Clinical trial NCT02057198
Conditions: C. Difficile Diarrhea Enterocolitis
Sponsor: Duke University
Start date: 2014-06-10; Completion date: 2017-06-27
Enrollment: 33 participants; Allocation: RANDOMIZED; Intervention model: PARALLEL

Brief summary:
The overall aim is to characterize and to compare the extent and quantity of C. difficile stool shedding, perianal colonization and environmental contamination in patients who received oral fidaxomicin, oral metronidazole, or oral vancomycin. This is a prospective, randomized, microbiologic and molecular, study of environmental contamination from patients with proven C. difficile associated diarrhea (CDAD).

Detailed description:
Background and Significance:

C. difficile has emerged as one of the most important pathogens that threaten the health and quality of life for many populations. Data from different studies clearly indicate that shedding of viable spores and subsequent contamination of environmental surfaces play an important role in the transmission of C. difficile. We aim to perform an analysis of the impact of different oral antibiotic therapy on microbiologic kinetics in patients with C. difficile diarrhea, such as: shedding, colonization and environmental contamination. We believe data from this study can inform whether drug therapies may be used to interrupt disease transmission and to improve the infection control of C. difficile.

Purpose of the Study:

The purposes of this study are to 1) determine the impact of oral fidaxomicin, oral metronidazole and oral vancomycin on the baseline and the temporal variation of C. difficile isolated from specific body sites of a patient with microbiology-proven CDAD and 2) determine the impact of oral fidaxomicin, oral metronidazole and oral vancomycin on the baseline and the temporal variation of C. difficile isolated from targeted surfaces in a hospital room. , More specifically, we will establish the extent and quantity of C. difficile shedding, colonization and environmental contamination in patients who received oral fidaxomicin, oral metronidazole, or vancomycin and the duration that stool remains positive for C. difficile.

This study will prospectively study the role of the environment in Healthcare Associated Infections (HAIs) in the modern healthcare setting and will specifically address many limitations of previous studies. The study will use modern diagnostic and molecular methods to describe the microbiologic characteristics and concordance of cultures from the environment and from patient, describe temporal variation and relationship in the microbiologic profiles of cultures obtained from the environment and from the patient, assess confounders such as hand hygiene and quality of cleaning, and provide longitudinal follow up for subsequent outcomes.

This study will utilize microbiologic and molecular techniques to critically and prospectively examine the impact of the environmental bioburden on the risk of colonization and infection of hospitalized patients. Data from this study will provide novel, important information regarding the true impact of the hospital environment on the acquisition and spread of HAIs and Multi-Drug Resistant (MDR)-pathogens in hospitalized patients over time. As such, data collected in this study may provide important information about the mechanisms and relative frequency of how and when environmental sources of bacteria lead to colonization and infection in hospitalized patients. These data may in turn stimulate or justify the future development of novel preventive interventions.

Design and Procedures/Study Interventions:

This is a randomized, controlled study of patients with documented CDAD, defined as having polymerase chain reaction for C. difficile in a patient with more than 3 loose stools within 24 hours. Eligible patients for enrollment will be identified by microbiology-driven alerts or by orders for contact isolation for C. difficile. Study team will be alerted to approach the patient to provide information about the study and to obtain informed consent.

This study will obtain microbiological cultures from 2 sources: 1) environmental surfaces in the room and 2) body surfaces of the patient at predefined intervals starting the day of enrol1ment. Cultures will be obtained on Day 1 (day of enrol1ment), Day 3 and Day 7 following admission to the room, at the end of each subsequent week (Day 14, Day 21, etc.), and on the day of discharge from the hospital room. Microbiological cultures will be obtained from the following body sites: perianal and stool specimens. Microbiological cultures will be obtained from 5 high-touch environmental surfaces as outlined in the protocol.

Selection of Subjects:

A total of 30 patients are anticipated to be enrolled in this study, 10 in each of the three treatment arms. Patients will be block-randomized to receive one of the three antibiotic treatments for CDAD described above. The study will enroll 10 patients receiving metronidazole therapy, 10 patients receiving oral vancomycin therapy and 10 patients receiving oral fidaxomicin therapy.

As soon as the PI or study coordinator finds that a patient has a positive C. difficile result, the primary care provider (PCP) in hospital will be contacted to discuss the patient. If the PCP agrees to allow potential enrollment, the PCP will introduce the study to the patient. If the patient indicates willingness to participate, the PI or study coordinator will be introduced by the PCP or another caregiver known to the patient. The informed consent process will take place if the patient is interested in participating. The patient will be enrolled as a study subject if all eligibility criteria are met. The PCP will formally prescribe fidaxomicin, metronidazole or vancomycin following randomization. Fidaxomicin will be supplied by the study sponsor. Metronidazole and vancomycin will not be supplied by the sponsor. If the subject is randomized to receive fidaxomicin, the PI or study coordinator will notify the Duke Investigational Drug Service (IDS) that a subject is enrolling and will order this drug through the IDS. As soon as the 10th subject who is prescribed fidaxomicin enrolls, then enrollment will be closed to patients prescribed fidaxomicin. Enrollment will be closed to subjects taking metronidazole and vancomycin as soon as the 10th subject in each group is enrolled. The subject will begin treatment with the medication prescribed by the PCP in hospital.

No compensation is being offered for participation in this study.

Consent Process:

The consent process will be conducted by a study coordinator or the principal investigator. This will typically occur in the patient's hospital room..

Subject's Capacity to Give Legally Effective Consent:

Subjects will need to be able to give consent to participate in this study.

Risk/Benefit Assessment:

The risks are minimal for this study. First, patients may experience adverse effects from the antibiotics that they consent to receive. Each of three agents is recommended for the treatment of CDAD. Second, the microbiological samples that will be taken may cause some discomfort and minor bleeding which will be discussed with the patient during the consenting process. Declining to participate in the study will not affect the clinical care of the patient. Results of study specimens will not be analyzed in real-time and will not be sent back to clinicians.

SAEs are not anticipated for this study. Any standard SAE events that may occur will be reported to the manufacturer and to the IRB.

There is no direct benefit to the patient in the study. The sponsor will supply Fidaxomicin if this is prescribed for a patient enrolled in the study. The data from this study may prompt future studies that examine the use oral antibiotics to reduce the transmissibility of C. difficile.

Data Analysis and Statistical Considerations:

Descriptive statistics will be used to correlate culture results from the environment and the patient.

Data and Safety Monitoring:

PI will review and sign off on all adverse events or problems as they occur and will submit reports of such events to the IRB in accordance with HRPP policies and to the sponsor in accordance with the protocol.

Privacy, Data Storage and Confidentiality:

Privacy during swabbing shall be maintained by swabbing the patient in the patient's room with the door closed as would be appropriate for other patient care, using Universal Precautions. To ensure privacy the patient and environmental samples will use an automatically generated ID and room number in place of name, MRN or other personal identifiers.

Data collected by the study will be entered into secure Access databases. All connections to the system, both external and internal, occur over encrypted channels. Access to components of the system is role-based and can only be granted by administrators of the system. All collected information is stored on a server hosted by Duke Medicine.

Arms: arm 1: 200 mg. 2 times a day for 10 days arm 2: 500 mg.orally 3 times daily for 10 days arm 3: 125 mg. orally 4 times a day for 10 days
Interventions: intervention 1: Fidaxomicin intervention 2: Metronidazole intervention 3: Vancomycin
Intervention descriptions: intervention 1: None intervention 2: None intervention 3: None

Protocol documents:
Prot_000.pdf: 
Exploratory Study of Impact of Oral Metronidazole, Vancomycin and Fidaxomicin on the Extent and 
Quantity of Host Carriage and Environmental Contamination with C. difficile 
Principal Investigator: Daniel Sexton 
NCT02057198 
Version Date: 2/28/19 
Purpose of the Study 
 We aim to perform an exploratory analysis on the impact of different oral antibiotic therapy on 
microbiologic kinetics in patients with C. difficile diarrhea, such as: shedding, colonization and 
environmental contamination. We believe data from this study can inform whether drug therapies may 
be used to interrupt disease transmission and to improve the infection control of C. difficile. 
Background & Significance 
C. difficile has emerged as one of the most important pathogens that threaten the health and quality of 
life for many populations. Data from different studies clearly indicate that shedding of viable spores and 
subsequent contamination of environmental surfaces play an important role in the transmission of C. 
difficile.  We aim to perform an exploratory analysis on the impact of different oral antibiotic therapy on 
microbiologic kinetics in patients with C. difficile diarrhea, such as: shedding, colonization and 
environmental contamination. We believe data from this study can inform whether drug therapies may 
be used to interrupt disease transmission and to improve the infection control of C. difficile. 
  
Clinical and in vitro data suggest fidaxomicin may be useful in reducing shedding, carriage and 
environmental contamination of C. difficile. These features include: 
• Fidaxomicin has 8‐fold higher bactericidal activity against C. difficile compared to vancomycin in in 
vitro studies. 
• Fidaxomicin is associated with lower post‐treatment spore counts as compared to vancomycin. 
• Fidaxomicin is associated with less disturbance of non‐Clostridial GI flora 
• Fidaxomicin has prolonged post‐antibiotic effect compared to vancomycin. 
• Fidaxomicin therapy, compared with vancomycin, was associated with slightly shorter time to 
resolution of diarrhea. 
Design & Procedures 
General. Duke University Health System is uniquely positioned to study the impact of fidaxomicin on the 
microbiologic kinetics of C. difficile, including bacterial shedding, colonization and environmental 
contamination. In 2011, the Duke Program for Infection Prevention and collaborators from University of 
North Carolina, Chapel Hill were jointly awarded a five‐year Preventions Epicenter grant by the Centers 
for Disease Control and Prevention (CDC). The keystone project funded by the Epicenters grant will 
study the efficacy of ultraviolet light and novel cleaning strategies in reducing environmental 


contamination and disease incidence due to 4 main pathogens: MRSA, VRE, Acinetobacter and C. 
difficile. In Phase III of the Epicenter study, we will study bacterial shedding, level of bacterial 
colonization and level of environmental contamination starting from the time a patient is admitted into 
a freshly cleaned room. Microbiologic cultures will be obtained from enrolled patients and the 
designated surfaces of their rooms.  
  
We propose an exploratory study that will describe and compare the impact of 3 oral antibiotic 
therapies on the microbiologic kinetics of C. difficile shedding, colonization and environmental 
contamination among patients with laboratory confirmed CDAD. The proposed study will take 
advantage of much of the infrastructure, study coordination and enrollment strategies already created 
for phase III of the CDC Epicenter study, resulting in high cost‐effectiveness. 
We will undertake a prospective, randomized controlled trial (RCT) to evaluate the impact of antibiotic 
treatment choice on environmental shedding and contamination with C. difficile spores.  The proposed 
research will be a parallel study to the CDC Phase II (Duke IRB #Pro00032718 and Phase III studies (Duke 
IRB #Pro00036470). 
Specific Aims. The specific aims of this study are to: 
1) characterize the baseline and the temporal variation in the profile of C. difficile isolated from targeted 
surfaces in a hospital room; 
2)  determine the impact of oral fidaxomicin, oral metronidazole and oral vancomycin on the above 
relationships over time and specifically establish: 
a. Extent and quantity of C. difficile shedding, colonization and environmental contamination in patients 
who received oral fidaxomicin vs. oral metronidazole or vancomycin. 
b. Duration of diarrhea that were positive for CDAD. 
This is a RCT of patients with documented CDAD, defined as any patients with a positive polymerase 
chain reaction (PCR) test for C. difficile in a patient with more than 3 loose stools within 24 hours.  
Eligible patients will be identified by microbiology‐driven alerts or by orders for contact isolation for C. 
difficile. Study team will be alerted to approach the patient to provide information about the study and 
to obtain informed consent. 
Outcomes.  The primary outcome will be median total colony forming units (CFU) of C. difficile identified 
in the hospital room environment for each antibiotic.  More specifically, the median environmental 
contamination in patients who receive fidaxomicin will be compared to the median environmental 
contamination in patients who receive vancomycin and to the median environmental contamination in 
patients who receive metronidazole.  Secondary outcomes will include molecular relatedness of C. 
difficile isolates, changes in environmental contamination over time, and duration of diarrhea.  
Inclusion criteria  
Adult patients ( > 18 years )with microbiology‐proven CDAD, who are able to provide informed consent 
and are eligible to receive oral antibiotic therapy. 


Exclusion criteria  
Prisoners, pregnant women and children <18 years will be excluded (see Protection of Human Subjects 
and Inclusion of Children), 
Patients requiring intravenous therapy for treatment of CDAD, 
Patients who do not consent and those who withdraw consent, etc. 
 Patient Participation 
This study will obtain microbiologic cultures from 2 sources: 1) environmental surfaces in the room and 
2) stool or perianal swabs from the patient at predefined intervals starting the day of enrollment. The 
environmental cultures as well as the stool and perianal swabs will be labeled with a unique study 
number. Cultures will be obtained on Day 1 (day of enrollment), Day 3 and Day 7 following admission to 
the room, at the end of each subsequent week (Day 14, Day 21, etc.), and on the day of discharge from 
the hospital room.  Microbiologic cultures will be obtained, including perianal swabs and stool 
specimens.  Microbiologic cultures will be obtained from 5 high‐touch environmental surfaces 
A total of 30 patients are anticipated in this study; 10 patients will be included in each of the three study 
arms. Patients will always receive anti‐C. difficile therapy for CDAD; the exact drug will be assigned 
based on block‐randomization of fidaxomicin, metronidazole or vancomycin. Thus, the study will enroll 
10 patients receiving metronidazole therapy, 10 patients receiving oral vancomycin therapy and 10 
patients receiving oral fidaxomicin therapy. Patients will receive 10 days of therapy. 
Subjects will be asked to return 7 days after discharge from hospital for an outpatient visit. Subjects will 
also be asked for a stool sample if possible. If not, a perianal swab will be obtained. 
We will adhere to all Good Clinical Practice (GCP) guidelines. The protocol, clinical record form, and 
consent form will be submitted to the Institutional Review Boards for approval. 
Onsite study coordinators will obtain informed consent. Study coordinators or a trained designee will 
collect specimens from patients using standard methodology. Results of study specimens will not be 
analyzed in real‐time and will not be fed back to clinicians. Declination of participation in the study will 
not affect the clinical care of the patient. 
Specimens from different environmental sites obtained at different time‐points will be tested to 
determine the presence of C. difficile. The count and proportion of specimens from patients that are 
positive for the bacteria will be calculated for each time point. Relatedness of bacteria will be 
determined using antibiotic susceptibility and molecular techniques, including PFGE, ribotyping, and 
MLST methods for C. difficile that are found from patient and from the environment of the patient 
room.  Statistical analysis of the final data set will include adjustments for length of stay and the average 
number of cultures taken per patient and per patient room.  
  
Microbiologic cultures from the environment will be sent to UNC Hospital Epidemiology Microbiology 
laboratory (headed by Dr William Rutala) and swab and stool samples from subjects will be sent to the 
Duke VA Medical Center Molecular Epidemiology Research Laboratory (headed by Dr Chris Woods) for 


analysis.  All samples sent to UNC and the Duke VA are de‐identified and labeled with a unique study 
number. 
Selection of Subjects 
Inclusion criteria  
Adult patients ( > 18 years )with microbiology‐proven CDAD, who are able to provide informed consent 
and are eligible to receive oral antibiotic therapy. 
  
Exclusion criteria  
Prisoners, pregnant women and children <18 years will be excluded (see Protection of Human Subjects 
and Inclusion of Children), 
Patients requiring intravenous therapy for treatment of CDAD, 
Patients who do not consent and those who withdraw consent, etc. 
Subject Recruitment and Compensation 
Describe recruitment procedures, including who will introduce the study to potential subjects. Describe 
how you will ensure that subject selection is equitable and all relevant demographic groups have access 
to study participation (per 45 CFR 46.111(a) (3)). Include information about approximately how many 
DUHS subjects will be recruited. If subjects are to be compensated, provide specific prorated amounts to 
be provided for expenses such as travel and/or lost wages, and/or for inducement to participate. 
A Waiver or Alteration of Consent and HIPAA Authorization will be submitted to the IRB for approval. 
Subjects will be identified through review of hospital records including lab results for C. difficile. 
  
As soon as the PI or study coordinator identifies a patient with a positive C. difficile result, the primary 
service team (PST) in hospital will be contacted to discuss the patient. If the PST agrees that the patient 
is eligible and agrees to the drug‐allocation schema outlined above the PST will introduce the study and 
the study coordinator to the patient and the study coordinator will go over the informed consent with 
the patient.  The patient will be enrolled as a study subject if all eligibility criteria are met and after the 
informed consent is signed and dated by the patient. C difficile therapy will be assigned by block 
randomization. If the patient is allocated to oral vancomycin or oral metronidazole, then the PST will 
prescribe the drug as per usual practice. If the patient is assigned fidaxomicin, the study investigators 
will prescribe the drug from the Investigational Drug Service (IDS). The study sponsor will supply 
fidaxomicin, but not metronidazole or vancomycin. 
Subject’s Capacity to Give Legally Effective Consent 
If subjects who do not have the capacity to give legally effective consent are included, describe how 
diminished capacity will be assessed. Will a periodic reassessment occur? If so, when? Will the subject 
be consented if the decisional capacity improves? 


Subjects will need to be able to give consent to participate in this study. 
Risk/Benefit Assessment 
The three treatment options included in this study are part of routine care for CDAD.  Vancomycin and 
metronidazole are recommended for the treatment of CDAD in multi‐society guidelines.  Fidaxomicin is 
FDA‐approved for the treatment of CDAD, but is not included in guidelines because of its cost.  
Nevertheless, all antibiotics can lead to adverse events.  Thus, patients may experience adverse effects 
from the antibiotics that they consent to receive as part of usual clinical care for CDAD. Secondly, the 
microbiological samples that will be taken may cause some discomfort and minor bleeding which will be 
discussed with the patient during the consenting process. Declining to participate in the study will not 
affect the clinical care of the patient. Results of study specimens will not be analyzed in real‐time and 
will not be sent back to clinicians. 
The PI will review and sign off on all adverse events or problems as they occur. SAEs are not anticipated 
for this study. Any standard SAE events that may occur will be reported to the manufacturer and to the 
IRB.  
There is no direct benefit to the patient in the study. The sponsor will supply Fidaxomicin free of charge 
if the patient is randomized to this drug. The data from this study may prompt future studies that 
examine the use of oral antibiotics to reduce the transmissibility of C. difficile. 
Costs to the Subject 
The sponsor will supply Fidaxomicin free of charge if the patient is randomized to this drug. 
Data Analysis & Statistical Considerations 
Describe endpoints and power calculations. Provide a detailed description of how study data will be 
analyzed, including statistical methods used, and how ineligible subjects will be handled and which 
subjects will be included for analysis. Include planned sample size justification. Provide estimated time 
to target accrual and accrual rate. Describe interim analysis including plans to stop accrual during 
monitoring. Phase I studies, include dose escalation schema and criteria for dose escalation with 
definition of MTD and DLT. 
Outcomes.  The primary outcome will be median total colony forming units (CFU) of C. difficile identified 
in the hospital room environment for each antibiotic.  More specifically, the median environmental 
contamination in patients who receive fidaxomicin will be compared to the median environmental 
contamination in patients who receive vancomycin and to the median environmental contamination in 
patients who receive metronidazole.  Secondary outcomes will include molecular relatedness of C. 
difficile isolates, changes in environmental contamination over time, and duration of diarrhea.  
Specimens from different environmental sites obtained at different time‐points will be tested to 
determine the presence of C. difficile. The count and proportion of specimens from patients that are 
positive for the bacteria will be calculated for each time point. Relatedness of bacteria will be 
determined using antibiotic susceptibility and molecular techniques, including PFGE, ribotyping, and 
MLST methods for C. difficile that are found from patient and from the environment of the patient 
room.  Statistical analysis of the final data set will include adjustments for length of stay and the average 
number of cultures taken per patient and per patient room.  


Microbiologic cultures from the environment will be sent to UNC Hospital Epidemiology Microbiology 
laboratory (headed by Dr William Rutala) and swab and stool samples from subjects will be sent to the 
Duke VA Medical Center Molecular Epidemiology Research Laboratory (headed by Dr Chris Woods) for 
analysis.  All samples sent to UNC and the Duke VA are de‐identified and labeled with a unique study 
number. 
 Statistics – Descriptive statistics would be used to correlate culture results from the environment and 
the patient.  Medians will be compared using standard statistical tests such as Wilcoxon rank sums. 
Data & Safety Monitoring 
Summarize safety concerns, and describe the methods to monitor research subjects and their data to 
ensure their safety, including who will monitor the data, and the frequency of such monitoring. If a data 
monitoring committee will be used, describe its operation, including stopping rules and frequency of 
review, and if it is independent of the sponsor (per 45 CFR 46.111(a) (6)). 
Data 
Data collected by the study will be entered into secure REDCap databases managed by the Duke Office 
of Clinical Research. All connections to the system, both external and internal, occur over encrypted 
channels. Access to components of the system is role‐based and can only be granted by administrators 
of the system. All collected information is stored on a secure server hosted by Duke Medicine 

SAP_001.pdf: 
Exploratory Study of Impact of Oral Metronidazole, Vancomycin and Fidaxomicin on the Extent and 
Quantity of Host Carriage and Environmental Contamination with C. difficile 
Principal Investigator: Daniel Sexton 
NCT02057198 
Statistical Analysis Plan 
Nicholas Turner MD MHSc 
Version date: 25 October 2018  
Study Design and Participants 
We performed a prospective, unblinded randomized controlled trial of eligible and enrolled inpatients at 
Duke University Hospital.  All adult inpatients diagnosed with CDI were eligible for inclusion; CDI was 
defined as a positive NAAT test in the setting of >3 loose stools in a 24-hour period.  Eligible patients 
were excluded if prisoners, pregnant, required intravenous therapy for treatment of CDI, unable to 
consent, or received two or more doses of empiric therapy for CDI (with any agent).  Eligible patients 
with no exclusion criteria were approached for enrollment. 
Randomization 
Enrolled patients were randomized to one of three study arms with 1:1:1 allocation: metronidazole 
500mg PO q6, vancomycin 125mg PO q6, or fidaxomicin 200mg PO q12.  Treatment was provided a 
minimum of 10 days following enrollment.  Patients and providers were unblinded to study arm and 
treatment choice.  The metronidazole treatment arm was considered to be the reference arm. 
Outcomes 
The primary outcome was the change in total environmental burden, measured as the total colony 
forming units (CFUs) of C. difficile isolated from each patient’s hospital environment. Environmental 
sampling was conducted from 5 pre-specified locations (bedrails, overbed table, sink, toilet seat and 


bathroom floor). 5 replicate Rodac plates (covering an area of 25 cm2) were collected from each site.  
Secondary outcomes included total environmental burden (as measured by percent of hospital 
environmental samples positive according to each treatment group), C. difficile shedding over time 
(assessed as CFU/g of stool from serial patient samples), and molecular relatedness of isolates (assessed 
as the percent of environmental isolates sharing the same ribotype as the strain isolated from each 
patient’s stool samples).  
Study Procedures 
Eligible patients were identified by microbiology-driven alerts or by orders for contact isolation 
for C. difficile.  The study team was alerted of a potentially eligible patient.  After confirmation of 
eligibility, the study coordinator approached the treating clinician and patient for potential enrollment 
and informed consent.  
 
After obtaining informed consent, cultures were acquired from two sources: 1) environmental 
surfaces in the room and 2) stool samples from the patient. Cultures were obtained from these sources 
at predefined intervals starting the day of enrollment (day 0), days 3 and 7 following admission to the 
room, at the end of each subsequent week (days 14, 21, etc) and on the day of discharge from the 
hospital room (Figure 1).  Environmental cultures were obtained from five high-touch environmental 
surfaces (bedside rail, bedside table, sink, toilet seat, and bathroom floor, toilet seat) and sampled in 5 
replicates for each site. 
Microbiological methods 
The concentration of C. difficile in stool was obtained using ethanol shock followed by 
quantitative culture on CDSA plates to determine CFUs/g of stool on each sampling day. A minimum of 
five environmental sites were cultured in 5 replicates from each room using Rodac plates containing 
Clostridium difficile Selective Agar.  All plates were anaerobically incubated at 37oC for 48 hours.  For C. 


difficile, the total number of CFUs of the targeted pathogen present on each plate was determined by 
identifying morphologies suggestive of the target organisms.  These colonies were then sub-cultured 
and identity confirmed using a latex agglutination kit targeting C. difficile-specific cell wall antigens 
(Oxoid, UK).   
We performed ribotying of C. difficile strains to assess whether environmental strains matched 
C. difficile shed by study subjects. Ribotyping was conducted on all initial patient stool specimens as well 
as environmental samples from each site. Ribotyping was performed according to the methods 
described previously by Bidet et al.11 Cluster analysis to determine strain relatedness was conducted 
with Bionumerics imaging analysis software, using Dice coefficients and the unweighted paired group 
method with arithmetic mean (UPGMA). Band position tolerance was set at 1.25% and strains were 
considered identical if they exhibited a >99% match. 
Statistical Methods 
Standard descriptive statistics were used including medians and interquartile ranges (IQR) for 
non-normally distributed continuous variables. Comparisons of proportions were conducted with two-
sample proportional z-tests.  
To model the reduction in C. difficile shedding over time, stool or environmental C. difficile 
concentrations (CFU/g) were plotted for each subject over time. Inspection suggested an exponential 
decay curve. Concentrations (CFU/g) were then log transformed, providing linear decay curves for 
regression modeling. A linear mixed effects model (with subject identity as the random effects term) 
was employed to properly account for the correlation inherent in repeated sampling within subjects 
over time. All regression modeling was conducted in R (version 3.4.3) with the regression modeling 
package lme4.12 Graphs were constructed using ggplot2.13