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1 2 3 4 5 6 7 8 9 Title: Regional variability in fecal microbiota transplantation practices: a descriptive study of the 10 11 Southern Fecal microbiota Transplantation (SOFT) Movement 12 13 Authors: Susy S. Hota MD MSc 1, 2 , Salman Surangiwala BSc (C) 3, Aimee S. Paterson MSc 3, Bryan 14 2, 4 3, 5 15 Coburn MD PhD and Susan M. Poutanen MD MPH for the Southern Ontario Fecal microbiota 16 Transplantation Movement (SOFT Movement) 17 18 19 SOFT Movement: B. Coburn MD PhD 2, 4 , Nick Daneman MD MSc 2, 6 , Mark Downing MD 7

20 8 1,2 7,9 21 ,Christopher Graham MD , Susy S. Hota MDConfidential MSc , Jennie Johnstone MD PhD , Christine Lee MD 22 10, 11 , Janine McCready MD 12 , Elaine O. Petrof MD MSc 13, 14 , Susan M. Poutanen MD MPH 3, 5 , Jeff 23 24 Powis MD MSc 2, 12 , Daniel Ricciuto MD 15, and Michael Silverman MD 16, 17. 25 26 1Department of Infection Prevention and Control, University Health Network, , Canada 27 28 2Department of Medicine, , Toronto, Canada 29 30 3Department of Microbiology, University Health Network/, Toronto, Canada

31 4 32 Toronto General Research Institute 33 5Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada 34 35 6Sunnybrook Health Sciences Center, Toronto, Canada 36 37 7St. Joseph’s Health Center, Toronto, Canada

38 8 39 , Mississauga, Canada 40 9Public Health Ontario, Toronto, Canada 41 42 10St. Joseph’s Healthcare, Hamilton, Canada 43 11 44 McMaster University, Hamilton, Canada 45 12 , Toronto, Canada 46 47 13 Kingston General Hospital, Kingston, Canada 48 49 14 Queen’s University 50 15 51 Lakeridge Health, Oshawa, Canada 52 53 54 1 55 56 57 58 59 60 For Peer Review Only Page 3 of 40

1 2 3 4 5 6 7 8 9 16St. Joseph’s Hospital, London, Canada

10 17 11 Western University, London, Canada 12 13 14 Keywords: Fecal microbiota transplantation; recurrent Clostridium difficile infection; Canada; survey 15 16 Running Title: Fecal microbiota transplantation in Ontario, Canada 17 18 19 Dr. Susy Hota (Corresponding Author) Dr. Susan M. Poutanen (Alternate) 20 21 Medical Director, UHN IPAC Confidential Medical Microbiologist / Inf. Diseases Specialist 22 Assistant Professor, Division of Infectious Diseases Associate Professor, University of Toronto 23 24 University of Toronto University Health Network/Sinai Health System 25 26 8 PMB Rm 103, Toronto General Hospital Department of Microbiology 27 200 Elizabeth Street 600 University Avenue, Room 1485 28 29 Toronto ON M5G 2C4 Toronto ON M5G 1X5 30 31 Office: 416-340-4800 x 7801 or 7287 Office: 416-586-4800 x 3139 32 33 Fax: 416-340-5047 Fax: 416-586-8746 34 Email: [email protected] Email: [email protected] 35 36 Funding 37 38 39 This work was supported by a Department of Medicine Integrating Challenge Grant and the Department 40 of Laboratory Medicine and Pathobiology at the University of Toronto. 41 42 43 Potential Competing Interests 44 45 S.S. Hota has received a grant and honoraria from serving as a consultant and on the advisory board of 46 47 Cubist (Merck) pharmaceuticals. S. M. Poutanen has received honoraria related to advisory boards from 48 49 Merck, Paladin Labs, and Accelerate Diagnostics and honoraria from Merck related to talks. C. Lee is a 50 member of advisory board for Rebiotix and received grants from Merck, Actelion and Rebiotix for 51 52 clinical research. E.O. Petrof is a co-founder and serves on the Scientific Advisory Board of Nubiyota 53 54 2 55 56 57 58 59 60 For Peer Review Only Page 4 of 40

1 2 3 4 5 6 7 8 9 LLC. D. Ricciuto has received a grant from Astellas. M.Silverman has received speaker honoraria from 10 11 Merck. The remainder of authors have no competing interests to declare. 12 13 14 15 16 17 18 19 20 21 22 Confidential 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 3 55 56 57 58 59 60 For Peer Review Only Page 5 of 40

1 2 3 4 5 6 7 8 9 Abstract 10 Background: There is growing evidence that fecal microbiota transplantation (FMT) is a cost-effective 11 12 treatment for recurrent Clostridium difficile infection. However, little guidance exists for implementation 13 14 of FMT programs. This study summarizes the program characteristics and protocols of 9 planned or 15 16 operating FMT programs in Southern Ontario (Southern Ontario Fecal microbiota Transplantation – 17 SOFT- Movement), in order to inform FMT policy in Canada. 18 19 20 Methods: A 59-item survey was administered electronically to clinical leads of the SOFT Movement on 21 22 June 2, 2016. Six domains were evaluated:Confidential 1) FMT program characteristics; 2) FMT recipients; 3) donor 23 screening and selection; 4) FMT manufacturing; 5) FMT administration; 6) good manufacturing 24 25 procedures/biosafety procedures; and, 7) infection control procedures. Descriptive statistics were used to 26 27 analyze quantitative data. 28 29 Results: All nine programs responded to the survey. Of nearly 1300 FMT performed between 2003 and 30 31 2016 within these programs, most (5/6 operating programs) utilized enema administration. Programs were 32 33 primarily driven by physicians. All programs used universal FMT donors and followed Health Canada 34 screening guidelines, with significant variability in screening frequency (every 3 – 6 months) and 35 36 modality. Locations for FMT preparation and manufacturing protocols were heterogeneous. FMT stool 37 38 masses ranged from 20g to 150g and FMT volume, from 25mL to 300mL. 39 40 Interpretation: The experience of this high-volume, Canadian, regional FMT network highlights current 41 42 challenges in program development, including a high reliance upon physicians and the costly nature of 43 44 donor screening. Standardization and optimization through development of regional centers of excellence 45 for FMT donor recruitment and administration should be explored. 46 47 48 49 50 51 52 53 54 4 55 56 57 58 59 60 For Peer Review Only Page 6 of 40

1 2 3 4 5 6 7 8 9 Introduction 10 Over the past decade, fecal microbiota transplantation (FMT) has emerged as a novel option for the 11 12 treatment of recurrent Clostridium difficile infection (rCDI). To date, multiple randomized controlled 13 14 trials have demonstrated that FMT using various methodologies is at least as effective if not superior to 15 16 conventional antibiotic treatments for rCDI, and several cost-effectiveness analyses have demonstrated its 17 value (1-10). However, for clinicians and centers considering offering FMT, little to no guidance exists 18 19 on how to optimally approach program development. In part, this stems from a lack of accepted standards 20 21 for FMT methodologies. Within FMT research, variables such as FMT patient selection, timing of FMT, 22 Confidential 23 FMT pre-treatment (with suppressive antibiotics and bowel lavage), donor selection, donor screening, 24 FMT manufacturing and storage conditions, FMT route of administration, and number of FMT 25 26 administrations have not been adequately standardized and validated (11, 12). The impact of 27 28 heterogeneity in FMT methodologies on recipient outcome remains unclear. 29 30 In 2015, Health Canada issued brief, interim guidance regarding the use of FMT in patients with C. 31 32 difficile infection (CDI) not responding to conventional treatment, focusing primarily on the safety 33 34 aspects of donor selection and screening (13). While various expert bodies have produced guidelines for 35 FMT that include further details on how to manufacture and perform FMT, these recommendations are 36 37 predominantly based on expert opinion (14, 15). In the absence of evidence-informed guidance, 38 39 individual centers in Canada offering the treatment have largely created their own protocols. The 40 41 characteristics of Canadian FMT programs have not been summarized and widely shared. 42 43 In November 2015, the Southern Ontario Fecal microbiota Transplantation (SOFT) Movement was 44 45 created with the dual purpose of sharing FMT experience between long-standing and new programs and 46 removing barriers to FMT provision in Ontario, Canada. As an initial step, we performed an 47 48 environmental scan of practices by surveying our members on FMT program characteristics and 49 50 methodologies. Here, we describe the key features of FMT programs in Southern Ontario. 51 52 53 54 5 55 56 57 58 59 60 For Peer Review Only Page 7 of 40

1 2 3 4 5 6 7 8 9 Methods 10 11 A 59-item survey on FMT program characteristics and protocols (Appendix 1) was developed by two 12 13 study investigators (SH and SMP) and reviewed for content validity by a third investigator (BC). Open- 14 15 ended and multiple-choice questions were used to evaluate the following domains: 1) FMT program 16 characteristics; 2) FMT recipients; 3) donor screening and selection; 4) FMT manufacturing; 5) FMT 17 18 administration; 6) good manufacturing procedures/biosafety procedures; and, 7) infection control 19 20 procedures. 21 Confidential 22 The survey was built using SurveyGizmo© and administered electronically on June 2, 2016. Twelve 23 24 SOFT Movement members representing 9 hospital corporations in Southern Ontario (Figure 1) received 25 26 the survey by email, with instructions to complete one survey per institution. One reminder email was 27 sent. The data were analyzed using standard descriptive statistics on Microsoft Excel©. Consent to 28 29 participate in this study was implicit to completing the survey. Institutional research ethics board approval 30 31 was not deemed necessary as participation was voluntary, the survey did not request patient information 32 33 or elicit personal opinions, and results were to be presented in aggregate. 34 35 Results 36 37 All 9 institutions responded to the survey request, with 6 providing complete responses. One institution 38 39 shared FMT standard operating procedures that were developed but did not have clinical experience to 40 41 report. Two institutions were in the process of forming FMT programs and therefore provided incomplete 42 43 or no survey responses. 44 45 FMT program characteristics 46 47 48 Since 2003, approximately 1300 FMT have been administered across 6 institutions in Southern Ontario 49 (Figure 1). The earliest program began in 2003, with the remainder of programs starting after 2008. Two 50 51 programs had not yet launched their programs. One program performed FMT for clinical care only while 52 53 54 6 55 56 57 58 59 60 For Peer Review Only Page 8 of 40

1 2 3 4 5 6 7 8 9 the other respondents planned or performed FMT for both clinical care and research purposes. Programs 10 11 were all staffed by physicians, with five programs having inter-professional clinical support (program co- 12 ordinator, clinical nurses and infectious diseases physician assistant) and two employing research staff 13 14 (research nurse and summer student). 15 16 FMT recipients 17 18 19 All active programs administered FMT for adult patients with CDI. One center additionally performed 20 21 research into FMT for inflammatory bowelConfidential disease, another had planned or ongoing research on FMT for 22 non-alcoholic fatty liver disease and multiple sclerosis and a third was planning research into FMT for 23 24 obesity and bipolar depression. FMT indications used by the programs for CDI patients are summarized 25 26 in Figure 2. Major exclusions for FMT recipients included: severe, uncontrollable diarrhea (n = 3); bloody 27 diarrhea (n = 2); any immunocompromise (n = 1); neutropenia (n = 1), irreversible bleeding disorder (n = 28 29 1). No center had an upper limit of age for FMT recipients. 30 31 32 Donor screening and selection 33 All surveyed programs used or planned to use universal FMT donors. At all sites, universal donors 34 35 underwent screening at baseline. Five of the 7 institutions (71%) screened universal donors every 6 36 37 months thereafter, while one institution screened every 3 months and another screened every 3 months 38 and at the end of the donation cycle. Three programs performed microbiota analysis of the donor feces but 39 40 none used these data as selection criteria for donors. 41 42 43 All programs applied the following suggested donor exclusions recommended by Health Canada: recent 44 antibiotics; systemic immunosuppressive or biological agents; systemic antineoplastic agents; exogenous 45 46 glucocorticoids; antidiarrheal drugs; mineral oil; bismuth; and kaolin. One program allowed magnesium 47 48 consumption in donors. Additional exclusions used by all programs included a history of cancer, and by 49 50 some programs, a history of chronic medical conditions, ongoing use of medications, and certain food 51 consumptions depending on recipients’ allergies. 52 53 54 7 55 56 57 58 59 60 For Peer Review Only Page 9 of 40

1 2 3 4 5 6 7 8 9 Figure 3, which lists Health Canada-recommended donor exclusion criteria, summarizes the infectious 10 11 diseases laboratory screening modalities used by programs to adhere to these guidelines. A significant 12 proportion of infectious diseases screening occurred through reference laboratories. Gastroenteritis 13 14 (diarrhea) due to agents not directly screened for in laboratory tests (e.g. Listeria ), malaria, Chagas 15 16 disease, babesiosis, Creutzfeld-Jacob disease and other prion disease exclusions were derived from 17 medical assessment in all cases, with one center also performing laboratory testing for malaria. Although 18 19 not specifically recommended by Health Canada, 71% and 57% of programs additionally screened for 20 21 carbapemenase-producing Enterobacteriaceae a nd extended spectrum beta-lactamase-producing 22 Confidential 23 organisms. 24 25 FMT manufacturing 26 27 Three (3/6) active programs manufactured FMT within a clinical microbiology laboratory, 2 performed 28 29 these steps in a research laboratory and one used a shared clinical/research space. In 3 programs, a 30 31 physician manufactured the FMT all or some of the time; in other programs, FMT manufacturing 32 33 involved a: nurse (n=1); laboratory technologists (n=1); research technologist (n=1), PhD microbiologist 34 (n=1) or physician assistant (n=1). 35 36 37 Four (4/7) respondents undertook manufacturing validation studies prior to finalizing protocols. The 38 39 majority (4/7) recommended that donor feces be stored in household refrigerators prior to transporting to 40 the FMT program. Most strived to manufacture FMT within 24 hours of donation, although 2 centers 41 42 accepted samples up to 48 and 72 hours after donation. 43 44 There was a wide range of donor stool mass and diluent volume used in manufacturing FMT (Table 1). 45 46 Diluents varied with 50% of programs using saline, 17% using water, and 33% using saline for FMT 47 48 administered by enema and water for FMT administered by nasoduodenal/nasojejunal (ND/NJ). Six 49 50 programs manufactured frozen FMT, with one institution additionally offering lyophilized FMT. Only 51 52 53 54 8 55 56 57 58 59 60 For Peer Review Only Page 10 of 40

1 2 3 4 5 6 7 8 9 one program used a cryoprotectant (glycerol) in the frozen FMT product. When frozen, FMT was

10 o o 11 maintained at both -20 C and -80 C. 12 13 FMT administration 14 15 The most common route of FMT administration was enema, with 3 programs offering FMT by enema 16 17 alone, 1 providing enema and colonoscopy administration and 1 providing enema and ND/NJ 18 19 administration. One institution performed FMT by ND/NJ route only. 20 21 FMT was performed in either a clinic setting, inpatient room or day unit. FMT was most commonly 22 Confidential 23 administered by a physician (n = 5 programs), sometimes with assistance from a physician trainee, 24 25 physician assistant, or nurse. In the majority of cases when FMT was being administered to patients with 26 CDI, oral vancomycin therapy was stopped 24-48 hours before FMT, although one site stopped it 48-96 27 28 hours prior and another, <24 hours before FMT. Only one program used a bowel preparation after 29 30 stopping vancomycin before FMT administration. In those performing FMT by enema, 2 programs 31 32 administered FMT once, 3 provided it up to 3 times and 1 provided more than 5 FMT if necessary. In the 33 2 programs providing FMT by colonoscopy, a single administration was given. One program provided a 34 35 single FMT by ND/NJ route-time while another provided up to 3 ND/NJ administrations. When multiple 36 37 FMT administrations were given, they were most frequently given 2-4 days apart. 38 39 At 3 sites, patients were not routinely followed post-FMT, whereas 4 sites reported variable follow-up 40 41 durations ranging from 1-36 months. For CDI, failure of FMT was based on return of CDI symptoms 42 43 alone at 2 programs while 5 programs additionally required laboratory confirmation. 44 45 Good manufacturing procedures/biosafety procedures 46 47 48 All programs manufactured FMT in a biosafety cabinet. Two programs used disposable equipment for 49 manufacturing and the remainder disinfected the manufacturing equipment and space using a sporicidal 50 51 agent. 52 53 54 9 55 56 57 58 59 60 For Peer Review Only Page 11 of 40

1 2 3 4 5 6 7 8 9 Infection control procedures 10 11 Fluid-resistant gowns and gloves were used by all programs during FMT manufacturing and 12 13 administration, while procedure masks and face shields were used variably. Shoe covers were only used 14 15 during FMT administration at one institution. Four programs performed more than one FMT per day. 16 Between cases, two of these programs requested environmental services to disinfect rooms with a 17 18 sporicidal agent; one relied on FMT program staff do this; and one only changed linens between cases. 19 20 All programs requested environmental services to disinfect rooms used for FMT with a sporicidal agent 21 22 after the last or only procedure of the day wasConfidential completed. 23 24 Interpretation 25 26 We provide a comprehensive description of a high volume network of FMT programs in Canada. 27 28 National surveys of FMT practices in the UK and Ireland have focused primarily on identifying 29 30 where FMT is offered, and analysing barriers to FMT uptake without detailing protocols for 31 32 manufacturing and administration (16-18). Others have reported on the development of single-site FMT 33 programs (19, 20) but to our knowledge, a larger scale comparison of protocols and practices between 34 35 FMT programs has not been performed. Collectively, our programs have performed about 1300 FMT 36 37 primarily on patients with rCDI, but programs are expanding to include other indications in the context of 38 39 research. FMT is most commonly administered by enema, although colonoscopic and NJ administrations 40 are also available. To date, no definite data supports one route of administration over another in terms of 41 42 FMT efficacy for rCDI (3, 21-25). 43 44 With growing evidence to support the cost-effectiveness of FMT for rCDI, deregulation by Health 45 46 Canada for this indication and increasing research applications of FMT for other health conditions, there 47 48 has been renewed interest in FMT programs across Canada. In July 2016, Health Quality Ontario, an 49 50 arms-length organization that advises the Ontario Ministry of Health and Long Term Care on quality in 51 healthcare, made a recommendation for public funding of FMT for rCDI based on an independent review 52 53 54 10 55 56 57 58 59 60 For Peer Review Only Page 12 of 40

1 2 3 4 5 6 7 8 9 of the cost-effectiveness of FMT and patient experience with rCDI (26). As individual centers and the 10 11 provincial healthcare systems determine how to best structure and fund FMT programs, providing a view 12 into current FMT programs can highlight successes and points of vulnerability. 13 14 15 In Southern Ontario, FMT programs are heavily driven by physicians. While FMT by enema or NJ tube 16 may be administered by other health practitioners such as nurses and physician assistants, a physician 17 18 with expertise in gastroenterology, infectious diseases and/or microbiology is required to oversee the 19 20 procedure, the donor screening steps and recipient follow-up. As there is currently no mechanism for 21 22 compensating physicians for this service inConfidential Ontario, physicians are donating time and expertise to provide 23 this needed service. Likewise, hospitals are absorbing costs associated with building and supporting FMT 24 25 programs. A fair, transparent and cost-effective means for providing seamless service should be 26 27 developed in order to facilitate access to FMT. 28 29 Universal FMT donors are widely employed in these programs, primarily to provide stool samples that 30 31 are processed then frozen and banked for later use. This approach is cost-effective, validated (4, 27-29) 32 33 and favorable in terms of logistics for providing FMT on demand. The optimal frequency for screening 34 universal donors is not clear and variability exists among the surveyed programs. Comprehensive donor 35 36 screening, as recommended by Health Canada, is expensive, and not all tests are readily available to all 37 38 institutions. There remains a heavy reliance upon reference laboratories for specialized testing (eg. stool 39 40 for ova and parasites, enteric viruses). In some cases, validated or reliable tests do not exist (eg. testing of 41 stool for Listeria ) yet medical assessment alone may not necessarily exclude the possibility of infection or 42 43 carriage. 44 45 FMT manufacturing is highly variable across sites. The total weight of stool used, the volume of diluent, 46 47 and the method of preparation differed between programs. Locating a space for this task is a frequent 48 49 barrier for FMT programs, and this has resulted in physicians using research laboratory space to 50 51 manufacture a clinical therapeutic. The use of commercial systems that contain the FMT product and that 52 53 54 11 55 56 57 58 59 60 For Peer Review Only Page 13 of 40

1 2 3 4 5 6 7 8 9 can be carefully disinfected between uses is highly desirable for infection control but these approaches are 10 11 associated with significant costs and therefore are inconsistently used. Disposable equipment may be one 12 alternative to decrease manufacturing costs (4, 30) but further research into validating FMT 13 14 manufacturing is needed. While some sites in our survey did undertake validation studies to support their 15 16 manufacturing processes and storage conditions, no industry standard exists regarding metrics for 17 validation studies. 18 19 20 Our study has limitations. The study sites may not represent all sites where FMT has been performed 21 22 within our region. Two of the surveyed sitesConfidential were in the process of developing FMT programs and survey 23 response may not represent their final approaches. Finally, we aimed to simply describe the FMT 24 25 programs and did not collect data on clinical outcome of FMT recipients, which would be important for 26 27 guiding future recommendations for FMT programs. 28 29 In summary, our study has identified a significant diversity in practices for FMT within a circumscribed 30 31 region of Ontario, Canada servicing 12 million people. Site-based FMT protocols are driven by multiple 32 33 factors including costs, local administrative pressures and availability of screening tests and these barriers 34 have limited FMT uptake (16-18). The two largest costs of FMT in the region are physician time for 35 36 coordinating, manufacturing and administering FMT and FMT donor screening. While public funding for 37 38 FMT is being explored, FMT costs in Ontario are currently absorbed by individual hospital budgets and 39 40 research funding. In planning future FMT programs in Canada, opportunities for systems-wide 41 efficiencies should be explored – such as creating regional centers of excellence for FMT donor 42 43 recruitment and administration. A recently released European guidance document on FMT echoes these 44 45 concepts, recommending implementation of a clinical governance that would oversee the administrative 46 47 aspects of FMT programs and deal with any organizational barriers that may hinder their efficiency to 48 deliver FMT to rCDI patients in need (15). Such an approach would concentrate expertise in FMT, ensure 49 50 consistency in procedures and practices, enable trace-backs in the event of possible FMT-related adverse 51 52 53 54 12 55 56 57 58 59 60 For Peer Review Only Page 14 of 40

1 2 3 4 5 6 7 8 9 events, and reduce the need for numerous institutions to introduce costly donor screening tests and 10 11 equipment into laboratories. 12 13 Acknowledgements (none) 14 15 Author Contributions 16 17 18 S. S. Hota and S. M. Poutanen. co-led the design of the study and the development of the survey. S. S. 19 20 Hota drafted the manuscript and submitted it for publication. S. Surangiwala administered the survey and 21 completed the initial analysis of data. A. Paterson. completed additional data analysis. B. Coburn 22 Confidential 23 reviewed and approved the survey prior to administration. The SOFT Movement includes physician leads 24 25 of FMT programs in Southern Ontario as follows: B. Coburn (University Health Network), N. Daneman 26 (Sunnybrook Health Sciences Centre), M. Downing (St. Joseph’s Health Center – Toronto), C. Graham 27 28 (Trillium Health Partners), S. S. Hota (University Health Network), J. Johnstone (Public Health Ontario, 29 30 St. Joseph’s Health Care - Toronto), C. Lee (St. Joseph’s Healthcare - Hamilton), J. McCready (Michael 31 32 Garron Hospital), E. O. Petrof (Kingston General Hospital), S. M. Poutanen (Sinai Health Center, 33 University Health Network), J. Powis (Michael Garron Hospital), D. Ricciuto (Lakeridge Health), and M. 34 35 Silverman (St. Joseph’s Hospital - London). All SOFT Movement leads and authors reviewed the study 36 37 data for integrity, provided feedback on results, contributed to manuscript preparation and approved the 38 39 final draft. All authors agree to be accountable for the data presented within the manuscript. 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 13 55 56 57 58 59 60 For Peer Review Only Page 15 of 40

1 2 3 4 5 6 7 8 9 References 10 1 Van Nood E, Vrieze A, Nieuwdorp M, et al. Duodenal infusion of donor feces for recurrent 11 12 Clostridium difficile . N Engl J Med 2013; 368: 407-415. 13 14 2 Cammarota G, Masucci L, Ianiro G, et al. Randomized clinical trial: faecal microbiota 15 16 transplantation by colonoscopy vs vancomycin for the treatment of recurrent Clostridium difficile 17 infection. Aliment Pharmacol Ther 2015; 41: 835-843. 18 19 3 Youngster I, Sauk J, Pindar C et al. Fecal microbiota transplant for relapsing Clostridium difficile 20 21 infection using a frozen inoculum from unrelated donors: a randomized, open-label, controlled 22 Confidential 23 pilot study . Clin Infect Dis 2014; 58: 1515-1522. 24 4 Lee CH, Steiner T, Petrof EO et al. Frozen vs fresh fecal microbiota transplantation and clinical 25 26 resolution of diarrhea in patients with recurrent Clostridium difficile infection: a randomized 27 28 clinical trial. JAMA 2016; 315:142-149. 29 30 5 Kelly CR, Khoruts A, Staley C et al. Effect of fecal microbiota transplantation on recurrence in 31 multiply recurrent Clostridium difficile infection. Ann Intern Med 2016;165: 609-16. 32 33 6 Hota SS, Sales V, Tomlinson G, et al. Oral Vancomycin Followed by Fecal Transplantation 34 35 Versus Tapering Oral Vancomycin Treatment for Recurrent Clostridium difficile Infection: An 36 Open-Label, Randomized Controlled Trial . Clin Infect Dis 2017; 64: 265-71. 37 38 7 Konijeti GG, Sauk J, Shrime MG, Gupta M, Ananthakrishnan AN. Cost-effectiveness of 39 40 competing strategies for management of recurrent Clostridium difficile infection: a decision 41 42 analysis. Clin Infect Dis 2014; 58: 1507-14. 43 8 Varier RU, Biltaji E, Smith KJ et al. Cost-effectiveness analysis of fecal microbiota 44 45 transplantation for recurrent Clostridium difficile infection. Infect Control Hosp Epidemiol 2015; 46 47 36: 438-44. 48 49 9 Baro E, Galperine T, Denies F et al. Cost-effectiveness analysis of five competing strategies for 50 the management of multiple recurrent community-onset Clostridium difficile infection in France. 51 52 PLOS One 2017; 12: e0170258. doi: 10:1371/journal.pone.0170258. 53 54 14 55 56 57 58 59 60 For Peer Review Only Page 16 of 40

1 2 3 4 5 6 7 8 9 10 LaPointe-Shaw L, Tran KL, Coyte PC et al. Cost-effectiveness analysis of six strategies 10 11 to treat recurrent Clostridium difficile infection. PLOS One 2016; 11: e0149521. doi: 12 13 10.1371/journal.pone.0149521. 14 11 Hota SS, Tomlinson G, Poutanen SM. Reply to Galperine and Jensen. Clin Infect Dis 2017; 64: 15 16 1293-5. 17 18 12 Kassam Z, Lee CH, Hunt RH. Review of the emerging treatment of Clostridium difficile 19 infection with fecal microbiota transplantation and insights into future challenges. Clin Lab Med 20 21 2014; 34 : 787-798. 22 Confidential 23 13 Health Canada. Guidance document: Fecal microbiota therapy used in the treatment of 24 25 Clostridium difficile infection not responsive to conventional therapies. Available at: 26 http://www.hc-sc.gc.ca/dhp-mps/consultation/biolog/fecal_microbiota-bacterio_fecale-eng.php . 27 28 Accessed 6 May 2016. 29 30 14 Bakken J, Borody T, Brandt L et al. Treating recurrent Clostridium difficile infection with fecal 31 32 microbiota transplantation. Clin Gastroenterol and Hepatol . 2011; 9: 1044-9. 33 15 Cammarota G, Ianiro G, Tilg H et al. European consensus conference on fecal microbiota 34 35 transplantation in clinical practice. Gut 2017; 66: 569-80. 36 37 16 Porter RJ, Fogg C. Faecal microbiota transplantation for Clostridium difficile infection in the 38 39 United Kingdom. Clin Microbiol Infect 2015; 21: 578-82. 40 17 Prior AR, Kevans D, McDowell L, Cudmore S, Fitzpatrick F. Treatment of Clostridium difficile 41 42 infection: a national survey of clinician recommendations and the use of faecal microbiota 43 44 transplantation. J Hosp Infect 2017; 95: 438-441. 45 18 Quraishi MN, Segal J, Mullish B et al. National survey of practice of faecal microbiota 46 47 transplantation for Clostridium difficile infection in the UK. J Hosp Infect 2017; 95: 442-6. 48 49 50 51 52 53 54 15 55 56 57 58 59 60 For Peer Review Only Page 17 of 40

1 2 3 4 5 6 7 8 9 19 Costello SP, Tucker EC, La Brooy J, Schoeman MN, Andrews JM. Establishing a fecal 10 11 microbiota transplantation service for the treatment of Clostridium difficile infection. Clin Infect 12 Dis 2016; 62: 908-14. 13 14 20 Tauxe WM, Dhere T, Ward A, Rasca LD, Varkey JB, Kraft CS. Fecal microbiota transplant 15 16 protocol for Clostridium difficile infection. Lab Med 2015: 46: e19-e23. 17 21 Kassam Z, Lee CH, Yuan Y et al. Fecal microbiota transplantation for Clostridium difficile 18 19 infection: Systematic review and meta-analysis. Am J Gastroenterol 2013; 108: 500-508. 20 21 22 Guo B, Harstall C, Louie T, et al. Systematic review: Faecal transplantation for the treatment of 22 Confidential 23 Clostridium difficile -associated disease. Aliment Pharmacol Ther 2012; 35: 865-875. 24 23 Gough E, Shaikh H, Manges AR. Systematic review of intestinal microbiota transplantation 25 26 (fecal bacteriotherapy) for recurrent Clostridium difficile infection. Clin Infect Dis 2011; 53: 994- 27 28 1002. 29 30 24 Cammarota G, Ianiro G, Gasbarrini A. Fecal microbiota transplantation for the treatment of 31 Clostridium difficile infection: a systematic review. J Clin Gastroenterol , 2014 ; 48: 693-702. 32 33 25 Drekonja D, Reich J, Gezahegn S, et al. Fecal microbiota transplantation for Clostridium difficile 34 35 infection: A systematic review. Ann Int Med, 2015 ; 162: 630-638. 36 26 Health Quality Ontario. Fecal microbiota therapy for Clostridium difficile infection: A health 37 38 technology assessment. Ont Health Technol Assess Ser [Internet].2016 July; 16 (17): 1-69. 39 40 Available at http://www.hqontario.ca/evidence-to-improve-care/journal-ontario-health- 41 42 technology-assessment-series . Accessed on July 18, 2017. 43 27 Hamilton MJ, Weingardent AR, Sadowsky MJ, Khoruts A. Standardized frozen preparation for 44 45 transplantation of fecal microbiota for recurrent Clostridium difficile infection. Am J 46 47 Gastroenterol 2012; 102: 761-7. 48 49 28 Tanga G, Yin W, and Liu W. Is frozen fecal microbiota transplantation as effective as fresh fecal 50 microbiota transplantation in patients with recurrent or refractory Clostridium difficile infection: 51 52 A meta-analysis . Diagn Micro and Inf Dis 2017; 88: 322-29. 53 54 16 55 56 57 58 59 60 For Peer Review Only Page 18 of 40

1 2 3 4 5 6 7 8 9 29 Terveer EM, van Beurden YH, Goorhuis A et al. How to: Establish and run a stool bank. Clin 10 11 Micro and Infection 2017. Available at http://dx.doi.org/10.1016/j.cmi.2017.05.015 . Accessed on 12 July 18, 2017. 13 14 30 Perez E, Lee CH, Petrof EO. A Practical Method for Preparation of Fecal Microbiota 15 16 Transplantation. Methods Mol Biol 2016; 1476: 259-67. 17

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1 2 3 4 5 6 7 8 9 Table 1. Range of donor stool mass and diluent volume used for fecal microbiota transplantation (FMT) 10 11 manufacturing within the 7 SOFT Movement institutions with finalized protocols. 12 13 Route of Range of mass of stool Range of diluent 14 Administration used (g) used (mL) 15 Min Max Min Max 16 Enema 20 100 25 300 17 18 Colonoscopy 30 150 200 300 19 ND/NJ 30 100 70 250 20 21 22 Confidential 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 18 55 56 57 58 59 60 For Peer Review Only Page 20 of 40

1 2 3 4 5 6 7 8 9 Figure 1. Location of fecal microbiota transplantation (FMT) programs in SOFT Movement, 2016 10

11 Formatted: Highlight 12 13 14 15 16 17 18 19 20 21 22 Confidential 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 FMT programs included: 38 39 A. St. Joseph’s Hospital, London 40 B. St. Joseph’s Healthcare, Hamilton 41 42 C. Trillium Health Partners, Mississauga 43 44 D. University Health Network/Sinai Health System, Toronto 45 46 E. Michael Garron Hospital, Toronto 47 F. St. Joseph’s Health Centre, Toronto* 48 49 G. Sunnybrook Health Science Centre, Toronto* 50 51 H. Lakeridge Health, Oshawa 52 53 54 19 55 56 57 58 59 60 For Peer Review Only Page 21 of 40

1 2 3 4 5 6 7 8 9 I. Kingston General Hospital, Kingston 10 11 *Sunnybrook Health Sciences Centre and St. Joseph’s Health Centre (Toronto) were not operating at the 12 time of the survey 13 14 15 16

17 18 19 20 21 22 Confidential 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 20 55 56 57 58 59 60 For Peer Review Only Page 22 of 40

1 2 3 4 5 6 7 8 9 Figure 2. Proportion of the 7 operating SOFT Movement programs providing FMT to each of the 10 11 following subgroups of patient Clostridium difficile infection (CDI) or recurrent CDI (rCDI) 12 13 14 15 16 17 18 19 20 21 22 Confidential 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 21 55 56 57 58 59 60 For Peer Review Only Page 23 of 40

1 2 3 4 5 6 7 8 9 Figure 3. Proportion of the 7 operating SOFT Movement programs completing laboratory testing for the 10 infectious disease agents recommended by Health Canada 11 12 13 14 15 16 17 18 19 20 21 22 Confidential 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 22 55 56 57 58 59 60 For Peer Review Only Page 24 of 40

1 2 3 4 5 SOFT Movement Survey of FMT Programs 6 7 8 9 10 Part 1: General Information about your Fecal Microbiota 11 12 Transplant (FMT) Program 13 14 1) Please fill out the information below: 15 16 First Name: ______17 18 Last Name: ______19 20 Title: ______21 Please enter an email address we can use to communicate with you.: 22 Confidential 23 ______24 Please fill out the start date of this survey below.: 25 ______26 27 28 2) Please enter the name of the institution and city where your FMT program is based: 29 30 Institution name: ______31 32 City: ______33 34 3) Have you begun performing FMTs at your location? 35 36 37 ( ) Yes 38 ( ) No 39 40 41 4) Approximately what year did you start performing FMT? If you have not, what year do 42 you anticipate you will be starting to perform FMTs? 43 44 ( ) Please enter year: ______45 46 ( ) Not applicable 47 48 5) If applicable, please enter the number of FMTs performed since the program started? If 49 50 not applicable, please enter 0 (zero). 51 52 ______53 54 55 56 57 58 59 60 1

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1 2 3 6) Have you performed FMT in the context of a research study, for clinical care or both? 4 5 6 ( ) Research only 7 8 ( ) Clinical care only 9 ( ) Both 10 11 12 7) Which approvals or endorsements did you require before starting your FMT 13 program (check all that apply): 14 15 [ ] Medical Advisory Committee 16 17 [ ] Hospital Senior Administrators 18 19 [ ] Research Ethics Board 20 [ ] Other (please specify): ______21 22 Confidential 23 8) Approximately how long does it take for a patient to get a FMT from initial clinical 24 assessment to first administration? 25 26 ( ) < 1week 27 28 ( ) 1-4 weeks 29 30 ( ) 4-12 weeks 31 ( ) >12 weeks 32 33 34 9) Aside from the persons who manufacture and administer FMT, who else supports the 35 program and in what capacity (select all that apply and please list duties below)? 36 37 [ ] Coordinator: ______38 39 [ ] Clinical nurse: ______40 41 [ ] Research nurse: ______42 [ ] Trainee MD: ______43 44 [ ] Students: ______45 46 [ ] Volunteers: ______47 [ ] Other (please specify): ______48 49 [ ] Not applicable 50 51 52 53 54 55 56 57 58 59 60 2

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1 2 3 4 5 6 Part 2: Donor Selection and Screening 7 8 10) Please attach your Standard Operating Procedures for FMT donor screening (if 9 available) below. 10 11 12 Please attach on web survey 13 14 11) Do you use universal FMT donors? 15 16 17 ( ) Yes 18 ( ) No 19 20 21 12) If you use universal FMT donors, how often do you screen them? 22 Confidential 23 ( ) Every month 24 25 ( ) Every 2 months 26 ( ) Every 3 months 27 28 ( ) Every 4 months 29 30 ( ) Every 5 months 31 ( ) Every 6 months 32 33 ( ) I do not use universal donors 34 35 ( ) Other (please specify): ______36 37 13) If you do not use universal FMT donors, when do you perform donor screening? 38 39 40 ( ) Within 2 weeks of donation for FMT 41 ( ) Within 4 weeks of donation for FMT 42 43 ( ) Within 3 months of donation for FMT 44 45 ( ) Within 6 months of donation for FMT 46 ( ) Other (please specify): ______47 48 49 14) Do you perform microbiota analysis of donor feces? 50 51 ( ) Yes 52 53 ( ) No 54 55 56 57 58 59 60 3

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1 2 3 15) If you perform microbiota analysis of donor feces, do you use this as part of your 4 5 selection criteria for choosing donors? 6 7 ( ) Yes 8 9 ( ) No 10 ( ) Not applicable 11 12 13 16) Which of the following agents suggested by Health Canada do you use as exclusion 14 criteria when screening donors for FMT? 15 16 [ ] Systemic immunosuppressive or biological agents 17 18 [ ] Systemic antineoplastic agents 19 20 [ ] Exogenous glucocorticoids 21 [ ] Anti-diarrheal drugs 22 Confidential 23 [ ] Mineral oil 24 25 [ ] Bismuth 26 27 [ ] Magnesium 28 [ ] Kaolin 29 30 [ ] Recent use of antibiotics (if yes, please specify your definition of recent use): 31 ______32 33 [ ] All of the above 34 35 17) Do you screen for additional agents not included in Health Canada's suggestions? 36 37 38 ( ) Yes (please specify): ______39 ( ) No 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 4

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1 2 3 18) Which of the following microorganisms or diseases suggested by Health Canada do you 4 5 use as exclusion criteria routinely in FMT donors? (Enter all that apply) 6 7 [ ] Cancer 8 Salmonella 9 [ ] species 10 [ ] Shigella 11 12 [ ] Campylobacter 13 [ ] Sorbitol-negative Escherichia coli 0157-H7 14 15 [ ] Shiga toxin 16 [ ] Yersinia 17 18 [ ] Plesiomonas 19 20 [ ] Aeromonas 21 [ ] Vibrio 22 Confidential 23 [ ] Listeria 24 [ ] Helicobacter pylori 25 26 [ ] Clostridium difficile 27 28 [ ] Vancomycin-resistant enterococci (VRE) 29 [ ] Methicillin-resistant Staphylococcus aureus (MRSA) 30 31 [ ] Syphilis 32 [ ] Neisseria gonorrhea 33 34 [ ] Chlamydia trachomatis 35 36 [ ] Norovirus 37 [ ] Rotavirus 38 39 [ ] Adenovirus 40 [ ] HIV 1/2 41 42 [ ] HTLV-I/II 43 44 [ ] Hepatitis B/C 45 [ ] Ova and parasites 46 47 [ ] Malaria 48 [ ] Chagas disease 49 50 [ ] Babesiosis 51 52 [ ] Creuztfeldt-Jakob disease 53 [ ] Prion-related diseases from dural mater grafts 54 55 [ ] All of the above 56 57 58 59 60 5

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1 2 3 19) What screening modality do you use to screen for the above microorganisms/diseases? 4 5 6 Risk Medical 7 Laboratory test factors assessment 8 Test type 9 (please 10 Test Test enter 11 Test performed 12 Risk Medical performed below if performed at site 13 factors assessment at your applicable) at PHL other than 14 site 15 PHL 16 17 Salmonella [ ] [ ] ______18 species 19 20 Shigella [ ] [ ] ______21 Confidential 22 Campylobacter [ ] [ ] ______23 24 Sorbitol- [ ] [ ] ______25 negative 26 Escherichia 27 28 coli 0157-H7 29 Shiga toxin [ ] [ ] ______30 31 Yersinia [ ] [ ] ______32 33 Plesiomonas [ ] [ ] ______34 35 Aeromonas [ ] [ ] ______36 37 Vibrio [ ] [ ] ______38 39 Listeria [ ] [ ] ______40 41 Helicobacter [ ] [ ] ______42 pylori 43 44 Clostridium [ ] [ ] ______45 difficile 46 47 Vancomycin- [ ] [ ] ______48 resistant 49 enterococci 50 (VRE) 51 52 Methicillin- [ ] [ ] ______53 54 resistant 55 Staphylococcus 56 aureus 57 (MRSA) 58 59 60 6

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1 2 3 4 Syphilis [ ] [ ] ______5 6 Neisseria [ ] [ ] ______7 gonorrhea 8 9 Chlamydia [ ] [ ] ______10 trachomatis 11 12 Norovirus [ ] [ ] ______13 14 Rotavirus [ ] [ ] ______15 16 Adenovirus [ ] [ ] ______17 18 HIV 1/2 [ ] [ ] ______19 HTLV-I/II [ ] [ ] ______20 21 Hepatitis B/C [ ] [ ] ______22 Confidential 23 Ova and [ ] [ ] ______24 parasites 25 26 Malaria [ ] [ ] ______27 28 Chagas disease [ ] [ ] ______29 30 Babesiosis [ ] [ ] ______31 32 Creuztfeldt- [ ] [ ] ______33 Jakob disease 34 35 Prion-related [ ] [ ] ______36 diseases from 37 dural mater 38 39 grafts 40 Cancer [ ] [ ] ______41 42 43 44 45 46 20) Do you screen for any additional microorganisms or diseases not included by Health 47 Canada suggestions? 48 49 ( ) Yes (please specify): ______50 51 ( ) No 52 53 54 55 56 57 58 59 60 7

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1 2 3 21) Do you collect a dietary history of FMT donors in the event recipients have food 4 5 allergies? 6 7 ( ) Yes 8 9 ( ) No 10 11 12 13 Part 3: FMT Manufacturing 14 15 22) Please attach your Standard Operating Procedures for FMT manufacturing (if 16 available) below. 17 18 19 Please attach on web survey 20 21 23) Where is FMT manufactured in your centre (select more than one if applies)? 22 Confidential 23 [ ] Clinical microbiology laboratory 24 25 [ ] Research laboratory 26 27 [ ] Pharmacy 28 29 [ ] Clinic 30 [ ] Other (please specify) 31 32 33 24) Who manufactures FMT (select all that apply)? 34 35 [ ] MD 36 37 [ ] Trainee MD 38 [ ] Clinical nurse 39 40 [ ] Research nurse 41 42 [ ] Laboratory technologist 43 44 [ ] Clinical microbiology technologist/technician 45 [ ] Research technologist/technician 46 47 [ ] Other (please specify): ______48 49 50 51 52 53 54 55 56 57 58 59 60 8

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1 2 3 25) Approximately what mass of donor stool do you use for each FMT (please select all that 4 5 apply)? 6 7 8 Other 9 amount 10 10g 20g 30g 40g 50g 100g 150g (please

11 enter 12 below) 13 14 15 Enema [ ] [ ] [ ] [ ] [ ] [ ] [ ] ___ 16 17 Colonoscopy [ ] [ ] [ ] [ ] [ ] [ ] [ ] ___ 18 Nasogastric/nasojejunal [ ] [ ] [ ] [ ] [ ] [ ] [ ] ___ 19 20 21 22 Confidential 23 24 26) Approximately what volume of diluent do you use for each FMT (check all that apply if 25 more than one route of administration at your center)? 26 27 28 Other 29 amount 30 25mL 50mL 100mL 150mL 200mL 300mL 400mL 500mL (please

31 enter 32 33 below) 34 35 Enema [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] ___ 36 37 Colonoscopy [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] ___ 38 39 Nasogastric/nasojejunal [ ] [ ] [ ] [ ] [ ] [ ] [ ] [ ] ___ 40 41 42 43 44 27) What type of diluent do you use for FMT? 45 46 [ ] Tap water 47 48 [ ] Sterile water 49 [ ] Sterile normal saline 50 51 [ ] Other (please specify): ______52 53 54 55 56 57 58 59 60 9

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1 2 3 28) What form of FMT do you manufacture (select all that apply)? 4 5 6 [ ] Fresh 7 8 [ ] Frozen 9 [ ] Capsules 10 11 [ ] Lyophilized (freeze-dried) 12 13 [ ] Other (please specify): ______14 15 29) What are your recommended storage conditions for donor feces prior to FMT 16 manufacturing? 17 18 19 ( ) Household freezer 20 ( ) Household fridge 21 22 ( ) Room temperature Confidential 23 24 ( ) Other (please specify): ______25 26 30) How long do you allow donor feces to be stored prior to delivery to your unit for FMT 27 manufacturing? 28 29 30 ( ) Up to 24 hour 31 ( ) Up to 48 hour 32 33 ( ) Up to 72 hour 34 35 ( ) Other (please specify): ______36 37 31) What storage conditions for donor feces do you use after receiving donor feces for FMT 38 manufacturing? 39 40 41 ( ) Room temperature 42 ( ) 4-5C 43 44 ( ) -20C 45 46 ( ) -80C 47 ( ) Other (please specify): ______48 49 50 51 52 53 54 55 56 57 58 59 60 10

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1 2 3 32) How long do you allow donor feces to be stored in your unit before manufacturing for 4 5 FMT? 6 7 ( ) A few hours 8 9 ( ) A few hours to 24 hours 10 ( ) 24-48 hours 11 12 ( ) 48-72 hours 13 14 ( ) Other (please specify): ______15 16 33) If you use frozen FMT, which cryoprotectant do you use? 17 18 19 ( ) Glycerol (please enter concentration in final FMT): 20 ______21 ( ) Other (please specify): ______22 Confidential 23 ( ) No cryoprotectant 24 25 ( ) Not applicable 26 27 34) If you use frozen FMT, at what temperature is the sample frozen? 28 29 30 ( ) -20C 31 ( ) -80C 32 33 ( ) Other (please specify): ______34 35 ( ) Not applicable 36 37 35) What is the maximum acceptable time from FMT donation to patient administration in 38 your institution? 39 40 41 ( ) 3 hours 42 ( ) 6 hours 43 44 ( ) 12 hours 45 46 ( ) 24 hours 47 ( ) 48 hours 48 49 ( ) 96 hours 50 51 ( ) >96 hours 52 53 ( ) Not applicable 54 55 56 57 58 59 60 11

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1 2 3 36) Did you undertake any manufacturing validation studies prior to starting your FMT 4 5 program? 6 7 ( ) Yes 8 9 ( ) No 10 11 37) What are your rejection criteria for donor stools at the time of donation (select all that 12 apply)? 13 14 15 [ ] Clinical criteria only (donor has active fever, diarrhea etc.) 16 [ ] Unformed stool provided for donation 17 18 [ ] Urine mixed in donated stools 19 20 [ ] Mucous in donated stools 21 [ ] Insufficient quantity of donated stools 22 Confidential 23 [ ] Blood in donated stools (if so, do you do Fecal Occult Blood Testing?): 24 ______25 26 [ ] Other (please specify): ______27 28 29 30 31 32 33 Part 4: Good Manufacturing/Biosafety Procedures 34 35 38) Do you manufacture FMT in a biosafety cabinet? 36 37 38 ( ) Yes 39 ( ) No 40 41 42 39) How do you disinfect your manufacturing equipment (select all that apply)? 43 44 [ ] Disinfect with sporicidal agent pre- and post-FMT 45 46 [ ] Disinfect with non-sporicidal disinfectant pre- and post-FMT 47 48 [ ] Use only disposable equipment for all manufacturing steps 49 [ ] Other (please specify) 50 51 52 53 54 55 56 57 58 59 60 12

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1 2 3 40) What personal protective equipment is used by the FMT manufacturer (select all that 4 5 apply)? 6 7 [ ] Single pair of gloves 8 9 [ ] Double gloves 10 [ ] Fluid-resistant gown 11 12 [ ] Non-fluid-resistant gown 13 14 [ ] Procedure mask 15 [ ] Face shield 16 17 [ ] Hair coverings 18 19 [ ] Shoe protection 20 21 [ ] Other (please specify): ______22 Confidential 23 24 25 Part 5: Patients 26 27 41) For which of the follow conditions do you administer FMT? 28 29 [ ] Clostridium difficile infection 30 31 [ ] Inflammatory bowel disease 32 33 [ ] Irritable bowel syndrome 34 35 [ ] Other (please specify): ______36 37 42) To which of the following subgroups of Clostridium difficile infection (CDI) do you 38 administer FMT (select all that apply)? 39 40 [ ] Initial episode of CDI as part of treatment for acute disease or immediately thereafter (ie. 41 42 within 2 weeks of symptom-onset) 43 [ ] First recurrent CDI episode as part of treatment for acute disease or immediately thereafter 44 45 (ie. within 2 weeks of symptom-onset) 46 [ ] Second or greater recurrent CDI episode(s) as part of treatment for acute disease or 47 immediately thereafter (ie. within 2 weeks of symptom-onset) 48 49 [ ] Patients with a history of recurrent CDI after they have been treated and are asymptomatic off 50 therapy (i.e. beyond 2 weeks of symptom onset) 51 52 [ ] Patients with a history of recurrent CDI on chronic suppressive oral vancomycin 53 54 [ ] Patients with CDI who are unresponsive to antimicrobial treatment 55 [ ] Critically-ill patients with CDI 56 57 [ ] Immunocompromised patients with CDI 58 59 60 13

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1 2 3 [ ] Those with concurrent underlying GI disease with CDI 4 5 [ ] Other (please specify): ______6 7 [ ] Not applicable 8 9 43) What are your major exclusion criteria for FMT receipt (select all that apply)? 10 11 12 [ ] Age over 90 years 13 [ ] Immunocompromised status 14 15 [ ] Bleeding disorder (i.e. irreversible) 16 17 [ ] Severe, uncontrollable diarrhea 18 [ ] Bloody diarrhea 19 20 [ ] Other (please specify): ______21 22 Confidential 23 24 25 26 Part 6: Clinical Procedures for FMT Administration 27 28 44) Please attach your Standard Operating Procedures for FMT administration (if 29 available) below. 30 31 32 Please attach on web survey 33 34 45) Where do you perform FMT (select all that apply)? 35 36 37 [ ] Clinic room 38 [ ] Day unit 39 40 [ ] Inpatient room 41 42 [ ] Outside of hospital 43 [ ] Other (please specify): ______44 45 46 46) Who administers FMT to patients (select all that apply)? 47 48 [ ] MD 49 50 [ ] Trainee MD 51 52 [ ] Nurse 53 [ ] Other (please specify): ______54 55 56 47) How long before FMT do you stop oral vancomycin (or other antibiotic) if a patient is 57 on treatment/suppression? 58 59 60 14

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1 2 3 ( ) <24 hours 4 5 ( ) 24-48 hours 6 7 ( ) 48-96 hours 8 9 ( ) >96 hours 10 ( ) Not applicable 11 12 13 48) What route(s) of administration do you use for FMT? 14 15 [ ] Enema 16 17 [ ] Colonoscopy 18 [ ] Nasogastric/nasojejunal tube 19 20 [ ] Other (please specify): ______21 Confidential 22 49) On average, how long does the FMT procedure take? 23 24 25 10-30 30-60 >60 Not 26 <10minutes 27 minutes minutes minutes applicable 28 29 30 Enema [ ] [ ] [ ] [ ] [ ] 31 32 Colonoscopy [ ] [ ] [ ] [ ] [ ] 33 34 35 Nasogastric/nasojejunal [ ] [ ] [ ] [ ] [ ] 36 37 38 39 40 50) How many FMTs do you perform per patient? 41 42 43 Up Up 44 Only >5 if Not 45 to to 1 necessary applicable 46 3 5 47 48 49 Enema [ ] [ ] [ ] [ ] [ ] 50 51 52 Colonoscopy [ ] [ ] [ ] [ ] [ ] 53 54 Nasogastric/nasojejunal [ ] [ ] [ ] [ ] [ ] 55 56 57 58 59 60 15

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1 2 3 4 5 6 51) If you administer multiple FMTs per patient, what is the frequency of FMT? 7 8 9 Other 10 Every Every Every (please Not 11 Daily 2-4 4-7 Weekly 10-14 enter a applicable 12 days days days value 13 14 below) 15 16 Enema [ ] [ ] [ ] [ ] [ ] ___ ( ) 17 18 Colonoscopy [ ] [ ] [ ] [ ] [ ] ___ ( ) 19 20 Nasogastric/nasojejunal [ ] [ ] [ ] [ ] [ ] ___ ( ) 21 Confidential 22 23 24 25 52) What are your criteria for failure of FMT? 26 27 ( ) Return of CDI symptoms 28 29 ( ) Return of CDI symptoms and laboratory confirmation 30 31 ( ) Other (please specify): ______32 33 53) What is your routine follow-up post-FMT? 34 35 ( ) I only see post-FMT patient’s as needed, if they have concerns 36 37 ( ) I see post-FMT patients regularly, at the following time points (other please specify):: 38 ______39 40 41 54) Do you perform microbiota analysis of FMT recipient feces prior to FMT 42 administration? 43 44 ( ) Yes 45 46 ( ) No 47 48 55) Do you perform microbiota analysis of FMT recipient feces following FMT 49 administration? 50 51 52 ( ) Yes (please specify frequency): ______53 ( ) No 54 55 56 57 58 59 60 16

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1 2 3 4 5 6 Part 7: Infection Control Procedures 7 8 56) What personal protective equipment is worn by the individual administering FMT 9 (select all that apply)? 10 11 12 [ ] Single pair of gloves 13 [ ] Double gloves 14 15 [ ] Fluid-resistant gown 16 17 [ ] Non-fluid-resistant gown 18 19 [ ] Procedure mask 20 [ ] Face shield 21 22 [ ] Hair coverings Confidential 23 24 [ ] Shoe protection 25 [ ] Other (please specify): ______26 27 28 57) How is the FMT procedure room/area disinfected between FMTs, if multiple FMTs are 29 scheduled back to back? 30 31 ( ) I never have more than one FMT in a day 32 33 ( ) Wipe down with non-sporicidal hospital disinfectant by FMT team 34 35 ( ) Wipe down with sporicidal disinfectant by FMT team 36 ( ) Cleaning by housekeeping staff using non-sporicidal hospital disinfectant 37 38 ( ) Cleaning by housekeeping staff using sporicidal disinfectant 39 40 ( ) Other (please specify): ______41 42 58) How is the FMT procedure room/area disinfected after FMT procedures are done for 43 the day? 44 45 46 ( ) Wipe down with non-sporicidal disinfectant by FMT team 47 ( ) Wipe down with sporicidal disinfectant by FMT team 48 49 ( ) Cleaning by housekeeping staff using non-sporicidal disinfectant 50 51 ( ) Cleaning by housekeeping staff using sporicidal disinfectant 52 53 ( ) Other (please specify): ______54 55 56 57 58 59 60 17

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1 2 3 4 5 6 Remarks 7 8 9 10 11 59) Do you have any other questions/comments/concerns to share? 12 13 ______14 15 ______16 ______17 18 ______19 20 21 22 Confidential

23 24 25 Thank You! 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 18

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