Prevention of Clostridium Difficile-associated Diarrhea by Daily Intake of Kefir
Phase: PHASE2
Conditions: Clostridium Difficile Infection, Diarrhea
Sponsor: St. Luke's Hospital of Duluth

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Prevention of Clostridium difficile-associated diarrhea by daily intake of kefir 
 
 
Johan S. Bakken MD, PhD, FIDSA 
Associate Professor 
Department of Family Medicine  
University of Minnesota, Duluth 
St. Luke's Infectious Diseases 
1001 East Superior Street, Ste L201 
Duluth, MN 55802 
 
Andrew Thompson, MD 
St. Luke's Infectious Diseases 
1001 East Superior Street, Ste L201 
Duluth, MN 55802 
 
Libby Maas, RN, BSN 
Clinical Supervisor-7 West 
St. Luke’s Hospital 
Duluth, MN 55805 
 
Traci Lundeen, PharmD. 
Department of Pharmacy 
St. Luke’s Hospital 
Duluth, MN 55805 
 
Jane Gilbert-Howard, RN 
Infection Prevention 
St. Luke’s Hospital 
Duluth, MN 55805 
 
Paula Bursch, RD., LD. 
Clinical Nutrition/Diabetes Care 
St. Luke’s Hospital 
Duluth, MN 55805 
 
Renuga Vivekanandan, M.D. 
Assistant Professor 
Department of Medicine 
Creighton University 
601 North 30th Street, Suite 5800 
Omaha, NE 68131 
 
Ron Regal, Ph.D. 
Department of Mathematics 
University of Minnesota Duluth  
Duluth, MN 55812 
 
Xuan Li, Ph.D. 
Department of Mathematics 
University of Minnesota Duluth  
Duluth, MN 55812 
 
 

Protocol Version 3 
Updated 21 Jan 2016 (LJR) 
 
 
 
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Key Study Personnel: 
Marilyn Odean, M.S. 
Whiteside Institute for Clinical Research 
St. Luke’s Hospital 
Duluth, MN 55805 
 
Lynsie Radovich, Ph.D. 
Whiteside Institute for Clinical Research 
University of Minnesota Medical School Duluth  
Duluth, MN 55812 
 
 
 
 
 
Research Question 
 
This study is being conducted to investigate the potential benefits of probiotic intake for 
preventing antibiotic associated diarrhea and Clostridium difficile infection (CDI) in patients 
undergoing a systemic antibiotic treatment. Primary research question: can daily kefir 
consumption reduce the incidence of diarrhea and CDI in patients during antibiotic treatment? 
 
Specific Aims 
 
§ Enroll a total of 1190 patients into three, randomized study groups:  
 
Patients prescribed antibiotics and receive no kefir 
 
 
Patients prescribed antibiotics and receive kefir during their hospital stay only 
Patients prescribed antibiotics and receive kefir for the duration of their antibiotic 
regimen, for a maximum of 30 days 
 
§ Monitor and record clinical findings specifically related to diarrhea, for example the 
incidence, duration, and recurrence of diarrhea, for patients enrolled in the study.  
 
§ Carry out statistical data analyses in order to assess the efficacy of daily kefir intake 
on reducing the incidence of diarrhea and CDI 
 
 
Background and Significance 
 
Clostridium difficile infections are of great concern for hospitals nationwide and C. difficile remains 
the most common nosocomial infection in North America 1.  The majority of patients with C. 
difficile infection respond to orally administered metronidazole or vancomycin, but 5-30% of 
patients go on to develop recurrent infection and diarrhea, despite antibiotic treatments2. The 
idea that gut microbiota influence susceptibility and recovery from disease is becoming more 
widely reported3. Disruption of normal bacterial flora in the gut during systemic antibiotic use has 
been attributed to the uncontrolled growth of bacteria that are otherwise suppressed such as C. 

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difficile. Even after an antibiotic regimen has concluded, restoration of the normal gut microbiota 
is thought to be paramount to interrupting the cycle of C. difficile infection. The idea of 
reintroducing normal microbial flora to patients with recurrent C. difficile infections has been the 
foundation upon which the use of probiotic agents, including fecal transplants, has been 
introduced4. The use of probiotics to treat antibiotic-associated diarrhea, and specifically C. 
difficile infections, has been studied and successes have been reported, and in particular by our 
group4,5.  The emerging idea, however, is that probiotic consumption can be used to prevent the 
onset of a C. difficile infection, which requires further study. Meta-analyses have been conducted 
on previously reported data and ultimately conclude that the use of probiotics is safe and 
effective6. However, there remains a need for a focused and controlled study assessing the efficacy 
of kefir consumption on the incidence of C. difficile infections at St. Luke’s Hospital in Duluth, MN, 
and CHI Creighton University Medical Center in Omaha, NE. The data collected from this study 
have the potential to change clinical practice at not only our institutions, but at any hospital or 
institution that has a population of patients undergoing systemic antibiotic treatment.  
Risk factors for persistent C. difficile infection include age greater than 65 years, poor nutritional 
status, recent abdominal surgery, prolonged hospitalization and recent stay in the ICU2. The 
purpose of this study is to determine if administering at-risk patients a daily regimen of kefir can 
reduce the incidence of C. difficile infections.  Because treatment for C. difficile infections is difficult 
and expensive, and recurrent infections are common, a way to prevent these infections is of great 
interest. A preventive measure that reduces the incidence of diarrhea and C. difficile infections will 
clearly improve patient health, and will have a multi-fold impact on how patients are cared for 
while in the hospital as well as post-discharge.  There is potential for cost-saving, as well, in the 
form of the direct cost of antibiotic treatments and prolonged hospital stays. Additionally, the cost 
in time and effort to prevent the spread of these infections will be reduced, as well, all of which 
ultimately improve patient care.   
 
Preliminary Studies 
 
Many studies have been published indicating a potential for probiotics as a prophylactic against 
diarrhea associated with antibiotic use in humans6. Additionally, a recent report in a rodent model 
suggests that kefir consumption concomitantly with antibiotic treatment may prevent the 
development of C. difficile-associated diarrhea7. However, to our knowledge there have not been 
any studies published that have investigated the preventative effects of kefir consumption 
specifically related C. difficile infection in human patients.  This protocol will serve as an initial 
study for a subset of at-risk patients and the data collected will provide guidance for future studies 
to include a more broad range of at-risk patients. 
 
Research Design and Methods 
 
Subjects 
The objective is to identify a population of at-risk patients that are undergoing treatment at St. 
Luke’s Hospital (Duluth, MN) and CHI Creighton University Medical Center (Omaha, NE). The 
study will include patients who have been prescribed a systemic antibiotic of any kind 
(administered by oral or parenteral route), but have not yet begun the treatment regimen. There 
will be three study groups: 
 
 

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Patients prescribed antibiotics and receive no kefir 
 
Patients prescribed antibiotics and receive kefir during their hospital stay only 
Patients prescribed antibiotics and receive kefir for the duration of their antibiotic 
regimen, for a maximum of 30 days 
 
All patients will receive a journal to track their kefir intake (if in Group C) and any loose stools or 
diarrhea for 30 days after their hospital stay. Additionally, all patients will receive a follow-up 
phone 3-5 days after discharge from the hospital, and weekly thereafter for 30 days, to determine 
if diarrhea has occurred (total of 4 phone calls). Three attempts will be made to reach the patient 
for each scheduled phone call. All patients will be instructed to call their physician if symptoms of 
diarrhea occur. The aims of this study are to determine the incidence of antibiotic-associated 
diarrhea in each of the study groups as well as the presence of C. difficile in the stool of those 
patients that report having diarrhea.  
 
 
 
Risk factors for C. difficile infection: 
 
Age over 65 years 
 
Prolonged stay in an intensive care unit 
 
Antibiotic use 
 
Hypoalbuminemia 
 
Compromised immune system 
 
Inclusion criteria for this study: Patients who have 
Been admitted to the medical unit on 7 West at St. Luke’s Hospital (Duluth, MN), the 4600 
or 5500 floor at CHI Creighton University Medical Center (Omaha, NE) 
Been prescribed a systemic antibiotic of any kind (administered by oral or parenteral 
route), and have not yet started taking antibiotics or have started taking antibiotics within 
6 hours prior to study enrollment  
Consented to be randomized and take part in the study and are adults greater than 19 
years of age 
 
Exclusion criteria for this study: Patients who are/have 
Tube feeding 
Undergoing dialysis and other renal treatment 
An existing C. difficile infection 
A recent history of C. difficile infection (within the last 3 months) 
A recent history of antibiotic use (within the last 3 months) 
Inflammatory bowel disease, Crohn’s disease, or other chronic gastrointestinal syndrome 
Transferred from the ICU 
A history of acquired of genetic immunodeficiencies; active, acute or chronic serious 
infections (i.e., viral hepatitis, HIV/AIDS), or autoimmune disorders 
Undergoing gastrointestinal surgery, radiation, or cytotoxic chemotherapy 
Allergy to milk protein  
 
 
Randomization Plan 

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Patients will be randomized into each of three study groups by using a computer-generated 
random number system. As patients are enrolled onto the study, a number will be drawn 
from an envelope that has previously been assigned to one of the three study groups. 
Patients will be enrolled into the study group that corresponds to the number drawn. 
 
Data Collection and Accrual Methods 
Patients who meet inclusion criteria and consent to be part of the study will be assigned to one of 
the three study groups at random: 
 
Group A: Receive no kefir 
 
Group B: Receive kefir during their hospital stay only 
Group C: Receive kefir for the duration of their antibiotic regimen, for a maximum of 30 
days 
 
During the standard admissions interview, patients are asked about any allergies, including milk 
protein allergy. This type of allergy will exclude patients from participating in the study. Because 
kefir is 99% lactose free, lactose intolerance will not exclude individuals from participating. Per 
standard of care, a physical exam will be performed and a symptom-directed exam will be 
performed at any follow-up appointments, typically one month after discharge from the hospital.  
 
The consent process will be carried out by Jenna Wentzlaff, PharmD., with assistance from 
pharmacy interns on rotation at St. Luke’s Hospital in Duluth, MN.  Consenting will be carried out 
by John M. Horne, M.D., Leopoldo Alberto Dobronski Jacome, M.D., and Javeria Syed, MD at the 
medical center in Omaha, NE. The consenting process will be carried out at the institution at which 
the patient is hospitalized. This process will be done on a continuous and at-need basis such that 
patients who enroll on this study are not delayed their antibiotic and/or kefir regimens.  
 
Patients in study groups consuming kefir will receive a postcard that includes the nutrition facts 
for a 4-ounce serving of kefir. Lifeway brand Kefir® will be used as it is widely available and 
comes in several palatable flavors. The probiotic content of Lifeway Keir remains constant, 
regardless of flavor. 
 
Patients in Group A will receive their prescribed antibiotics during their hospital stay and will not 
receive kefir. These patients will be instructed to not consume any yogurt, kefir, or other probiotic 
products during their hospital stay and for 30 days post-discharge.  
 
Patients in Groups B and C will begin receiving kefir on the same day that their prescribed 
antibiotic regimen begins. At least 4 ounces of kefir will be administered 3 times a day to patients 
enrolled on this study. A 4 oz. glass of kefir will be provided with every mealtray, and nursing staff 
at each of the participating institutions will administer the kefir to the patients. The amount of 
kefir consumed by the patient will be recorded by the nursing staff and entered in the electronic 
medical record. Four ounces is a standard serving of yogurt and is well-tolerated by patients. This 
serving size will help maintain ongoing live probiotic cultures in the individuals receiving kefir. 
 
For patients in Group B, administration of kefir by the nursing staff will continue for the duration 
of the patients’ hospital stay only. For patients in Group C, kefir will be prescribed at the same 

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minimum dose as given during their hospital stay (at least 4 ounces of kefir 3 times each day, not 
to exceed 12 ounces per day).  
 
All patients will be given a journal in which they can record any symptoms of a C. difficile infection 
(i.e., diarrhea). Additionally, patients in Group C will record their kefir consumption on a daily 
basis.  All patients will receive a follow-up phone 3-5 days after discharge from the hospital, then 
weekly for a total of 30 days from their hospital discharge (a total of 4 phone calls). Three 
attempts will be made to reach the patient for each scheduled phone call. Patients will be asked if 
they have had any incidence of diarrhea in order for nursing staff and physicians to assess if C. 
difficile infection has occurred.  
 
All patients will be asked to contact their physician at the hospital at which they received 
treatment if they experience diarrhea after their hospital stay. These patients will be offered a 
fecal C. difficile test, as per standard of care, from the laboratory within the hospital from which 
they received care. A clinical diagnosis is required to determine if an individual has a C. difficile 
infection. The criterion that must be met is a patient who has 3 or more watery stools in a 24 hour 
period. Stool collection and testing will be carried out per treatment guidelines8.  
 
Patients that develop a C. difficile infection during the study will be immediately treated per 
standard of care and will be considered treatment failures8. However, these patients will be 
contacted for follow-up information pertinent to the study (i.e., duration of symptoms, and efficacy 
of standard treatment). Follow up contacts will be made via telephone; an initial call will be made 
3-5 days after discharge from the hospital and patients will be contacted weekly thereafter for 30 
days (a total of 4 phone calls). Three attempts will be made to reach the patient for each scheduled 
phone call. During these phone calls, patients will be asked if they have any concerns or 
symptoms, specifically related to diarrhea.  
 
If at any point during the hospitalization or during the follow-up timeframe a patient receiving 
kefir displays signs or symptoms of an invasive bacterial, yeast, or fungal infection, blood cultures 
and other cultures as deemed clinically appropriate (urine culture, sputum culture, wound culture, 
etc.) will be obtained. Signs and symptoms of an invasive infection include, but are not limited to, 
the following: fever, chills, elevated WBC concentration, elevated serum C-reactive protein (CRP) 
and/or procalcitonin levels, and hypotension. 
If a suspected invasive infection occurs during the course of kefir administration, the following 
empiric treatment regimen will be considered:  
• Intravenous administration of vancomycin plus piperacillin/tazobactam plus fluconazole 
o Intravenous daptomycin will be used for patients with a previously documented 
vancomycin allergy 
o An intravenous  fluoroquinolone (ciprofloxacin or moxifloxacin) will be used for 
patients with a documented penicillin allergy 
o Intravenous micafungin will be used for patients with a documented fluconazole 
allergy 
Initial intake screening for inclusion in the kefir research study will include an evaluation of 
known allergies.  Antibiotic therapy will be adjusted in accordance with identification of the 
causative organism(s) and corresponding antibiotic susceptibilities. Treatment duration will be 
determined based on standards of care for the clinical situation and the causative organism.  

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Data Analysis 
The primary outcome variables will be 1) any diarrhea post antibiotic administration and 2) any C. 
difficile infection post antibiotic administration.  No further typing of isolates will be performed on 
samples obtained as it is beyond the scope of this study. The three treatment groups will be 
compared using logistic regression with covariates of study location, age, gender, antibiotic type 
and doses, hypoalbuminemia, and compromised immune system.  Model selection based on the 
Akaike Information Criterion will be used to select covariates in final models.  The treatment 
groups will also be compared without covariate adjustment.  As needed, missing data will be 
handled using multiple imputation after assessment of missing at random considerations. 
Dependent and independent variables in planned analyses will be included in imputations along 
with any auxiliary variables thought to be potentially related to predicting the missing data. In 
addition, in order to include other auxiliary covariates in the imputations that are potentially 
related to missingness, logistic regression will be performed with the dependent variable 
missing/not missing. Only imputed values of independent variables will be used in the 
analyses.  Multiple imputation will be performed with the R package mi.9 
 
 
The data being collected from the patient diaries are to be used to monitor compliance with 
antibiotic use, kefir consumption, and any symptoms of C. diff infection. These data will be 
particularly useful in the event that there is no difference seen in C. diff infection rates among the 
study groups. From the self-reported patient data, compliance can be monitored and exclusion 
from the study may be warranted in the case of non-compliance.  
 
 
Settings 
Patients will be drawn from the identified population on 7 West at St. Luke’s Hospital (Duluth, 
MN) and the 4600 or 5500 floor at CHI Creighton University Medical Center (Omaha, NE). Data 
will be collected during the patients’ stay and will be collected from the patient journals post-
discharge. All data collected will be shared among co-investigators named on this study from St. 
Luke’s Hospital (Duluth, MN) and CHI Creighton University Medical Center (Omaha, NE). 
 
 
Measurement Endpoints 
Primary Endpoint: The primary endpoint will be the incidence of diarrhea among the three 
randomized study groups. 
 
Co-Primary Endpoint: The co-primary endpoint will be an assessment of the safety of kefir when 
administered to individuals undergoing antibiotic treatment. 
 
Secondary Endpoints:  The secondary endpoint will be the incidence of C. difficile infection among the 
three randomized study groups. No further isolate typing will be performed on samples obtained in 
this study. 
 
 

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Data Management Plan 
Data on subjects will be obtained by the nursing staff on 7 West of St. Luke’s Hospital in Duluth, 
MN. Clinical information, as outlined above in Data Collection and Accrual Methods, will be 
entered into the electronic medical record as advised by the Clinical Research Nurse at each of the 
institutions/departments participating in this study. Additionally, data will be entered into an 
electronic database on an ongoing basis throughout the study in order to facilitate data analysis 
after the study has concluded. 
 
Evaluation Plan 
The conduct of the study will be evaluation on the basis of: 
 
Accrual of the adequate number of patients to populate the study groups 
 
Completion of all components of the study 
 
Successful dissemination of the results and findings 
 
Analysis Plan 
Data from this study will be analyzed using the methods described above. Data will be submitted 
for statistical analysis after patient identifiers have been removed and only the assigned study 
number is used.  
 
Study Limitations 
A limitation of this study is patient compliance with consumption of appropriate amounts of kefir 
for the assigned study group. For example, it is imperative that the patients who are asked to not 
drink any kefir, or are asked to only drink kefir during their hospital stay but not at home until the 
conclusion of the study comply with their kefir regimen. Additionally, the use of kefir as the 
probiotic agent introduces a broad range of microbiota to the patient and the particular 
organism(s) that may be responsible for improving the incidence of C. difficile infections will not 
be identified. 
 
 
Timeline 
The duration of this study will be approximately 6 months; this should allow for an appropriate 
number of patients to be enrolled in the study, per current patient load at our institutions, and will 
allow time for follow-up interviews to be conducted.  At the conclusion of the study, the primary 
and secondary endpoints will be analyzed in order to develop a manuscript for reporting our 
findings, the duration of which will take approximately 1 year.   
 
 
Dissemination of Results 
A manuscript describing our findings will be completed and submitted for publication. In addition, 
these data may be presented to local or national audiences at conferences or meetings as deemed 
appropriate.  
 
References 

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1.  
Zilberberg MD, Shorr AF, Kollef MH. Increase in adult Clostridium difficile-related 
hospitalizations and case-fatality rate, United States, 2000-2005. Emerg Infect Dis. 
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Gerding DN, Muto CA, Owens RC. Treatment of Clostridium difficile infection. Clin Infect Dis. 
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Vecchio A Lo, Cohen MB. Fecal microbiota transplantation for Clostridium difficile infection: 
benefits and barriers. Curr Opin Gastroenterol. 2014;30(1):47-53. 
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Bakken JS. Staggered and Tapered Antibiotic Withdrawal With Administration of Kefir for 
Recurrent Clostridium difficile Infection. Clin Infect Dis. June 2014:ciu429 - . 
doi:10.1093/cid/ciu429. 
5.  
Bakken JS. Resolution of recurrent Clostridium difficile-associated diarrhea using staggered 
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http://europepmc.org/abstract/MED/19708314. Accessed August 1, 2014. 
6.  
Goldenberg JZ, Ma SSY, Saxton JD, et al. Probiotics for the prevention of Clostridium difficile-
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doi:10.1002/14651858.CD006095.pub3. 
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Bolla PA, Carasi P, Bolla M de los A, De Antoni GL, Serradell M de los A. Protective effect of a 
mixture of kefir-isolated lactic acid bacteria and yeasts in a hamster model of Clostridium 
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Stuart H. Cohen M, Dale N. Gerding M, Stuart Johnson M, et al. Clinical Practice Guidelines for 
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Su, Yu-Sung, et al. "Multiple imputation with diagnostics (mi) in R: Opening windows into 
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