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Fecal Microbial Transplantation and Its Expansion Into the Treatment of Other Diseases

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Fecal Microbial Transplantation and Its Expansion Into the Treatment of Other Diseases Fecal Microbial Transplantation and its Expansion into the Treatment of Other Diseases by Braden Thomas Millan A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science Department of Medicine University of Alberta ©Braden Thomas Millan, 2016 Abstract Background: Fecal Microbial Transplantation (FMT) has gained popularity due to its efficacy in the treatment of recurrent Clostridium difficile infection (RCDI). RCDI is associated with prolonged courses of antibiotics with high recurrence rates following the initial resolution of symptoms. The increased use of antibiotics in both healthcare and agriculture has led to increased prevalence of antibiotic-resistant microbes. Therefore, we first tested the hypothesis that patients with RCDI would harbor high numbers of antibiotic-resistant bacteria and secondly, that FMT would reduce the number of antibiotic-resistant gene containing bacteria. Furthermore, the association between microbial dysbiosis and inflammatory bowel disease (IBD) has enhanced interest in therapies targeting the microbiota. For RCDI, resolution of the infection using FMT correlates with efficient engraftment of the donor microbiota. The purpose of our mouse studies was to determine the efficiency of donor microbiota engraftment into the recipient following a short pre-FMT treatment regimen and investigate if this changed the FMTs ability to reduce the development of colitis in Interleukin-10 knockout (IL-10 -/-) mice. Methods: Using shotgun metagenomics, we sequenced the microbiota of 20 RCDI patients. The libraries from the RCDI patients and a healthy cohort (n=87) obtained from the Human Microbiome Project (HMP) were aligned against the NCBI bacterial taxonomy database and the Comprehensive Antibiotic Resistance Database (CARD). Results were corroborated through a DNA microarray containing 354 antibiotic resistance (ABR) genes. In mice, the microbiota was analyzed at baseline (day 0), following treatment (day 3), three days after FMT (day 7) and 31 days following FMT (day 35) using real-time PCR and 16S rRNA sequencing. Sequencing data was processed using the QIIME pipeline. Gastrointestinal inflammation was quantified by measuring cytokines from the stool, cecum tissue, small intestine tissue, and serum, as well as histology scoring of the small intestine and colon. Conclusion: RCDI patients have increased numbers of antibiotic-resistant organisms. FMT is effective in the eradication of pathogenic antibiotic-resistant organisms and elimination of antibiotic-resistance genes. Regardless of the pre-FMT treatment regimen, strong engraftment of the donor microbiota into a healthy recipient was observed and remarkably was maintained after four weeks. In an IBD model, our results indicate that preparation of the host has substantial effects on the efficacy of FMT and should be considered moving forward in FMT research for other diseases. ii Preface This thesis is an original work by Braden T. Millan. All research projects, of which this thesis is a part, received research ethics approval from the University of Alberta Research Ethics Board: Fecal microbiota transplantation (FMT) in the management of recurrent Clostridium difficile infection (CDI), Pro00049006, October 2014. Probiotic bacteria and epithelial cells and Breeding Colony, AUP00000293, August 2014. Chapter 2 of this thesis has been published as Millan B, Park H, Hotte N, Mathieu O, Burguiere P, Tompkins TA, Kao D, & Madsen KL. Fecal microbial transplants reduce antibiotic-resistant genes in patients with recurrent Clostridium difficile infection. Clin Infect Dis. 2016 Mar 29. KM, TT, and DK designed the study; BM and HP conducted the research; BM, HP, NH, OM, PB, JD carried out the data analysis; DK performed patient assessments and fecal microbial transplants; BM, HP, and KM wrote the manuscript; All authors read and approved the final manuscript. iii Acknowledgements First, I would like to thank my supervisor Dr. Karen Madsen for all the guidance she has provided me with throughout my graduate studies. Without her, the contents of this thesis would not be possible. I would also like to thank my committee members, Dr. Dina Kao and Dr. Richard Fedorak who helped guide me through my graduate studies and provided me with much- needed career guidance. All the members of the Madsen laboratory helped support me through my graduate studies, in particular, Naomi Hotte whose invaluable knowledge helped guide me through each day; as well as Dr. Heekuk Park who wrote all the bioinformatics pipelines and taught me how to use them. Finally, I would like to thank my parents for all the opportunities they have provided me with in my life and hope that they understand that my success is a direct indication of how amazing they truly are. iv Table of Contents Abstract ........................................................................................................................... ii Preface............................................................................................................................ iii Acknowledgements ........................................................................................................ iv List of Tables ............................................................................................................... viii List of Figures ................................................................................................................ ix List of Abbreviations ................................................................................................... xiii Chapter 1: The Microbiota in Clostridium difficile Infection and Inflammatory Bowel Disease and Implications for Fecal Microbiota Transplantation ........................................ 1 1.1 Introduction ............................................................................................................... 1 1.2 Clostridium difficile infection ................................................................................... 5 1.2.1 Introduction ............................................................................................................................................. 5 1.2.2 Epidemiology and Pathology ............................................................................................................ 6 1.2.3 Treatment and Recurrence ................................................................................................................. 8 1.2.4 Fecal Microbial Transplantation in CDI and RCDI ................................................................... 9 1.3 Inflammatory Bowel Disease .................................................................................. 12 1.3.1 Introduction ........................................................................................................................................... 12 1.3.2 Epidemiology ....................................................................................................................................... 13 1.3.3 Treatment ............................................................................................................................................... 14 1.3.4 Economic Costs ................................................................................................................................... 15 1.3.5 Genetics .................................................................................................................................................. 16 1.3.6 Environmental Factors ...................................................................................................................... 18 1.3.7 Microbiome and the Immune System ........................................................................................... 19 1.3.8 Fecal Microbial Transplants in IBD .............................................................................................. 24 Chapter 2: Fecal microbial transplants reduce antibiotic-resistant genes in patients with recurrent Clostridium difficile infection............................................................................ 50 Abstract ......................................................................................................................... 51 2.1 Introduction ............................................................................................................. 53 2.2 Materials and Methods ............................................................................................ 54 2.2.1 Patient Cohorts ..................................................................................................................................... 54 2.2.2 Donor Selection ................................................................................................................................... 54 2.2.3 Fecal Microbial Transplantation (FMT) ...................................................................................... 55 2.2.4 DNA Extraction and Metagenomic Analysis ............................................................................. 55 v 2.2.5 DNA Microarray Analysis ............................................................................................................... 56 2.2.6 Statistical analysis ............................................................................................................................... 57 2.3 Results ....................................................................................................................
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