Antimicrobial Resistant Organism Decolonization After Microbiome Perturbation (ARO-DECAMP): protocol for a multi-centre, randomized, placebo-controlled feasibility pilot trial

Antimicrobial Resistant Organism Decolonization After Microbiome Perturbation (ARO-DECAMP): protocol for a multi-centre, randomized, placebo-controlled feasibility pilot trial | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Research Article Antimicrobial Resistant Organism Decolonization After Microbiome Perturbation (ARO-DECAMP): protocol for a multi-centre, randomized, placebo-controlled feasibility pilot trial Noelle Yee, Maria Kulikova, Derek MacFadden, Nick Daneman, Ana Konvalinka, and 7 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-3895021/v1 This work is licensed under a CC BY 4.0 License Status: Under Revision Version 1 posted 5 You are reading this latest preprint version Abstract Background: Antimicrobial resistance (AMR) is a threat to effective treatment of bacterial infections. Gastrointestinal colonization with an antimicrobial resistant organism (ARO) is a risk factor for subsequent systemic infection, and increasing resistance is associated with increased infection recurrence. Patient-level interventions to decrease or minimize antimicrobial harms and reduce gastrointestinal colonization and translocation without worsening selection for AMR have tremendous potential for clinical impact. Despite the prevalence and mortality associated with bloodstream infections, there are no effective therapies for decolonization of the gut microbiome in attempts to potentially decrease the risk of recurrence. Reconstituting the perturbed microbiome is a novel therapeutic modality with the potential to decrease ARO colonization and subsequent infection and combat AMR without additional selection pressure for further AMR. No clinical trial has yet assessed the potential of a therapeutic microbial consortium for ARO decolonization and infection prevention after antibiotic treatment. Methods: Antimicrobial Resistant Organism Decolonization After Microbiome Perturbation (ARO-DECAMP) is a multi-centre, placebo-controlled, pilot randomized controlled feasibility trial using the microbial consortium Microbial Ecosystem Therapeutic-2. Non-intensive care unit hospitalized patients > 18 years of age receiving antibiotic treatment for a bloodstream infection caused by an ARO will be included. Participants will be randomized in a 1:1 ratio to receive either MET-2 or placebo for 10 days, with treatment initiation 2-3 days after completion of antibiotics. Participants will be followed for 180 days, and biological samples will be collected periodically for clinical, ecological, and biomarker outcomes. Recruitment rate and study intervention adherence will be evaluated for feasibility. Discussion: This study is designed to determine if a trial of administration of microbial consortia after antibiotic treatment for bloodstream infections is feasible. Results of this pilot study will inform the design and sample size of a definitive trial powered to assess the effectiveness of the intervention as a therapeutic strategy for augmenting the microbiome and improving clinical outcomes. Trial registration: ClinicalTrials.gov, NCT06214403. Registered 19 January 2024, https://clinicaltrials.gov/study/NCT06214403 antimicrobial resistance microbiome microbial consortia decolonization antibiotic resistant infection bacteremia BACKGROUND Antimicrobial resistance (AMR) is a globally recognized challenge (1). Carriage of antimicrobial resistant organisms (AROs) is a risk factor for infection across age (2–4), infectious syndromes (5–9), host immune status (10,11) and care setting (12). The risk of recurrent infection with a pathogen increases along with increasing resistance in the infecting organism (13). In individuals with bloodstream infection (BSI) due to Gram-negative pathogens, recurrence rates are 5–10% in the first year after incident infections (13–15); recurrence risk can approach 50% in the highest risk populations (16,17). Disruption of the microbial ecosystem in the gut observed in numerous human diseases has common features, including depletion of health-associated anaerobes, overgrowth of pathogenic taxa (such as Streptococcus, Enterococcus, Proteobacteria ), and decreased diversity compared to healthy controls. These ecological features generally co-occur and are associated with increased risk of infection and immune pathology (including rejection in the setting of transplantation). Antibiotic exposure, particularly to agents with significant anti-anaerobic activity, results in large-scale disruptions of the gut microbiome, including loss of health-associated anaerobes and increased colonization with and relative abundance of pathogenic taxa (18–22). A diverse gut microbiome rich in obligate anaerobic bacteria is causally implicated in resistance to pathogen colonization and infection (23), and therapeutic augmentation of the microbiome is a target for the eradication of AROs and prevention of infection (24). Probiotics (single or limited-species cultivated microbes) do not replicate the ecological complexity of the human gut microbiome (25) and have failed to prevent infections in some high-risk populations, but are generally safe, scalable, and may be effective in some settings (26). Conversely, fecal microbiota transplantation (FMT) transfers the full ecological and functional complexity of the donor microbiome but is not scalable or reproducible and has been associated with safety concerns (27,28). In a systematic review of FMT for Clostridioides difficile infection and other indications, FMT was associated with ARO eradication rates of 37.5–87.5%, indicating that reconstitution of a healthy, diverse microbiome may be effective for ARO eradication (29). Therapeutic microbial consortia – cultivated or isolated multi-species communities of 10s to 100s of organisms – offer a compromise between the practical benefits of probiotics and the ecological complexity of FMT. In three human interventional trials, bacterial consortia administered after antibiotic treatment or recurrent Clostridioides difficile infection (rCDI) reconstituted stool microbial diversity, increased microbes and microbial metabolites that confer ARO colonization resistance, decreased pathogenic species abundance, and were effective for the treatment of rCDI (25,30,31). The investigational product, Microbial Ecosystem Therapeutic-2 (MET-2), is a defined microbial community derived from healthy donor stool. MET capsules are orally administered mixtures of pure cultures characterized for bacterial genotype and phenotype, including for AMR cultured from the stool of a healthy donor. In a Phase 1a clinical trial in 19 patients with rCDI, MET-2 was safe and well tolerated among patients (31). In a post-hoc analysis of stool from participants in this study, MET-2 exposure was associated with significant decreases in the relative abundance of potential pathogens and antimicrobial resistance genes at a level similar to or greater than FMT (32). The aim of this multi-centre, randomized, placebo-controlled pilot study is to assess whether a trial of MET-2 after antimicrobial treatment for BSI is feasible, to assess protocol adherence at multiple sites, and to establish clinical and biomarker outcome pilot data to inform a definitive trial powered for clinical outcomes. Ultimately, if the pilot trial is successful, the main trial will aim to determine if targeted therapeutic augmentation of the microbiome decreases recurrent infection, as well as secondary clinical, microbiologic, microbial ecological, physiological, and biological (biomarker) outcomes. METHODS Study Design This is a placebo-controlled, pilot and feasibility randomized control trial in 4 hospitals in Ontario, Canada. Research coordinators will screen all non-Intensive Care Unit (ICU) hospitalized patients with a diagnosis of BSI with qualifying organisms that are being treated with antibiotics. The study intervention will start at least 2 and no more than 3 full calendar days following completion of antibiotics (i.e., with a minimum 2-day and maximum 3-day antibiotic-free period prior to initiation of the investigational agent). Participants will be randomized to oral MET-2 or placebo through central randomization to ensure allocation concealment. The placebo is identical in appearance to MET-2. Antimicrobial Resistant Organism Decolonization After Microbiome Perturbation (ARO-DECAMP) is an investigator-initiated study sponsored by the University Health Network. The trial is funded by the Canadian Institutes of Health Research (CIHR). NuBiyota, the manufacturer of MET-2, is providing MET-2 and placebo in-kind. None of these groups played a role in the design, conduct, analysis, interpretation, or writing of this protocol. Eligibility Criteria Inclusion criteria: Adult ( > 18 years old) inpatient not admitted to the ICU or equivalent at the time of screening (step-up and step-down units are eligible) Positive blood culture with one of the following organisms: AmpC beta-lactamase producing species: Enterobacter cloacae, Citrobacter spp., Klebsiella aerogenes, Serratia spp., Morganella morganii, Hafnia alvei Extended-spectrum beta-lactamase-producing Gram-negative bacilli Receiving treatment (or intent to initiate treatment) for the bloodstream infection at the time of screening Exclusion criteria: Inability to swallow oral MET-2 or placebo capsule Recipient of small bowel transplant Inflammatory bowel disease, short bowel syndrome, diverting/non-diverting ileo/colostomy Use of >3 days over-the-counter or prescription probiotics (not including food additives) in the 10 days prior to enrolment Receipt of FMT within 3 months of enrolment Absolute neutrophil count 42 days Known pregnancy, planning to become pregnant during the study period, or breastfeeding Any other reason in view of the site investigator or treating team Trial Interventions Participants randomized to the intervention will consume the investigational drug, MET-2, once daily for 10 days. MET-2 capsules are administered orally at 0.5 g per capsule, containing 3.1 x 10 5 -10 11 colony forming units (CFUs). An initial loading dose of 10 MET-2 capsules/day will be taken for 2 days (5 grams total). This is expected to deliver a therapeutic dose of MET-2 in the range of 10 6 -10 12 CFU. For the following 8 days, participants will take a maintenance dose of 3 MET-2 capsules/day (1.5 grams total) (24). Participants randomized to the placebo will receive microcrystalline cellulose in a capsule, identical in appearance to MET-2 but not containing live bacteria. The placebo is also prepared by the MET-2 manufacturer. Participants will take the placebo in the same dosing schedule as MET-2: 10 capsules daily for 2 days, followed by 3 capsules daily for 8 days. Primary Feasibility Outcomes The two primary feasibility outcomes are: Recruitment rate of eligible patients into the study. This is determined by the numbers of eligible, consented, and randomized patients overall and by study site per month. Successful recruitment is defined as > 85 patients over an 18-month period. Adherence to MET-2 or placebo for the treatment duration. Successful adherence is defined as >80% of the prescribed interventional loading dose (16/20 pills) and >75% of daily doses (18/24 pills) for the maintenance period. This is determined by returned unused capsules and records of missed doses (in the medical chart or patient study drug diary). Secondary Feasibility Outcomes The secondary feasibility outcomes will aim to evaluate study generalizability and sample collection feasibility, and to establish biomarker pilot data to inform a definitive trial. These will include descriptive microbiologic and demographic features of the study population, adherence to biomarker sample collection (successful adherence is defined as >80% of participants having samples suitable for analysis at 30 days post-intervention), and descriptive distribution of microbiologic, ecological and biomarker values in pre- and post-randomization stool, blood, and urine samples. Safety and Clinical Outcomes Safety and clinical outcomes recorded will include: Adverse event (AE) frequency, grade, and attribution to study product in each treatment arm, and the rate of discontinuance due to AEs; Infection rate at 90- and 180-days post-intervention. Infection is defined as either isolation of a pathogenic species from any sterile site, or the initiation of a therapeutic course of antimicrobials with or without isolation of a pathogenic species from a sterile or non-sterile site. Available data for > 80% and >60% of study participants at 90 and 180 days, respectively, will constitute successful data collection; ARO colonization by culture at 30- and 90-days post-intervention, defined as any positive result for AROs from any site; Recurrence and re-infection rates (with the same organism) at 90- and 180-days post-intervention in each treatment arm; AMR gene complement by sequencing at 30- and 90-days post-intervention; All-cause mortality at 90- and 180-day; ICU and hospital lengths of stay; C. difficile carriage at days 30 and 90. Follow-up The total time in the study for each participant is approximately 6 months. Table 1 details the Schedule of Assessments. Table 1: Schedule of Assessments Screening Baseline Intervention Follow-Up Antibiotic period Antibiotic washout period (48-72 hours) Day 1-2 Day 3-10 Day 30 ( + 3) Day 90 ( + 7) Day 180 ( + 7) Eligibility screening X Informed consent X Randomization X MET-2 or Placebo Loading dose of 10 capsules/day Maintenance dose of 3 capsules/day Stool collection X X X Rectal swab collection X X X X* Blood collection X X X Urine collection X X X AE documentation X X X Collect data per case report form X X X X X *optional Sample size and recruitment With an anticipated rate of 85% adherence to treatment allocation, a sample size of 100 individuals (randomized 1:1) is required to provide an estimate of adherence within error margin of ±7% with 95% confidence. The data we obtain on recruitment, willingness to participate, and adherence to the study procedures will directly inform the estimates of attrition and recruitment needed to calculate the appropriate sample size and study duration of a definitive, separate trial. Statistical analysis Analysis will be performed at the end of the trial. No interim or subgroup analyses will be performed on collected data due to the short duration of the trial and sample size. For primary feasibility outcomes, recruitment rates will be described overall and per site as per month recruitment, and adherence to the intervention and biomarker sample collection will be described as proportions. Descriptive baseline characteristics in the secondary feasibility outcomes will be defined as medians/ranges (for continuous variables such as age) or proportions (for categorical variables). Adherence to biomarker sample collection will be described as rates per individual and per timepoint. Biomarker values will be reported as means (with standard deviations) with logarithmic transformation when appropriate. The safety and clinical outcomes reporting will vary by outcome. AEs will be reported as frequency/grade. Infection and all-cause mortality will be reported for each timepoint as frequencies. ARO and C. difficile carriage will be reported as proportions. AMR gene complement will be assessed by sequencing and reported as AMR gene richness and relative abundance both overall and by mechanism and resistance by drug class. Comparisons between categorical variables will be assessed using tests of proportion (e.g., Chi-Square), and continuous variables will be assessed using comparisons of means or non-parametrically when appropriate. Any deviation from this statistics section of the protocol along with the accounting for missing, unused, and spurious data will be described in the final report. Data management and monitoring The Data and Safety Monitoring Board (DSMB) will provide independent review of study reports, procedures, indicators of trial management, and emerging safety and AE data. After the first 10 and 25 participants have reached Day 30 and after the first 50 participants have reached Day 90, the DSMB will review all available data and decide if the study has any safety concerns. The DSMB will meet on an ad hoc basis in the case of any unexpected serious safety issue or unexpected death. Recommendations made by the DSMB to alter the conduct of the study for the protection of the safety of study participants will be forwarded to the sponsor for review and for a final decision. The sponsor or its designee will notify investigative sites and regulatory authorities, as appropriate, of DSMB recommendations. All unexpected AEs and serious AEs will be reported to the Research Ethics Board. Serious and unexpected adverse drug reactions will be reported to Health Canada. DISCUSSION The composition and function of the human microbiome is susceptible to large-scale ecological perturbation that has been associated with increased risk of disease and death. Antimicrobial therapy affects the composition of the human microbiome, decreasing microbial diversity and promoting the overgrowth of pathogenic taxa. In humans, loss of anaerobes is associated with increased risk of infection and death, especially in the highest risk populations such as those with solid organ or allogeneic stem cell transplants (11,17,33). Considering the associations between pathogen colonization, disruption of the microbiota, and risk of infection, the microbiome may be an effective target to enhance ARO decolonization and prevent infection after antibiotic exposure. It is important to understand the therapeutic potential of microbial consortia in eradicating AROs and re-establishing a diverse gut microbiome, given the intervention provides the ecological complexity required for a therapeutic effect. The strengths of this trial include multicentre enrolment and inclusion of high-risk populations to emphasize generalizability, flexible enrolment period to promote high recruitment of eligible patients, and extensive follow-up to monitor safety, clinical and microbiologic/biomarker outcomes. To reduce barriers to enrolment (investigator-, site-, or patient-identified), appropriate protocol modifications or procedural improvement strategies will be implemented. If trial components that are not essential to achieving primary outcomes are negatively affecting overall recruitment rates (e.g. biological sample collection), these will be modified or removed. New approaches to the eradication of carriage and infection with AROs are needed. The ARO-DECAMP pilot and feasibility trial represents an opportunity to tackle AMR and ARO biology through a novel therapeutic approach. If this trial indicates MET-2 administration after antimicrobial treatment for BSI is feasible, it will inform a definitive phase 3 RCT designed and powered to determine the effectiveness of microbial consortia as a therapeutic strategy for augmenting the microbiome, and decreasing recurrent infection after BSI with an ARO. Abbreviations AE: adverse event AMR: antimicrobial resistance ARO: antimicrobial resistant organism BSI: bloodstream infection CFU: colony forming units DSMB: data and safety monitoring board FMT: fecal microbiota transplant ICU: intensive care unit MET: Microbial Ecosystem Therapeutics rCDI: recurrent Clostridioides difficile infection Declarations Ethics Approval and Consent to Participate This study was approved by Health Canada on November 10, 2023. The study was reviewed and approved by the University Health Network Research Ethics Board (17-5147) as the central ethics committee, as well as the ethics review board at each participating site. Informed consent to participate in the trial will be obtained from all participants. Research will be conducted in accordance with the Declaration of Helsinki and all applicable regulatory, ethics, and institutional requirements. Consent for Publication Not applicable. Availability of Data and Materials Not applicable. Competing Interests The authors declare that they have no competing interests. Funding This is an investigator-initiated trial funded by Canadian Institutes of Health Research. NuBiyota, will provide MET-2 and placebo in-kind. Neither funder nor product manufacturer were involved in the study design and will not be involved in data analysis or interpretation of results. Authors’ Contributions NY, MK, and BC designed the study. NY and BC drafted the manuscript. 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Supplementary Files 231221ARODECAMPSPIRITChecklist.doc Cite Share Download PDF Status: Under Revision Version 1 posted Editorial decision: Minor revision 04 Oct, 2024 Reviewers agreed at journal 30 Jul, 2024 Reviewers invited by journal 21 Apr, 2024 Editor assigned by journal 20 Mar, 2024 First submitted to journal 25 Jan, 2024 You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-3895021","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":293662232,"identity":"beca0ad9-0a8c-472f-a1de-77f555bee6a1","order_by":0,"name":"Noelle 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Network","correspondingAuthor":false,"prefix":"","firstName":"Sharon","middleName":"","lastName":"Walmsley","suffix":""},{"id":293662243,"identity":"77032ddf-cdad-400c-83ee-3b06bfd7c995","order_by":11,"name":"Bryan Coburn","email":"","orcid":"https://orcid.org/0000-0003-0150-4510","institution":"UHN: University Health Network","correspondingAuthor":false,"prefix":"","firstName":"Bryan","middleName":"","lastName":"Coburn","suffix":""}],"badges":[],"createdAt":"2024-01-24 19:11:19","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-3895021/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-3895021/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":55210752,"identity":"8e3b5846-c60a-4d01-aad8-0fc2d27f294a","added_by":"auto","created_at":"2024-04-24 06:25:02","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":322499,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-3895021/v1/efab9e63-93a0-4f45-8b96-b503c8b59cd5.pdf"},{"id":55210479,"identity":"71fe3ea4-8b1f-4f60-990b-38071538550a","added_by":"auto","created_at":"2024-04-24 06:17:02","extension":"doc","order_by":4,"title":"","display":"","copyAsset":false,"role":"supplement","size":139264,"visible":true,"origin":"","legend":"","description":"","filename":"231221ARODECAMPSPIRITChecklist.doc","url":"https://assets-eu.researchsquare.com/files/rs-3895021/v1/1fe2b6ce5d40f9bee6ceea60.doc"}],"financialInterests":"","formattedTitle":"Antimicrobial Resistant Organism Decolonization After Microbiome Perturbation (ARO-DECAMP): protocol for a multi-centre, randomized, placebo-controlled feasibility pilot trial","fulltext":[{"header":"BACKGROUND","content":"\u003cp\u003eAntimicrobial resistance (AMR) is a globally recognized challenge (1). Carriage of antimicrobial resistant organisms (AROs) is a risk factor for infection across age (2\u0026ndash;4), infectious syndromes (5\u0026ndash;9), host immune status (10,11) and care setting (12). The risk of recurrent infection with a pathogen increases along with increasing resistance in the infecting organism (13). In individuals with bloodstream infection (BSI) due to Gram-negative pathogens, recurrence rates are 5\u0026ndash;10% in the first year after incident infections (13\u0026ndash;15); recurrence risk can approach 50% in the highest risk populations (16,17).\u003c/p\u003e \u003cp\u003eDisruption of the microbial ecosystem in the gut observed in numerous human diseases has common features, including depletion of health-associated anaerobes, overgrowth of pathogenic taxa (such as \u003cem\u003eStreptococcus, Enterococcus, Proteobacteria\u003c/em\u003e), and decreased diversity compared to healthy controls. These ecological features generally co-occur and are associated with increased risk of infection and immune pathology (including rejection in the setting of transplantation). Antibiotic exposure, particularly to agents with significant anti-anaerobic activity, results in large-scale disruptions of the gut microbiome, including loss of health-associated anaerobes and increased colonization with and relative abundance of pathogenic taxa (18\u0026ndash;22).\u003c/p\u003e \u003cp\u003eA diverse gut microbiome rich in obligate anaerobic bacteria is causally implicated in resistance to pathogen colonization and infection (23), and therapeutic augmentation of the microbiome is a target for the eradication of AROs and prevention of infection (24). Probiotics (single or limited-species cultivated microbes) do not replicate the ecological complexity of the human gut microbiome (25) and have failed to prevent infections in some high-risk populations, but are generally safe, scalable, and may be effective in some settings (26). Conversely, fecal microbiota transplantation (FMT) transfers the full ecological and functional complexity of the donor microbiome but is not scalable or reproducible and has been associated with safety concerns (27,28). In a systematic review of FMT for \u003cem\u003eClostridioides difficile\u003c/em\u003e infection and other indications, FMT was associated with ARO eradication rates of 37.5\u0026ndash;87.5%, indicating that reconstitution of a healthy, diverse microbiome may be effective for ARO eradication (29).\u003c/p\u003e \u003cp\u003eTherapeutic microbial consortia \u0026ndash; cultivated or isolated multi-species communities of 10s to 100s of organisms \u0026ndash; offer a compromise between the practical benefits of probiotics and the ecological complexity of FMT. In three human interventional trials, bacterial consortia administered after antibiotic treatment or recurrent \u003cem\u003eClostridioides difficile\u003c/em\u003e infection (rCDI) reconstituted stool microbial diversity, increased microbes and microbial metabolites that confer ARO colonization resistance, decreased pathogenic species abundance, and were effective for the treatment of rCDI (25,30,31).\u003c/p\u003e \u003cp\u003eThe investigational product, Microbial Ecosystem Therapeutic-2 (MET-2), is a defined microbial community derived from healthy donor stool. MET capsules are orally administered mixtures of pure cultures characterized for bacterial genotype and phenotype, including for AMR cultured from the stool of a healthy donor. In a Phase 1a clinical trial in 19 patients with rCDI, MET-2 was safe and well tolerated among patients (31). In a post-hoc analysis of stool from participants in this study, MET-2 exposure was associated with significant decreases in the relative abundance of potential pathogens and antimicrobial resistance genes at a level similar to or greater than FMT (32).\u003c/p\u003e \u003cp\u003eThe aim of this multi-centre, randomized, placebo-controlled pilot study is to assess whether a trial of MET-2 after antimicrobial treatment for BSI is feasible, to assess protocol adherence at multiple sites, and to establish clinical and biomarker outcome pilot data to inform a definitive trial powered for clinical outcomes. Ultimately, if the pilot trial is successful, the main trial will aim to determine if targeted therapeutic augmentation of the microbiome decreases recurrent infection, as well as secondary clinical, microbiologic, microbial ecological, physiological, and biological (biomarker) outcomes.\u003c/p\u003e"},{"header":"METHODS","content":"\u003cp\u003e\u003cstrong\u003eStudy Design\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThis is a placebo-controlled, pilot and feasibility randomized control trial in 4 hospitals in Ontario, Canada. Research coordinators will screen all non-Intensive Care Unit (ICU) hospitalized patients with a diagnosis of BSI with qualifying organisms that are being treated with antibiotics. The study intervention will start at least 2 and no more than 3 full calendar days following completion of antibiotics (i.e., with a minimum 2-day and maximum 3-day antibiotic-free period prior to initiation of the investigational agent). Participants will be randomized to oral MET-2 or placebo through central randomization to ensure allocation concealment. The placebo is identical in appearance to MET-2.\u003c/p\u003e\n\u003cp\u003eAntimicrobial Resistant Organism Decolonization After Microbiome Perturbation (ARO-DECAMP) is an investigator-initiated study sponsored by the University Health Network. The trial is funded by the Canadian Institutes of Health Research (CIHR). NuBiyota, the manufacturer of MET-2, is providing MET-2 and placebo in-kind. None of these groups played a role in the design, conduct, analysis, interpretation, or writing of this protocol.\u0026nbsp;\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eEligibility Criteria\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eInclusion criteria:\u003c/p\u003e\n\u003col\u003e\n \u003cli\u003eAdult (\u003cu\u003e\u0026gt;\u003c/u\u003e18 years old) inpatient not admitted to the ICU or equivalent at the time of screening (step-up and step-down units are eligible)\u003c/li\u003e\n \u003cli\u003ePositive blood culture with one of the following organisms:\u003cul\u003e\n \u003cli\u003eAmpC beta-lactamase producing species: \u003cem\u003eEnterobacter cloacae, Citrobacter spp., Klebsiella aerogenes, Serratia spp., Morganella morganii, Hafnia alvei\u0026nbsp;\u003c/em\u003e\u003c/li\u003e\n \u003cli\u003eExtended-spectrum beta-lactamase-producing Gram-negative bacilli\u003c/li\u003e\n \u003c/ul\u003e\n \u003c/li\u003e\n \u003cli\u003eReceiving treatment (or intent to initiate treatment) for the bloodstream infection at the time of screening\u003c/li\u003e\n\u003c/ol\u003e\n\u003cp\u003eExclusion criteria:\u003c/p\u003e\n\u003col\u003e\n \u003cli\u003eInability to swallow oral MET-2 or placebo capsule\u003c/li\u003e\n \u003cli\u003eRecipient of small bowel transplant\u003c/li\u003e\n \u003cli\u003eInflammatory bowel disease, short bowel syndrome, diverting/non-diverting ileo/colostomy\u003c/li\u003e\n \u003cli\u003eUse of \u0026gt;3 days over-the-counter or prescription probiotics (not including food additives) in the 10 days prior to enrolment\u003c/li\u003e\n \u003cli\u003eReceipt of FMT within 3 months of enrolment\u003c/li\u003e\n \u003cli\u003eAbsolute neutrophil count \u0026lt;0.5x10\u003csup\u003e9\u003c/sup\u003e/L\u003c/li\u003e\n \u003cli\u003eDeath expected within 72 hours of enrolment\u003c/li\u003e\n \u003cli\u003ePlanned continuation of non-prophylaxis antimicrobial therapy active against the bloodstream isolate for \u0026gt;42 days\u003c/li\u003e\n \u003cli\u003eKnown pregnancy, planning to become pregnant during the study period, or breastfeeding\u0026nbsp;\u003c/li\u003e\n \u003cli\u003eAny other reason in view of the site investigator or treating team\u0026nbsp;\u003c/li\u003e\n\u003c/ol\u003e\n\u003cp\u003e\u003cstrong\u003e\u003cem\u003eTrial Interventions\u003c/em\u003e\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eParticipants randomized to the intervention will consume the investigational drug, MET-2, once daily for 10 days. MET-2 capsules are administered orally at 0.5 g per capsule, containing 3.1 x 10\u003csup\u003e5\u003c/sup\u003e-10\u003csup\u003e11\u003c/sup\u003e colony forming units (CFUs). An initial loading dose of 10 MET-2 capsules/day will be taken for 2 days (5 grams total). This is expected to deliver a therapeutic dose of MET-2 in the range of 10\u003csup\u003e6\u003c/sup\u003e-10\u003csup\u003e12\u003c/sup\u003e CFU. For the following 8 days, participants will take a maintenance dose of 3 MET-2 capsules/day (1.5 grams total) (24).\u003c/p\u003e\n\u003cp\u003eParticipants randomized to the placebo will receive microcrystalline cellulose in a capsule, identical in appearance to MET-2 but not containing live bacteria. The placebo is also prepared by the MET-2 manufacturer. Participants will take the placebo in the same dosing schedule as MET-2: 10 capsules daily for 2 days, followed by 3 capsules daily for 8 days.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003e\u003cem\u003ePrimary Feasibility Outcomes\u003c/em\u003e\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe two primary feasibility outcomes are:\u003c/p\u003e\n\u003col\u003e\n \u003cli\u003eRecruitment rate of eligible patients into the study. This is determined by the numbers of eligible, consented, and randomized patients overall and by study site per month. Successful recruitment is defined as \u003cu\u003e\u0026gt;\u003c/u\u003e85 patients over an 18-month period.\u0026nbsp;\u003c/li\u003e\n \u003cli\u003eAdherence to MET-2 or placebo for the treatment duration. Successful adherence is defined as \u0026gt;80% of the prescribed interventional loading dose (16/20 pills) and \u0026gt;75% of daily doses (18/24 pills) for the maintenance period. This is determined by returned unused capsules and records of missed doses (in the medical chart or patient study drug diary).\u003c/li\u003e\n\u003c/ol\u003e\n\u003cp\u003e\u003cstrong\u003e\u003cem\u003eSecondary Feasibility Outcomes\u003c/em\u003e\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe secondary feasibility outcomes will aim to evaluate study generalizability and sample collection feasibility, and to establish biomarker pilot data to inform a definitive trial. These will include descriptive microbiologic and demographic features of the study population, adherence to biomarker sample collection (successful adherence is defined as \u0026gt;80% of participants having samples suitable for analysis at 30 days post-intervention), and descriptive distribution of microbiologic, ecological and biomarker values in pre- and post-randomization stool, blood, and urine samples.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003e\u003cem\u003eSafety and Clinical Outcomes\u003c/em\u003e\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eSafety and clinical outcomes recorded will include:\u0026nbsp;\u003c/p\u003e\n\u003col\u003e\n \u003cli\u003eAdverse event (AE) frequency, grade, and attribution to study product in each treatment arm, and the rate of discontinuance due to AEs;\u003c/li\u003e\n \u003cli\u003eInfection rate at 90- and 180-days post-intervention. Infection is defined as either isolation of a pathogenic species from any sterile site, or the initiation of a therapeutic course of antimicrobials with or without isolation of a pathogenic species from a sterile or non-sterile site. Available data for \u003cu\u003e\u0026gt;\u003c/u\u003e80% and \u0026gt;60% of study participants at 90 and 180 days, respectively, will constitute successful data collection;\u003c/li\u003e\n \u003cli\u003eARO colonization by culture at 30- and 90-days post-intervention, defined as any positive result for AROs from any site;\u003c/li\u003e\n \u003cli\u003eRecurrence and re-infection rates (with the same organism) at 90- and 180-days post-intervention in each treatment arm;\u003c/li\u003e\n \u003cli\u003eAMR gene complement by sequencing at 30- and 90-days post-intervention;\u003c/li\u003e\n \u003cli\u003eAll-cause mortality at 90- and 180-day;\u003c/li\u003e\n \u003cli\u003eICU and hospital lengths of stay;\u003c/li\u003e\n \u003cli\u003e\u003cem\u003eC. difficile\u003c/em\u003e carriage at days 30 and 90.\u003c/li\u003e\n\u003c/ol\u003e\n\u003cp\u003e\u003cstrong\u003eFollow-up\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe total time in the study for each participant is approximately 6 months. Table 1 details the Schedule of Assessments.\u0026nbsp;\u003c/p\u003e\n\u003cp\u003eTable 1: Schedule of Assessments\u003c/p\u003e\n\u003ctable border=\"1\" cellspacing=\"0\" cellpadding=\"0\" width=\"627\"\u003e\n \u003ctbody\u003e\n \u003ctr\u003e\n \u003ctd width=\"16.586921850079744%\"\u003e\n \u003cp\u003e\u003cstrong\u003e\u0026nbsp;\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"13.556618819776714%\"\u003e\n \u003cp\u003e\u003cstrong\u003eScreening\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"15.151515151515152%\"\u003e\n \u003cp\u003e\u003cstrong\u003eBaseline\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"30.14354066985646%\" colspan=\"2\"\u003e\n \u003cp\u003e\u003cstrong\u003eIntervention\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"24.56140350877193%\" colspan=\"3\"\u003e\n \u003cp\u003e\u003cstrong\u003eFollow-Up\u003c/strong\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd width=\"16.56050955414013%\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"13.535031847133759%\"\u003e\n \u003cp\u003e\u003cem\u003eAntibiotic period\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"15.127388535031848%\"\u003e\n \u003cp\u003e\u003cem\u003eAntibiotic washout period\u003c/em\u003e\u003c/p\u003e\n \u003cp\u003e\u003cem\u003e(48-72 hours)\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"14.968152866242038%\"\u003e\n \u003cp\u003e\u003cem\u003eDay 1-2\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"15.127388535031848%\"\u003e\n \u003cp\u003e\u003cem\u003eDay 3-10\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"9.07643312101911%\"\u003e\n \u003cp\u003e\u003cem\u003eDay\u003c/em\u003e\u003c/p\u003e\n \u003cp\u003e\u003cem\u003e30\u003c/em\u003e\u003c/p\u003e\n \u003cp\u003e\u003cem\u003e(\u003cu\u003e+\u003c/u\u003e 3)\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"7.484076433121019%\"\u003e\n \u003cp\u003e\u003cem\u003eDay\u003c/em\u003e\u003c/p\u003e\n \u003cp\u003e\u003cem\u003e90\u003c/em\u003e\u003c/p\u003e\n \u003cp\u003e\u003cem\u003e(\u003cu\u003e+\u003c/u\u003e 7)\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"8.121019108280255%\"\u003e\n \u003cp\u003e\u003cem\u003eDay\u003c/em\u003e\u003c/p\u003e\n \u003cp\u003e\u003cem\u003e180\u003c/em\u003e\u003c/p\u003e\n \u003cp\u003e\u003cem\u003e(\u003cu\u003e+\u003c/u\u003e 7)\u003c/em\u003e\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd width=\"16.56050955414013%\"\u003e\n \u003cp\u003eEligibility screening\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"13.535031847133759%\"\u003e\n \u003cp\u003eX\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"15.127388535031848%\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"14.968152866242038%\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"15.127388535031848%\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"9.07643312101911%\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"7.484076433121019%\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"8.121019108280255%\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd width=\"16.56050955414013%\"\u003e\n \u003cp\u003eInformed consent\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"13.535031847133759%\"\u003e\n \u003cp\u003eX\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"15.127388535031848%\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"14.968152866242038%\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"15.127388535031848%\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"9.07643312101911%\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"7.484076433121019%\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"8.121019108280255%\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd width=\"16.56050955414013%\"\u003e\n \u003cp\u003eRandomization\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"13.535031847133759%\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"15.127388535031848%\"\u003e\n \u003cp\u003eX\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"14.968152866242038%\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"15.127388535031848%\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"9.07643312101911%\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"7.484076433121019%\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"8.121019108280255%\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd width=\"16.56050955414013%\"\u003e\n \u003cp\u003eMET-2 or Placebo\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"13.535031847133759%\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"15.127388535031848%\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"14.968152866242038%\"\u003e\n \u003cp\u003eLoading dose of 10 capsules/day\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"15.127388535031848%\"\u003e\n \u003cp\u003eMaintenance dose of 3 capsules/day\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"9.07643312101911%\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"7.484076433121019%\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"8.121019108280255%\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd width=\"16.56050955414013%\"\u003e\n \u003cp\u003eStool collection\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"13.535031847133759%\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"15.127388535031848%\"\u003e\n \u003cp\u003eX\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"14.968152866242038%\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"15.127388535031848%\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"9.07643312101911%\"\u003e\n \u003cp\u003eX\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"7.484076433121019%\"\u003e\n \u003cp\u003eX\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"8.121019108280255%\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd width=\"16.56050955414013%\"\u003e\n \u003cp\u003eRectal swab collection\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"13.535031847133759%\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"15.127388535031848%\"\u003e\n \u003cp\u003eX\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"14.968152866242038%\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"15.127388535031848%\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"9.07643312101911%\"\u003e\n \u003cp\u003eX\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"7.484076433121019%\"\u003e\n \u003cp\u003eX\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"8.121019108280255%\"\u003e\n \u003cp\u003eX*\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd width=\"16.56050955414013%\"\u003e\n \u003cp\u003eBlood collection\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"13.535031847133759%\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"15.127388535031848%\"\u003e\n \u003cp\u003eX\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"14.968152866242038%\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"15.127388535031848%\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"9.07643312101911%\"\u003e\n \u003cp\u003eX\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"7.484076433121019%\"\u003e\n \u003cp\u003eX\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"8.121019108280255%\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd width=\"16.56050955414013%\"\u003e\n \u003cp\u003eUrine collection\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"13.535031847133759%\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"15.127388535031848%\"\u003e\n \u003cp\u003eX\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"14.968152866242038%\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"15.127388535031848%\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"9.07643312101911%\"\u003e\n \u003cp\u003eX\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"7.484076433121019%\"\u003e\n \u003cp\u003eX\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"8.121019108280255%\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd width=\"16.56050955414013%\"\u003e\n \u003cp\u003eAE documentation\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"13.535031847133759%\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"15.127388535031848%\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"14.968152866242038%\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"15.127388535031848%\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"9.07643312101911%\"\u003e\n \u003cp\u003eX\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"7.484076433121019%\"\u003e\n \u003cp\u003eX\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"8.121019108280255%\"\u003e\n \u003cp\u003eX\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003ctr\u003e\n \u003ctd width=\"16.56050955414013%\"\u003e\n \u003cp\u003eCollect data per case report form\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"13.535031847133759%\"\u003e\n \u003cp\u003eX\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"15.127388535031848%\"\u003e\n \u003cp\u003eX\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"14.968152866242038%\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"15.127388535031848%\"\u003e\n \u003cp\u003e\u0026nbsp;\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"9.07643312101911%\"\u003e\n \u003cp\u003eX\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"7.484076433121019%\"\u003e\n \u003cp\u003eX\u003c/p\u003e\n \u003c/td\u003e\n \u003ctd width=\"8.121019108280255%\"\u003e\n \u003cp\u003eX\u003c/p\u003e\n \u003c/td\u003e\n \u003c/tr\u003e\n \u003c/tbody\u003e\n\u003c/table\u003e\n\u003cp\u003e*optional\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eSample size and recruitment\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eWith an anticipated rate of 85% adherence to treatment allocation, a sample size of 100 individuals (randomized 1:1) is required to provide an estimate of adherence within error margin of \u0026plusmn;7% with 95% confidence. The data we obtain on recruitment, willingness to participate, and adherence to the study procedures will directly inform the estimates of attrition and recruitment needed to calculate the appropriate sample size and study duration of a definitive, separate trial.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eStatistical analysis\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eAnalysis will be performed at the end of the trial. No interim or subgroup analyses will be performed on collected data due to the short duration of the trial and sample size.\u003c/p\u003e\n\u003cp\u003eFor primary feasibility outcomes, recruitment rates will be described overall and per site as per month recruitment, and adherence to the intervention and biomarker sample collection will be described as proportions.\u003c/p\u003e\n\u003cp\u003eDescriptive baseline characteristics in the secondary feasibility outcomes will be defined as medians/ranges (for continuous variables such as age) or proportions (for categorical variables). Adherence to biomarker sample collection will be described as rates per individual and per timepoint. Biomarker values will be reported as means (with standard deviations) with logarithmic transformation when appropriate.\u003c/p\u003e\n\u003cp\u003eThe safety and clinical outcomes reporting will vary by outcome. AEs will be reported as frequency/grade. Infection and all-cause mortality will be reported for each timepoint as frequencies. ARO and \u003cem\u003eC. difficile\u003c/em\u003e carriage will be reported as proportions. AMR gene complement will be assessed by sequencing and reported as AMR gene richness and relative abundance both overall and by mechanism and resistance by drug class.\u003c/p\u003e\n\u003cp\u003eComparisons between categorical variables will be assessed using tests of proportion (e.g., Chi-Square), and continuous variables will be assessed using comparisons of means or non-parametrically when appropriate.\u0026nbsp;\u003c/p\u003e\n\u003cp\u003eAny deviation from this statistics section of the protocol along with the accounting for missing, unused, and spurious data will be described in the final report.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eData management and monitoring\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe Data and Safety Monitoring Board (DSMB) will provide independent review of study reports, procedures, indicators of trial management, and emerging safety and AE data. After the first 10 and 25 participants have reached Day 30 and after the first 50 participants have reached Day 90, the DSMB will review all available data and decide if the study has any safety concerns. The DSMB will meet on an ad hoc basis in the case of any unexpected serious safety issue or unexpected death. Recommendations made by the DSMB to alter the conduct of the study for the protection of the safety of study participants will be forwarded to the sponsor for review and for a final decision. The sponsor or its designee will notify investigative sites and regulatory authorities, as appropriate, of DSMB recommendations. All unexpected AEs and serious AEs will be reported to the Research Ethics Board. Serious and unexpected adverse drug reactions will be reported to Health Canada.\u003c/p\u003e"},{"header":"DISCUSSION","content":"\u003cp\u003eThe composition and function of the human microbiome is susceptible to large-scale ecological perturbation that has been associated with increased risk of disease and death. Antimicrobial therapy affects the composition of the human microbiome, decreasing microbial diversity and promoting the overgrowth of pathogenic taxa. In humans, loss of anaerobes is associated with increased risk of infection and death, especially in the highest risk populations such as those with solid organ or allogeneic stem cell transplants (11,17,33). Considering the associations between pathogen colonization, disruption of the microbiota, and risk of infection, the microbiome may be an effective target to enhance ARO decolonization and prevent infection after antibiotic exposure. It is important to understand the therapeutic potential of microbial consortia in eradicating AROs and re-establishing a diverse gut microbiome, given the intervention provides the ecological complexity required for a therapeutic effect.\u003c/p\u003e \u003cp\u003eThe strengths of this trial include multicentre enrolment and inclusion of high-risk populations to emphasize generalizability, flexible enrolment period to promote high recruitment of eligible patients, and extensive follow-up to monitor safety, clinical and microbiologic/biomarker outcomes. To reduce barriers to enrolment (investigator-, site-, or patient-identified), appropriate protocol modifications or procedural improvement strategies will be implemented. If trial components that are not essential to achieving primary outcomes are negatively affecting overall recruitment rates (e.g. biological sample collection), these will be modified or removed.\u003c/p\u003e \u003cp\u003eNew approaches to the eradication of carriage and infection with AROs are needed. The ARO-DECAMP pilot and feasibility trial represents an opportunity to tackle AMR and ARO biology through a novel therapeutic approach. If this trial indicates MET-2 administration after antimicrobial treatment for BSI is feasible, it will inform a definitive phase 3 RCT designed and powered to determine the effectiveness of microbial consortia as a therapeutic strategy for augmenting the microbiome, and decreasing recurrent infection after BSI with an ARO.\u003c/p\u003e"},{"header":"Abbreviations","content":"\u003cp\u003eAE: adverse event\u003c/p\u003e\n\u003cp\u003eAMR: antimicrobial resistance\u003c/p\u003e\n\u003cp\u003eARO: antimicrobial resistant organism\u003c/p\u003e\n\u003cp\u003eBSI: bloodstream infection\u003c/p\u003e\n\u003cp\u003eCFU: colony forming units\u003c/p\u003e\n\u003cp\u003eDSMB: data and safety monitoring board\u003c/p\u003e\n\u003cp\u003eFMT: fecal microbiota transplant\u003c/p\u003e\n\u003cp\u003eICU: intensive care unit\u003c/p\u003e\n\u003cp\u003eMET: Microbial Ecosystem Therapeutics\u003c/p\u003e\n\u003cp\u003erCDI: recurrent \u003cem\u003eClostridioides difficile\u0026nbsp;\u003c/em\u003einfection\u003c/p\u003e"},{"header":"Declarations","content":"\u003cp\u003e\u003cu\u003e\u003cstrong\u003eEthics Approval and Consent to Participate\u003c/strong\u003e\u003c/u\u003e\u003c/p\u003e\n\u003cp\u003eThis study was approved by Health Canada on November 10, 2023. The study was reviewed and approved by the University Health Network Research Ethics Board (17-5147) as the central ethics committee, as well as the ethics review board at each participating site. Informed consent to participate in the trial will be obtained from all participants. Research will be conducted in accordance with the Declaration of Helsinki and all\u0026nbsp;applicable regulatory, ethics, and institutional requirements.\u003c/p\u003e\n\u003cp\u003e\u003cu\u003e\u003cstrong\u003eConsent for Publication\u003c/strong\u003e\u003c/u\u003e\u003c/p\u003e\n\u003cp\u003eNot applicable.\u003c/p\u003e\n\u003cp\u003e\u003cu\u003e\u003cstrong\u003eAvailability of Data and Materials\u003c/strong\u003e\u003c/u\u003e\u003c/p\u003e\n\u003cp\u003eNot applicable.\u003c/p\u003e\n\u003cp\u003e\u003cu\u003e\u003cstrong\u003eCompeting Interests\u003c/strong\u003e\u003c/u\u003e\u003c/p\u003e\n\u003cp\u003eThe authors declare that they have no competing interests.\u003c/p\u003e\n\u003cp\u003e\u003cu\u003e\u003cstrong\u003eFunding\u003c/strong\u003e\u003c/u\u003e\u003c/p\u003e\n\u003cp\u003eThis is an investigator-initiated trial funded by Canadian Institutes of Health Research. NuBiyota, will provide MET-2 and placebo in-kind. Neither funder nor product manufacturer were involved in the study design and will not be involved in data analysis or interpretation of results.\u0026nbsp;\u003c/p\u003e\n\u003cp\u003e\u003cu\u003e\u003cstrong\u003eAuthors\u0026rsquo; Contributions\u003c/strong\u003e\u003c/u\u003e\u003c/p\u003e\n\u003cp\u003eNY, MK, and BC designed the study. NY and BC drafted the manuscript. All authors provided revisions to the draft study design. All authors revised the manuscript. All authors read and approved the final manuscript.\u003c/p\u003e\n\u003cp\u003e\u003cu\u003e\u003cstrong\u003eAcknowledgements\u003c/strong\u003e\u003c/u\u003e\u003c/p\u003e\n\u003cp\u003eThe development of this protocol was supported by a grant to BC from the Weston Family Microbiome Initiative.\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\n\u003cli\u003eWorld Health Organization. Antimicrobial resistance: global report on surveillance. Vol. 61, World Health Organization. 2014. \u003c/li\u003e\n\u003cli\u003eHealy DB, Anthony Ryan C, Paul Ross R, Stanton C, Dempsey EM. Clinical implications of preterm infant gut microbiome development. Nat Microbiol. 2022;7:22\u0026ndash;33. \u003c/li\u003e\n\u003cli\u003eStewart CJ, Ajami NJ, O\u0026rsquo;brien JL, Hutchinson DS, Smith DP, Wong MC, et al. Temporal development of the gut microbiome in early childhood from the TEDDY study. Nature. 2018;562(7728):583\u0026ndash;8. \u003c/li\u003e\n\u003cli\u003eShimasaki T, Seekatz A, Bassis C, Rhee Y, Yelin RD, Fogg L, et al. Increased Relative Abundance of Klebsiella pneumoniae Carbapenemase-producing Klebsiella pneumoniae Within the Gut Microbiota Is Associated With Risk of Bloodstream Infection in Long-term Acute Care Hospital Patients. Clinical Infectious Diseases. 2019 May 30;68(12):2053\u0026ndash;9. \u003c/li\u003e\n\u003cli\u003eVan Ruissen MCE, Bos LD, Dickson RP, Dondorp AM, Schultsz C, Schultz MJ. Manipulation of the microbiome in critical illness-probiotics as a preventive measure against ventilator-associated pneumonia. Intensive Care Med Exp. 2019;7(Suppl 1):37. \u003c/li\u003e\n\u003cli\u003eMagruder M, Edusei E, Zhang L, Albakry S, Satlin MJ, Westblade LF, et al. Gut commensal microbiota and decreased risk for Enterobacteriaceae bacteriuria and urinary tract infection. Gut Microbes. 2020;12(1):e1805281. \u003c/li\u003e\n\u003cli\u003eStoma I, Littmann ER, Peled JU, Giralt S, van den Brink MRM, Pamer EG, et al. Compositional Flux Within the Intestinal Microbiota and Risk for Bloodstream Infection With Gram-negative Bacteria. Clinical Infectious Diseases. 2021 Dec 6;73(11):e4627\u0026ndash;35. \u003c/li\u003e\n\u003cli\u003eTamburini FB, Andermann TM, Tkachenko E, Senchyna F, Banaei N, Bhatt AS. Precision identification of diverse bloodstream pathogens in the gut microbiome. Nat Med. 2018 Dec 15;24:1809\u0026ndash;14. \u003c/li\u003e\n\u003cli\u003eBerkell M, Mysara M, Xavier BB, van Werkhoven CH, Monsieurs P, Lammens C, et al. Microbiota-based markers predictive of development of Clostridioides difficile infection. Nat Commun. 2021 Dec 1;12:2241. \u003c/li\u003e\n\u003cli\u003eTaur Y, Pamer EG. The Intestinal Microbiota and Susceptibility to Infection in Immunocompromised Patients. Curr Opin Infect Dis. 2013 Aug;26(4):332. \u003c/li\u003e\n\u003cli\u003eTaur Y, Xavier JB, Lipuma L, Ubeda C, Goldberg J, Gobourne A, et al. Intestinal domination and the risk of bacteremia in patients undergoing allogeneic hematopoietic stem cell transplantation. Clinical Infectious Diseases. 2012;55(7):905\u0026ndash;14. \u003c/li\u003e\n\u003cli\u003eFreedberg DE, Zhou MJ, Cohen ME, Annavajhala MK, Khan S, Moscoso DI, et al. Pathogen colonization of the gastrointestinal microbiome at intensive care unit admission and risk for subsequent death or infection. Intensive Care Med. 2018;44:1203\u0026ndash;11. \u003c/li\u003e\n\u003cli\u003eWoudt SHS, De Greeff SC, Schoffelen AF, Vlek ALM, Bonten MJM, Cohen Stuart JWT, et al. Antibiotic Resistance and the Risk of Recurrent Bacteremia. Clinical Infectious Diseases. 2018;66(11). \u003c/li\u003e\n\u003cli\u003eAl-Hasan MN, Eckel-Passow JE, Baddour LM. Bacteremia complicating gram-negative urinary tract infections: A population-based study. Journal of Infection. 2010;60(4). \u003c/li\u003e\n\u003cli\u003eJensen US, Knudsen JD, Wehberg S, Gregson DB, Laupland KB. Risk factors for recurrence and death after bacteraemia: A population-based study. Clinical Microbiology and Infection. 2011;17(8). \u003c/li\u003e\n\u003cli\u003eAurora A, Le TD, Akers KS, Blyth DM, Graybill JC, Clemens MS, et al. Recurrent bacteremia: A 10-year retrospective study in combat-related burn casualties. Burns. 2019;45(3). \u003c/li\u003e\n\u003cli\u003eNguyen MH, Shields RK, Chen L, William Pasculle A, Hao B, Cheng S, et al. Molecular Epidemiology, Natural History, and Long-Term Outcomes of Multidrug-Resistant Enterobacterales Colonization and Infections Among Solid Organ Transplant Recipients. Clinical Infectious Diseases. 2022;74(3). \u003c/li\u003e\n\u003cli\u003ePatel J, Kittleson M, Rashidi S, Singer-Englar T, Patel N, Kransdorf E, et al. Apparent Immune Effect of Clostridium Difficile in Post-Heart Transplant Recipients. The Journal of Heart and Lung Transplantation. 2021;40(4). \u003c/li\u003e\n\u003cli\u003eBuffie CG, Jarchum I, Equinda M, Lipuma L, Gobourne A, Viale A, et al. Profound alterations of intestinal microbiota following a single dose of clindamycin results in sustained susceptibility to Clostridium difficile-induced colitis. Infect Immun. 2012;80(1). \u003c/li\u003e\n\u003cli\u003eDonskey CJ, Chowdhry TK, Hecker MT, Hoyen CK, Hanrahan JA, Hujer AM, et al. Effect of Antibiotic Therapy on the Density of Vancomycin-Resistant Enterococci in the Stool of Colonized Patients. New England Journal of Medicine. 2000 Dec 28;343(26):1925\u0026ndash;32. \u003c/li\u003e\n\u003cli\u003eRooney AM, Timberlake K, Brown KA, Bansal S, Tomlinson C, Lee KS, et al. Each Additional Day of Antibiotics Is Associated With Lower Gut Anaerobes in Neonatal Intensive Care Unit Patients. Clinical Infectious Diseases. 2020;70(12):2553\u0026ndash;60. \u003c/li\u003e\n\u003cli\u003eDethlefsen L, Huse S, Sogin ML, Relman DA. The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16s rRNA sequencing. PLoS Biol. 2008;6(11):2383\u0026ndash;400. \u003c/li\u003e\n\u003cli\u003ePickard JM, Zeng MY, Caruso R, N\u0026uacute;\u0026ntilde;ez G. Gut microbiota: Role in pathogen colonization, immune responses, and inflammatory disease. Immunol Rev. 2017 Sep 1;279:70\u0026ndash;89. \u003c/li\u003e\n\u003cli\u003eSorbara MT, Pamer EG. Microbiome-based therapeutics. Nat Rev Microbiol. 2022; \u003c/li\u003e\n\u003cli\u003eSuez J, Zmora N, Zilberman-Schapira G, Mor U, Dori-Bachash M, Bashiardes S, et al. Post-Antibiotic Gut Mucosal Microbiome Reconstitution Is Impaired by Probiotics and Improved by Autologous FMT. Cell. 2018 Sep 6;174(6):1406-1423.e16. \u003c/li\u003e\n\u003cli\u003eJohnstone J, Meade M, Lauzier F, Marshall J, Duan E, Dionne J, et al. Effect of Probiotics on Incident Ventilator-Associated Pneumonia in Critically Ill Patients: A Randomized Clinical Trial. JAMA. 2021 Sep 21;326(11):1024\u0026ndash;33. \u003c/li\u003e\n\u003cli\u003eDeFilipp Z, Bloom PP, Torres Soto M, Mansour MK, Sater MRA, Huntley MH, et al. Drug-Resistant E. coli Bacteremia Transmitted by Fecal Microbiota Transplant. New England Journal of Medicine. 2019 Nov 21;381(21):2043\u0026ndash;50. \u003c/li\u003e\n\u003cli\u003eHota SS, Poutanen SM. Microbiome-based therapeutics for Clostridioides difficile infection: helpful solutions or unclear cocktails? Lancet Infect Dis. 2023 Sep 1;23(9):999\u0026ndash;1000. \u003c/li\u003e\n\u003cli\u003eSaha S, Tariq R, Tosh PK, Pardi DS, Khanna S. Faecal microbiota transplantation for eradicating carriage of multidrug-resistant organisms: a systematic review. Vol. 25, Clinical Microbiology and Infection. Elsevier B.V.; 2019. p. 958\u0026ndash;63. \u003c/li\u003e\n\u003cli\u003eFeuerstadt P, Louie TJ, Lashner B, Wang EEL, Diao L, Bryant JA, et al. SER-109, an Oral Microbiome Therapy for Recurrent Clostridioides difficile Infection. New England Journal of Medicine. 2022 Jan 20;386(3):220\u0026ndash;9. \u003c/li\u003e\n\u003cli\u003eKao D, Wong K, Franz R, Cochrane K, Sherriff K, Chui L, et al. The effect of a microbial ecosystem therapeutic (MET-2) on recurrent Clostridioides difficile infection: a phase 1, open-label, single-group trial. Lancet Gastroenterol Hepatol. 2021 Apr 1;6(4):282\u0026ndash;91. \u003c/li\u003e\n\u003cli\u003eRooney AM, Cochrane K, Fedsin S, Yao S, Anwer S, Dehmiwal S, et al. A microbial consortium alters intestinal Pseudomonadota and antimicrobial resistance genes in individuals with recurrent Clostridioides difficile infection. mBio. 2023 Aug 31;14(4):e0348222. \u003c/li\u003e\n\u003cli\u003ePeled JU, Gomes ALC, Devlin SM, Littmann ER, Taur Y, Sung AD, et al. Microbiota as Predictor of Mortality in Allogeneic Hematopoietic-Cell Transplantation. New England Journal of Medicine. 2020;382(9). \u003c/li\u003e\n\u003c/ol\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":true,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":false,"isAuthorSuppliedPdf":false,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"pilot-and-feasibility-studies","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"pafs","sideBox":"Learn more about [Pilot and Feasibility Studies](http://pilotfeasibilitystudies.biomedcentral.com/)","snPcode":"","submissionUrl":"https://www.editorialmanager.com/PAFS/default.aspx","title":"Pilot and Feasibility Studies","twitterHandle":"@MedicalEvidence","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"em","reportingPortfolio":"BMC/SO AJ","inReviewEnabled":true,"inReviewRevisionsEnabled":true},"keywords":"antimicrobial resistance, microbiome, microbial consortia, decolonization, antibiotic resistant infection, bacteremia","lastPublishedDoi":"10.21203/rs.3.rs-3895021/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-3895021/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003e\u003cstrong\u003eBackground:\u0026nbsp;\u003c/strong\u003eAntimicrobial resistance (AMR) is a threat to effective treatment of bacterial infections.\u003cstrong\u003e \u003c/strong\u003eGastrointestinal colonization with\u003cstrong\u003e \u003c/strong\u003ean antimicrobial resistant organism (ARO) is a risk factor for subsequent systemic infection, and increasing resistance is associated with increased infection recurrence. Patient-level interventions to decrease or minimize antimicrobial harms and reduce gastrointestinal colonization and translocation without worsening selection for AMR have tremendous potential for clinical impact. Despite the prevalence and mortality associated with bloodstream infections, there are no effective therapies for decolonization of the gut microbiome in attempts to potentially decrease the risk of recurrence. Reconstituting the perturbed microbiome is a novel therapeutic modality with the potential to decrease ARO colonization and subsequent infection and combat AMR without additional selection pressure for further AMR. No clinical trial has yet assessed the potential of a therapeutic microbial consortium for ARO decolonization and infection prevention after antibiotic treatment.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eMethods:\u0026nbsp;\u003c/strong\u003eAntimicrobial Resistant Organism Decolonization After Microbiome Perturbation (ARO-DECAMP) is a multi-centre, placebo-controlled, pilot randomized controlled feasibility trial using the microbial consortium Microbial Ecosystem Therapeutic-2. Non-intensive care unit hospitalized patients \u003cu\u003e\u0026gt;\u003c/u\u003e18 years of age receiving antibiotic treatment for a bloodstream infection caused by an ARO will be included. Participants will be randomized in a 1:1 ratio to receive either MET-2 or placebo for 10 days, with treatment initiation 2-3 days after completion of antibiotics. Participants will be followed for 180 days, and biological samples will be collected periodically for clinical, ecological, and biomarker outcomes. Recruitment rate and study intervention adherence will be evaluated for feasibility.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eDiscussion:\u0026nbsp;\u003c/strong\u003eThis study is designed to determine if a trial of administration of microbial consortia after antibiotic treatment for bloodstream infections is feasible. Results of this pilot study will inform the design and sample size of a definitive trial powered to assess the effectiveness of the intervention as a therapeutic strategy for augmenting the microbiome and improving clinical outcomes.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eTrial registration:\u0026nbsp;\u003c/strong\u003eClinicalTrials.gov, NCT06214403. 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