1. FECAL MICROBIOTA TRANSPLANTATION: THE ULTIMATE PROBIOTIC DR MARCO ANDRES BERGEVIN, MD, FRCPC INFECTIOUS DISEASES AND MEDICAL MICROBIOLOGY, CITÉ DE LA SANTÉ HOSPITAL, LAVAL, QC MARCO.BERGEVIN@GMAIL.COM

2. DISCLOSURE Received renumeration for consultation services and/or conferences from: Pendopharm; Paladin; Merck and Cubist No conflicts of interest I have practiced FMT only for recurrent C. Difficile and I accept consults only for such patients at the present time

3. PRESENTATION OVERVIEW 1.Defining the gut microbiota and it’s physiological role 2.Microbiome-Host interactions in IBD 3.How is FMT performed 4.Evidence for use of FMT in IBD 5.Closing remarks

4. HUMAN GUT MICROBIOME SECTION ONE

5. HUMAN GUT MICROBIOME Definition of microbiome: A collection of different microbes and their functions or genes found in an environmental habitat (1) Scientific exploration of the microbiome is in it’s infancy Knowledge has expanded due to next generation sequencing Studies biased towards western societies Studies focused mainly on bacteria ignoring the role of viruses and eukaryotic components Sampling is usually with stool ignoring proximal intestine and mucosa associated bacteria 1.The gut microbiota and host health: a new clinical frontier. Marchesi et al. Gut 2016; 65:330-339 2.Tyler et al. Analyzing the Human Microbiome: A “How To” guide for PhysiciansAm J Gastroenterol 2014; 109: 983-993. 3.Wlodarska et al. An Integrative View of Microbiome-Host Interactions in Inflammatory Bowel Diseases Cell Host and Microbe 17, May 13, 2015.

6. HUMAN GUT MICROBIOME 1.de Meij et al. FASEB journal. Vol 30. April 2016

7. HUMAN GUT MICROBIOME The gut microbiome contains 500-1000 different bacterial species and millions of genes (2) The microbiome composition varies significantly in abundance and bacterial types across the intestinal tract Physiological roles of the microbiome Synthesis of vitamins (biotin, folate, B 5, B 6, riboflavin, thiamin,) Carbohydrate metabolism Immune maturation and maintenance both local and systemic Inhibition of pathogenic species (niche occupation) Communication with the enteric nervous system (Gut:brain axis) 1.The gut microbiota and host health: a new clinical frontier. Marchesi et al. Gut 2016; 65:330-339 2.Tyler et al. Analyzing the Human Microbiome: A “How To” guide for PhysiciansAm J Gastroenterol 2014; 109: 983-993. 3.Wlodarska et al. An Integrative View of Microbiome-Host Interactions in Inflammatory Bowel Diseases Cell Host and Microbe 17, May 13, 2015.

8. Figure 1 Cell Host & Microbe 2015 17, 577-591DOI: (10.1016/j.chom.2015.04.008) 1.Wlodarska et al. An Integrative View of Microbiome-Host Interactions in Inflammatory Bowel Diseases Cell Host and Microbe 17, May 13, 2015.

9. Figure 1 Cell Host & Microbe 2015 17, 577-591DOI: (10.1016/j.chom.2015.04.008) 1.Wlodarska et al. An Integrative View of Microbiome-Host Interactions in Inflammatory Bowel Diseases Cell Host and Microbe 17, May 13, 2015.

10. HUMAN GUT MICROBIOME There is a bi-directional relationship between host and microbiome (1,2) What constitutes a healthy microbiome is not yet fully elucidated (1) Diversity, Richness, Resistance, Resilience Which are Keystone Species, Foundation species? Factors that influence the microbiome (1,2) : Age Diet Genetics Host immune system Antibiotic use Environment / Hygiene 1.The intestinal microbiome and health. Tuddenham S. Curr Opin Infect Dis 2015, 28:464-470 2.The gut microbiota and host health: a new clinical frontier. Marchesi et al. Gut 2016; 65:330-339

11. EARLY YEARS MAY BE CRITICAL IN ESTABLISHING MICROBIOME 1.Arrieta et al. The Intestinal Microbiome in Early Life: Health and Disease. Frontiers in Immunology 2014; (5) 427

12. DIET, LIFESTYLE AND ENVIRONMENT MODIFY THE MICROBIOME

13. THE MICROBIOME AND IBD SECTION 2

14. WHY PAY INTEREST TO THE MICROBIOME IN IBD? In animal models of IBD, gut microbiota is essential in inducing inflammation Diversion of the fecal stream has been shown to improve symptoms for Crohn’s disease Antibiotics have been shown to be helpful in certain situations ( anal fistula, post-operative recurrence, pouchitis) IBD susceptibility genes mainly involve microbe processing, T cell function and mucosal barrier function The recent increased prevalence in IBD cannot be explained by genetics alone (diet? ; hygiene?) Microbiome studies have shown dysbiosis associated to IBD 1.Matsuoka et al. The gut microbiota and inflammatory bowel disease. Semin Immunopathol 2015; 37: 47-55 2.Jostins et al. Nature. 2012. November 1; 491 (7422): 119-124

15. 1.Jostins et al. Nature. 2012. November 1; 491 (7422): 119-124 2.Liu et al. Nature Genetics (2015). 47 (9), 979 - 986. issn: 1061-4036 Genome wide analysis has revealed around 200 different genetic loci associated with IBD They only account for 13.1% and 8.2% of the variance in disease liability for Crohn’s disease and ulcerative colitis respectively

16. STUDIES SHOWING LINK BETWEEN MICROBIOME AND IBD 1.Matsuoka et al. The gut microbiota and inflammatory bowel disease. Semin Immunopathol 2015; 37: 47-55

17. STUDIES SHOWING LINK BETWEEN MICROBIOME AND IBD 1.Gevers et al. The treatment naive microbiome in new- onset Crohn’s disease. Cell Host Microbe 15, 382-392

18. IBD PATHOGENESIS AND TREATMENT An aberrant immune response against the gut microbiota triggered by environmental factors in a genetically susceptible host http://www.intechopen.com/books/inflammatory-bowel-disease/insights- to-the-ethiopathogenesis-of-the-inflammatory-bowel-disease Diet / Prebiotics Probiotics ? FMT ? Antibiotics Diet / Prebiotics Probiotics ? FMT ? Antibiotics 5-ASA, prednisone, azathioprine, anti TNF- alpha

19. FECAL MICROBIOTA TRANSPLANTATION (FMT) SECTION 3

20. FECAL MICROBIOTA TRANSPLANTATION What is it? Administration of fecal material containing distal gut microbiota from a healthy person to a patient with a disease or condition related to dysbiosis Why do it? Restore phylogenetic diversity and therefore microbiome physiological functions Replace and or inhibit pathogenic species Does it work? For recurrent C. difficile infections the efficacy of FMT is now undisputed, with cure rates of 85-90% in case series One randomised trial: efficacy was 81% for a first infusion and 93,8% with a second infusion vs 30% for vancomycin Success of FMT in C. Difficile has sparked interest for treating other conditions associated with dysbiosis including IBD 1.Van Nood et al. Duodenal Infusion of Donor Feces for Recurrent Clostridium difficile NEJM 368;5 2.Kelly et al. Update on Fecal Microbiota Transplantation 2015: Indications, Methodologies, Mechanisms and Outlook. Gastroenterology 2015; 149: 223-237

21. Relative abundances of most abundant OTUs in donor and pre- and post-FMT samples. Anna M. Seekatz et al. mBio 2014; doi:10.1128/mBio.00893- 14

22. FMT “HOW TO” 1.Donor Selection 1.Donor Screening 1.Stool collection and preparation 1.Patient preparation and stool administration

23. DONOR SELECTION AND SCREENING Unrelated volunteer vs family, partner or friend Chosen donor must be healthy and devoid of any microbiota associated (IBS, Obesity, constipation, GI malignancy) or potentially transmittable illness Donor must not have taken antibiotics recently Only 30% of candidates were acceptable when screened at one facility (2) 1.Kelly et al. Update on Fecal Microbiota Transplantation 2015: Indications, Methodologies, Mechanisms and Outlook. Gastroenterology 2015; 149: 223-237 2.Costello et al. Establishing a fecal microbiota transplant service for the treatment of Clostridium difficile Infection. CID 2016: 62 April 1

24. DONOR SELECTION AND SCREENING 1.Costello et al. Establishing a fecal microbiota transplant service for the treatment of Clostridium difficile Infection. CID 2016: 62 April 1

25. STOOL COLLECTION AND PREPARATION (NO CONSENSUS) 1.Costello et al. Establishing a fecal microbiota transplant service for the treatment of Clostridium difficile Infection. CID 2016: 62 April 1 Fresh stool in ziplock container Blended with 400ml saline in new magic bullet Filter out larger particles Place into barium enema kit

26. PATIENT PREPARATION AND ROUTE OF ADMINISTRATION (NO CONSENSUS) Stop antibiotics 24h-72h before Colonoscopy preparation the night before Main routes Retention enema Patient is laying down in slight tredelenburg position Turns over during the procedure Usually waits 30 minutes after complete infusion Colonoscopy Naso-duodenal infusion Oral pills of encapsulated fecal material

27. SAFETY OF FMT Multiple theoretical risks associated with FMT Transmission of infection Transmission of microbiota associated disease Complications during the procedure Health Canada now requires registration FMT is generally very well tolerated NEJM RANDOMISED TRIAL 1.Van Nood et al. Duodenal Infusion of Donor Feces for Recurrent Clostridium difficile NEJM 368;5

28. ADVERSE EVENTS IN FAECAL MICROBIOTA TRANSPLANT: A REVIEW OF THE LITTERATURE BAXTER ET AL. JOURNAL OF HOSPITAL INFECTION 92 (2016) 117-127 Compiled n= 1555 patients 1190 treated for CDI, 186 for UC, 67 for CD Serious complications CDI: 2 deaths related to aspiration pneumonia 2 perforations during colonoscopy 1 related bacteremia (24h after) Exacerbated IBD in 6 cases

29. ADVERSE EVENTS IN FAECAL MICROBIOTA TRANSPLANT: A REVIEW OF THE LITTERATURE BAXTER ET AL. JOURNAL OF HOSPITAL INFECTION 92 (2016) 117-127

30. EVIDENCE FOR FMT IN IBD SECTION 4

31. FECAL MICROBIOTA TRANSPLANTATION AS THERAPY FOR INFLAMMATORY BOWEL DISEASE: A SYSTEMATIC REVIEW AND META-ANALYSIS COLMAN ET AL. J CROHN’S COLITIS 2014 DECEMBER 1; 8 (12) 1569-1581 Meta analysis of 18 studies, only one randomised Total of 122 patients ( 79 with UC, 39 Crohn’s, 4 unclassified) Overall, 45% achieved clinical remission (54 / 119) Cohort studies had 36.2% remission Ulcerative colitis 22% remission Crohn’s disease 60.5% remission Conclusions Risk of study bias No serious safety concerns as of yet Randomised studies needed with clinical and microbiota data

32. FECAL MICROBIOTA TRANSPLANTATION INDUCES REMISSION IN PATIENTS WITH ACTIVE ULCERATIVE COLITIS IN A RANDOMIZED CONTROLLED TRIAL MOAYEDDI ET AL. GASTROENTEROLOGY 2015; 149: 102-109 Randomised controlled trial Weekly 50ml FMT for 6 weeks vs placebo water enema N=70 (36 FMT, 34 placebo) Clinical remission 24% vs 5% favoring FMT (p=0.03) Treatment success with donor B 39% vs 10% with other donors (p=0.06) Increased response of FMT with immunosuppression 5/11(46%) vs 4/27 without (15%) Recent diagnosis (<1 year) 3/4 responded (75%) vs 6/34 (18%) for chronic disease (p=0.04) Conclusion: First randomised trial to demonstrate that FMT can be efficacious in UC

33. FINDINGS FROM A RANDOMISED CONTROLLED TRIAL OF FECAL TRANSPLANTATION FOR PATIENTS WITH ULCERATIVE COLITIS ROSSEN ET AL. GASTROENTEROLOGY 2015; 149: 110-118 Randomised controlled trial 2 donor vs autologous FMT via nasogastric tube at 3 week interval N=48 (23 donor, 25 autologous) Clinical and endoscopic remission 30.4% for donor stool vs 20% for autologous FMT (p=0.51) In the per-protocol analysis 41.2% vs 25% (p=0.29) Donor FMT esponders shifted towards microbiota profiles of their donors Autologous FMT responders also shifted their microbiota Conclusion: Negative study, further research warranted

34. HEALTH CANADA GUIDANCE “To date, CDI is the only indication for which FMT has demonstrated safety and efficacy. Therefore, this is the only condition for which FMT merits consideration outside the direct regulatory provisions of an investigational clinical trial, provided that the conditions noted in this guidance document are followed” Fecal Microbiota Therapy Used in the Treatment of Clostridium difficile Infection Not Responsive to Conventional Therapies

35. CLOSING REMARKS SECTION 5

36. MICROBIOME Study of the microbiome is a new frontier of science The microbiome plays a role in IBD Much work is still needed to refine our understanding of the interaction between the microbiome and inflammatory bowel disease Which species are harmful or protective? Is there a relation between genotype and those species? Is early life important in predisposition? Is dysbiosis a cause, a consequence or a little of both? Are viruses and eukaryotes also important?

37. FECAL MICROBIOTA THERAPY We are still in the stone age of FMT Stool banks with frozen stool are a step up Don’t requiring “same day” delivery Permit post donation screening Have been shown to be as efficacious Next generation FMT is just around the corner for C. difficile Standardised pharmaceutical grade, preparations of a beneficial mixture of bacteria RBX2660 for C. difficile had 87.1% success in a phase 2 trial (1) 1.Oreinstein et al. Safety and Durability of RBX2660 (Microbiota Suspension) for Recurrent Clostridium difficile Infection: Results of the PUNCH CD Study. CID 2016 Mar 1;62(5):596-602

38. IBD AND FMT Will definitions of IBD change to include genetic factors and microbiota composition? Ex: Ileal “transmucosal” IBD, NOD2 mutant, with an excess of adherent-invasive E.coli and depletion of F. prausnitzii The one size fits most of FMT for C.Diff seems less likely for IBD… Will we be able to profile and predict beneficial donors? Stool banks with success rate compilations? Will multiple next-generation FMT preps be created for different disease patterns and microbiota profiles? Research MUST be advanced in this field

39. THANK YOU