analyses. Overall, the clinical cure rate from physician-reported data 
across all delivery modalities and CDI patient populations was 84.0%. The most common indication for FMT, 
recurrent CDI, had an 87.0% (1150/1322) clinical cure rate by lower gastrointestinal (GI) delivery (Figure 1). 
Across the entire cohort, 85.0% (n=1742) of patients were treated with 250mL lower GI delivery fecal 
microbiota preparation (FMP) and 15.0% used 30mL upper GI delivery FMP. FMT by colonoscopy (85.8% 
clinical cure, n=1441) was superior to upper endoscopy (74.1% clinical cure, n=201) (p<0.01). The 
relationship between fecal preparation type and efficacy was statistically significant (p<0.05), with 85.1% 
efficacy for 250mL preparations and 77.9% efficacy for 30mL preparations. CDI classification had a 
statistically significant impact on the rate of clinical efficacy (Figure 1). From a safety perspective, 42 AEs 
were reported; however, no AEs were determined to be “definitely related” to FMT, 3 were “possibly related” 
to FMT and 39 “not related” based on NIH criteria. 
 
Conclusions: To our knowledge, this is the largest FMT study reported, and suggest in a large, real-world 
patient cohort that includes severe and refractory CDI patients, FMT from a public stool bank appears to be 
a safe and effective treatment for CDI not responsive to standard therapy. 
 

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Figure 1: Efficacy of FMT by Clostridium difficile infection classification and fecal microbiota preparation type 
 
Clostridium. 
difficile 
infection   
Classification 
Total 
250 mL 
30mL 
N 
Efficacy 
(%) 
P-
value 
N 
Efficacy
(%) 
P-
value 
N 
Efficacy 
(%) 
P-
value 
Recurrent 
1542 85.9 
<0.001 
1322
87.0 
<0.001 
220
79.5 
0.278 
Mixed 
(e.g. 
recurrent and 
severe) 
259 
79.2 
0.021 
229 
80.0 
0.047 
30 
66.7 
0.118 
Refractory 
159 
74.2 
<0.001 
126 
75.4 
<0.01 
33 
69.7 
0.228 
Severe 
90 
83.3 
0.85 
65 
81.5 
<0.01 
25 
88 
0.205 
 
 
 
 

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16.2. Dubois et al. ID Week 2015 
 
Title: Prospective Assessment of Donor Eligibility for Fecal Microbiota Transplantation at a Public Stool Bank: 
Results From the Evaluation of 1,387 Candidate Donors  
 
Authors: Nancy E. Dubois MN, MBA1, Kelly Ling1, Majdi Osman MD, MPH1, Laura Burns1, Gina Mendolia1, 
Dan Blackler, James Burgess1, Carolyn Edelstein MPA1, Andrew Noh1, Elaine Vo PhD, Eric Alm PhD1,2,3, 
Mark Smith PhD1,2 Zain Kassam MD, MPH1,2  
 
1. OpenBiome 
2. Massachusetts Institute of Technology 
3. Broad Institute 
 
Character count: 1,948/1,950 
 
Background: Recurrent Clostridium difficile infection is a major public health threat and fecal microbiota 
transplantation is a promising therapy. Public stool banks have emerged to meet increasing demand, 
supplied with fecal material from rigorously screened, universal donors. However, limited data exists 
regarding best practices for donor assessment. Accordingly, we aim to outline a donor screening framework, 
capture etiology of exclusion, and quantify the number of qualified stool donors.  
 
Methods: Enrollment was conducted prospectively over a 1-year period. Candidates were directed to an 
online registry to complete a pre-screening survey to rule out common exclusion criteria. Eligible participants 
were invited for a 109-point, in-person clinical assessment by a nurse or physician and overseen by an 
internal medicine specialist to exclude risk factors for transmissible diseases and potential microbiome-
mediated conditions. Candidate donors completed stool and serologic screening by a CLIA-approved 
laboratory (Figure 1).  
 
Results: Overall, 1,387 participants enrolled in the donor program. At Stage 1, candidates completed a pre-
screen survey with 910 (66%) individuals excluded, commonly for abnormal body mass index, logistic 
constraints and recent antimicrobial use. At Stage 2, remaining participants underwent a clinical assessment 
with 403 (84%) participants excluded, most commonly for loss to follow-up with 235 (58%) candidates failing 
to attend an invited assessment. During the clinical interview, psychiatric illness, medications and infectious 
disease risk factors were identified as the most common reasons for exclusion. At Stage 3, remaining 
candidates underwent laboratory investigation with 35 (47%) candidates excluded, commonly for rotavirus 
and C. difficile. Overall, 39 participants qualified as stool donors resulting in a 2.8% acceptance rate (Figure 
2). 
 
Conclusions: Healthy, rigorously screened stool for use in FMT is rare with only 2.8% donors qualifying. An 
unanticipated, large number of asymptomatic potential donors were not eligible and logistics as well as loss 
to follow-up appear to be important factors for stool banks. Consensus-based guidelines are urgently needed 
to ensure safe standards for stool donors. 
 
 

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17. APPENDIX II 
17.1. Study Schematic 
 

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17.2. Study Calendar 
 
Screening  
Enrollment/ 
Baseline 
Visit* 
Daily for 
Duration 
of 
Antibiotic 
regimen 
+7 days 
Every 3 days 
(+/-1 day) 
from 
Enrollment to 
intervention 
end 
Follow-
up 
Calls 
48-72 hours 
post 
Antibiotic 
Completion* 
7 Days 
Post 
Antibiotic 
Completion 
Unscheduled 
Visit* 
Weekly 
Post-FMT 
Follow-Up 
Sample 
Collection1 
 
1 Month 
Post-FMT 
Call 
6 month 
Post-FMT 
assessment 
Verification of Inclusion 
and Exclusion Criteria 
X 
X 
 
 
 
 
 
 
 
 
 
Invited to participate 
X 
 
 
 
 
 
 
 
 
 
 
Informed Consent 
 
X 
 
 
 
 
 
 
 
 
 
Pregnancy test 
 
D2 
 
 
 
S2 
 
 
 
 
 
Test Capsule 
 
D 
 
 
 
S 
 
 
 
 
 
CMV/ EBV PCR testing 
 
X3 
 
 
 
 
 
 
 
 
 
Vitals Collection 
 
X 
 
 
 
S 
 
X 
 
 
 
Physical Exam 
 
X 
 
 
 
S 
 
X 
 
 
 
Clinical Symptoms 
Assessment 
 
X 
 
 
X 
S 
 
X 
X 
X 
 
Dietary Assessment 
 
X 
 
 
X 
S 
D 
X 
 
X 
 
Risk Factor 
Assessment 
 
X 
 
 
 
 
 
 
 
 
 
Demographics 
collection 
 
X 
 
 
 
 
 
 
 
 
 
Medical History 
 
X 
 
 
 
 
 
 
 
 
X 
Concomitant 
Medications 
 
X 
 
 
X 
S 
D 
X 
X 
X 
 
FMT or Placebo 
Administration 
 
D 
D 
 
 
S 
D 
 
 
 
 
Stool Sample 
Collection 
 
X 
 
X 
X 
S 
D 
 
X 
 
 
Antibiotic Resistant 
Bacteria Testing 
 
X 
 
X 
 
S 
D 
 
X 
 
 
Patient diary 
 
X 
X 
X 
X 
X 
X 
 
X 
 
  
Post-ingestion 
Observation 
 
D 
 
 
 
S 
 
 
 
 
 
Adverse Events 
Assessments 
 
D 
 
 
X 
S 
D 
X 
 
X 
X 
X-Indicates all groups 
 D-indicates daily dosing groups (Groups 1 and 3) only   
S-indicates single dose group (Group 2) only 
*Indicates a clinic visit 
1Lasts a duration of 4 weeks 
2Women of childbearing potential only 
3 Patients at risk of CMV/EBV associated disease only 
 
 

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17.3. NIH Common Terminology Criteria for Adverse Events (CTCAE) 
 
 
 
 

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17.4. Adverse Event Assessment Flow Chart