Conditions: Crohn Disease
Allocation: RANDOMIZED | Intervention model: PARALLEL
Enrollment: 10
Healthy volunteers: no

Brief summary:
The purpose of this study is to determine the effect of a novel gut microbiota-targeted therapeutic regimen (bowel lavage and antibiotics with or without an antifungal) in the management of active Crohn's Disease (CD) or indeterminate colitis (IBDU) that is refractory to conventional, immunosuppressive therapy. In addition, the study will determine the effect of PEG lavage alone on fecal calprotectin and gut microbiota in patients who are undergoing a PEG lavage for clinical care.

Detailed description:
Investigators will evaluate the efficacy of a novel treatment regimen, employing non-immunosuppressive medications, in the management of refractory CD or IBDU. Refractory patients include those patients who have experienced loss of responsiveness (LOR) or primary nonresponse to an immunomodulator or a biologic. Investigators will treat participants with a combination of gut microbiota-targeted therapies to restore a healthy gut microbiome composition. Investigators believe that this strategy will both treat the gut inflammation associated with inflammatory bowel disease (IBD) as well as salvage response to immune suppressive therapies.

Investigators will also evaluate the effect of PEG lavage alone on fecal calprotectin and gut microbiota. Participants in this arm, will be undergoing a PEG lavage in preparation for a endoscopy for clinical care. They will be asked to provide stool samples, prior to and after their PEG lavage. Participants will not be receiving any investigational treatments.

Arms:
arm 1: Vancomycin oral suspension four times daily (Day 1-14), plus neomycin orally three times daily (Days 1-3), plus ciprofloxacin orally twice daily (Day 4-14), plus Polyethylene Glycol 3350 (Miralax) dissolved in Gatorade on day 2, plus fluconazole orally once daily (Day 1-14). arm 2: Vancomycin oral suspension four times daily (Day 1-14), plus neomycin orally three times daily (Days 1-3), plus ciprofloxacin orally twice daily (Day 4-14), plus Polyethylene Glycol 3350 (Miralax) dissolved in Gatorade on day 2, plus placebo. arm 3: Collect stool samples for calprotectin in patients undergoing colonoscopy for clinical care to evaluate effect of bowel lavage alone on calprotectin.

Interventions: intervention 1: Vancomycin intervention 2: Neomycin intervention 3: Ciprofloxacin intervention 4: Polyethylene Glycol 3350 intervention 5: Fluconazole
Intervention descriptions: intervention 1: Oral suspension 4 times daily (Day 1-14) intervention 2: Oral three times daily (Days 1-3) intervention 3: Oral twice daily (Days 4-14) intervention 4: Dissolved in Gatorade on day 2 intervention 5: Orally once daily (Day 1-14)

Protocol document:
Prot_SAP_001.pdf: 
 
 
  
Title: 
A Randomized Pilot Study of Fundamental Modification of the 
Gut Microbiota in the Treatment of Refractory Crohn’s 
Disease 
Short Title 
Holiday 
Drug or Device 
Name(s): 
Polyethylene glycol, neomycin, vancomycin, ciprofloxacin, 
fluconazole 
Sponsor: 
The Broad Medical Research Program at CCFA, the National 
Institutes of Health National Institute of Diabetes and Digestive and 
Kidney Diseases 
Secondary Funder: 
The Children's Hospital of Philadelphia 
eIRB Number: 
17-014343 
Protocol Date: 
March 13, 2018 
Amendment 1 Date: October 19, 2018 
Amendment 3 Date: August 16, 2019 
Amendment 2 Date: March 1, 2019 
Amendment 4 Date: September 20, 2019 
Amendment 5 Date: December 16, 2019 
Amendment 6: December 20, 2019 
 
Study Principal Investigator: Lindsey Albenberg, DO 
  
Division of Pediatric Gastroenterology 
The Children’s Hospital of Philadelphia 
Roberts Center, 14-140 
2716 South St, Philadelphia, PA 19146 
Phone: 215-590-7801 
email: albenbergl@chop.edu 
 
 


  
 
 
 
 
 
 
 
ii 
TABLE OF CONTENTS 
Table of Contents ................................................................................................................... ii 
Abbreviations and Definitions of Terms .............................................................................. v 
Abstract ................................................................................................................................. vi 
Protocol Synopsis ................................................................................................................. vii 
Table 1: Schedule of Study Procedures for Intervential Group (Group 1) .................... xii 
Table 2: Schedule of study procedures for group 2 ......................................................... xiv 
Figure 1: Study Diagram, Group 1 ................................................................................... xiv 
1 
BACKGROUND INFORMATION AND RATIONALE ........................................................................1 
1.1 
INTRODUCTION ......................................................................................................................................1 
1.2 
BACKGROUND AND RELEVANT LITERATURE ........................................................................................1 
1.2.1 
Inflammatory Bowel Disease: Current Therapies and Treatment Challenges ................................1 
1.2.2 
History of Gut Microbiota-Targeted Therapies for IBD ..................................................................2 
1.2.3 
Preliminary Data ..............................................................................................................................3 
1.3 
SELECTION OF DRUGS AND DOSAGES ...................................................................................................8 
1.4 
COMPLIANCE STATEMENT .....................................................................................................................8 
2 
STUDY OBJECTIVES ...............................................................................................................................9 
2.1 
PRIMARY OBJECTIVE (OR AIM) .............................................................................................................9 
2.2 
SECONDARY OBJECTIVES (OR AIM) .......................................................................................................9 
3 
INVESTIGATIONAL PLAN .....................................................................................................................9 
3.1 
GENERAL SCHEMA OF STUDY DESIGN ..................................................................................................9 
3.1.1 
Screening & Enrollment Phase ......................................................................................................10 
3.1.2 
Study Treatment Phase ...................................................................................................................11 
3.1.3 
Optional Intervention Extension Phase (14 day repeat drug regimen) .........................................12 
3.1.4 
Follow Up Phase ............................................................................................................................12 
3.2 
ALLOCATION TO TREATMENT GROUPS AND BLINDING .......................................................................12 
3.3 
STUDY DURATION, ENROLLMENT AND NUMBER OF SITES ..................................................................12 
3.3.1 
Duration of Study Participation .....................................................................................................12 
3.3.2 
Total Number of Study Sites/Total Number of Subjects Projected .................................................13 
3.4 
STUDY POPULATION ............................................................................................................................13 
3.4.1 
Group 1: Interventional Group; Participants who have had primary non-response or loss of 
response to conventional, immunosuppressive treatment ...........................................................................13 
3.4.2 
Group 2: Observational Group; Participants undergoing clinically indicated PEG lavage in 
preparation for a GI endoscopy. .................................................................................................................15 
4 
STUDY PROCEDURES ...........................................................................................................................15 
4.1 
GROUP 1 PARTICIPANTS ......................................................................................................................15 
4.1.1 
Screening Visit ................................................................................................................................15 
4.1.2 
Enrollment Phase (Visit 1) .............................................................................................................16 
4.1.3 
Study Treatment Phase (Days 1-15 including Visits 2-4): In-person Study Visits .........................16 
4.1.4 
Daily Surveys ..................................................................................................................................16 
4.1.5 
Study Visit 2 (Day 5) ......................................................................................................................17 
4.1.6 
Study Visit 3 (Day 8) ......................................................................................................................17 
4.1.7 
Study Visit 4 (Day 15) ....................................................................................................................17 
4.1.8 
Follow-up Phase ............................................................................................................................18 
4.1.9 
Concomitant Medication ................................................................................................................18 
4.1.10 
Rescue Medication Administration ............................................................................................19 
4.2 
GROUP 2 PARTICIPANTS ......................................................................................................................19 
4.2.1 
Visit 1: Baseline Sample Prior to bowel cleanout ..........................................................................19 
4.2.2 
Visit 2: Day 5 (+/- 24 hours) after GI endoscopy ..........................................................................19 


 
 
 
 
 
 
 
 
iii 
4.2.3 
Visit 3: Day 12 (+/- 24 hours) after GI endoscopy ........................................................................19 
4.3 
SUBJECT COMPLETION/WITHDRAWAL ................................................................................................19 
4.3.1 
Early Termination Study Visit ........................................................................................................20 
5 
STUDY EVALUATIONS AND MEASUREMENTS ............................................................................21 
5.1 
SCREENING AND MONITORING EVALUATIONS AND MEASUREMENTS .................................................21 
5.1.1 
Group 1 ..........................................................................................................................................21 
5.1.2 
Group 2 ..........................................................................................................................................24 
5.2 
EFFICACY EVALUATIONS ....................................................................................................................24 
5.2.1 
Diagnostic Tests, Scales, Measures, etc. ........................................................................................24 
5.2.2 
Fecal calprotectin ..........................................................................................................................25 
5.2.3 
C-reactive protein (CRP) ...............................................................................................................26 
5.2.4 
Microbial DNA sequencing ............................................................................................................26 
5.3 
SAFETY EVALUATION ..........................................................................................................................26 
6 
STATISTICAL CONSIDERATIONS .....................................................................................................27 
6.1 
PRIMARY ENDPOINT ............................................................................................................................27 
6.2 
SECONDARY ENDPOINTS .....................................................................................................................27 
6.3 
STATISTICAL METHODS .......................................................................................................................27 
6.3.1 
Safety Analysis ................................................................................................................................29 
7 
STUDY MEDICATION ............................................................................................................................30 
7.1 
INTERVENTION DESCRIPTION AND REGIMEN .......................................................................................30 
7.1.1 
Dispensing ......................................................................................................................................31 
7.1.2 
Receipt ............................................................................................................................................31 
7.1.3 
Storage ...........................................................................................................................................31 
7.1.4 
Preparation and Packaging ...........................................................................................................31 
7.1.5 
Administration and Accountability .................................................................................................31 
7.1.6 
Participant Compliance Monitoring ..............................................................................................31 
7.1.7 
Return or Destruction of Investigational Product ..........................................................................32 
8 
SAFETY MANAGEMENT ......................................................................................................................32 
8.1 
CLINICAL ADVERSE EVENTS ...............................................................................................................32 
8.2 
ADVERSE EVENT REPORTING ..............................................................................................................32 
8.3 
DEFINITION OF AN ADVERSE EVENT ...................................................................................................32 
8.4 
DEFINITION OF A SERIOUS ADVERSE EVENT (SAE) ............................................................................32 
8.4.1 
Relationship of SAE to study drug or other intervention ...............................................................33 
8.5 
IRB/IEC NOTIFICATION OF SAES AND OTHER UNANTICIPATED PROBLEMS ......................................33 
8.5.1 
Follow-up report ............................................................................................................................33 
8.6 
MEDICAL EMERGENCIES .....................................................................................................................33 
9 
STUDY ADMINISTRATION ..................................................................................................................34 
9.1 
TREATMENT ASSIGNMENT METHODS .................................................................................................34 
9.1.1 
Randomization ................................................................................................................................34 
9.1.2 
Blinding ..........................................................................................................................................34 
9.1.3 
Unblinding ......................................................................................................................................34 
9.2 
DATA COLLECTION AND MANAGEMENT .............................................................................................34 
9.3 
CONFIDENTIALITY ...............................................................................................................................35 
9.4 
RECORDS RETENTION ..........................................................................................................................35 
9.5 
REGULATORY AND ETHICAL CONSIDERATIONS ..................................................................................35 
9.5.1 
Data and Safety Monitoring Plan ..................................................................................................35 
9.5.2 
Risk Assessment ..............................................................................................................................36 
9.5.3 
Potential Benefits of Trial Participation ........................................................................................42 
9.5.4 
Risk-Benefit Assessment .................................................................................................................42 
9.6 
RECRUITMENT STRATEGY ...................................................................................................................42 


  
 
 
 
 
 
 
 
iv 
9.6.1 
Group 1 Participants ......................................................................................................................42 
9.6.2 
Group 2 Participants ......................................................................................................................43 
9.7 
INFORMED CONSENT/ASSENT AND HIPAA AUTHORIZATION .............................................................43 
9.8 
PAYMENT TO SUBJECTS/FAMILIES ......................................................................................................45 
9.8.1 
Gifts ................................................................................................................................................45 
10 
PUBLICATION .........................................................................................................................................46 
11 
REFERENCES ..........................................................................................................................................46 
 


  
 
 
 
 
 
 
 
v 
ABBREVIATIONS AND DEFINITIONS OF TERMS 
 
 
 
AE 
 
Adverse event 
CBC 
 
Complete blood count 
CD 
 
Crohn’s disease 
CDAI 
 
Crohn’s Disease Activity Index 
CMP 
 
Comprehensive metabolic panel 
CMV 
 
Cytomegalovirus 
CRF 
 
Case Report Form 
CRP 
 
C-reactive protein 
CTRC 
 
Clinical Translational Research Center 
EKG 
 
Electrocardiogram 
ESR 
 
Erythrocyte sedimentation rate 
FCP 
 
Fecal calprotectin 
GI 
 
Gastrointestinal 
HBI 
 
Harvey Bradshaw Index 
IBD 
 
Inflammatory bowel disease 
IBDU 
 
Indeterminate colitis 
ICE 
 
Idiopathic chronic enterocolitis 
IDS 
 
Investigational Drug Service 
IRB 
 
Institutional Review Board 
ITS 
 
Internal Transcribed Spacer 
LOR 
 
Loss of responsiveness 
MRN 
 
Medical Record Number 
PEG 
 
Polyethylene glycol 
PENN 
 
University of Pennsylvania 
PCDAI 
 
Pediatric Crohn’s Disease Activity Index 
PUCAI 
 
Pediatric Ulcerative Colitis Activity Index 
SAE 
 
Serious adverse event 
TUNPRC 
 
Tulane University National Primate Center 
UC 
 
Ulcerative Colitis 


  
 
 
 
 
 
 
 
vi 
ABSTRACT 
Context:   
Recent evidence suggests that the gut microbiota is responsible for the stimulation of the 
intestinal immune system in Inflammatory Bowel Disease (IBD). Such research indicates 
that if gut flora plays a role in the pathogenesis of IBD, then perhaps targeting commensal 
microbes rather than or in addition to the immune system would be more efficacious. 
 
Objectives:  
The primary objective is to determine the effect of a novel gut microbiota-targeted 
therapeutic regimen in the management of active Crohn’s Disease (CD) or IBDU that is 
refractory to conventional, immunosuppressive therapy. The regimen will deeply modify the 
gut microbiota and help to treat the gut inflammation associated with IBD, as well as rescue 
response to biologic or immunomodulator therapies.  
Study Design:  
This will be a randomized, placebo-controlled, double blind Phase 2a trial.  
Setting/Participants: 
The interventional arm (Group 1) of the study will recruit pediatric patients 6-18 years old 
with moderately active CD or IBDU who have had a loss of response to one or more 
biologic or immunomodulator therapies. Group 2 (observational arm) of the study will 
recruit patients aged 10 and older  who are undergoing a GI endoscopy due to suspicion for 
active intestinal inflammation determined by physician global assessment (PGA).Study 
Interventions and Measures:  
Only participants in the Group 1 of the study will undergo the study intervention. The study 
intervention includes a bowel lavage and oral antibiotics (3 days of vancomycin and 
neomycin followed by 11 days of vancomycin and ciprofloxacin) with or without an 
antifungal (fluconazole). Measures will be obtained for the evaluation of disease activity 
(PCDAI), fecal calprotectin, and C-reactive protein. Changes in the composition of the gut 
microbiota will also be assessed.Group 2 participants will not undergo the study 
intervention. Group 2 will be an observational group who are undergoing a bowel lavage as 
part of clinical care. Participants will provide stool samples before and after completing a 
PEG bowel lavage. Measures will be obtained for the evaluation of fecal calprotectin. 
Changes in the composition of the gut microbiota will also be assessed. 


 
vii  
 
 
 
 
 
 
 
PROTOCOL SYNOPSIS 
Study Title 
Fundamental Modification of the Gut Microbiota in the Treatment 
of Refractory Crohn’s Disease 
Funder 
The Broad Medical Research Program at CCFA, the National 
Institutes of Health, National Institute of Diabetes and Digestive and 
Kidney Diseases 
Clinical Phase 
Phase II 
Study Rationale 
The available evidence suggests that it is the commensal gut 
microbiota responsible for the stimulation of the intestinal immune 
system in the inflammatory bowel diseases. Thus, many IBD 
researchers and providers have questioned the current therapeutic 
approach.  For instance, if the gut flora plays a role in the 
pathogenesis of IBD, then perhaps targeting the microbes rather 
than the immune system, or a combination of the two, would be 
more efficacious.  Most IBD providers would agree that immune 
suppressive medications are the most reliable therapies that we have 
available right now, but that a therapeutic approach which targets 
both the gut microbes and the immune system is much more logical 
based on what we know regarding the pathogenesis of these 
diseases.  
 
We hypothesize that immune suppressive medications lead to 
persistent colonization with potentially pathogenic microbes that 
perpetuate disease chronicity in IBD patients.  Additionally, we 
hypothesize that host immunosuppression could allow indolent 
colonizers of the colonic mucosa (symbionts) to behave as 
pathobionts, thereby causing progressive loss of response (LOR) to 
immune suppression. 
This study will evaluate the efficacy of a novel treatment regimen, 
employing non-immunosuppressive medications, in the 
management of refractory CD or IBDU.   Refractory patients 
include those patients who have experienced LOR or primary 
nonresponse to an immunomodulator or a biologic.  We will treat 
patients with a combination of gut microbiota-targeted therapies to 


 
viii  
 
 
 
 
 
 
 
restore a healthy gut microbiome composition.  We believe that this 
strategy will both treat the gut inflammation associated with IBD as 
well as salvage response to immune suppressive therapies. 
 
In addition, the study will determine the effect of PEG lavage alone 
on fecal calprotectin and gut microbiota in patients with active CD 
or IBDU.  
Study Objective(s) 
Primary  
• 
To determine the effect of a novel gut microbiota-targeted 
therapeutic regimen (bowel lavage and antibiotics with or 
without an antifungal) in the management of active CD or IBDU 
that is refractory to conventional, immunosuppressive therapy.  
Secondary 
• 
To correlate the effectiveness in reducing bacterial 16S rRNA 
copy number and fungal 18S rRNA copy number, with the use 
of the regimen in the primary objective, with improvement of 
disease activity in patients with CD or IBDU refractory to 
immunosuppressive therapy. 
• 
To determine the relationship between the effectiveness of the 
proposed therapies with changes in gut microbiota composition. 
• 
To determine the effect of PEG lavage alone on the microbiome 
and the fecal calprotectin. 
 
Study Design 
 
Randomized, placebo-controlled, double blind Phase 2a trial 
Subject Population 
Key criteria for 
Inclusion and 
Exclusion: 
Group 1-Intervention Participants 
Inclusion Criteria 
 
1. Parental/guardian permission (informed consent) and if 
appropriate, child assent. 


 
ix  
 
 
 
 
 
 
 
2. Males or females 6-18 years of age 
3. Current weight >10 kg (or 22 lb) 
4. Ability to swallow pills 
5. Normal kidney function 
6. Normal AST, ALT, and alkaline phosphatase 
7. Active CD or IBDU defined as PCDAI>30 
8. CRP > 15mg/L (or 1.5mg/dL) or fecal calprotectin 
(FCP)>350mcg/g (within one month of enrollment) 
9. Have had primary nonresponse or an initial response for 8 or 
more weeks, followed by loss of responsiveness (LOR) 
(self-reported worsening of symptoms for at least 7 days), to 
one or more of the following therapies*: azathioprine, 6-
mercaptopurine, methotrexate, adalimumab, certolizumab, 
golimumab, infliximab, natalizumab, vedolizumab, or 
ustekinumab 
*Must be administered at standard, therapeutic dosages 
 
10. Girls who have menses and/or are ³ 11 years of age must 
have a negative urine/serum pregnancy test and must use an 
acceptable method of contraception 
Exclusion Criteria 
11. Unwillingness to provide consent 
12. Known allergy or intolerance to aminoglycosides or any of 
the medications used in this study, including medications 
within the same class 
13. Current use of one of more of the following medications: 5-
fluorouracil, digoxin, anticoagulants, theophylline, 
phenytoin, probenecid, duloxetine, clozapine, sildenafil, 
hydrochlorothiazide, cyclosporine, hypoglycemics, 


 
x  
 
 
 
 
 
 
 
terfenadine, tacrolimus, rifabutin, midazolam, and 
voriconazole 
14. Known diagnosis of diabetes mellitus 
15. Known or suspected stricturing disease producing 
obstructive symptoms 
16. Active Clostridium difficile infection 
17. Prolonged QTc interval as seen on enrollment EKG 
18. Current use of antibiotics 
19. Starting or increasing the dose of an IBD related medication 
within 4 weeks of screening 
20. Participants who may be non-compliant with the study 
schedules or procedures 
 
Group 2-Observational Arm Participants  
Inclusion Criteria 
1. Males or females 10 years of age and older.  
2.  Patients undergoing a clinical GI endoscopy due to 
suspicion for active intestinal inflammation determined by 
physician global assessment (PGA). 
3. Undergoing a bowel preparation as part of clinical care. 
4. Parental/guardian permission (informed consent) and if 
appropriate, child assent. 
Exclusion Criteria 
1. Antibiotic use within the past 30 days.  
2.   Current presence of an ostomy bag.  
3.   Patients undergoing a non- polyethylene glycol 3350 
cleanout. 
4. Unwillingness to provide informed consent.  
5. Parents/guardians or subjects who, in the opinion of the 
Investigator, may be non-compliant with study schedules or 
procedures. 
 


 
xi  
 
 
 
 
 
 
 
Number Of Subjects  
 
60 pediatric participants will be enrolled with an estimated yield of 
35 evaluable participants. Subjects will be enrolled from CHOP. 
Study Duration 
Group 1 subject participation will last 6-8 months; Group 2 subject 
participation could last up to two months. The entire study is 
expected to last 2 years. 
Study Phases  
For Group 1 participants:  
Screening 
Enrollment 
Treatment Phase 
Follow-Up  
 
Efficacy Evaluations 
Our estimates of efficacy will use a disease activity score (PCDAI) 
for clinical response (interventional patients only), FCP for mucosal 
inflammation, and CRP for systemic inflammation (for 
interventional patients only).  
Safety Evaluations 
For Group 1 participants:  
Primary measurements that will be used to assess safety include 
vital signs, laboratory results, EKG for QTc interval, disease 
activity scores, and screening for medication side effects and 
adverse events. 
Statistical And 
Analytic Plan 
The two arms of Group 1 will be compared using standard 
descriptive statistics. Categorical variables will be compared using 
Fisher’s exact test and continuous variables will be compared using 
the unpaired t-test or Wilcoxon rank sum test if the data are not 
normally distributed. 
DATA AND SAFETY 
MONITORING PLAN 
The PI is responsible for data quality management and ongoing 
assessment of safety. 
 
 
 
 


 
xii  
 
 
 
 
 
 
 
 
 
 
 
TABLE 1: SCHEDULE OF STUDY PROCEDURES FOR INTERVENTIAL GROUP (GROUP 1) 
 
Screening/ 
Recruitment 
Enrollment/ Day  
-17 - 0 
 
Day 1 
Day 5 
Day 8 
Day 15 
Day 22 
Day 29 
 
Day 36-64 
(Optional visit) 
3 mos 
6 mos 
Study Visit 
Visit 0 
Visit 1 
Study Drug 
Start 
Visit 2 
Visit 3 
Visit 4 
Visit 5 
Visit 6 
Visit 6.1 
Visit 7 
Visit 8 
Phase of Study 
 
Intervention Phase 
Follow-up Phase 
Telephone visit 
X 
 
x 
 
 
 
X 
 
X 
X 
X 
Web-based screening survey 
X 
 
 
 
 
 
 
 
 
 
 
Daily Surveya 
 
X 
 
X 
X 
X 
X 
X 
Xb  
Xb  
Xb  
Medical record review 
X 
X 
 
 
 
 
 
 
 
X 
X 
Study Treatment 
 
 
x 
X 
X 
 
 
 
 
 
 
Physical exam including vital 
signs 
 
X 
 
X 
X 
X 
 
X 
 
 
 
Urine pregnancy test for 
female participants 
 
X 
 
 
 
 
 
 
 
 
 
Stool collection for 
microbiome analysis 
 
X 
 
X 
X 
X 
X 
X 
 
 
 
Stool C. difficile toxin 
Xc 
 
 
 
 
 
 
 
 
 
 
Rectal swabs for mucosal 
analysis 
X 
Xd 
 
 
X 
X 
 
X 
 
 
 
FCP 
Xe 
 
 
 
X 
X 
X 
X 
 
 
 
CBC (no diff) 
 
X 
 
Blood draw to 
store for 
future use 
X 
X 
 
X 
 
 
 
CMP 
 
X 
 
X 
X 
 
X 
 
 
 
ESR 
 
X 
 
X 
X 
 
X 
 
 
 
CRP 
 
X 
 
X 
X 
 
X 
 
 
 
Serum Cystatin C 
 
X 
 
 
 
 
 
 
 
 
Infliximab or adalimumab 
levelf 
 
X 
 
 
 
 
 
 
 
 
Vancomycin levelg 
 
 
 
Xg 
Xg 
Xg 
 
 
 
 
 
PCDAI 
X (within 1 
month) 
X 
 
X 
X 
X 
 
X 
 
 
 
EKG 
 
X 
 
 
X 
 
 
 
 
 
 
a. Online Redcap survey completed daily (Day-7 through Day 29). 
b. Online Redcap survey completed once a week (Day 36 through 6 months). 


 
xiii  
 
 
 
 
 
 
 
c. C.diff will be performed if no record of negative C.diff within 1 month of enrolment. 
d. Rectal swab samples will be collected once, either during screening or at the enrolment visit. 
e. FCP will be performed if no record of test within 1 month of enrolment. 
f. For participants on infliximab or adalimumab. 
g. Serum vancomycin level will be tested as described in Section 5.1.5.


 
page xiv 
  
 
 
 
TABLE 2: SCHEDULE OF STUDY PROCEDURES FOR GROUP 2 
Study Procedure 
Screening/ 
Recruitment 
(up to Day -1) 
Day -1 
 
Day 0 
Day 5 
Post 
Procedure 
(+/- 24 hours) 
Day 12 Post 
Procedure 
(+/- 24 hours) 
Study Visit 
Visit 0 
Day of Bowel 
Lavage* 
Day of 
Procedure* 
Visit 2 
Visit 3 
Verbal Informed Consent 
X 
 
 
 
 
Medical record review 
X 
 
 
 
 
Distribution of study supplies 
X 
 
 
X 
 
Stool collection for 
microbiome analysis 
X 
 
 
X 
X 
Stool collection for FCP 
analysis  
X** 
 
 
X 
X 
*Clinical care procedures 
**Not completed if participant has a FCP of >350 within 1 month of enrollment available in 
their clinical chart.   
 
FIGURE 1: STUDY DIAGRAM, GROUP 1 
 
 


 
  
 
 
 
1 
1 
BACKGROUND INFORMATION AND RATIONALE 
1.1 Introduction 
Recent evidence suggesting that the commensal gut microbiota, or the “gut microbiome,” is 
responsible for stimulation of the intestinal immune system in inflammatory bowel disease 
(IBD) has caused many researchers and providers in the field to question current therapeutic 
approaches.  Though most IBD providers would agree that immunosuppressive medications 
are currently the most reliable therapies, such research indicates that if gut flora plays a role 
in the pathogenesis of IBD, then perhaps targeting commensal microbes rather than or in 
addition to the immune system would be more efficacious.  
This protocol seeks to test the hypothesis that a therapeutic approach that deeply alters the 
composition and bacterial/fungal load of the gut microbiota will be efficacious in patients 
with refractory Crohn’s Disease (CD) or IBDU who have primary nonresponse or secondary 
loss of response to conventional, immune suppressive therapies. This study will evaluate the 
efficacy of a novel treatment regimen employing non-immunosuppressive medications in 
the management of refractory CD.  Patients will be treated with a combination of gut 
microbiota-targeted therapies to deeply modify the dysbiotic gut microbiota that has been 
consistently reported in patients with CD[1].  We believe this strategy will both treat the gut 
inflammation associated with IBD, as well as rescue response to biologic or 
immunomodulator therapies.    
Additionally, this protocol will assess the effect of PEG lavage alone on the microbiome and 
the fecal calprotectin in patients with active IBDU or Crohn’s disease.  
 
1.2 Background and Relevant Literature 
1.2.1 Inflammatory Bowel Disease: Current Therapies and Treatment 
Challenges 
Inflammatory bowel disease (IBD), including CD, UC, and IBDU affects approximately 1.5 
million Americans and the incidence is increasing worldwide [2].  Current evidence 
indicates that the pathogenesis of IBD involves an inappropriate and persistent inflammatory 
response to the gut microbiota in genetically susceptible individuals [3].  In support of this 
notion, several studies utilizing animal models have shown that the development of 
intestinal inflammation requires microbial colonization of the gut [4, 5].  Clinical 
observations of IBD further implicate the role of the commensal gut microbiota, as IBD 
usually affects intestinal regions with the highest bacterial load, and both fecal diversion and 
antibiotic treatment can be effective in the management of CD [6, 7]. 
However, standard treatments for IBD do not focus on restoring immune tolerance to 
commensal microbes but rather depend on immunosuppression.  Although effective in 
inducing and maintaining remission for many patients, there is substantial risk of side effects 
associated with the use of immunosuppressive medications, namely steroids, 
immunomodulators (e.g., thiopurines and methotrexate) and biologics (e.g., infliximab and 
adalimumab) [8].  In addition, a significant proportion of patients will experience primary 


 
  
 
 
 
2 
nonresponse or a loss of response (LOR) to immunosuppression over time in a way that 
cannot be explained by the pharmacokinetics of the drug [9]. 
When nonresponse or LOR occurs, providers must escalate dosage or change the treatment 
medication(s).  Because of the limited number of medications and concern for the 
exhaustion of non-surgical options, maintaining patients with IBD on an effective 
medication for as long as possible becomes a priority of clinical care.   
1.2.2 History of Gut Microbiota-Targeted Therapies for IBD 
Antibiotics 
There is clear evidence for the effectiveness of antibiotics in the treatment of inflammation 
in animal models of IBD [10-12].  For example, IL-10 knockout mice develop a phenotype 
comparable to human IBD and at least two studies have shown that antibiotics such as 
neomycin, ciprofloxacin, vancomycin, and metronidazole may both prevent and treat 
intestinal inflammation [10, 12].  However, the evidence for the effectiveness of antibiotics 
in the treatment of humans with IBD has historically been less robust.  Within the past 
several years, two meta-analyses of randomized controlled trials have documented a small 
but statistically significant benefit of antibiotics to induce remission in both CD and UC [13, 
14].  In addition, several studies have now shown that antibiotic combination therapy 
significantly improves rates of remission and also steroid withdrawal in UC [15-18].   
Most notably, Turner and colleagues have recently published their experience using a two- 
to three-week course of combination antibiotic therapy in pediatric UC and indeterminate 
colitis refractory to standard immunosuppressive medications [18]. Patients were treated 
with combination oral amoxicillin, metronidazole, and doxycycline, except in children 2-7 
years old where doxycycline was substituted with ciprofloxacin, and in infants under 2 years 
old where doxycycline was substituted with gentamicin.  In addition, in cases of allergy the 
allergenic drug was substituted with gentamicin, and in hospitalized children vancomycin 
was added to the regimen. The antibiotic regimen was definitively effective in 7/15 (47%) of 
patients, inducing complete clinical remission as defined by the Pediatric Ulcerative Colitis 
Activity Index (PUCAI).  For the patients defined as primary responders (n=9), i.e., clinical 
remission at three weeks after initiating antibiotic therapy, reduction in CRP and PUCAI 
were statistically significant.  Finally, all patients repeatedly tested negative for fecal C. 
difficile and bacterial cultures indicative of developed resistance. Only one patient tested 
positive for CMV and was subsequently treated with ganciclovir.  These findings 
demonstrate the potential efficacy of an antibiotic therapeutic strategy in the treatment of 
refractory IBD.   
Antifungals 
In addition to the bacterial component, there appears to be a relationship between IBD and 
the fungal gut microbiota. The authors of a recent study demonstrated that mice lacking 
Dectin-1, a C-type leptin receptor that recognizes β-glucans in the fungal cell wall, had 
increased susceptibility to chemically induced colitis due to their altered immunological 
responses to indigenous fungi [19]. Significantly, a polymorphism in the gene encoding 
Dectin-1 (CLEC7A) was found to be associated with a severe form of ulcerative colitis in 


 
  
 
 
 
3 
humans [19]. A connection between high dietary concentrations of yeast and increased 
disease activity in patients with CD has also been suggested [20].   
 
In terms of fungal-targeted therapies for IBD, preliminary evidence suggests that 
fluconazole treatment may reduce intestinal inflammation in animal models of colitis and in 
patients with IBD [21]. We recently demonstrated a significant difference in the composition 
of the fungal microbiota in pediatric patients with IBD as compared to healthy controls [2], 
further suggesting a relationship between fungi and the pathogenesis of IBD.  
Bowel Lavage 
Given the potential role of the gut microbiota in the pathogenesis of IBD, therapies that 
deplete commensal flora in the gastrointestinal (GI) tract have been suggested. For example, 
in the 1980’s, intestinal lavage with normal saline was studied in patients hospitalized with 
acute exacerbations of severe CD. A small, controlled study demonstrated reduction in 
disease severity and also duration of hospitalization [23, 24]. Failure to further develop 
bowel lavage as an independent therapeutic option is likely secondary to advancements in 
pharmacological therapies. Recent evidence has indeed shown that bacterial diversity in the 
gut is significantly decreased following colonoscopy preparations [25].  It is unknown the 
effects of PEG lavage on the gut microbiome composition and FCP. It is expected that the 
effect of the PEG lavage on gut microbiota composition and fecal calprotectin will be 
comparable across patients who have been diagnosed with inflammatory bowel disease. 
1.2.3 Preliminary Data 
Effectiveness of Antibiotics in Mouse Models versus Humans, What’s the Difference? 
The observation that antibiotics as currently used have only modest efficacy in the treatment 
of CD and UC represents a challenge to the notion that antimicrobials could be used to 
deplete the microbiota in patients with IBD. One possible explanation is that the use of 
antibiotics in animal models is more effective in reducing intestinal bacterial load in mice 
than in humans. Indeed, in preliminary data [3], we show that two specific oral antibiotics 
dramatically reduce bacterial load by greater than 4 logs in mice within 72 hours, as 
quantified by 16S gene copy number.   


 
  
 
 
 
4 
 
 
We believe that an antibiotic therapeutic strategy capable of significantly reducing bacterial 
load in patients with CD will show greater levels of efficacy in the treatment of active 
disease than in previously reported studies [26-28]. Additionally, based on data suggesting 
the potential importance of gut fungi in IBD, we hypothesize that to focus exclusively on gut 
bacterial load may represent a missed opportunity. 
Efficacy of the Holiday Regimen for Treatment of Chronic Enterocolitis in Rhesus 
Macaques (Macaca mulatta) 
Idiopathic chronic enterocolitis (ICE) is one of the most significant causes of morbidity and 
mortality in captive nonhuman primates and remains a diagnostic and therapeutic challenge 
for veterinarians working with these species.  Current evidence suggests that ICE is a 
multifactorial disease involving perturbations in gastrointestinal bacterial populations, as 
well as the response of the host immune system to these changes [29].  Our group is 
currently collaborating with Tulane University National Primate Center (TUNPRC) on a 
study where rhesus macaques with ICE and a negative stool infectious work-up (n=6 at 
present) were treated with an anti-microbial regimen similar to the one proposed here.  The 
animals receive the following regimen: 125 mg total vancomycin hydrochloride four times 
daily, 50 mg/kg neomycin twice daily, and fluconazole 2 mg/kg twice daily.  Therapy was 
administered for a total of 14 days.  Thus far, four of the six animals have experienced no 
signs of diarrhea since completion of the treatment protocol.  Soft stool was observed for 
one day in the remaining two monkeys since completion of treatment, with normal stool 
observed on other days for both animals.  Based upon daily observations of 
mentation/behavior, activity level, and appetite as well as pre-treatment and intra-treatment 
CBC and serum chemistries, this treatment regimen was well-tolerated by all animals with 
no adverse effects noted. 
Efficacy of Combination Antibiotic Therapy for Refractory IBD at CHOP 
Figure 2: Time course of 16S rRNA gene copy number during oral antibiotic treatment (14 days of 
vancomycin plus neomycin) and upon discontinuing antibiotics on day 15 compared to control. 


 
  
 
 
 
5 
Since the paper by Turner and colleagues [18] was presented at a national meeting in 2014, 
physicians within the CHOP Center for Inflammatory Bowel Disease have been utilizing a 
combination antibiotic approach clinically for patients with IBD refractory to standard 
therapy.  As a means of preliminary efficacy evaluation, a retrospective study (CHOP IRB 
#15-011806) was performed to review CHOP’s experience treating refractory IBD with 
combination antibiotic therapy.  Information collected included patient demographics, 
disease characteristics, immunotherapy history, indication for antibiotic therapy, and type, 
dosage, and duration of antibiotics prescribed.  Eligible patients were ages 3-21 and 
prescribed treatment with three or more oral antibiotics concomitantly for the treatment of 
IBD.  Clinical outcomes were evaluated based on changes in disease activity, as measured 
by the Pediatric Crohn’s Disease Activity Index (PCDAI) in participants with CD, or the 
Pediatric Ulcerative Colitis Activity Index (PUCAI) in patients with UC or indeterminate 
colitis, at the time of initiation of combination antibiotic therapy and at multiple subsequent 
time points.  Disease morbidity outcomes were additionally measured, including referral to 
and/or scheduling of surgery, as well as escalation of therapy to an experimental medication.  
The incidence of adverse reactions during and following combination antibiotic therapy was 
also assessed. 
  
Of the enrolled patients (n=14), four participants had CD (29%) and the remainder had UC 
or indeterminate colitis (IBDU) (Table 1).  In 13 participants, the indication for combination 
antibiotic therapy was disease refractory to standard immunosuppressive therapies and in the 
remaining participant the indication for antibiotic therapy was induction and maintenance of 
remission.  Participants were prescribed combination antibiotic therapy for an average of 
29.5 days (range 9-71).  
TABLE 1: PEDIATRIC IBD PATIENTS TREATED AT CHOP WITH COMBINATION 
ANTIBIOTICS 
Case 
Number 
Agea 
IBD 
Type 
LOR to 
Medicationsb 
Antibiotic 
Regimenc 
Duration 
in Days 
Surgery Referral 
Experimental 
Therapyd 
Rescue of 
Response 
1 
13.2 
UC 
IFX+MTX 
MAC 
14 
Cancelled 
No escalation 
IFX+MTX 
2 
12.3 
UC 
IFX 
MADV 
71 
Delayed (96 days) 
n/a 
IFX 
3 
16.4 
CD 
IFX+MTX, ADA+MTX 
MCV 
23 
n/a 
No escalation 
ADA+MTX 
4 
10.8 
CD 
IFX+MTX 
MAC 
9 
Proceeded 
n/a 
n/a 
5 
13.1 
IBDU 
IFX, ADA+MTX 
MAC 
24 
Cancelled 
n/a 
ADA+MTX 
6 
15.7 
CD 
IFX+MTX 
MACV 
28 
n/a 
Escalation 
n/a 
7 
13.6 
UC 
IFX+MTX 
MAC 
21 
n/a 
n/a 
n/a 
8 
18.5 
UC 
IFX+MTX 
MAC 
59 
Cancelled 
No escalation 
n/a 


 
  
 
 
 
6 
9 
11.5 
UC 
IFX 
RCV 
35 
n/a 
n/a 
IFX+MTX 
10 
10.7 
IBDU 
IFX+MTX, ADA 
MCV 
19 
Delayed (22 days) 
No escalation 
n/a 
11 
6.5 
CD 
IFX+MTX, ADA+MTX 
MCV 
36 
n/a 
n/a 
ADA+MTX 
12 
16.1 
CD 
IFX 
MCDV 
31 
n/a 
No escalation 
IFX+MTX 
13 
12.3 
UC 
n/a 
MCV 
21 
n/a 
n/a 
n/a 
14 
10.4 
UC 
IFX 
MCDV 
22 
Cancelled 
n/a 
n/a 
 
 
 
 
 
 
 
 
 
aAge at initiation of antibiotic therapy 
 
bAll demonstrated LOR; IFX=infliximab monotherapy, IFX+MTX=IFX plus methotrexate dual therapy, 
ADA+MTX=adalimumab plus methotrexate dual therapy 
cA=amoxicillin, C=ciprofloxacin, D=doxycycline, M=metronidazole, R=rifaximin, V=vancomycin 
 
dReferral or discussion of eligibility screening for vedolizumab (Entyvio) or ustekinumab (Stelara)  
 
Because of the limitations inherent to the review of existing medical records, disease activity 
scores at all study time points were not available for each participant.  However, for those 
participants with available data, PUCAI and PCDAI scores showed decreases in disease 
activity both two weeks post-initiation and post-completion of their prescribed antibiotic 
combination regimen. 
There were four documented adverse reactions that occurred during the course of therapy or 
shortly following therapy termination.  All were mild and only one was probably related to 
the medication regimen (black, hairy tongue); all resolved without sequelae.  In addition, 
there were two severe and one life-threatening adverse event; however, all occurred two 
weeks after termination of therapy and based on clinical expertise were unlikely related to 
the antibiotic therapy.  Only one additional event was possibly related to the prescribed 
antibiotic therapy – a vaginal yeast infection that occurred four weeks post-termination of 
therapy and which also resolved without sequelae. 
Efficiency of Combination Antibiotic Therapy for Refractory IBD at PENN 
Lindsey Albenberg, DO is performing a clinical trial in adults with a similar IRB-approved 
protocol at the University of Pennsylvania, which has shown potential for benefit and safety 
of the drug regimen. The primary endpoint in the Penn protocol is the change in disease 
activity, as measured by the Harvey Bradshaw Index (HBI) score, and FCP concentration, 
between the enrollment visit and Day 15. A reduction of HBI by 3 or more points is 
considered a clinically significant change in HBI. 
Five adult participants have been enrolled. All five participants had lost response to anti-
TNF alpha therapy and were not responding to either vedolizumab or ustekinumab. The first 
participant demonstrated a significant improvement in HBI that persisted to at least 2 
months post antimicrobial therapy. This participant also had normalization of his fecal 
calprotectin from enrollment to day 15. The second two participants had decreases in the 


 
  
 
 
 
7 
HBI from enrollment to day 15. However, neither of these participants had a significant 
change in fecal calprotectin. One of these participants developed acute diarrhea on day 17. 
Stool infectious studies (including C. difficile) were negative. It was determined that the 
worsening of his diarrhea was related to progression of his already very severe CD. The 
fourth participant also demonstrated a significant improvement in HBI as well as 
normalization of the fecal calprotectin and this individual is still in the follow-up phase. The 
fifth participant is currently in the intervention phase, but this participant had an 
improvement in his HBI and normalization of his fecal calprotectin by day 8. Of note, there 
was one serious adverse event, but it was unrelated to the study procedures. There have been 
no other serious adverse events. 
We are observing very significant reductions in fecal calprotectin from baseline to day 8 and 
day 15 in about half of the participants. We suspect that this represents healing of the 
mucosa in these very sick patients with IBD. However, given how robust the response has 
been (better response than expected), we want to be sure that the reduction in calprotectin 
truly represents healing of the tissue versus the PEG lavage flushing out the neutrophils. 
This will be examined in Group 2. 
 
Table 2 shows change in HBI after completing the two week study regimen. These findings 
demonstrate the potential for benefit of the therapy proposed in this protocol.  
TABLE 2: CHANGE IN HARVEY BRADSHAW INDEX (HBI) & DISEASE 
CATEGORY FOR HOLIDAY PARTICIPANTS AT PENN 
Participant 
Number 
HBI at 
Enrollment 
HBI on 
Day 15 
Number of 
Points 
Decreased  
Clinically 
Significant 
(Y/N)* 
Disease Category 
at Enrollment 
Disease Category 
on Day 15 
11001 
11 
3 
8 
Y 
Moderate 
Remission 
11003 
13 
7 
5 
Y 
Moderate 
Mild 
11005 
9 
5 
4 
Y 
Moderate 
Mild 
11007 
8 
4 
4 
Y 
Moderate 
Remission 
11011 
7 
5 
2 
N 
Mild 
Mild 
*A reduction of HBI by 3 or more points is considered a clinically significant change in HBI. 
Only one participant has shown an improvement in fecal calprotectin from baseline to day 
15. However, it was a dramatic improvement. The n is still quite small. 
This proposal will test the hypothesis that the gut microbiota is fundamentally involved in 
the perpetuation of CD that is refractory to conventional strategies and that a strategy that 
dramatically alters the composition and/or biomass of the gut microbiota (both bacteria and 
fungi) will lead to clinical improvement and reduction of inflammation.   


 
  
 
 
 
8 
1.3 Selection of Drugs and Dosages 
In this protocol, we will allow the gastrointestinal tract a “Holiday” from gut microbes that 
may be perpetuating the inflammatory response.  We will attempt to reduce the microbial 
load in the gut through an intestinal lavage followed by short-term (14 days) treatment with 
broad-spectrum antibiotics with or without an antifungal.  The intestinal lavage protocol was 
chosen based on the standard bowel cleanse protocol utilized at Children’s Hospital of 
Philadelphia prior to colonoscopy and are also widely accepted in the literature [30].  In the 
animal study above (Figure 1) demonstrated ability to significantly reduce 16S rRNA gene 
copy number with a combination of two oral antibiotics – neomycin and vancomycin.  This 
protocol has been adapted for human use because of the risk of ototoxicity, which is 
associated with long-term neomycin therapy. Thus, using neomycin only for the first three 
days, and then neomycin will be replaced with ciprofloxacin. Ciprofloxacin will be an 
appropriate replacement as it is well known to be deeply disruptive to the gut microbiota [4]. 
For the antifungal, the study will use fluconazole, which is used to treat a variety of fungal 
infections, because it is considered to be a safer option than other systemic antifungals such 
as amphotericin.   
Animal studies have shown that the 16S rRNA gene copy number decreases after three days 
of therapy and returns to baseline five days after antibiotics are discontinued. Fourteen (14) 
days of therapy was chosen for this study so that there would be continued suppression of 
bacterial load to allow sufficient time for healing of the gastrointestinal tract. This protocol 
chose standard pediatric dosing for the treatment of systemic or gastrointestinal infections 
(see Section 7.1 for dosages). 
Participants in this study will not be required to stop any prior medications (including 
immunosuppressive medications), with the exception of probiotics and antibiotics. If 
potential participants are on prescribed antibiotics related to their IBD, they are required to 
stop those antibiotics in order to participate in this study. If potential participants are on 
antibiotics for a non-IBD related reason, they will be required to complete their current 
course before being enrolled in this study. Furthermore, participants already on steroids as 
part of their IBD regimen will be required to maintain their dosage and regimen during the 
14 days (Days 1-14) of the study drug intervention. If steroid dosage is increased during the 
14 day study drug regimen, the participant will be considered to have started rescue therapy 
and study drugs will be stopped. 
1.4 Compliance Statement 
This study will be conducted in full accordance all applicable Children’s Hospital of 
Philadelphia Research Policies and Procedures and all applicable Federal and state laws and 
regulations including 45 CFR 46, 21 CFR Parts 50, 54, 56, 312, 314 and 812 and the Good 
Clinical Practice: Consolidated Guideline approved by the International Conference on 
Harmonisation (ICH). All episodes of noncompliance will be documented. 
The investigators will perform the study in accordance with this protocol, will obtain 
consent and assent, and will report unanticipated problems involving risks to subjects or 
others in accordance with The Children’s Hospital of Philadelphia IRB Policies and 
Procedures and all federal requirements. Collection, recording, and reporting of data will be 


 
  
 
 
 
9 
accurate and will ensure the privacy, health, and welfare of research subjects during and 
after the study.  
2 
STUDY OBJECTIVES 
The purpose of the study is to determine the efficacy of a novel treatment regimen, 
employing non-immunosuppressive medications, in the management of refractory CD or 
IBDU.   Refractory patients include those patients who have experienced LOR or 
nonresponse to an immunomodulator or a biologic.  LOR is defined as patients who were 
doing well initially on an appropriate dosage of an immunomodulator or a biologic and 
subsequently developed increased disease activity.  We will treat patients with a 
combination of bowel lavage and oral antimicrobials.  We hypothesize that this strategy will 
both treat the gut inflammation associated with IBD as well as salvage response to therapy. 
2.1 Primary Objective (or Aim) 
The primary objective of this study is to determine the efficacy of a novel gut microbiota-
targeted therapeutic regimen, comprised of a bowel lavage and oral antibiotics with or 
without an antifungal, in the management of active CD or IBDU that is refractory to 
conventional, immunosuppressive therapy. 
2.2 Secondary Objectives (or Aim) 
The secondary objectives are to: 
• Correlate effectiveness in reducing bacterial 16S and fungal 18S rRNA gene copy 
number, by the use of the regimen in the primary objective, with improvement in 
disease activity for patients with CD or IBDU refractory to immunosuppression. 
 
• Determine the relationship between the effectiveness of the proposed therapies with 
changes in gut microbiota composition. 
 
• To determine the effect of PEG lavage alone on the microbiome and the fecal 
calprotectin. 
3 
INVESTIGATIONAL PLAN 
3.1 General Schema of Study Design 
“Holiday” will be a randomized, placebo controlled, double blind Phase 2a trial. Participants 
will be enrolled into one of two groups. Group 1 will consist of pediatric CD or IBDU 
patients who have moderately active disease that is refractory to conventional, 
immunosuppressive therapy and will be receiving study intervention. Group 2 will consist of 
pediatric patients undergoing a clinically indicated PEG lavage in preparation for a 
clinically-indicated GI endoscopy and will not be receiving study intervention. We expect to 
enroll 60 participants to produce 20 evaluable participants in Group 1 and 15 evaluable 
participants in Group 2.A similar IRB-approved protocol is being conducted in adults at the 
University of Pennsylvania. The ultimate enrollment goal between both sites is 30 adults and 
30 children (Group 1 only) to yield 20 evaluable participants in each group.  


 
  
 
 
 
10 
 Group 1 recruitment will target patients who have demonstrated nonresponse or LOR to 
immunosuppressive therapy, and may be facing escalation of therapy or even surgery.  
Group 2 recruitment will target patients undergoing clinically indicated PEG lavage in 
preparation for a GI endoscopy.  
Once enrolled, participants in Group 1 will be treated with bowel lavage and oral antibiotics 
with or without an antifungal over a period of 14 days. Clinical efficacy will be assessed at 
defined time points through scoring on the Pediatric Crohn’s Disease Activity Index 
(PCDAI) and the Short Crohn’s Disease Activity Index (sCDAI), the fecal calprotectin 
(FCP), a clinical marker of intestinal inflammation, and the C-reactive protein (CRP), a 
marker of systemic inflammation. At the stool collection time points, the composition of the 
gut microbiota will also be determined using 16S gene qPCR, 18S gene qPCR, 16S gene 
sequencing, and internal transcribed spacer (ITS) gene sequencing to determine effects on 
bacterial and fungal load and microbiota composition.  
 
Participants in Group 2 will submit stool samples both before and after undergoing clinically 
indicated bowel lavage in preparation for a clinical GI endoscopy. The effect of the bowel 
lavage alone on disease activity (determined via fecal calprotectin levels) and composition 
of gut microbiota (determined via 16S gene qPCR, 18S gene qPCR, 16S gene sequencing, 
and ITS gene sequencing) will be assessed. 16S gene qPCR determines bacterial load. 18S 
gene qPCR determines fungal load. 16S gene sequencing determines bacterial microbiota 
composition. ITS gene sequencing determines fungal microbiota composition.  
 
3.1.1 Screening & Enrollment Phase 
Potential participants will be identified through medical chart review, clinic schedules, 
inpatient lists, as well as physician referrals. Families will be contacted by a research team 
member and informed consent will be obtained.  For prospective Group 1 participants, a  
REDCap Screening Questionnaire will be completed to confirm eligibility, and an 
enrollment visit will be scheduled. Participants will be given study supplies necessary for 
appropriate specimen collection. For prospective Group 2 subjects, consent will be obtained 
over the phone. 
3.1.1.1 Group 1(Interventional Group)  
For Group 1 participants, a verbal screening consent form will be obtained before collecting 
screening information. Once verbal consent is obtained, potential participants will be sent a 
REDCap Screening Questionnaire. Participants who seem to meet all inclusion criteria (see 
Section 3.4.1.1) will be scheduled for an enrollment visit and will be given study supplies. 
The screening consent will allow the subject to complete the screening questionnaire and 
provide samples at their first visit. Written informed consent, and assent when appropriate, 
will be obtained before undergoing any other study procedures.  The study will be explained 
to each participant and their legal guardian when they come to the study site.  If the subject 
and/or guardian agrees to participate, they will sign the written consent form.The enrollment 
visit will include a physical examination to determine eligibility based on clinical 


 
  
 
 
 
11 
parameters. Blood and stool samples will also be obtained at the enrollment visit for baseline 
values.  If not completed clinically within 1 month of enrollment, the stool sample may be 
tested to rule out Clostridium difficile infection.  If a participant tests positive for C. difficile 
infection at enrollment, they will be withdrawn from the study and their primary GI 
physician will be notified so that antibiotic therapy can be continued on a clinical basis. 
These participants can be re-screened once C. difficile has been treated and they have been 
tested negative for C. difficile infection. The enrollment visit blood sample will also be 
assessed for serum creatinine to ensure no participants with impaired kidney function are 
actively enrolled. Female participants who have menses and/or are > 11 years old will have 
a urine pregnancy test. All participants will undergo electrocardiogram (EKG) to assess QTc 
interval at baseline. Participants and their parents will also be asked to complete 7 days of an 
online “Daily Survey” through REDCap to record their baseline symptoms before starting 
any study drug. 
 
3.1.1.2 Group 2 (Observational Group)  
 
For Group 2 participants, a verbal informed consent form will be obtained before 
collecting a baseline stool sample and starting their clinically indicated bowel 
preparation. We will target patients who had a clinical disease activity score, physician 
global assessment, or laboratory values suggestive of ongoing active inflammation. If a 
clinical fecal calprotectin level greater than or equal to 350 mcg/g is not available within 
a month prior to enrollment, the baseline stool sample will be tested for fecal calprotectin 
level.  . If the baseline fecal calprotectin is ³350 mcg/g and if the patient’s primary GI 
does not intend to start the patient on a corticosteroid or biologic within the 7 days 
following the procedure, subjects will then provide additional stool samples at time 
points 5 days and 12 days after their clinically-indicated procedure. These stool collection 
time points align with those of Group 1 participants, relative to their PEG lavage. 
 
3.1.2 Study Treatment Phase  
For Group 1 participants who are fully eligible, medications will be dispensed from The 
University of Pennsylvania’s Investigational Drug Services (Penn IDS) and shipped to the 
participant’s home address. There will be no more than 17 days between the enrollment visit 
and the start of the intervention phase. The antimicrobial regimen will include 3 days of 
vancomycin and neomycin followed by 11 days of vancomycin and ciprofloxacin. 
Participants will also be randomized 1:1 in a double-blinded fashion to fluconazole or 
placebo for 14 days. See Section 7.1 for details about dose, frequency and duration of all 
study drugs.  
On Day 2, participants will also undergo a bowel preparation with polyethylene glycol 
(PEG) 3350. On this day, the diet will be limited to clear liquids. There will be no other 
dietary modifications during the course of the study. 


 
  
 
 
 
12 
On Days 1-14, participants and/or their parent/guardian will record their symptoms daily 
through a secure, web-based portal (REDCap).  This information will be used to calculate 
the sCDAI score.  In– person study visits will take place on days 5, 8, and 15. The indicated 
clinical and laboratory parameters will be assessed at the time of these visits.  
There is a +/- 2 day window within which the Day 15 visit must occur. 
3.1.3 Optional Intervention Extension Phase (14 day repeat drug regimen) 
Group 1 participants who achieve clinical response (reduction of PCDAI by 15 or more 
points) or clinical remission (PCDAI <15) to the study intervention at Day 15, but have 
relapsed (PCDAI > 30 or sCDAI > 20) between days 30 and 64 (2 months), will be offered 
the option to repeat the 14 day study regimen. Once the study team is aware of a 
participant’s disease relapse, the participant’s symptoms will be observed for 2 weeks 
through the survey before starting their extension phase to confirm relapse. Participants who 
repeat the regimen will not require rescreening or a repeat enrollment visit. To reduce the 
risk of a prolonged QTc interval, the repeated regimen will exclude fluconazole/ placebo. 
The PEG lavage will also be excluded. An additional telephone visit (visit 6.1) will be 
conducted. This visit will take place at the end of the extension phase. All participants will 
have a 3 month visit (visit 7) and the last study visit for all participants will be at 6 months. 
3.1.4 Follow Up Phase 
The follow-up phase will include Day 16 until 6 months following the end of the 
intervention phase.  The purpose of the follow-up phase is to determine the durability of the 
effect of the intervention over time.  A telephone follow-up will occur on Day 22.  An in-
person study visit will take place on Day 29.  The indicated clinical and laboratory 
parameters will be assessed at the time of these visits (See Table 1, Study Schedule of 
Procedures). There is a +/- 3 day window for these two visits (Day 22 and 29). Finally, 
telephone follow-ups will occur at 3 months and 6 months following the intervention phase.  
There will be a 14-day window for the 3 month and 6 month follow-up telephone visits. 
3.2 Allocation to Treatment Groups and Blinding 
Within Group 1, participants will be randomized to one of two arms, one which will be 
receiving fluconazole in addition to antibiotics and one which will receive placebo. The 
randomization schedule will be generated by Penn IDS. Neither the participant, the study 
team, nor the clinical site personnel will know the treatment group to which any participant 
is randomized. 
3.3 Study Duration, Enrollment and Number of Sites 
3.3.1 Duration of Study Participation 
3.3.1.1 Group 1 Participants 
The study duration per Group 1 participant will be approximately 6-8 months, with up to 30 
days for screening (from telephone verbal consent to the enrollment visit), 2 weeks for the 
intervention phase, and up to 6 months for the follow-up phase.   


 
  
 
 
 
13 
Participants who meet criteria and opt to undergo the extension phase of the antimicrobial 
regimen will prolong their participation in the study by approximately 2 weeks.  
3.3.1.2 Group 2 Participants 
The study duration per Group 2 participant could be up to 2 months.   
3.3.2 Total Number of Study Sites/Total Number of Subjects Projected 
The study will be performed at one site, The Children’s Hospital of Philadelphia. A similar 
IRB-approved protocol is being conducted in adults at the University of Pennsylvania. The 
research will include outcome data from the Penn protocol. Data from these individuals will 
not be included in the enrollment numbers for this study and research activities under the 
Penn protocol will not be reported as part of the continuing review. 
We expect to enroll 60 participants to produce 20 evaluable participants in Group 1 and 15 
evaluable participants in Group 2. 
3.4 Study Population 
3.4.1 Group 1: Interventional Group; Participants who have had primary non-
response or loss of response to conventional, immunosuppressive treatment 
3.4.1.1 Inclusion Criteria —  
1. Parental/guardian permission (informed consent) and if appropriate, child assent. 
2. Males or females 6-18 years of age 
3. Current weight >10 kg (or 22 lb) 
4. Ability to swallow pills 
5. Normal kidney function, defined by eGFR >90 mL/min/1.73m3, estimated using 
serum cystatin C, creatinine, BUN, and height in the combined comprehensive eGFR 
equation.  
6. Normal AST, ALT, and alkaline phosphatase, < 1.5 than the upper limit of normal 
for the reference range for the child’s age, according to CHOP lab reference ranges. 
7. Active CD or IBDU defined as PCDAI>30 
*Patients who have a partial PCDAI  of at least 20, including only the subjective 
reporting of symptoms over the past week (see Section 5.2.1), will be considered 
eligible for scheduling of an enrollment visit and will only be actively enrolled with a 
definite PCDAI score of 30 or above, inclusive of the physical examination and 
abdominal mass component.  
8. CRP >15mg/L (or 1.5mg/dL) or fecal calprotectin (FCP) > 350mcg/g (within one 
month of enrollment) 
9. Have been treated with one of the following therapies** for at least 8 weeks with 
primary nonresponse or an initial response, followed by LOR (self-reported 


 
  
 
 
 
14 
worsening of symptoms for ≥ 7 days): azathioprine, 6-mercaptopurine, methotrexate, 
adalimumab, certolizumab, golimumab, infliximab, natalizumab, vedolizumab, or 
ustekinumab 
If taking steroids, dose must be stable for at least 2 weeks prior to screening 
**These medications must have been administered at standard, therapeutic dosages. 
10. Girls who have menses and/or are ³ 11 years of age must have a negative 
urine/serum pregnancy test and must use an acceptable method of contraception, 
including abstinence, a barrier method (diaphragm or condom), Depo-Provera, or an 
oral contraceptive, for the duration of the study. 
3.4.1.2 Exclusion Criteria —  
1. Unwillingness to provide informed consent  
2. Allergy or intolerance to aminoglycosides or any of the medications used in this 
study, including medications within the same class 
3. Current use of one or more of the following medications: 5-fluorouracil, digoxin, 
anticoagulants, theophylline, phenytoin, probenecid, duloxetine, clozapine, 
sildenafil, hydrochlorothiazide, cyclosporine, hypoglycemics, terfenadine, 
tacrolimus, rifabutin, midazolam, and voriconazole 
4. Known diagnosis of diabetes mellitus 
5. Known or suspected stricturing disease producing obstructive symptoms 
6. Active Clostridium difficile infection 
7. Baseline QTc interval on EKG as follows: 
a. 3-5 yo: >412ms in males or >417ms in females 
b. 5-8 yo: >411ms in males or >409ms in females 
c. 8-12 yo: >407ms in males or >414ms in females 
d. >18 yo: > 430ms in males or > 450ms in females 
8. Current use of antibiotics 
9. Starting or increasing the dose of a IBD related medication within 4 weeks of 
screening including: 
e. Azathioprine or 6-mercaptopurine (6MP) 
f. Infliximab, adalimumab, certolizumab, or golimumab 
g. Natalizumab, vedolizumab, or ustekinumab 


 
  
 
 
 
15 
h. Methotrexate 
i. Any 5-ASA compound (e.g. Lialda, Asacol, etc) 
j. Prednisone, budesonide or other steroids delivered orally or rectally 
10. Participants who, in the opinion of the investigator, may be non-compliant with 
study schedules or procedures 
3.4.2 Group 2: Observational Group; Participants undergoing clinically indicated 
PEG lavage in preparation for a GI endoscopy.  
3.4.2.1 Inclusion Criteria —  
1. Males or females 10 years of age and older.  
 
2.  Patients undergoing a clinical GI endoscopy due to suspicion for active intestinal 
inflammation determined by physician global assessment (PGA). 
3. Undergoing a bowel preparation as part of clinical care. 
4. Parental/guardian permission (informed consent) and if appropriate, child assent. 
3.4.2.2 Exclusion Criteria —  
1. Antibiotic use within the past 30 days.  
 
2. Current presence of an ostomy bag.  
3.   Patients undergoing a non- polyethylene glycol 3350 cleanout. 
4. Unwillingness to provide informed consent.  
5. Parents/guardians or subjects who, in the opinion of the Investigator, may be non-
compliant with study schedules or procedures. 
Subjects that do not meet all of the enrollment criteria may not be enrolled. Any violations 
of these criteria must be reported in accordance with IRB Policies and Procedures.  
4 
STUDY PROCEDURES 
4.1 
Group 1 Participants 
4.1.1 Screening Visit 
Screening visit will include: 
• Informed consent  
• Email or complete screening questionnaire  
• Schedule enrollment visit  
• Distribute study supplies 


 
  
 
 
 
16 
 
4.1.2 
Enrollment Phase (Visit 1) 
Eligible participants will be seen by a study team investigator and study coordinator at the 
enrollment visit.  The written informed consent form may be signed at this visit if not 
already completed.  Enrollment will include: 
• Written informed consent & assent (if applicable) 
• Review and documentation of eligibility criteria  
• Obtain collected stool sample for analysis of microbiome  
o If no record of negative C. difficile toxin  within 1 month of enrollment, stool 
will be used to test for C. difficile toxin  
o If no record of fecal calprotectin within 1 month of enrollment, stool will be 
used to test fecal calprotectin 
• Vital signs 
• Anthropometric measurements 
• Physical exam, including CD disease symptom assessment for PCDAI 
• Rectal swabs (2) for mucosally-associated microbiome analysis 
• Blood sample (CBC, CMP, CRP, ESR, serum cystatin C, biologic levels if applicable 
with extra stored for future use) 
• Urine pregnancy test for female participants (if applicable) 
• EKG 
• Medication education 
• Distribution of Gatorade (and a pitcher) 
• Distribution of supplies 
 
4.1.3 
Study Treatment Phase (Days 1-15 including Visits 2-4): In-person Study 
Visits 
Day 1 is defined as the day that a participant starts the study drug regimen. The study team 
will instruct the participant to start taking study drugs on the upcoming Monday, Thursday, 
or Friday, in order to enhance compliance and ensure that in-person study visits do not fall 
on weekends.  
4.1.4 
Daily Surveys 
The participant and/or their parent/guardian will be asked to complete an online survey 
through REDCap asking a variety of questions to monitor disease activity. Participants and 
their parent/guardian will be prompted to identify any concerns including medication side 
effects and/or worsening of symptoms.  This survey will be completed as listed in Table 1, 
Schedule of Study Procedures. 
Survey responses will be monitored by study staff through REDCap on a regular basis. If 
surveys are not completed as scheduled, the coordinator may contact the participant to 
ensure compliance.  
If a participant is enrolled in the study who does not have daily access to the internet and/or 
email, a daily survey paper diary will be provided to them. In order to ensure compliance for 


 
  
 
 
 
17 
this group, they will be required to ship the completed paper surveys to the study team on a 
weekly basis. Shipping labels will be provided in advance to enable this practice. 
4.1.5 
Study Visit 2 (Day 5) 
The visit will include: 
• Vital signs 
• Anthropometric measurements 
• Physical exam, including CD disease symptom history for PCDAI 
• Blood sample (vancomycin level, with extra stored for future use to evaluate 
metabolomics and neomycin levels) 
• Obtain stool sample 
• Adverse event assessment (see Section 8) 
• Study drug compliance assessment 
• Update current medications log 
• Daily Survey  
• Distribution of supplies 
4.1.6 
Study Visit 3 (Day 8) 
The visit will include: 
• Vital signs 
• Anthropometric measurements 
• Physical exam, including CD disease symptom assessment for PCDAI 
• EKG 
• Rectal swab for mucosally-associated microbiome analysis 
• Blood sample (CBC, CMP, CRP, ESR with extra stored for future use and vancomycin 
level, if applicable) 
• Obtain stool sample  
• Adverse event assessment (see Section 8) 
• Study drug compliance assessment 
• Update current medications log 
• Daily Survey  
• Distribution of supplies 
4.1.7 
Study Visit 4 (Day 15) 
The visit will include: 
• Vital signs 
• Anthropometric measurements 
• Physical exam, including CD disease symptom assessment for PCDAI 
• Rectal swab for mucosally-associated microbiome analysis 
• Blood sample (CBC, CMP, CRP, ESR with extra stored for future use and vancomycin 
level, if applicable) 
• Collect stool sample  


 
  
 
 
 
18 
• Adverse event assessment (see Section 8) 
• Study drug compliance assessment and collect any unused study drug 
• Update current medications log 
• Daily Survey  
• Distribution of supplies 
4.1.8 
Follow-up Phase 
Participants will be followed from Day 16 through 6 months.  The study team will conduct a 
telephone call on Day 22 and an in-person visit on Day 29.  From Day 30 through 6 months 
post-treatment, participants and/or their parent/guardian will continue to record symptoms 
weekly in REDCap. Telephone follow-up will occur at 3 months and 6 months. 
4.1.8.1 Telephone Follow-Up: Visit 5 (Day 22) 
A telephone follow-up will be conducted on Day 22 (+/- 3 days). During the telephone 
session, questions will be asked to assess the general state of the participant’s IBD and their 
current medication regimen. The participant’s electronic medical record will be reviewed. 
Any recent surgeries, hospitalizations, and C difficile test results since their last study visit 
will be recorded. Participants and their parent/guardian will be reminded to ship or bring in a 
stool sample. 
4.1.8.2 Study Visit 6 (Day 29) 
The visit will be conducted on Day 29 (+/- 3 days). The visit will include: 
• Vital signs 
• Anthropometric measurements 
• Physical exam, including CD disease symptom assessment for PCDAI 
• Rectal swab for mucosally-associated microbiome analysis 
• Blood sample (CBC, CMP, CRP, ESR with extra stored for future use) 
• Collect stool sample  
• Adverse event assessment (see Section 8) 
• Study drug compliance assessment 
• Update current medications log 
• Daily Survey  
4.1.8.3 Telephone Follow-Ups: 3 Months & 6 Months 
Telephone follow-up will also occur at 3 months and 6 months (+/- 2 weeks). Questions will 
be asked to assess the general state of the participant’s IBD and their current medication 
regimen. The participant’s electronic medical record will be reviewed. Any recent surgeries, 
hospitalizations, and C difficile test results since their last study visit will be recorded. 
4.1.9 
Concomitant Medication 
All prior and concomitant medications used within 30 days prior to the screening visit and 
through the end of the study will be recorded. The dates of administration, dosage, and 
reason for use will be collected.  All concomitant medications will be continued with the 
exception of probiotics and antibiotics which must be discontinued prior to the start of the 


 
  
 
 
 
19 
intervention phase (day 1-14). If potential participants are on prescribed antibiotics related to 
their IBD, they will be required to stop those antibiotics in order to participate in this study. 
If potential participants are on antibiotics for non-IBD related reasons, they will be required 
to complete their current course before enrolling in this study. Participants already on 
steroids as part of their IBD regimen will be required to maintain their dose and regimen 
during the 14 days (Days 1-14) of the study drug intervention. If steroid dosage is increased 
during the 14 day study drug regimen, the participant will be considered to have started 
rescue therapy and study drugs will be stopped. 
4.1.10 
Rescue Medication Administration 
If a participant’s condition worsens during the course of the study, the PI, in conjunction 
with the participant’s primary provider, will make a decision on whether or not to withdraw 
the participant from the study.  If the participant receives rescue medication(s) during Days 
1-14 of the study, the study drugs will be stopped and they will be considered a non-
responder. Participants will be followed until the end of the 6 month time point of the study 
schedule.  
4.2 Group 2 Participants 
4.2.1 Visit 1: Baseline Sample Prior to bowel cleanout 
• Obtain informed consent 
• Medical Record Review 
• Distribution of study supplies 
• Collect stool sample  
4.2.2 Visit 2: Day 5 (+/- 24 hours) after GI endoscopy 
• Medical Record Review 
• Collect stool sample  
• Distribute supplies for next sample collection  
4.2.3 Visit 3: Day 12 (+/- 24 hours) after GI endoscopy  
• Medical Record Review 
• Collect stool sample  
 
 
4.3 Subject Completion/Withdrawal 
Participants may withdraw from the study at any time without prejudice to their clinical 
care.  They may also be discontinued from the study at the discretion of the PI for lack of 
adherence to study treatment or visit schedules, AEs, lack of response, reasons of safety, 
administrative reasons and/or need for rescue medication during the enrollment or 
intervention phase.  Participants who require rescue medication or surgery after completion 
of the intervention regimen (Day 15 or later) will continue to be followed by the study with 
their permission. If a subject withdraws from the study all research samples and data 
collected prior to withdraw will remain part of the study.   It will be documented whether or 


 
  
 
 
 
20 
not each participant completes the clinical study. If the PI becomes aware of any serious, 
related adverse events after the participant completes or withdraws from the study, they will 
be recorded in the adverse event log of the study and to the IRB (when applicable). 
4.3.1 Early Termination Study Visit 
Group 1 participants who withdraw from the study will have all procedures enumerated for 
the last visit as the early termination visit. Participants who are withdrawn during the 
intervention phase will be asked to return the investigational product. 


 
  
 
 
 
21 
5 
STUDY EVALUATIONS AND MEASUREMENTS 
5.1 Screening and Monitoring Evaluations and Measurements 
5.1.1 Group 1 
5.1.1.1 Medical Record Review 
Include a listing of the variables that will be abstracted from the medical chart (paper or 
electronic). 
• Date of birth 
• MRN 
• Mailing address 
• Email address 
• Telephone number 
• Sex 
• Race 
• Height 
• Weight 
• IBD history (including date of diagnosis, and disease location) 
• Prior use of medications 
• Current medications 
• Medication allergies 
• Surgical history (including all surgeries regardless of relation to IBD) 
• Co-morbid medical conditions 
• History of stricturing or fistulizing disease 
• Interview with participant (such as bowel frequency, abdominal pain, general well-
being) 
• Physical examination 
• Laboratory tests (including ESR, CRP, albumin, hematocrit, hemoglobin, fecal 
calprotectin, stool C. difficile toxin, drug levels for biologics) 
5.1.1.2 Physical Examination 
A physical examination will be performed in order to calculate the PCDAI at all in-person 
study visits for Group 1 participants. A study investigator will document whether there is an 
abdominal mass (0=no tenderness, no mass, 5= tenderness, no mass without tenderness, 10 
= tenderness, involuntary guarding, definite mass). A study investigator will also document 
any extraintestinal manifestations of disease, including arthralgia, uveitis, erythema 
nodosum, aphthous ulcers, Pyoderma gangrenosum, anal fissure, new fistula, and/or 
abscess. Documentation may be completed in EPIC. 
5.1.1.3 Vital Signs 
Oral temperature will be obtained using a digital thermometer.  Heart rate and blood 
pressure will be obtained using an automated device while the patient is seated.  Height and 
weight will also be obtained as listed in Table 1, Schedule of Procedures. 


 
  
 
 
 
22 
5.1.1.4 EKG 
An EKG will be performed by trained staff on Day 0 (the enrollment visit) and on Day 8 
(Visit 3). EKG is indicated because both ciprofloxacin and fluconazole carry some risk of 
QTc interval prolongation. Prolonged QTc intervals are defined in section 3.4.2. Participants 
with a prolonged QTc interval at baseline will be excluded. Participants with a prolonged 
QTc interval on Day 8 will discontinue the fluconazole/ placebo aspect of the study 
medication regimen. The study coordinator will remove the fluconazole/ placebo from the 
blister pack to avoid accidental doses. 
5.1.1.5 Laboratory Blood Evaluations 
Blood will be collected and processed by trained staff. The following testing will be 
performed: 
• ESR  
 
ESR will be evaluated at the enrollment visit, day 8, day 15, and day 29. 
 
• CRP 
 
CRP will be evaluated at the enrollment visit, day 8, day 15, and day 29. 
 
• CMP 
 
CMP will be evaluated at the enrollment visit, day 8, day 15, and day 29. 
 
• CBC without differential 
CBC without differential will be evaluated at the enrollment visit, day 8, day 15, and 
day 29. 
• Serum cystatin C  
 
Serum cystatin C will be evaluated at the enrollment visit. Serum cystatin C, 
creatinine, BUN, and height will be used in the combined comprehensive eGFR 
equation to estimate eGFR in order to confirm eligibility. 
 
• Vancomycin Level 
 
Serum vancomycin levels will be tested on day 5 to monitor for systemic absorption 
of vancomycin. If the result is above the therapeutic range, vancomycin will be 
discontinued and serum vancomycin will be tested on day 8. If on day 8, serum 
vancomycin level is below the therapeutic range, vancomycin will be restarted, but 
the dose will be decreased by 25%. If the serum vancomycin level remains 
therapeutic or above therapeutic, vancomycin will not be restarted and the serum 
level will be rechecked on day 15. 
 


 
  
 
 
 
23 
• Drug levels for participants on biologics stored for future testing 
 
At the enrollment visit, blood will be obtained for drug level and antibody testing for 
patients who are being treated with infliximab or adalimumab (ARUP laboratories). 
Serum will be stored frozen in ARUP transport tubes. Serum will be stored for future 
use so that it will be possible to correlate response to this regimen with biologic drug 
levels and presence or absence of biologic medication antibodies. 
 
 
 
• Extra blood for storage for future testing 
Extra blood will be drawn and will be stored for future metabolomics studies at the 
enrollment visit, day 5, day 8, day 15, and day 29.  
Total blood draws will not exceed 3ml/kg or 50 ml (whichever is greater) within an 8-week 
period. 
5.1.1.6 Pregnancy Testing 
A urine pregnancy test will be performed for female subjects ³ 11 years of age and girls <11 
years who are physically capable of becoming pregnant. 
5.1.1.7 Stool Collection, Shipping, and Analysis 
Each participant will be provided with stool collection kits to take home during the course of 
the study. Participants will be instructed to collect a bowel movement at 5 time points – 
enrollment, Day 8, Day 15, Day 22, and Day 29. Stool samples will be returned to CHOP 
using pre-paid mailers, by dropping it off at the main hospital or a satellite location, or by 
submitting it to a study team member at a study visit. 
All specimens remaining after the study is complete will be retained for possible future use 
or it is deemed by the investigators that the specimens are no longer needed. 
Stool sample from the enrollment will be sent to a CHOP lab for C. difficile testing (if not 
tested clinically within one month of enrollment).  
Stool samples will be aliquoted for FCP testing and microbiome analyses. The remaining 
Stool will be stored in the laboratory of Dr. Gary Wu at the University of Pennsylvania. 
Microbiome analysis will occur through the PennCHOP Microbiome Center. 
At the enrollment visit, Study Visit 3, Study Visit 4, and Study Visit 6, participants will 
undergo a rectal swab for assessment of the mucosally-associated gut microbiota. Swabs 
will stored in a -80 freezer at the University of Pennsylvania.   
All frozen swabs will be analyzed by the PennCHOP Microbiome Center. 


 
  
 
 
 
24 
5.1.2 Group 2 
5.1.2.1 Medical Record Review 
• Date of birth 
• MRN 
• Mailing address 
• Email address 
• Telephone number 
• Sex 
• IBD  history (including date of diagnosis, and disease location) 
• Prior use of medications 
• Current medications 
• Procedure reports and phone encounters associated with bowl prep  
• Physical examination 
• Laboratory tests (including ESR, CRP, albumin, hematocrit, hemoglobin, fecal 
calprotectin, stool C. difficile toxin, drug levels for biologics) 
The above data elements will be abstracted manually from the electronic medical record by 
study staff.  
5.1.2.2 Sample Collection  
Stool samples will be collected at specified time points during the study, before and 
after undergoing PEG lavage. If participants are not seen in clinic during the study 
timeframe, specimen collection direction and supplies will be mailed to the participant. The 
family will use a stool collection hat to obtain the stool. Samples will be returned to CHOP. 
Samples will be processed for microbiome analysis identically to those of Group 1 
participants.   
5.2 Efficacy Evaluations 
5.2.1 Diagnostic Tests, Scales, Measures, etc. 
The Pediatric Crohn’s Disease Activity Index is a validated, non-invasive scale that is 
widely used in clinical trials to assess Crohn’s disease activity among children [31].   The 
PCDAI scale incorporates self-reported symptoms, historical features, laboratory data 
(hematocrit, albumin, and ESR), and physical examination findings for an overall score of 0 
to 100 [31].  The PCDAI includes the following measurements: 1. Subjective reporting of 
the degree of abdominal pain, stool pattern, and general well-being (recall over the past 
week). 2. Presence of extraintestinal manifestations, such as fever, arthritis, rash, and uveitis. 
3. Physical examination findings. 4. Weight change and either height change or height 
velocity. 5. Hematocrit (HCT), erythrocyte sedimentation rate (ESR), and serum albumin.  
 
A partial PCDAI score will be used to evaluate patients at enrollment. This will consist of 
the PCDAI score without the physical exam or laboratory component (HCT, ESR, and 
albumin) of the assessment. The subject reports the degree of abdominal pain, stools per 
day, and general well-being over the previous week. The scoring system is outlined in Table 
3.The partial PCDAI is calculated as the sum of the scores from the 3 subjective questions in 


 
  
 
 
 
25 
the PUCAI, and ranges from 0 to 30. The partial PCDAI includes the following three 
measurements; scoring for each measurement is indicated in parentheses: 
 
Table 3: Partial PCDAI Score Criteria  
 
Symptom 
Degree 
Score 
 
None  
0 
Abdominal Pain 
Mild: Brief, does not interfere with activities  
5 
 
Moderate/Severe: Daily, longer lasting, affects activities, 
nocturnal  
10 
 
0-1 liquid stools, no blood  
0 
Stools (per day) 
Up to 2 semi-formed with small blood, or 2-5 liquid 
5 
 
Gross bleeding, or >6 liquid, gross blood, or nocturnal diarrhea  10 
 
No limitation of activities, well 
0 
Patient Functioning, 
General well-being 
Occasional difficulty in maintaining age-appropriate activities, 
below par 
5 
 
Frequent limitation of activity, very poor 
10 
Active disease will be defined as a PCDAI score >10 regardless of the FCP concentration 
[43].  To be defined as having achieved a full clinical response (remission), patients must 
have a PCDAI ≤10 or a 15 point reduction from week 0, and a FCP concentration ≤200 
mcg/g. Group 1 participants with PCDAI≤10 or a 15 point reduction from week 0 but with 
elevated FCP (i.e. >200 mcg/g) will be considered partial responders.  The sCDAI, a 
modified score validated in adults that includes only the history elements[34], will be 
administered through the daily REDCap surveys on Day 1-29 and then weekly thereafter 
(see Section 4.3.1). The sCDAI is validated in the adult population, but there is no 
equivalent measure in the pediatric population. Therefore, the sCDAI will be used to 
evaluate disease activity in daily surveys.  
Both PCDAI and sCDAI are validated measures of CD disease activity. The sCDAI is 
validated only in the adult population, but there is no equivalent measure in the pediatric 
population. Therefore, the sCDAI will be used to evaluate disease activity in daily surveys.  
 
5.2.2 Fecal calprotectin 
Evidence suggests that fecal calprotectin (FCP) represents an excellent surrogate marker of 
intestinal inflammation and disease activity. Calprotectin is 36 kDa calcium- and zinc-
binding protein that represents 60% of cytosolic proteins in granulocytes [35].  Furthermore, 
calprotectin is highly stable in feces when stored at room temperature for up to 1 week [6].  
Clinically, the concentration of calprotectin in feces (FCP) is used as a non-invasive 
measure of neutrophilic infiltrate in the bowel mucosa, and thus intestinal inflammation. The 
correlation of decreased FCP concentration to mucosal healing has been demonstrated by 
endoscopy in ulcerative colitis and Crohn’s disease [7]. This has been confirmed in both 
adult and pediatric populations with Crohn’s disease [8, 9]. A recent meta-analysis identified 
a cut point of 250 mcg/g as optimal to distinguish the presence or absence of endoscopically 
detectable mucosal inflammation [41]. However, reduction in FCP is also used to assess 


 
  
 
 
 
26 
improvement. For example, following treatment with anti-TNF therapy, FCP has been 
demonstrated to dramatically decline [42].   
 
In this study, FCP concentration will be assessed using ELISA methods. The results of each 
stool calprotectin will be entered into CHOP’s electronic medical record and shared with the 
participant’s primary gastroenterologist.  Stool calprotectin is used as a marker of intestinal 
inflammation.  It is standard-of-care at the CHOP Inflammatory Bowel Center to consider 
any stool calprotectin value above 250µg/g as significantly elevated.   
5.2.3 C-reactive protein (CRP) 
C-reactive protein is produced mainly in hepatocytes in response to acute phase stimuli such 
as inflammation.  Its production is driven by circulating cytokines. C-reactive protein is 
commonly used to screen the activity of chronic inflammatory diseases including IBD. In 
general, patients with CD have a high CRP when the disease is active and a normal CRP 
when the disease is quiescent.  CRP will be tested through a CHOP laboratory. 
5.2.4 Microbial DNA sequencing 
DNA will be prepared in the PennCHOP Microbiome Center. Samples will be sent to the 
center de-identified and coded with a study number. We will perform 16S rRNA and ITS gene 
sequencing to evaluate the bacterial and fungal microbiota, respectively, in stool and rectal 
swab samples. Isolated DNA will be quantified using the Picogreen system and 50 ng of DNA 
will be amplified.  Pyrosequencing will be carried out using barcoded primers as previously 
described [10].  For pyrosequencing of bacteria, primers annealing to the V1V2 region of the 
16S bacterial gene will be used.  The development of the ITS1 fungal primers is described in 
[10].  For pyrosequencing, we will use the Roche/454 Genome Sequencer Junior.  Sequence 
data will be processed using QIIME [11]. If warranted by the preliminary data, samples may 
be analyzed further using a metagenomic approach, in which DNA samples are nebulized, 
ligated to linkers, and subjected to pyrosequencing (IlluminaHiSeq).  This allows enumeration 
of the types of genes present in a sample. To determine bacterial and fungal load, respectively, 
we will determine 16S and 18S gene copy number from the stool and rectal swab samples. 
The qPCR methods including the details of the primers as well as PCR cycling conditions 
have been previously described [12]. 
5.3 Safety Evaluation 
Participant safety will be monitored by monitoring adverse events, medication side effects, 
vital signs, physical examinations, and laboratory data. The Principal Investigator and study 
team will specifically monitor participants for fever, nausea/vomiting, increased abdominal 
pain, and increased diarrhea from baseline (see Section 8).  Adverse events will be 
compared to all known side effects of the antimicrobials prescribed through the current 
study (see Section 9.5.2). All adverse events will be tracked and assessed by the PI. Adverse 
events will be reported according to CHOP Research Policy and Procedure – please see 
Section 9.5.1 for additional safety monitoring details for this study. 


 
  
 
 
 
27 
6 
STATISTICAL CONSIDERATIONS 
6.1 Primary Endpoint 
The primary endpoint will be the change in disease activity, as measured by PCDAI and 
FCP concentration, between the enrollment visit and Day 15 for Group 1 participants. All 
participants who withdraw for any reason prior to day 15 will be considered treatment 
failures.  
To be defined as having achieved a full clinical response (remission), patients must have: 
• A PCDAI ≤10 or a 15-point reduction from week 0, and a FCP concentration ≤200 
mcg/g.  
• Participants with PCDAI≤10 or a 15-point reduction from enrollment but with 
elevated FCP (i.e. > 200 mcg/g) will be considered partial responders. 
6.2 Secondary Endpoints 
Secondary endpoints will include the following: 
• The change in CRP between the enrollment visit and Day 15 
• Correlation of effectiveness in reducing bacterial 16S and fungal 18S rRNA copy 
number, by the use of oral antimicrobials combined with bowel lavage, with 
improvement of disease activity in patients with CD or IBDU that is refractory to 
immunosupression. 
• The relationship between the effectiveness of the proposed regimen with changes to 
the composition of the gut microbiota 
• Safety and tolerability of the treatment regimen based on medication side effects 
and/or adverse events (AEs). 
• The change in FCP between baseline, Day 5 after procedure, and Day 12 after 
procedure in Group 2 participants.  
 
6.3 Statistical Methods 
The two treatment arms in Group 1 will be compared using standard descriptive statistics. 
Categorical variables will be compared using Fisher’s exact test and continuous variables 
will be compared using the unpaired t-test or Wilcoxon rank sum test if the data are not 
normally distributed.   
Our estimates of efficacy will use four outcome measures: clinical response, clinical 
remission, reduction in FCP concentration, and reduction in CRP. For clinical response 
(reduction of score on PCDAI by 15 or more points) we will report the proportion and 
binomial 95% confidence intervals. Similar methods will be used for remission (PCDAI 
<10). Although 250 mcg/g has been recently recommended, there is no standard definition 
of a clinically meaningful reduction in FCP and many definitions have been used. Therefore, 
we will use a paired t-test (after applying a log transformation if necessary) to establish 


 
  
 
 
 
28 
whether the FCP concentration is lower following therapy than at baseline and we will also 
report the proportion of patients with reduction in FCP to less than 250 mcg/g among the 
subset with baseline FCP > 350 mcg/g.  Similarly, there is no standard definition of a 
clinically meaningful reduction in CRP.  Therefore, we will use a paired t-test (after 
applying a log transformation if necessary) to establish whether the CRP is lower following 
therapy than at baseline. 
As a Phase 2a study to determine the effectiveness of the two treatment arms to induce a 
clinical response or remission, with 20 participants, it is possible to generate the required 
data [44].  
 
We are not examining efficacy in Group 2. The primary outcome is reduction in FCP with 
PEG lavage. We will use a paired t-test (after applying a log transformation if necessary) to 
establish whether the FCP concentration is lower following PEG lavage than at baseline. 
From our preliminary data and the expected mean and standard deviation of the paired 
differences, 15 patients will allow us to achieve 80% power and a level of significance of 
5%. 
 
To detect reduction in bacterial and fungal load by 16S and 18S gene copy number we will 
use a paired t-test after applying a log transformation. Based on the preliminary data, it is 
assumed that the standard deviation of change will be approximately 0.4 log and that a 
minimum of a 2 log drop in copy number would be clinically significant. To have 90% 
power, this requires only 3 participants. Even if the standard deviation is greater, say 1 or 2 
log, the required sample size is 5 or 13, respectively.  We will measure the Pearson’s 
correlation to determine the relationship between copy numbers and the outcome measures 
listed above (PCDAI, FCP, and CRP). If all patients do not have >2 log drop in 16S and 18S 
copy number, we will compare clinical remission and response among those with and 
without >2 log drop using Fisher’s exact test. 
 
The main statistical and computational tool for comparing the bacterial gut microbiota 
among different groups (e.g. between samples from different time points) is the 
phylogenetic-based method as implemented in the program UniFrac [47, 48], which 
measures the similarity among the community based on phylogenetic distances determined 
by the 16S rRNA gene sequences of different bacteria. Based on these distances, we can 
cluster the microbiomes using the Principal Coordinate Analysis (PCoA) along axes of 
maximal variance.  The significant principal components can then be compared between two 
groups using the two sample t-tests. Permutations can be used to obtain the p-values. 
Alternatively, we can compare several principal components simultaneously by performing 
nonparametric permutation test for association between the two groups and the microbiome 
compositions. Specifically, we can randomize the labels of the groups and compare all 
distances between points that both come from the same group to all distances between points 
from different groups using t-tests. In such permutation test, we can obtain a nonparametric 
distribution of the t statistic that takes into account the correlations introduced by the pair-
wise distance matrix structures. For the fungal community distances, Jaccard and 
abundance-weighted Jaccard indices will be calculated. 


 
  
 
 
 
29 
6.3.1 Safety Analysis 
All subjects enrolled into the study will be included in the safety analysis. The frequencies 
of AEs by type, severity and relationship to study drug will be summarized. SAEs (if any) 
will be described in detail. 
AE incidence will be summarized along with the corresponding exact binomial 95% two-
sided confidence intervals. 
We expect that adverse events will occur because the participants included in this study will 
have active, refractory disease.  Thus, hospitalizations or even life-threatening events may 
occur.  However, we anticipate very few, if any, adverse events that are directly related to 
the proposed intervention. 


 
  
 
 
 
30 
7 
STUDY MEDICATION  
7.1 Intervention Description and Regimen 
Only Group 1 participants will be administered the study drug regimen. The antimicrobial 
regimen will include 3 days of vancomycin and neomycin followed by 11 days of 
vancomycin and ciprofloxacin. Group 1 participants will also be randomized in a double-
blinded fashion to fluconazole or placebo for 14 days.  
Drug 
Dosage Form 
Dosage 
Regimen 
Vancomycin 
500 mg/ 20 mL 
oral suspension 
40 mg/kg/day in 4 divided doses, 
rounded to the nearest 50mg; not to 
exceed 500 mg PO every 6 hours 
Days 1-14 
Neomycin 
500 mg tablet 
10-20 kg: 250 mg PO every 8 hours 
20-40 kg: 500 mg PO every 8 hours 
>40 kg: 1000 mg PO every 8 hours 
 
Day 1-3 
Ciprofloxacin 
250 mg tablet, 
500 mg tablet, 
750 mg tablet 
 
10-12.5 kg: 125 mg PO twice per day 
12.5-22.5 kg: 250 mg PO twice per day 
22.5-27.5 kg: 375 mg PO twice per day 
27.5-37.5 kg: 500 mg PO twice per day 
27.5-40 kg: 625 mg PO twice per day 
>40 kg:750 mg PO twice per day 
Days 4-14 
Encapsulated 
fluconazole or 
placebo capsule 
50 mg capsule, 
100 mg capsule 
10-20 kg: 50 mg PO in one dose daily  
20-25 kg: 100 mg PO in one dose daily 
25-30 kg: 150 mg PO in one dose daily 
30-40 kg: 200 mg PO in one dose daily 
40-50 kg: 250 mg PO in one dose daily 
50-60 kg: 300 mg PO in one dose daily 
>60 kg: 400 mg PO in one dose daily 
 
Days 1-14 
Miralax (PEG 
3350) 
Powder 
(dissolved in 
Gatorade or 
Crystal Lite) 
10-13 kg: 51 g dissolved in 24 oz 
14-17 kg: 68 g dissolved in 32 oz 
18-22 kg: 85 g dissolved in 40 oz 
23-26 kg: 102 g dissolved in 48 oz 
27-30 kg: 119 g dissolved in 56 oz 
31-34 kg: 136 g dissolved in 64 oz 
35-40 kg: 153 g dissolved in 64 oz 
41-42 kg: 170 g dissolved in 64 oz 
43-46 kg: 187 g dissolved in 64 oz 
47-50 kg: 204 g dissolved in 64 oz 
>50 kg: 238 g dissolved in 64 oz 
Day 2 
 


 
  
 
 
 
31 
7.1.1 Dispensing 
The University of Pennsylvania’s Investigational Drug Service (IDS) will prepare and 
dispense the drugs for this study. 
7.1.2 Receipt 
After confirmation of eligibility, participants will be sent the antimicrobial and lavage 
regimen listed above directly from Penn IDS to their home mailing address. Participants and 
their parent/guardian will be provided with a checklist of all study medications and will be 
instructed to report any discrepancies to a member of the study team. 
7.1.3 Storage 
Study medications will be prepared, stored, and dispensed by Penn IDS as described in the 
investigational brochures. 
7.1.4 Preparation and Packaging 
To promote participant compliance and minimize potential confusion, study medications 
will be packaged into 2 blister packs: one for Days 1-7 and the other Days 8-14. The rows of 
the blister packs will be labeled clearly, with each dose separated into blisters. The 
vancomycin suspensions will be packaged in separate Ziploc bags per day.  Each bag will 
contain four syringes containing the appropriate dosage of vancomycin. The Day 2 bag will 
additionally contain a bottle with PEG 3350.  At the enrollment visit, participants will be 
provided with a 64 ounce water pitcher plus either 2 32 ounce bottles of Gatorade.  
With the exception of vancomycin and fluconazole, all study medications will be distributed 
in their original formulation as per the manufacturer. For vancomycin, IDS will compound 
the prescribed total dosage for the oral suspension (500 mg/20 mL concentration) drawn up 
into individual syringes based on dosage. For fluconazole, IDS will encapsulate the original 
formulation tablets so that they will look identical to placebo capsules. 
7.1.5 Administration and Accountability 
Participants will be provided with all study medications by tracked courier to their preferred 
address following the enrollment visit and consequent confirmation of their eligibility.  
Participants will take all medications orally. All unused study medications and empty 
containers will be collected from each participant and/or their parent/guardian at the 
completion of their participation.   
7.1.6 Participant Compliance Monitoring 
Compliance will be monitored through study staff observation of empty blister packs and/or 
syringes at each in person visit (see Section 7.1.7). At each in-person visit, participants 
and/or their parent/guardian will be asked to bring in their used and unused blister packs, 
syringes, and PEG bottle for review by study staff.  Compliance will be reviewed with the 
participants and/or their parent/guardian throughout the study. 


 
  
 
 
 
32 
7.1.7 Return or Destruction of Investigational Product 
Adequate records of study drug receipt and disposition will be maintained by the University 
of Pennsylvania Investigational Drug Services. The purpose of these records is to ensure 
regulatory authorities that the investigational new drug will not be distributed to any person 
who is not a study subject under the terms and conditions set forth in this protocol. The 
study medication is to be prescribed by the Investigator or designee and may not be used for 
any purpose other than that described in this protocol. At study completion, all drug supplies 
including partially used and empty containers must be returned to the study team. 
8 
SAFETY MANAGEMENT 
8.1 Clinical Adverse Events 
Clinical adverse events (AEs) will be monitored throughout the study.  
8.2 Adverse Event Reporting 
Unanticipated problems related to the research involving risks to subjects or others that 
occur during the course of this study (including SAEs) will be reported to the IRB in 
accordance with CHOP IRB SOP 408: Unanticipated Problems Involving Risks to Subjects. 
AEs that are not serious but that are notable and could involve risks to subjects will be 
summarized in narrative or other format and submitted to the IRB at the time of continuing 
review.  
8.3 Definition of an Adverse Event 
An adverse event is any untoward medical occurrence in a subject who has received an 
intervention (drug, biologic, or other intervention).  The occurrence does not necessarily 
have to have a causal relationship with the treatment.  An AE can therefore be any 
unfavorable or unintended sign (including an abnormal laboratory finding, for example), 
symptom, or disease temporally associated with the use of a medicinal product, whether or 
not considered related to the medicinal product. 
All AEs (including serious AEs) will be noted in the study records and on the case report 
form with a full description including the nature, date and time of onset, determination of 
non-serious versus serious, intensity (mild, moderate, severe), duration, causality, and 
outcome of the event. 
8.4 Definition of a Serious Adverse Event (SAE) 
An SAE is any adverse drug experience occurring at any dose that results in any of the 
following outcomes:  
• death, 
• a life-threatening event (at risk of death at the time of the event),  
• requires inpatient hospitalization or prolongation of existing hospitalization, 
• a persistent or significant disability/incapacity, or 


 
  
 
 
 
33 
• a congenital anomaly/birth defect in the offspring of a subject.   
Important medical events that may not result in death, be life-threatening, or require 
hospitalization may be considered a serious adverse drug event when, based upon 
appropriate medical judgment, they may jeopardize the subject and may require medical or 
surgical intervention to prevent one of the outcomes listed in this definition. 
8.4.1 Relationship of SAE to study drug or other intervention 
The relationship of each SAE to the study intervention should be characterized using one of 
the following terms in accordance with CHOP IRB Guidelines: definitely, probably, 
possibly, unlikely or unrelated.  
8.5 IRB/IEC Notification of SAEs and Other Unanticipated Problems 
The Investigator will promptly notify the IRB of all on-site unanticipated, serious Adverse 
Events that are related to the research activity. Other unanticipated problems related to the 
research involving risk to subjects or others will also be reported promptly. Written reports 
will be filed using the eIRB system and in accordance with the timeline below.  
Type of Unanticipated 
Problem 
Initial Notification  
(Phone, Email, Fax) 
Written Report 
Internal (on-site) SAEs 
Death or Life Threatening  
24 hours 
Within 2 calendar days 
Internal (on-site) SAEs 
All other SAEs 
7 days 
Within 7 business days 
Unanticipated Problems 
Related to Research 
7 days  
Within 7 business days 
All other AEs 
N/A 
Brief Summary of important 
AEs may be reported at time 
of continuing review 
8.5.1 Follow-up report 
If an SAE has not resolved at the time of the initial report and new information arises that 
changes the investigator’s assessment of the event, a follow-up report including all relevant 
new or reassessed information (e.g., concomitant medication, medical history) will be 
submitted to the IRB. The investigator is responsible for ensuring that all SAE are followed 
until either resolved or stable.  
8.6 Medical Emergencies 
If any medical emergencies occur during the course of the study, patients will be treated for 
said medical emergency using standard hospital medical procedures.  One such medical 
emergency that may occur is a severe allergic reaction to a study medication. 


 
  
 
 
 
34 
9 
STUDY ADMINISTRATION 
9.1 Treatment Assignment Methods 
9.1.1 Randomization 
Stratified randomization to fluconazole versus placebo will be performed using a 1:1 ratio of 
treatment arms. The randomization order will be created by University of Pennsylvania’s 
Investigational Drug Service (IDS). 
9.1.2 Blinding 
The randomization schedule will be generated by Penn IDS. Neither the participant, the 
study team, nor the clinical site personnel will know the treatment group to which any 
participant is randomized. 
9.1.3 Unblinding 
If there is a serious adverse event, which is thought by the study team to be possibly or 
probably related to the coded medication, the principal investigator, when necessary for the 
safety of the participant, will unblind treatment group assignment.  The following 
procedures will be taken when the principal investigator deems that unblinding is necessary: 
The IDS will be notified by the study team that unblinding is necessary.  IDS will unblind 
the treatment group assignment and provide it to the study team. 
Unblinding of treatment assignment is anticipated to be an uncommon occurrence and is 
highly discouraged.  Unblinding should only be performed if deemed necessary for the 
safety of the participant.   
9.2 Data Collection and Management 
• In order to ensure confidentiality, all subjects will be given a study ID number that 
will used to identify them on all data collection documents. Data will also be 
recorded on a shared REDCap account, an online database shared amongst the study 
team members at CHOP and Penn. All information collected in this study will be 
kept confidential as required by law.  
• An enrollment log linking PHI to study ID number will be kept on a password 
protected excel document on the CHOP Research Secure Server (SAND). Only 
study personnel at the CHOP site will have access to the enrollment log. The study 
team will be responsible for data collection, data management and accurate record 
keeping. Upon completion of all study procedures and analyses, the enrollment log, 
linking PHI to subject study IDs will be destroyed when deemed no longer 
necessary.   
• The study team will oversee appropriate collection, storage and shipping of samples. 
For stool samples collected during post discharge follow ups, subjects will be asked 
to either bring samples to CHOP or ship the samples to the laboratory using provided 
pre-paid shippers. Samples will be processed and stored in a -80°C freezer. Subject 
will be instructed to properly label the samples with the date of collection, study ID 


 
  
 
 
 
35 
and visit number. Subjects will be reminded not to include any identifying 
information on samples. The PennCHOP Microbiome Program will receive the 
samples with study IDs, visit number and dates of collection. The lab will not receive 
any identifying information. 
9.3 Confidentiality 
All data and records generated during this study will be kept confidential in accordance with 
Institutional policies and HIPAA on subject privacy. The Investigator and other site 
personnel will not use such data and records for any purpose other than conducting the 
study. Data will not be reused or disclosed to any other person or entity, except as required 
by law or for authorized oversight of the research project. Safeguards to maintain subject 
confidentiality are described in the above section on data collection and management. The 
following groups of people at CHOP may have access to this information: the research team, 
Penn IDS, medical staff who are directly or indirectly involved in patients’ care, and the 
CHOP IRB.  
9.4 Records Retention 
Study documents and data will be retained in accordance with CHOP’s retention policy. 
9.5 Regulatory and Ethical Considerations 
9.5.1 Data and Safety Monitoring Plan 
An Investigational New Drug (IND) Exemption has been obtained from the University of 
Pennsylvania IND/IDE Support Unit within the Penn Office of Clinical Research. As part of 
an established safety and monitoring plan, the Primary Investigator will monitor adverse 
events and unanticipated problems during the study to monitor ongoing participant safety. A 
Safety Officer, Natalie Terry, MD, PhD, has been identified to provide additional 
monitoring for the study. This individual is a board-certified gastroenterologist in pediatric 
practice who is knowledgeable in the natural history and treatment of CD, but who is not 
directly involved in the study and has no conflict of interest, financial or otherwise.  
Following CHOP IRB guidelines, all onsite, unanticipated SAEs will be reported to the 
Safety Officer promptly (within 24 hours) in the form of a written narrative. This will 
include a copy of the completed Serious Adverse Event form and any other information that 
will assist the understanding of the event. Significant new information for ongoing serious 
adverse events should be provided promptly to the study sponsor. 
All other adverse events will be reported to the Safety Officer quarterly. Based on these 
reports, the Safety Officer will have the authority to suspend the study and to convene a 
Data and Safety Monitoring Board (DSMB) as necessary. We do not feel that a DSMB is 
necessary at the time of study launch given the open-label design and utilization of FDA-
approved medications. This monitoring plan, in addition to screening for prolonged QTc and 
kidney and liver dysfunction, has been established to ensure the safety of the investigational 
regimen in this population.  
During the trial, study medications will be paused in the event of a serious adverse event that 
qualifies as a CTCAE Grade 3 or Grade 4 and is definitely or probably related to the study 


 
  
 
 
 
36 
intervention. During the pause of study enrollment, the study team will review the SAE with 
the CHOP IRB and the Safety Officer to determine whether study procedures should be 
continued or stopped. If either entity determines that the study should be stopped, all 
recruitment, enrollment, sample collection and follow-up will be halted. Participants will be 
transitioned to standard of care under the guidance of their treating physician. His/her data 
will still be used in the final analyses.  
9.5.2 Risk Assessment 
9.5.2.1 Group 1 Participation 
There are potential risks to participants who agree to participate in this trial; however, the 
risks are relatively small and have been minimized by study design. Group 1 will have 
already been refractory to at least one conventional therapy. Many of these patients will 
otherwise be facing escalation of therapy to a medication that is considered experimental or 
will be facing surgery. The risks associated with this study are significantly less than the 
risks associated with surgery. The risks of each medication will be reviewed in detail as part 
of the consent process.   
As the participants’ concurrent therapies will not be discontinued and the intervention 
portion of this study lasts only two weeks, the probability of harm is very low. Participants 
can be withdrawn from the study at any time. Additionally, if a participants’ condition 
worsens and a rescue therapy is deemed necessary by the study team or primary 
gastroenterologist, the participant will be withdrawn. 
Risks Associated with Study Medications 
The therapeutic regimen described in this protocol is safe. These are medications that are 
already FDA approved for various indications. The protocol is using standard dosing. Also, 
many of the medications in the proposed regimen are already utilized in children and adults 
with CD. In the preliminary data, it was found a similar regimen to be safe in primates. No 
SAEs related to the drug regimen have been reported for the five subjects enrolled in the 
IRB-approved protocol being conducted through Penn. 
Subjects with a known allergy to any of the study medications will not be able to participate. 
Subjects who do not know how they will react to the study medications are at risk for an 
allergic reaction including anaphylaxis. Anaphylaxis is a severe, potentially life-threatening 
allergic reaction. It can occur within seconds or minutes of exposure to something someone 
is allergic to. The flood of chemicals released by the immune system during anaphylaxis can 
cause blood pressure to drop suddenly and airways can narrow, making it hard to breathe 
normally. Signs and symptoms of anaphylaxis include a rapid, weak pulse, a skin rash, 
nausea and vomiting. Anaphylaxis requires immediate medical attention including an 
injection of epinephrine. If anaphylaxis is not treated right away, it can lead to 
unconsciousness or even death.  
For any antibiotic, there is the possibility of “resistance” developing. Resistance means that 
specific, infection-causing bacteria that were treatable by the antibiotic are no longer as 
easily treated by that antibiotic. 


 
  
 
 
 
37 
For any antibiotic, there is also the possibility that subjects could develop Clostridium 
difficile. However, vancomycin, one of the study medications, is used to treat C. difficile and 
therefore, the chances of developing C. difficile while on study medications is extremely 
unlikely.  
Known Adverse Reactions to Study Medications 
Ciprofloxacin (Cipro) 
Reactions found in Clinical Trials in Pediatric Populations 
Common Reactions (occurs in > 5% of patients) 
• 
Temporary mild to moderate negative 
musculoskeletal reactions: 
o Joint pain 
o Joint sprains  
o Decreased range of joints  
o Degeneration of joints  
o Abnormal walking patterns 
o Body and muscle pain 
Less Common Reactions (occurs in 1-5% of patients) 
• 
Diarrhea 
• 
Vomiting 
• 
Abdominal pain  
• 
Stuffy nose 
• 
Indigestion 
• 
Nausea 
• 
Fever 
• 
Asthma 
• 
Rash  
• 
Dizziness 
• 
Nervousness 
• 
Trouble sleeping 
• 
Drowsiness 
• 
Laboratory value changes 
Reactions found in Clinical Trials in Adult Populations (possible in pediatric populations) 
Common Reactions (occurs in 1-2.5% of patients) 
• 
Nausea 
• 
Diarrhea 
• 
Abnormal liver function tests 
• 
Vomiting 
• 
Rash 
Rare but Potentially Dangerous Reactions (occurs in <1% of patients) 


 
  
 
 
 
38 
• 
Body related pain (i.e. headaches, 
abdominal pain, foot pain, etc.) 
 
• 
Blood flow (i.e. abnormal heart beat, high/ 
low blood pressure, heart attack, minor 
bleeds in the skin, swollen lymph nodes 
etc.) 
 
• 
Mental state (i.e. restlessness, dizziness, 
trouble sleeping, drowsiness, irritability, 
hallucinations, depression, poor appetite, 
etc.) 
 
• 
Gastrointestinal system (i.e. difficulty 
swallowing, intestinal perforation, GI 
bleeding, jaundice, hepatitis, etc.) 
 
• 
Metabolism and nutritional systems (i.e. 
increase in pancreas labs, high or low blood 
sugar) 
• 
Musculoskeletal system (i.e. joint, back, 
neck or chest pain, joint stiffness, achiness, 
gout flare up)  
 
• 
Kidneys, urinary or genital organs (i.e. 
kidney inflammation, kidney failure, 
bloody urine, breast pain, vaginal pain, 
discharge or itching, etc.) 
 
• 
Breathing (i.e. shortness of breath, nose 
bleeds, fluid in the lungs, inflamed larynx, 
hiccup, coughing up of blood, blood clot in 
lungs etc.) 
 
• 
Skin and sensitivity (i.e. allergic reaction, 
fever, chills, sweating, itchy skin, 
sensitivity to the sun, flushing, swelling of 
the face, neck, lips etc.) 
 
• 
Senses (i.e. blurred vision, change in color 
perception, vision loss, double vision, 
hearing loss, bad taste etc.) 
 
 
Vancomycin 
Reactions found in Clinical Trials in Adult Populations (possible in pediatric populations) 
Common Reactions (occurring in > 5% of patients) 
• 
Nausea 
• 
Abdominal pain 
• 
Vomiting 
• 
Diarrhea 
• 
Gassiness 
• 
Decreased potassium levels 
• 
Fever  
• 
Swelling of feet, ankles, or legs 
• 
Fatigue 
• 
Urinary tract infection 
• 
Back pain 
• 
Headache 
• 
Kidney failure 
• 
Increased kidney laboratory values 
Additional possible reactions. The likelihood of having these side effects is unknown. 
• 
Toxicity to the ear: (i.e. hearing loss 
(associated with IV therapy), vertigo, 
dizziness, hearing extraneous sounds i.e. 
ringing, clicking etc.) 
• 
Blood cells: (i.e. reversible low white blood 
cell count)  
 
• 
Miscellaneous (i.e. anaphylaxis, chills, 
rash, life-threatening skin condition, blood 
vessel destruction by inflammation) 


 
  
 
 
 
39 
 
Neomycin 
Reactions reported during treatment with Neomycin 
Common Reactions 
• 
Nausea 
• 
Diarrhea 
• 
Vomiting 
Other Adverse Reactions 
• 
Brain system: (i.e. nerve damage, damage 
to the inner ear (which could lead to 
temporary or permanent hearing loss and 
balance),  paralysis of the nerve and 
muscle systems, which may cause death, 
severe difficulty breathing, numbness, skin 
tingling, muscle twitching and 
convulsions) 
 
• 
Kidney: (i.e. damage to kidney, kidney 
failure) 
• 
Neonatal: (i.e. harm to an unborn baby 
when distributed to a pregnant woman,  
permanent hearing loss at the time of birth) 
 
• 
Miscellaneous: (i.e. yeast infection and 
other similar infections, inability to absorb 
certain nutrients, leading to increased fat, 
nitrogen, cholesterol, carotene, glucose, 
xylose, lactose, sodium, calcium, 
cyanocobalamin and iron in the stool) 
 
Fluconazole 
Reactions found in Clinical Trials in Pediatric Populations 
Common Reactions (occurs in 1-5% of patients) 
• 
Vomiting  
• 
Abdominal Pain  
• 
Nausea  
• 
Diarrhea  
• 
Abnormal liver function tests 
Reactions found in Clinical Trials in Adult Populations (possible in pediatric populations) 
Common Reactions (occurs in 1-5% of patients) 
• 
Headache 
• 
Nausea  
• 
Skin rash  
• 
Abdominal pain  
• 
Vomiting  
• 
Diarrhea  
• 
Dyspepsia  
• 
Dizziness 
• 
Taste perversion 
• 
Abnormal liver function tests 
Rare but Potentially Dangerous Reactions  


 
  
 
 
 
40 
• 
Liver: (i.e. gallbladder inflammation, 
yellowing of the skin, liver damage, serious 
liver infections like hepatitis, sudden liver 
failure which could lead to death in those 
with serious underlying medical conditions) 
• 
Miscellaneous (i.e. anaphylaxis, rapid 
swelling of the skin, birth defects when 
taken during early pregnancy)  
Other Post-Marketing Adverse Reactions 
• 
Heart  (i.e. irregular heart rhythms, 
abnormal heart rhythm disorders) 
 
• 
Blood cells (i.e. decreased white blood cells 
and platelets) 
 
• 
Body (i.e. abnormal weakness, lack of 
energy, tiredness, discomfort or uneasiness, 
fever) 
 
• 
Brain (i.e. seizures, dizziness, sleeping 
problems, sleepiness, tremor, vertigo, nerve 
damage- characterized by numbness or 
tingling, tickling, prickling, burning etc. of 
the skin without a physical cause) 
• 
Skin (i.e. rash caused by drug reaction, life-
threatening skin conditions, increased 
sweating, hair loss) 
 
• 
Metabolism and nutritional system (i.e. 
increased blood cholesterol, increased 
blood triglycerides, low blood potassium) 
 
• 
Gastrointestinal (i.e. blockage of bile to the 
duodenum, dry mouth, indigestion, 
vomiting, changes in taste) 
 
• 
Miscellaneous (i.e. anaphylaxis, rapid 
swelling of the skin, swelling of the face, 
severe itching of the skin, liver damage, 
muscle pain) 
 
 
MiraLax (PEG 3350) 
Reactions reported during treatment with MiraLax (PEG 3350) 
Common Reactions 
• 
Nausea 
• 
Abdominal Bloating 
• 
Cramping 
• 
Flatulence 
• 
Diarrhea and excessive stool frequency with 
high doses 
• 
Hives  
 
Reproductive Risks 
It is unknown what effect these treatments may have on an unborn child. Subjects of 
childbearing age will be asked to practice an effective method of birth control while 
participating in this study. Potential subjects will be made aware that taking oral antibiotics 
can potentially lower the effectiveness of oral birth control. If a subject becomes pregnant 


 
  
 
 
 
41 
during this study, as soon as their doctor is made aware, they will be asked to stop taking 
study medicine and will be withdrawn from the study. 
Blood Draws 
Blood draws can cause discomfort, bruising, have a small risk of infection, or a blood clot. 
Standard methods will be used to prevent infection.  
Stool Collection 
Any stool sample may contain germs that spread disease. Subjects will be asked to carefully 
wash their hands and use careful handling techniques to avoid spreading infection. Subjects 
will be provided with directions on how to properly and safely package and ship samples (if 
applicable). 
Rectal Swab Collection 
Subjects may experience minor physical discomfort while having the swabs taken. 
EKG 
Subjects may experience minor physical discomfort or anxiety while having the EKG 
procedure. 
9.5.2.2 Group 2 Participants 
The medical, physical and social risks are minimal for subjects of this arm of the study.  The 
primary risk is a breach of privacy and confidentiality, but we will take the measures noted 
in the main study to ensure privacy and confidentiality. 
Stool Collection  
 
Collecting stool may contain germs that spread disease. Subjects will be reminded to 
carefully wash their hands and use careful handling techniques to avoid spreading infection. 
Some people may feel uncomfortable or embarrassed when supplying a stool sample. There 
should be no pain while collecting the stool sample. However, if a subject is constipated, 
straining to pass stool may be painful. We will discuss this with the subject during the 
recruitment process and ensure that the individual subject is comfortable with the process.  
Breach of Confidentiality 
As with any study involving collection of data, there is the possibility of breach of 
confidentiality of data. Every precaution will be taken to secure participants' personal 
information to ensure confidentiality. 
At the time of participation, each participant will be assigned a study identification number. 
This number will be used on data collection forms and samples and in the database instead 
of names and other private information. 


 
  
 
 
 
42 
9.5.3 Potential Benefits of Trial Participation 
9.5.3.1 Potential Benefits to Group 1 Participants 
The direct benefit is improvement in disease activity and potential salvaged response to the 
prior treatment regimen (immunomodulator or biologic medication). In terms of indirect 
benefits, participation in this study will improve the understanding of the role of the gut 
microbiota in the inflammatory bowel diseases. Finally, the new knowledge about the gut 
microbiota that stands to be gained presents an additional benefit of this study, further 
contributing to the favorable balance of potential benefits to possible harms. 
9.5.3.2 Potential Benefits to Group 2 Participants  
There are no direct benefits to the individual participants in this study.  Primarily, the 
study has considerable potential benefit for all patients with IBD by better elucidating the 
effect of bowel lavage on the gut microbiota and the gut inflammatory marker, fecal 
calprotectin.  
9.5.4 Risk-Benefit Assessment 
9.5.4.1 Group 1 
The potential benefits outweigh any risks of participating in this study, as the treatment may 
help to salvage response to prior treatment regimens. The risks of participating in this study 
are small, and these risks are outweighed by the benefits to society to be gained from new 
knowledge about the gut microbiota and how it may play a role in inflammatory bowel 
disease management.  
9.5.4.2 Group 2  
There are no direct benefits to the subjects for their participation in this group of the 
study.  However, the risks of participating are minimal, and these risks are outweighed by 
the potential benefit of improving diagnosis and treatment of children with IBD.   
9.6 Recruitment Strategy 
9.6.1 Group 1 Participants 
Potential participants will be identified through outpatient clinic schedules, inpatient lists, 
endoscopy schedules and physician referrals. The study team will reach out to GI specialists 
at various hospital systems, such as St. Christopher’s Hospital for Children and Nemours 
Alfred I. duPont Hospital for Children, to request referrals and help propagate information 
about the study to potential subjects. Potential subjects may be provided with the study 
team’s contact information to contact CHOP directly. Non-CHOP physicians may also 
obtain permission from potential subjects to release limited contract information to the study 
team so they may contact interested individuals. 
Additionally, families may be approached at CHOP sponsored education meetings and 
events. Appropriate follow up from the study team may occur by phone or email. 
Contact information for the research team will be provided and a link to 
www.clinicaltrials.gov for more information. 


 
  
 
 
 
43 
An IRB approved flyer may also be distributed to potential participants. This document is 
attached in section 12.02 (1.0) of the IRB application. Flyers may be mailed, emailed, or 
handed out in-person. 
We also may be contacted through various websites and social media platforms, such as 
www.clinicaltrials.gov, the Crohn’s and Colitis Foundation of America (CCFA) Clinical 
Trial Registry, and the CHOP Clinical Research Finder public website by individuals 
outside of CHOP. Web-based advertising avenues, like eNewsletters, may be utilized in 
recruitment efforts including targeted advertising through local disease/health foundations 
such as the Crohn’s and Colitis Foundation of America (CCFA).  
We will conduct a social media campaign via the CCFA Facebook page. The Facebook 
posts will guide potential participants to contact IBDResearch@email.chop.edu to receive 
more information about the study. The study’s posts will be managed by the CCFA, who 
have their own team of experts to monitor posts/comments.  
There may be additional social media recruitment campaigns through the CHOP recruitment 
enhancement core or though the University of Pennsylvania. All materials and language 
posted will obtain IRB approval. If there are questions regarding initial eligibility, necessary 
information from the participant’s medical record will be obtained by the treating physician 
and/or a member of the study team. 
9.6.2 Group 2 Participants 
Potential participants will be identified through outpatient clinic schedules, inpatient lists, 
endoscopy schedules and physician referrals. Potential participants may be approached via 
phone, email, or at CHOP sponsored education meetings and events. Contact via email will 
be done with IRB approved language. Appropriate follow up from the study team may occur 
by phone or email. If there are questions regarding initial eligibility, necessary information 
from the participant’s medical record will be obtained by the treating physician and/or a 
member of the study team. 
 
9.7 Informed Consent/Assent and HIPAA Authorization 
Study personnel will obtain consent and assent for the study. Subjects may make a decision 
about study participation at that time, or may decide to enroll at a later visit.  
The study will be thoroughly explained by study personnel, including the study rationale and 
goals.  
For participants enrolled in Group 1, a physician on the study will explain the risks and 
benefits of the intervention and study procedures that are greater than minimal risk. A 
physician or another member of the research team, with consenting authority, will explain 
the rest of the consent form. Potential participants will be given the opportunity to ask 
questions to the physician and other study personnel about the study, risks, benefits, and 
confidentiality. Written consent will be obtained after all the questions and discussions have 
been completed. If a physician on the research study has not personally completed the 
consent form, signed and dated it himself/herself, a note will be included in either the 


 
  
 
 
 
44 
medical record or study record indicating that the consent conversation occurred. For the 
subjects under 18 years of age, assent will be obtained by explaining briefly the study while 
the parent/guardian is present. Participation in all areas of the study will be completely 
voluntary. Should the subjects become intolerant of any aspect of the study, their 
participation will be discontinued. Subjects who turn 18 during the course of the study will 
be re-consented. 
For participants recruited through the outpatient clinic, written consent will be obtained at 
that outpatient visit, a REDCap Screening Questionnaire will be completed, and participants 
will be scheduled for an enrollment CTRC visit.  
9.7.1.1 Verbal Consent & Waiver of Documentation of Consent  
We are requesting to obtain verbal consent and waiver of documentation of consent for 
participants enrolled in both Group 1 and Group 2 of the study.  
9.7.1.1.1 Group 1 
For participants recruited through physician referrals or for potential subjects who are not at 
CHOP prior to enrollment, they may be contacted and screened via telephone to obtain 
verbal consent. Once verbal consent is obtained, potential participants or their 
parent/guardian will be emailed a REDCap Screening Questionnaire. Participants who seem 
to meet all inclusion criteria (see Section 3.4) will be scheduled for an enrollment visit. The 
purpose of the verbal screening informed consent is to confirm the participant’s eligibility 
and obtain an IBD history. It is also to allow subjects to collect samples at home prior to 
their visit. Subjects are not always able to have a bowel movement while at the hospital and 
therefore, it will be helpful for subjects to collect the stool sample at home prior to their 
appointment. A stool collection kit will be given to or mailed to all participants and/or their 
parent/guardian so that a sample can be brought to the enrollment visit. 
When consent is obtained by telephone, the person obtaining consent will document the 
participant’s agreement to participate on the verbal consent form. We could not practicably 
carry out the research without the verbal consent, because it is possible that not all subjects 
will be seen at the main hospital within the timeframe of study recruitment. At the 
enrollment visit, the study will be reviewed in its entirety with the participant and the 
participant’s parents/guardian. Written consent and assent will be obtained. No samples will 
analyzed before obtaining written consent. 
9.7.1.1.2 Group 2 
As with those in Group 1, potential Group 2 participants may be contacted and 
screened via telephone to obtain verbal informed consent. The purpose of the verbal 
informed consent is to allow participants to collect a stool sample at home prior to their 
clinically-indicated PEG lavage. We could not practicably carry out the research without 
the verbal consent and waiver of documentation of consent as subjects do not typically 
come to the hospital to schedule a procedure and undergo a PEG lavage for clinical 
purposes. Instructions on when and how to undergo the lavage is given over the phone. 
 Subjects consented by telephone with the verbal consent with have the study 
procedures reviewed in their entirety before obtaining verbal consent. It will be made 


 
  
 
 
 
45 
clear to the potential subjects that they can refuse participation and it will not impact their 
care at CHOP. The subject will be given the opportunity to receive a copy of the consent. 
For subjects being consented via the telephone the following sections on waiver of assent, 
and waiver of HIPAA authorization apply.  
9.7.1.2 Waiver of Assent 
A full waiver of assent is requested for the verbal consent forms (Verbal Screening Informed 
Consent Form; to be used with Group 1 participants only and the Verbal Informed Consent 
Form; to be used with Group 2 participants only) which can be done over the telephone with 
parents/guardian and children may not be available. 
9.7.1.2.1 Group 1 
At the enrollment visit, the study will be reviewed in its entirety with the participant and 
the participant’s parents/guardian. Written assent will be obtained at this in-person visit 
and documented on the main consent form 
All Group 1 participants and/or their parent/guardian must provide written consent before 
undergoing any other study procedures. The study procedures will be explained to each 
participant and their parent/guardian at the time of pre-screening and written consent. If the 
participant agrees to further participate, the written informed consent form will be signed in-
person at either the outpatient clinic visit or the enrollment visit. 
 
9.7.1.3 Waiver of HIPPAA Authorization 
A partial waiver of HIPAA authorization to obtain verbal authorization is requested 
for both Group 1 and Group 2 participants. The waiver would allow Group 1 participants 
to collect the appropriate samples prior to their enrollment visit and enrolled Group 2 
participants to collect samples prior to being seen at CHOP or for subjects who will not 
require a visit to CHOP.  
 
9.8 Payment to Subjects/Families 
All participants will be provided compensation for their enrollment in this study. Participants 
will be compensated $10.00 per stool sample submitted on a pre-paid debit card. If all sample 
collections are completed an addition $70 will be provided. Group 1 participants can earn a 
maximum of $120 for their participation in the study. Group 2 participants can earn a 
maximum of $100 for their participation in the study. If a family is asked to repeat sample 
collection due to improper collection initially, the family will not be compensated for repeat 
samples. The bank issuing the debit card will have access to identifiable information. The 
bank will not have access to any medical information.  
9.8.1 Gifts 
Group 1 participants will be given a pitcher to prepare the Miralax (PEG 3350) solution for 
the day 2 bowel lavage. 


 
  
 
 
 
46 
10 PUBLICATION 
Data from this study, including preliminary data analyses, will be presented at national 
meetings and submitted for publication.  Confidentiality will be maintained during 
publication.   
11 REFERENCES 
1. Lewis, J.D., The utility of biomarkers in the diagnosis and therapy of inflammatory 
bowel disease. Gastroenterology, 2011. 140(6): p. 1817-1826 e2. 
2. Molodecky, N.A., et al., Increasing incidence and prevalence of the inflammatory 
bowel diseases with time, based on systematic review. Gastroenterology, 2012. 142(1): 
p. 46-54 e42; quiz e30. 
3. Sartor, R.B., Mechanisms of disease: pathogenesis of Crohn's disease and ulcerative 
colitis. Nat Clin Pract Gastroenterol Hepatol, 2006. 3(7): p. 390-407. 
4. Rath, H.C., et al., Different subsets of enteric bacteria induce and perpetuate 
experimental colitis in rats and mice. Infect Immun, 2001. 69(4): p. 2277-85. 
5. Elson, C.O., et al., Experimental models to study molecular mechanisms underlying 
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6. Harper, P.H., et al., Role of the faecal stream in the maintenance of Crohn's colitis. 
Gut, 1985. 26(3): p. 279-84. 
7. Rutgeerts, P., et al., Effect of faecal stream diversion on recurrence of Crohn's disease 
in the neoterminal ileum. Lancet, 1991. 338(8770): p. 771-4. 
8. Dave, M., et al., Opportunistic Infections Due to Inflammatory Bowel Disease 
Therapy. Inflamm Bowel Dis, 2013. 
9. Ben-Horin, S. and Y. Chowers, Review article: loss of response to anti-TNF 
treatments in Crohn's disease. Aliment Pharmacol Ther, 2011. 33(9): p. 987-95. 
10. Hoentjen, F., et al., Antibiotics with a selective aerobic or anaerobic spectrum have 
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deficient mice. Gut, 2003. 52(12): p. 1721-7. 
11. Kang, S.S., et al., An antibiotic-responsive mouse model of fulminant ulcerative colitis. 
PLoS Med, 2008. 5(3): p. e41. 
12. Madsen, K.L., et al., Antibiotic therapy attenuates colitis in interleukin 10 gene-
deficient mice. Gastroenterology, 2000. 118(6): p. 1094-105. 
13. Khan, K.J., et al., Antibiotic therapy in inflammatory bowel disease: a systematic 
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14. Wang, S.L., Z.R. Wang, and C.Q. Yang, Meta-analysis of broad-spectrum antibiotic 
therapy in patients with active inflammatory bowel disease. Exp Ther Med, 2012. 4(6): 
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15. Ohkusa, T., et al., Newly developed antibiotic combination therapy for ulcerative 
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16. Uehara, T., et al., Efficacy of antibiotic combination therapy in patients with active 
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17. Terao, S., et al., Antibiotic combination therapy for steroid withdrawal in steroid-
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18. Turner, D., et al., Combination of oral antibiotics may be effective in severe pediatric 
ulcerative colitis: A preliminary report. J Crohns Colitis, 2014. 
19. Iliev, I.D., et al., Interactions between commensal fungi and the C-type lectin receptor 
Dectin-1 influence colitis. Science, 2012. 336(6086): p. 1314-7. 
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disease. Scand J Gastroenterol, 1992. 27(3): p. 196-200. 
21. Zwolinska-Wcislo, M., et al., Effect of Candida colonization on human ulcerative 
colitis and the healing of inflammatory changes of the colon in the experimental model 
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22. Dollive, S., et al., Fungi of the Murine Gut: Episodic Variation and Proliferation 
during Antibiotic Treatment. PLoS One, 2013. 8(8): p. e71806. 
23. Wellmann, W. and F.W. Schmidt, Intestinal lavage in the treatment of Crohn's 
disease: a pilot study. Klin Wochenschr, 1982. 60(7): p. 371-3. 
24. Wellmann, W., P.C. Fink, and F.W. Schmidt, Whole-gut irrigation as 
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25. O'Brien, C.L., et al., Impact of colonoscopy bowel preparation on intestinal 
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Gastroenterol, 1996. 91(2): p. 328-32. 
27. Sutherland, L., et al., Double blind, placebo controlled trial of metronidazole in 
Crohn's disease. Gut, 1991. 32(9): p. 1071-5. 
28. Ursing, B., et al., A comparative study of metronidazole and sulfasalazine for active 
Crohn's disease: the cooperative Crohn's disease study in Sweden. II. Result. 
Gastroenterology, 1982. 83(3): p. 550-62. 
29. McKenna, P., et al., The macaque gut microbiome in health, lentiviral infection, and 
chronic enterocolitis. PLoS Pathogens, 2008. 4(2): p. 8. 
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colonoscopy: an endoscopic database study in a community hospital. J Clin 
Gastroenterol, 2012. 46(10): p. e96-e100. 
31. Hyams, J.S., et al., Development and validation of a pediatric Crohn's disease activity 
index.  J Pediatr Gastroenterol Nutr, 1991.  12(4): p. 439-47 
32. Harvey, R.F. and Bradshaw, J.M., A simple index of Crohn’s-dease activity. The 
Lancet, 1980, March 8: p. 514. 
33. Vermeire, S., et al., Correlation between the Crohn’s Disease Activity and Harvey–
Bradshaw Indices in assessing Crohn’s disease severity. Clin Gastroenterol Hepatol, 
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34. Thia, K., et al., Short CDAI: development and validation of a shortened and simplified 
Crohn's disease activity index. Inflamm Bowel Dis, 2011. 17(1): p. 105-11. 
35. Vermeire, S., G. Van Assche, and P. Rutgeerts, Laboratory markers in IBD: useful, 
magic, or unnecessary toys. Gut, 2006. 55: p. 436-31. 
36. Roseth, A.G., et al., Assessment of the neutrophil dominating protein calprotectin in 
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37. Roseth, A.G., E. Aadland, and K. Grzyb, Normalization of faecal calprotectin: a 
predictor of mucosal healing in patients with inflammatory bowel disease. 
Scandinavian Journal of Gastroenterology, 2004. 39(10): p. 1017-20. 
38. Roseth, A.G., et al., Assessment of disease activity in ulcerative colitis by faecal 
calprotectin, a novel granulocyte marker protein. Digestion, 1997. 58(2): p. 176-80. 
39. Walkiewicz, D., et al., Fecal calprotectin is useful in predicting disease relapse in 
pediatric inflammatory bowel disease. Inflammatory Bowel Diseases, 2008. 14(5): p. 
669-673. 
40. Roseth, A.G., et al., Assessment of disease activity in ulcerative colitis by faecal 
calprotectin, a novel granulocyte marker protein. Digestion, 1997. 58(2): p. 176-80. 
41. Lin, J.F., et al., Meta-analysis: fecal calprotectin for assessment of inflammatory 
bowel disease activity. Inflamm Bowel Dis, 2014. 20(8): p. 1407-15. 
42. Sipponen, T., et al., Fecal calprotectin, lactoferrin, and endoscopic disease activity in 
monitoring anti-TNF-alpha therapy for Crohn's disease. Inflamm Bowel Dis, 2008. 
14(10): p. 1392-8. 
43. Caporaso, J.G., et al., QIIME allows analysis of high-throughput community 
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trials of active Crohn's disease. Gastroenterology, 2004. 126(5): p. 1257-69. 
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treated with infliximab: a randomized trial. Ann Intern Med, 2007. 146(12): p. 829-
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46. Sandborn, W.J., et al., Vedolizumab as induction and maintenance therapy for Crohn's 
disease. N Engl J Med, 2013. 369(8): p. 711-21. 
47. Lozupone, C., M. Hamady, and R. Knight, UniFrac--an online tool for comparing 
microbial community diversity in a phylogenetic context. BMC Bioinformatics, 2006. 
7(371). 
48. Lozupone, C. and R. Knight, UniFrac: a new phylogenetic method for comparing 
microbial communities. Applied & Environmental Microbiology, 2005. 71(12): p. 
8228-35. 
49. Ciprofloxacin. Daily Med. U.S. National Library of Medicine, NIH Website. 
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89b2-f0eb63959a2f. Accessed September 8, 2017.  
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July 13, 2017.  


 
  
 
 
 
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ICF_000.pdf: 
CHOP IRB#: IRB 17-014343
Effective Date: 3/19/2020
Expiration Date: 12/17/2020
Page 1 of 9
Informed Consent Form and HIPAA Authorization
Study Title: 
A Randomized Pilot Study of Fundamental Modification of the Gut 
Microbiota in the Treatment of Refractory Crohn’s Disease (Holiday)
Version Date:  
March 12, 2020
Consent Name:
Group 2 Verbal Informed Consent Form
Principal Investigator:
Lindsey Albenberg
Telephone: (215) 590-1680
Emergency Contact:
On-call GI Attending
Telephone: (215) 590-1680
You, or your child may be eligible to take part in a research study. This form gives you 
important information about the study. It describes the purpose of this research study, and 
the risks and possible benefits of participating. 
If there is anything in this form you do not understand, please ask questions. Please take 
your time. You do not have to take part in this study if you do not want to. If you take 
part, you can leave the study at any time. 
In the sections that follow, the word “we” means the study doctor and other research 
staff. If you are a parent or legal guardian who is giving permission for a child, please 
note that the word “you” refers to your child.
Why are you being asked to take part in this study?
You are being asked to take part in this research study because you are undergoing a 
polyethylene glycol bowel lavage (more commonly known as a “bowel cleanout”) in 
preparation for a clinically indicated GI endoscopy (more commonly known as a 
“scope”). 
What is the purpose of this research study? 
Our bodies carry around trillions of tiny bacteria, fungi and viruses (called ‘microbes’) in 
many places on and inside of our bodies, such as the skin, the mouth, nose and gut. All of 
the different kinds of microbes that live on and inside of us, taken together, are called the 
“human microbiome.” 
Scientists want to know more about the microbiome in children with inflammatory bowel 
disease (IBD). Scientists have found that they may have differences in their gut 
microbiome. 
This research study is a part of a larger clinical trial which aims to determine whether a 
unique study drug combination can help children with IBD better respond to medications 
they already take for their disease. 
There will be two groups within the study. The first group (called Group 1) will take the 
study drug regimen, which will include medications that target the gut microbiome. Also, 
participants will have a bowel cleanout. We will then look at the gut microbiome and 
levels of gut inflammation before and after taking the study drug. 


CHOP IRB#: IRB 17-014343
Effective Date: 3/19/2020
Expiration Date: 12/17/2020
Page 2 of 9
The other group (Group 2) of the study will not receive any study drug. You are being 
asked to participate in Group 2. The purpose of this group is help us understand the effect 
that a bowel cleanout alone has on the presence of gut microbes and gut inflammation.  
We will compare both the microbiome and inflammation present in stool samples before 
and after bowel cleanout. Learning more about its relationship with the gut microbiome 
and gut inflammation may help us better understand the results of the main clinical trial 
and develop new therapies for children with IBD. 
How many people will take part?
About 60 individuals will take part in this study. 
What is involved in the study?
If you agree to take part in the study, you will be asked to collect a baseline stool sample 
prior to completing your clinically indicated bowel cleanout. Approximately 5 days after 
your procedure, you will be asked to submit another stool sample. The final stool sample 
will be collected 12 days after your procedure. We will use your samples in order to 
prepare and study DNA from the microbe samples. Additionally, we will be testing for 
the levels of a protein called calprotectin, which is present in stool when your GI tract is 
inflamed. Your participation in the study will not involve any additional hospital visits.
How long will you be in this study?
If you agree to take part, your participation will last for up to 2 months and will involve 
three study visits. 
What are the study procedures? 
Some of the procedures in this study will be repeated several times. Tests that are part of 
your regular, routine medical care will continue to be performed. The study involves the 
following tests and procedures: 
Stool Test: You will be asked for a sample of your stool 3 times during the study. Stool 
will need to be collected both prior to and after the bowel cleanout in preparation 
of your GI procedure. Stool sample collection kits and directions for their use will 
be provided to you. Stool sample collection kits can be mailed back if you will not 
be coming to CHOP for any appointments within the timeframe of the study. We 
will use your samples to prepare and study DNA from the microbes present in 
your stool.  We will also use your stool samples to perform a fecal calprotectin 
test which is used to measure intestinal inflammation. If stool samples are not 
collected in accordance with the instructions provided, you may be asked to 
repeat sample collection.
Medical Record Review: We will review your medical record and collect information 
related to your disease history and demographic information. Additionally, we 
will collect lab values and information related to your medical conditions and 
treatments. We will collect this data from your medical record until the end of the 
study. 


CHOP IRB#: IRB 17-014343
Effective Date: 3/19/2020
Expiration Date: 12/17/2020
Page 3 of 9
During the study, we will collect stool samples from you. By agreeing to 
participate in the study, you agree to give these samples to CHOP for research 
purposes.
Visit Schedule
Visit
Main Procedures
Duration
Visit 1, Baseline 
(prior to bowel 
cleanout)
Consent, Medical Record Review, Stool 
Sample Collection
1 hour
Visit 2, Day 5 
(post-procedure)
Medical Record Review, Stool Sample 
Collection
30 minutes
Visit 3, Day 12 
(post-procedure)
Medical Record Review, Stool Sample 
Collection
30 minutes
What are the risks of this study?
Taking part in a research study involves inconveniences and risks. If you have any 
questions about any of the possible risks listed below, you should talk to your study 
doctor or your regular doctor. 
As with any study involving collection of data, there is the possibility your confidential 
information will be shared with others. Every precaution will be taken to secure your 
personal information to ensure confidentiality.
Risks associated with study stool collection: 
Any stool sample may contain germs that spread disease. It is important to carefully wash 
your hands and use careful handling techniques to avoid spreading infection. 
Risks associated with data collection:
Sharing your information can risk a breach of confidentiality. However, your name will 
not be shared outside of CHOP. We will do our best to keep your information 
confidential.  A separate list will be maintained that links each participant's name to the 
study identification number for future reference and communication.
While we will take every precaution we can to keep your identity confidential, there is a 
small risk that some of the information we collect from you or learn from studying the 
DNA in your microbes or your own DNA (which can be mixed with the DNA of your 
microbes) could be linked back to you. Although there are no current methods that people 
can use to identify you from the DNA in your microbes and your own DNA, we cannot 
guarantee that there will not be new techniques developed in the future that could do this.
Are there any benefits to taking part in this study?
There will be no direct benefit to you from taking part in this study. The knowledge 
gained from this study may help doctors better understand how a bowel clean out affects 
the gut microbiome and inflammation. This will help us better understand the results of 
the main clinical trial and develop new therapies for children with IBD.


CHOP IRB#: IRB 17-014343
Effective Date: 3/19/2020
Expiration Date: 12/17/2020
Page 4 of 9
Do you need to give your consent in order to participate? 
If you decide to participate in this study, you must verbally agree. A copy of your signed 
consent form will be provided upon request. 
What are your responsibilities?
Please consider the study time commitments and responsibilities as a research subject 
when making your decision about participating in this study. 
What happens if you decide not to take part in this study? 
Participation in this study is voluntary. You do not have to take part in order to receive 
care at CHOP.
If you decide not to take part or if you change your mind later there will be no penalties 
or loss of any benefits to which you are otherwise entitled. 
Can you stop your participation in the study early?
You can stop being in the study at any time. You do not have to give a reason.
What about privacy, authorization for use of Personal Health Information (PHI) 
and confidentiality? 
As part of this research, health information about you will be collected. This will include 
information from medical records, procedures, and tests. Information related to your 
medical care at CHOP will go in your medical record. Medical records are available to 
CHOP staff. Staff will view your records only when required as part of their job. Staff are 
required to keep your information private. Information that could identify you will not be 
shared with anyone - unless you provide your written consent, or it is required or allowed 
by law. Laboratory test results will appear in your medical record. We will do our best to 
keep your personal information private and confidential. However, we cannot guarantee 
absolute confidentiality. Your personal information may be disclosed if required by law. 
The results of this study may be shown at meetings and published in journals to inform 
other doctors and health professionals. We will keep your identity private in any 
publication or presentation.
Several people and organizations may review or receive your identifiable information. 
They will need this information to conduct the research, to assure the quality of the data, 
or to analyze the data or samples. These groups include: 

Members of the research team and other authorized staff at CHOP and UPenn 

People from agencies and organizations that perform independent accreditation 
and/or oversight of research; such as the Department of Health and Human 
Services, Office for Human Research Protections.

The Broad Institute in Boston, Massachusetts, who is sponsoring this research.

The National Institutes of Health who is also sponsoring this research.

The Food and Drug Administration
By law, CHOP is required to protect your health information. The research staff will only 
allow access to your health information to the groups listed above.  By signing this 


CHOP IRB#: IRB 17-014343
Effective Date: 3/19/2020
Expiration Date: 12/17/2020
Page 5 of 9
document, you are authorizing CHOP to use and/or release your health information for 
this research. Some of the organizations listed above may not be required to protect your 
information under Federal privacy laws. If permitted by law, they may be allowed to 
share it with others without your permission.  
There is no set time for destroying the information that will be collected for this study. 
Your permission to use and share the information and data from this study will continue 
until the research study ends and will not expire. Researchers continue to analyze data for 
many years and it is not possible to know when they will be completely done. 


CHOP IRB#: IRB 17-014343
Effective Date: 3/19/2020
Expiration Date: 12/17/2020
Page 6 of 9
A Certificate of Confidentiality (CoC) issued by the NIH covers this research. A CoC 
helps protect your identifiable information and biological samples.
A CoC protects your private information from all legal proceedings. Unless you consent, 
information from this research study that identifies you will not be shared outside this 
research.
• No one can be forced to share your identifiable information or biological 
samples for a lawsuit.
•Your information can't be used as evidence even if there is a court subpoena.
If you consent, your information or biological samples could be shared for:
•your medical treatment and/or for use by your insurance company 
•other purposes not connected with this research. 
The CoC does not prevent some disclosures.
•The researchers can't refuse requests for information from those funding this 
research. The NIH may need information to assess this project. Also, the US Food 
and Drug Administration (FDA) may need information.
•You can still share information about yourself. You can also freely discuss your 
involvement in this research.
•The researchers must disclose things required by law. This includes suspected 
child abuse and neglect, harm to self or others, or communicable diseases.
•Some information from this study must go in your medical record.  
•Your information and biological samples may be shared for other research.
Can you change your mind about the use of personal information?
You may change your mind and withdraw your permission to use and disclose your 
health information at any time. To take back your permission, it is preferred that you 
inform the investigator in writing. 
Dr. Lindsey Albenberg 
The Children’s Hospital of Philadelphia
Department of Gastroenterology, Hepatology and Nutrition
Roberts Center, 14-140
2716 South St, Philadelphia, PA 19146


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Effective Date: 3/19/2020
Expiration Date: 12/17/2020
Page 7 of 9
In the letter, state that you changed your mind and do not want any more of your health 
information collected. The personal information that has been collected already will be 
used if necessary for the research. No new information will be collected. If you withdraw 
your permission to use your personal health information, you will be withdrawn from the 
study.
Additional Information 
A Data Safety and Monitoring Board, an independent group of experts, will be reviewing 
the data from this research throughout the study. 
Financial Information 
While you are in this study, the cost of your usual medical care – procedures, medications 
and doctor visits – will continue to be billed to you or your insurance.
Will there be any additional costs? 
There will be no additional costs to you by taking part in this study. 
Will you be paid for taking part in this study? 
If you decide to participate, you will be compensated $10.00 for each stool sample. If you 
complete all three sample collections, you will be compensated an additional $70.00. You 
may be compensated up to $100.00 for participating in the study. 
Payment will be in the form of a debit card. If you receive payment using a bankcard. 
The bank will have access to identifiable information. If samples are collected improperly 
and you are asked to repeat sample collection, you will not be compensated for repeat 
sample collections. 
Who is funding this research study?
The National Institutes of Health and the Broad Institute are providing funding for this 
study. 
The Children’s Hospital of Philadelphia is also funding this research. 
Please ask Dr. Albenberg if you have any questions about how the study is funded. 
What if you have questions about the study?
If you have questions about the study, call the study doctor, Dr. Lindsey Albenberg at 
215-590-1680. You may also talk to your own doctor if you have questions or concerns.
The Institutional Review Board (IRB) at The Children’s Hospital of Philadelphia has 
reviewed and approved this study. The IRB looks at research studies like these and makes 
sure research subjects’ rights and welfare are protected. If you have questions about your 
rights or if you have a complaint, you can call the IRB Office at 215-590-2830. 
A description of this clinical trial will be available on http://www.ClinicalTrials.gov, as 
required by U.S. Law.  This Web site will not include information that can identify you.  
At most, the Web site will include a summary of the results.  You can search this Web 
site at any time. 


CHOP IRB#: IRB 17-014343
Effective Date: 3/19/2020
Expiration Date: 12/17/2020
Page 8 of 9
Documentation of Verbal Consent to Take Part in this Research Study and 
Authorization to Use and Disclose Health Information for the Research
Name of Subject
The research study and consent form was explained to: 
Person Providing Consent
Relation to subject:
 Parent     
 Legal Guardian 
 Self
The person who provided consent confirmed that all of their questions had been 
answered and they agreed to their/their child’s participation in this research study. 
They confirmed that they were legally authorized to consent to their/their child’s 
participation.  
They agreed to let CHOP use and share their/their child’s health information. 
Person Obtaining Consent
Signature of Person Obtaining Consent
Date


CHOP IRB#: IRB 17-014343
Effective Date: 3/19/2020
Expiration Date: 12/17/2020
Page 9 of 9
Documentation of Verbal Assent to Take Part in this Research Study
For adults with diminished capacity capable of providing assent:
I have explained this study and the procedures involved to __________________ in 
terms he/she could understand and that he/she freely assented to take part in this study.
Person Conducting Assent
Signature of Person Conducting Assent
Date
For adults with diminished capacity unable to assent: 
I certify that __________________ was not capable of understanding the procedures 
involved in the study sufficiently to assent to study participation. 
Person Responsible for Conducting 
Assent
Signature of Person Responsible
Date