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Cotto C, Baker K, Fallon E, Rimon S. Fecal Microbiota, Live-jslm (RBL; REBYOTA ® ) for Prevention of Recurrent Clostridioides difficile Infection: What Gastroenterology Nurses Need to Know. Gastroenterol Nurs 2024; 47:378-382. [PMID: 39186389 DOI: 10.1097/sga.0000000000000847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 06/13/2024] [Indexed: 08/28/2024] Open
Affiliation(s)
- Candace Cotto
- Candace Cotto, RN, Medical Research Center of Connecticut, Hamden, Connecticut
- Kathy Baker, PhD, APRN, ACNS-BC, FCNS, FAAN, Texas Christian University, Harris College of Nursing & Health Sciences, Fort Worth, Texas
- Echo Fallon, PharmD, RPh, Ferring Pharmaceuticals Inc., Parsippany, New Jersey
- Sharon Rimon, MSN, FNP-BC, Reddy GI Associates, Mesa, Arizona
| | - Kathy Baker
- Candace Cotto, RN, Medical Research Center of Connecticut, Hamden, Connecticut
- Kathy Baker, PhD, APRN, ACNS-BC, FCNS, FAAN, Texas Christian University, Harris College of Nursing & Health Sciences, Fort Worth, Texas
- Echo Fallon, PharmD, RPh, Ferring Pharmaceuticals Inc., Parsippany, New Jersey
- Sharon Rimon, MSN, FNP-BC, Reddy GI Associates, Mesa, Arizona
| | - Echo Fallon
- Candace Cotto, RN, Medical Research Center of Connecticut, Hamden, Connecticut
- Kathy Baker, PhD, APRN, ACNS-BC, FCNS, FAAN, Texas Christian University, Harris College of Nursing & Health Sciences, Fort Worth, Texas
- Echo Fallon, PharmD, RPh, Ferring Pharmaceuticals Inc., Parsippany, New Jersey
- Sharon Rimon, MSN, FNP-BC, Reddy GI Associates, Mesa, Arizona
| | - Sharon Rimon
- Candace Cotto, RN, Medical Research Center of Connecticut, Hamden, Connecticut
- Kathy Baker, PhD, APRN, ACNS-BC, FCNS, FAAN, Texas Christian University, Harris College of Nursing & Health Sciences, Fort Worth, Texas
- Echo Fallon, PharmD, RPh, Ferring Pharmaceuticals Inc., Parsippany, New Jersey
- Sharon Rimon, MSN, FNP-BC, Reddy GI Associates, Mesa, Arizona
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2
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Zaidi SMH, Haider R, Kazmi SAB, Husnain A, Khan S, Merchant S, Tayyab H, Wazeen FR, Chaudhary AJ. Beyond Antibiotics: Novel Approaches in the Treatment of Recurrent Clostridioides difficile Infection. ACG Case Rep J 2024; 11:e01333. [PMID: 39081300 PMCID: PMC11286250 DOI: 10.14309/crj.0000000000001333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 03/06/2024] [Indexed: 08/02/2024] Open
Affiliation(s)
| | - Ramsha Haider
- Karachi Medical and Dental College, Karachi, Pakistan
| | | | - Ali Husnain
- Department of Medicine, King Edward Medical University, Lahore, Pakistan
| | - Saniah Khan
- Department of Medicine, King Edward Medical University, Lahore, Pakistan
| | | | - Hamnah Tayyab
- Department of Medicine, King Edward Medical University, Lahore, Pakistan
| | - Fazl Rahim Wazeen
- Department of Medicine, Greater Baltimore Medical Center, Towson, MD
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3
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Boyle BL, Khanna S. Fecal microbiota live - jslm (Rebyota™/RBL) for management of recurrent Clostridioides difficile infection. Future Microbiol 2024:1-9. [PMID: 38989699 DOI: 10.1080/17460913.2024.2364583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 06/03/2024] [Indexed: 07/12/2024] Open
Abstract
There is an unmet need for effective treatments of Clostridioides difficile infection, an emerging health crisis in the United States. The management of C. difficile infection should include treatment of active infection and a strategy to prevent recurrence. Current gold standard therapy includes oral antibiotics which predispose patients to gut dysbiosis and increase the risk of recurrent infection. Addressing dysbiosis via fecal microbiota transplantation is an active and promising area of research, but studies have lacked standardization which makes outcome and safety data difficult to interpret. Rebyota™, formerly known as RBX2660, is a live biotherapeutic product designed using a standardized protocol and manufacturing process that has been shown to be effective for preventing recurrent C. difficile infection.
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Affiliation(s)
| | - Sahil Khanna
- Division of Gastroenterology & Hepatology, Mayo Clinic, Rochester, MN 55905, USA
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4
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Quan M, Zhang X, Fang Q, Lv X, Wang X, Zong Z. Fighting against Clostridioides difficile infection: Current medications. Int J Antimicrob Agents 2024; 64:107198. [PMID: 38734214 DOI: 10.1016/j.ijantimicag.2024.107198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 04/18/2024] [Accepted: 05/04/2024] [Indexed: 05/13/2024]
Abstract
Clostridioides difficile (formerly Clostridium difficile) has been regarded as an 'urgent threat' and a significant global health problem, as life-threatening diarrhoea and refractory recurrence are common in patients with C. difficile infection (CDI). Unfortunately, the available anti-CDI drugs are limited. Recent guidelines recommend fidaxomicin and vancomycin as first-line drugs to treat CDI, bezlotoxumab to prevent recurrence, and faecal microbiota transplantation for rescue treatment. Currently, researchers are investigating therapeutic antibacterial drugs (e.g. teicoplanin, ridinilazole, ibezapolstat, surotomycin, cadazolid, and LFF571), preventive medications against recurrence (e.g. Rebyota, Vowst, VP20621, VE303, RBX7455, and MET-2), primary prevention strategies (e.g. vaccine, ribaxamase, and DAV132) and other anti-CDI medications in the preclinical stage (e.g. Raja 42, Myxopyronin B, and bacteriophage). This narrative review summarises current medications, including newly marketed drugs and products in development against CDI, to help clinicians treat CDI appropriately and to call for more research on innovation.
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Affiliation(s)
- Min Quan
- Center for Infectious Diseases, West China Hospital of Sichuan University, Chengdu, China
| | - Xiaoxia Zhang
- Center for Infectious Diseases, West China Hospital of Sichuan University, Chengdu, China
| | - Qingqing Fang
- Center for Infectious Diseases, West China Hospital of Sichuan University, Chengdu, China
| | - Xiaoju Lv
- Center for Infectious Diseases, West China Hospital of Sichuan University, Chengdu, China; Division of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, China
| | - Xiaohui Wang
- Center for Infectious Diseases, West China Hospital of Sichuan University, Chengdu, China; Division of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, China.
| | - Zhiyong Zong
- Center for Infectious Diseases, West China Hospital of Sichuan University, Chengdu, China; Division of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, China
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5
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Di Bella S, Sanson G, Monticelli J, Zerbato V, Principe L, Giuffrè M, Pipitone G, Luzzati R. Clostridioides difficile infection: history, epidemiology, risk factors, prevention, clinical manifestations, treatment, and future options. Clin Microbiol Rev 2024; 37:e0013523. [PMID: 38421181 PMCID: PMC11324037 DOI: 10.1128/cmr.00135-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024] Open
Abstract
SUMMARYClostridioides difficile infection (CDI) is one of the major issues in nosocomial infections. This bacterium is constantly evolving and poses complex challenges for clinicians, often encountered in real-life scenarios. In the face of CDI, we are increasingly equipped with new therapeutic strategies, such as monoclonal antibodies and live biotherapeutic products, which need to be thoroughly understood to fully harness their benefits. Moreover, interesting options are currently under study for the future, including bacteriophages, vaccines, and antibiotic inhibitors. Surveillance and prevention strategies continue to play a pivotal role in limiting the spread of the infection. In this review, we aim to provide the reader with a comprehensive overview of epidemiological aspects, predisposing factors, clinical manifestations, diagnostic tools, and current and future prophylactic and therapeutic options for C. difficile infection.
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Affiliation(s)
- Stefano Di Bella
- Clinical Department of
Medical, Surgical and Health Sciences, Trieste
University, Trieste,
Italy
| | - Gianfranco Sanson
- Clinical Department of
Medical, Surgical and Health Sciences, Trieste
University, Trieste,
Italy
| | - Jacopo Monticelli
- Infectious Diseases
Unit, Trieste University Hospital
(ASUGI), Trieste,
Italy
| | - Verena Zerbato
- Infectious Diseases
Unit, Trieste University Hospital
(ASUGI), Trieste,
Italy
| | - Luigi Principe
- Microbiology and
Virology Unit, Great Metropolitan Hospital
“Bianchi-Melacrino-Morelli”,
Reggio Calabria, Italy
| | - Mauro Giuffrè
- Clinical Department of
Medical, Surgical and Health Sciences, Trieste
University, Trieste,
Italy
- Department of Internal
Medicine (Digestive Diseases), Yale School of Medicine, Yale
University, New Haven,
Connecticut, USA
| | - Giuseppe Pipitone
- Infectious Diseases
Unit, ARNAS Civico-Di Cristina
Hospital, Palermo,
Italy
| | - Roberto Luzzati
- Clinical Department of
Medical, Surgical and Health Sciences, Trieste
University, Trieste,
Italy
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6
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DuPont HL, DuPont AW, Tillotson GS. Microbiota restoration therapies for recurrent Clostridioides difficile infection reach an important new milestone. Therap Adv Gastroenterol 2024; 17:17562848241253089. [PMID: 38800353 PMCID: PMC11119484 DOI: 10.1177/17562848241253089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Accepted: 04/18/2024] [Indexed: 05/29/2024] Open
Abstract
Microbiota restoration therapy has become a standard treatment for recurrent Clostridioides difficile infection (rCDI). In this article, we review the studies supporting the licensure of two live biotherapeutic products (LBPs) designed to prevent rCDI and to provide clinicians with a perspective on their differences. PubMed was reviewed on 1 October 2023, for all papers published concerning the current Food and Drug Administration allowance of the use of fecal microbiota transplantation (FMT) and the studies that led to the licensure of RBX2660 (REBYOTA™), generic name, fecal microbiota, live-jslm, and SER-109 (VOWST™), generic name, fecal microbiota spores, live-brpk. OpenBiome continues to produce fecal products for patients with rCDI at their treatment sites, and the American Gastroenterology Association has a National Registry focused on long-term safety of administering fecal microbiota products. The science behind the licensing of fecal microbiota, live-jslm, a consortium of fecal anaerobes found in stool augmented with strains of Bacteroidetes and fecal microbiota spores, live-brpk, a mixture of 50 species of purified Firmicutes spores is reviewed. Both products appear to be safe in clinical trials and effective in reducing rCDI episodes by mechanisms established for FMT, including normalization of α- and β-diversity of the microbiome and by increasing fecal secondary bile acids. The different makeup of the two LBPs suggests that rCDI responds to a variety of engrafting microbiota which explains why nearly all donors in FMT of rCDI are generally effective. Fecal microbiota, live-jslm has also been shown to successfully treat rCDI in elderly patients with advanced comorbidities. With the licensure of two novel LBPs, we are entering a new phase of microbiota replacement therapy. Having standardized manufacturing and proper monitoring of products, harnessing the microbiome to control and prevent disease has a new beginning.
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Affiliation(s)
- Herbert L. DuPont
- Infectious Diseases and Epidemiology, Department of Epidemiology, University of Texas School of Public Health, 1200 Pressler Street, Houston, TX 77030, USA
- Department of Internal Medicine, University of Texas McGovern Medical School, Houston, TX, USA
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
- Kelsey Research Foundation, Houston, TX, USA
| | - Andrew W. DuPont
- Division of Gastroenterology, University of Texas Health Science Center at Houston, Houston, TX, USA
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Obaid NA. Alternative treatment of recurrent Clostridioides difficile infection in adults by fecal transplantation: an overview of phase I-IV studies from Clinicaltrials.gov. Front Microbiol 2024; 15:1374774. [PMID: 38784794 PMCID: PMC11111976 DOI: 10.3389/fmicb.2024.1374774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 04/18/2024] [Indexed: 05/25/2024] Open
Abstract
Background Fecal microbiota transplantation (FMT) is an interventional approach to treat chronic and recurrent Clostridioides difficile infection (CDI). However, there is insufficient evidence regarding its effectiveness and safety. Clinical trials have been conducted to inspect the safety and effectiveness of FMT with and without comparison to pharmacological treatments. Aim This review explored the treatment of CDI in adults using FMT and evaluated the safety of this intervention based on phase I-IV studies registered on Clinicaltrials.gov. Method A comprehensive search of Clinicaltrials.gov was conducted to identify relevant studies that investigated CDI in adults. Data on study type, study design, sample size, intervention details, and outcomes related to FMT were examined and evaluated. Results In total, 13 clinical trials on FMT for CDI published through 17 November 2023 were identified, all of which were interventional studies. The investigation focused on both terminated and completed studies. Basic and advanced outcome measures were examined. Conclusion Some studies were terminated during phase II, and FMT was less effective than antibiotics such as vancomycin and fidaxomicin. However, colonoscopy and oral FMT were explored in several completed studies with promising results, but the evidence remains limited and inconclusive.
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Affiliation(s)
- Najla A. Obaid
- Pharmaceutical Sciences Department, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
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8
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Porcari S, Fusco W, Spivak I, Fiorani M, Gasbarrini A, Elinav E, Cammarota G, Ianiro G. Fine-tuning the gut ecosystem: the current landscape and outlook of artificial microbiome therapeutics. Lancet Gastroenterol Hepatol 2024; 9:460-475. [PMID: 38604200 DOI: 10.1016/s2468-1253(23)00357-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 10/04/2023] [Accepted: 10/10/2023] [Indexed: 04/13/2024]
Abstract
The gut microbiome is acknowledged as a key determinant of human health, and technological progress in the past two decades has enabled the deciphering of its composition and functions and its role in human disorders. Therefore, manipulation of the gut microbiome has emerged as a promising therapeutic option for communicable and non-communicable disorders. Full exploitation of current therapeutic microbiome modulators (including probiotics, prebiotics, and faecal microbiota transplantation) is hindered by several factors, including poor precision, regulatory and safety issues, and the impossibility of providing reproducible and targeted treatments. Artificial microbiota therapeutics (which include a wide range of products, such as microbiota consortia, bacteriophages, bacterial metabolites, and engineered probiotics) have appeared as an evolution of current microbiota modulators, as they promise safe and reproducible effects, with variable levels of precision via different pathways. We describe the landscape of artificial microbiome therapeutics, from those already on the market to those still in the pipeline, and outline the major challenges for positioning these therapeutics in clinical practice.
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Affiliation(s)
- Serena Porcari
- Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, Rome, Italy; UOC Gastroenterologia and UOC CEMAD Medicina Interna e Gastroenterologia, Department of Medical and Surgical Sciences, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - William Fusco
- Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, Rome, Italy; UOC Gastroenterologia and UOC CEMAD Medicina Interna e Gastroenterologia, Department of Medical and Surgical Sciences, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Igor Spivak
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel; Medical Clinic III, University Hospital Aachen, Aachen, Germany
| | - Marcello Fiorani
- Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, Rome, Italy; UOC Gastroenterologia and UOC CEMAD Medicina Interna e Gastroenterologia, Department of Medical and Surgical Sciences, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Antonio Gasbarrini
- Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, Rome, Italy; UOC Gastroenterologia and UOC CEMAD Medicina Interna e Gastroenterologia, Department of Medical and Surgical Sciences, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Eran Elinav
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel; Microbiome and Cancer Division, DKFZ, Heidelberg, Germany
| | - Giovanni Cammarota
- Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, Rome, Italy; UOC Gastroenterologia and UOC CEMAD Medicina Interna e Gastroenterologia, Department of Medical and Surgical Sciences, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Gianluca Ianiro
- Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, Rome, Italy; UOC Gastroenterologia and UOC CEMAD Medicina Interna e Gastroenterologia, Department of Medical and Surgical Sciences, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy.
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Paudel D, Nair DVT, Joseph G, Castro R, Tiwari AK, Singh V. Gastrointestinal microbiota-directed nutritional and therapeutic interventions for inflammatory bowel disease: opportunities and challenges. Gastroenterol Rep (Oxf) 2024; 12:goae033. [PMID: 38690290 PMCID: PMC11057942 DOI: 10.1093/gastro/goae033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 03/01/2024] [Accepted: 03/08/2024] [Indexed: 05/02/2024] Open
Abstract
Evidence-based research has confirmed the role of gastrointestinal microbiota in regulating intestinal inflammation. These data have generated interest in developing microbiota-based therapies for the prevention and management of inflammatory bowel disease (IBD). Despite in-depth understanding of the etiology of IBD, it currently lacks a cure and requires ongoing management. Accumulating data suggest that an aberrant gastrointestinal microbiome, often referred to as dysbiosis, is a significant environmental instigator of IBD. Novel microbiome-targeted interventions including prebiotics, probiotics, fecal microbiota transplant, and small molecule microbiome modulators are being evaluated as therapeutic interventions to attenuate intestinal inflammation by restoring a healthy microbiota composition and function. In this review, the effectiveness and challenges of microbiome-centered interventions that have the potential to alleviate intestinal inflammation and improve clinical outcomes of IBD are explored.
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Affiliation(s)
- Devendra Paudel
- Department of Nutritional Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Divek V T Nair
- Department of Nutritional Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Grace Joseph
- Department of Nutritional Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Rita Castro
- Department of Nutritional Sciences, The Pennsylvania State University, University Park, PA, USA
- Department of Pharmaceutical Sciences and Medicines, Faculty of Pharmacy, Universidade de Lisboa, Lisboa, Portugal
| | - Amit K Tiwari
- College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Vishal Singh
- Department of Nutritional Sciences, The Pennsylvania State University, University Park, PA, USA
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Oneto C, Khanna S. Prescription Microbiome Therapeutic for Recurrent Clostridioides difficile Infection: Fecal Microbiota Live-jslm. Am J Gastroenterol 2024; 119:S16-S21. [PMID: 38153221 DOI: 10.14309/ajg.0000000000002577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 10/22/2023] [Indexed: 12/29/2023]
Affiliation(s)
| | - Sahil Khanna
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA
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11
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McMillan AS, Theriot CM. Bile acids impact the microbiota, host, and C. difficile dynamics providing insight into mechanisms of efficacy of FMTs and microbiota-focused therapeutics. Gut Microbes 2024; 16:2393766. [PMID: 39224076 PMCID: PMC11376424 DOI: 10.1080/19490976.2024.2393766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 08/12/2024] [Accepted: 08/13/2024] [Indexed: 09/04/2024] Open
Abstract
Clostridioides difficile is a major nosocomial pathogen, causing significant morbidity and mortality worldwide. Antibiotic usage, a major risk factor for Clostridioides difficile infection (CDI), disrupts the gut microbiota, allowing C. difficile to proliferate and cause infection, and can often lead to recurrent CDI (rCDI). Fecal microbiota transplantation (FMT) and live biotherapeutic products (LBPs) have emerged as effective treatments for rCDI and aim to restore colonization resistance provided by a healthy gut microbiota. However, much is still unknown about the mechanisms mediating their success. Bile acids, extensively modified by gut microbes, affect C. difficile's germination, growth, and toxin production while also shaping the gut microbiota and influencing host immune responses. Additionally, microbial interactions, such as nutrient competition and cross-feeding, contribute to colonization resistance against C. difficile and may contribute to the success of microbiota-focused therapeutics. Bile acids as well as other microbial mediated interactions could have implications for other diseases being treated with microbiota-focused therapeutics. This review focuses on the intricate interplay between bile acid modifications, microbial ecology, and host responses with a focus on C. difficile, hoping to shed light on how to move forward with the development of new microbiota mediated therapeutic strategies to combat rCDI and other intestinal diseases.
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Affiliation(s)
- Arthur S. McMillan
- Genetics Program, Department of Biological Sciences, College of Science, North Carolina State University, Raleigh, NC, USA
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
| | - Casey M. Theriot
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
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12
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Lee C, Louie T, Bancke L, Guthmueller B, Harvey A, Feuerstadt P, Khanna S, Orenstein R, Dubberke ER. Safety of fecal microbiota, live-jslm (REBYOTA ™) in individuals with recurrent Clostridioides difficile infection: data from five prospective clinical trials. Therap Adv Gastroenterol 2023; 16:17562848231174277. [PMID: 37333464 PMCID: PMC10272687 DOI: 10.1177/17562848231174277] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 04/06/2023] [Indexed: 06/20/2023] Open
Abstract
Background Microbiota-based treatments reduce the incidence of recurrent Clostridioides difficile infections (rCDIs), but prospectively collected safety data needed to broaden patient access and protect public health have been limited. Objectives We provide cumulative safety data from five prospective clinical trials evaluating fecal microbiota, live-jslm (RBL) - the first microbiota-based live biotherapeutic product approved by the US Food and Drug Administration - for preventing rCDI in adults. Design Integrated safety analysis includes three phase II trials (PUNCH CD, PUNCH CD2, PUNCH Open-Label) and two phase III trials (PUNCH CD3, PUNCH CD3-OLS) of RBL. Methods Trial participants were at least 18 years of age with documented rCDI who completed standard-of-care antibiotic therapy before treatment with RBL. Assigned study treatment regimen was one or two doses of RBL (or placebo) administered rectally, depending on the trial design. In four of the five trials, participants with CDI recurrence within 8 weeks after RBL or placebo administration were eligible for treatment with open-label RBL. Treatment-emergent adverse events (TEAEs) were recorded for at least 6 months following last study treatment; in PUNCH CD2 and PUNCH Open-Label trials, TEAEs and serious TEAEs were collected through 12 and 24 months, respectively. Results Among the five trials, 978 participants received at least one dose of RBL (assigned treatment or after recurrence) and 83 participants received placebo only. TEAEs were reported in 60.2% of Placebo Only participants and 66.4% of RBL Only participants. Only abdominal pain, nausea, and flatulence were significantly higher in the RBL Only group compared with the Placebo Only group. Most TEAEs were mild or moderate in severity and were most frequently related to preexisting conditions. There were no reported infections for which the causative pathogen was traced to RBL. Potentially life-threatening TEAEs were infrequent (3.0% of participants). Conclusion Across five clinical trials, RBL was well tolerated in adults with rCDI. In aggregate, these data consistently demonstrated the safety of RBL.
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Affiliation(s)
- Christine Lee
- Medical Microbiologist and Researcher, Island Health, Clinical Professor, Department of Pathology and Laboratory Medicine, The University of British Columbia Faculty of Medicine, Vancouver, BC V6T 1Z3, Canada
- Island Medical Program University of British Columbia, University of Victoria, Victoria, BC, Canada
| | - Thomas Louie
- University of Calgary and Foothills Medical Center, Calgary, AB, Canada
| | - Lindy Bancke
- Rebiotix Inc., a Ferring Company, Roseville, MN, USA
| | | | - Adam Harvey
- Rebiotix Inc., a Ferring Company, Roseville, MN, USA
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13
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Gray AN, DeFilipp Z. Fecal Microbiota Transplantation for Acute Graft-versus-Host Disease After Allogeneic Hematopoietic Cell Transplantation: Expanding the Horizon into Pediatrics. Transplant Cell Ther 2023:S2666-6367(23)01289-7. [PMID: 37169290 DOI: 10.1016/j.jtct.2023.05.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 05/02/2023] [Accepted: 05/05/2023] [Indexed: 05/13/2023]
Abstract
The microbiome plays a vital role in maintaining homeostasis of the intestinal microenvironment and immune response in allogeneic hematopoietic cell transplantation (HCT) recipients. Disruption of the intestinal microbiome has been associated with the development of acute graft-versus-host disease (GVHD) of the lower GI tract and worse survival. Fecal microbiota transplantation (FMT) can achieve clinical responses in refractory GVHD, establishing the promise of microbiome-directed interventions in this population. While most data about microbial changes in HCT recipients have been generated from the adult population, children with refractory GVHD represent an important group that may benefit from FMT. In this review, we first highlight characteristics that distinguish the pediatric intestinal microbiome from adults. Subsequently, we explore multiple clinical factors that warrant careful consideration to optimize the application of FMT and other microbiome-directed therapeutics to children.
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Affiliation(s)
- Ashley N Gray
- Children's Hospital Los Angeles, Children's Center for Cancer and Blood Diseases, Division of Hematology, Oncology and Blood & Marrow Transplantation, Los Angeles, CA, USA.
| | - Zachariah DeFilipp
- Hematopoieitic Cell Transplant and Cell Therapy Program, Massachusetts General Hospital, Boston, MA
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14
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Javed QUA, Afzal M, Ilyas K, Sarfraz A, Sarfraz Z. Treatment efficacy of fecal microbiota-based live biotherapeutics (RBX2660) for the prevention of recurring Clostridioides difficile infection. Eur J Intern Med 2023; 111:130-132. [PMID: 36581474 DOI: 10.1016/j.ejim.2022.12.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 12/19/2022] [Accepted: 12/22/2022] [Indexed: 12/29/2022]
Affiliation(s)
| | - Muhammad Afzal
- University College of Medicine & Dentistry, Lahore, Pakistan
| | - Khola Ilyas
- Faisalabad Medical University, Faisalabad, Pakistan
| | | | - Zouina Sarfraz
- Research & Publications, Fatima Jinnah Medical University, Lahore 54000, Pakistan.
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15
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Chakaroun RM, Olsson LM, Bäckhed F. The potential of tailoring the gut microbiome to prevent and treat cardiometabolic disease. Nat Rev Cardiol 2023; 20:217-235. [PMID: 36241728 DOI: 10.1038/s41569-022-00771-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/05/2022] [Indexed: 12/12/2022]
Abstract
Despite milestones in preventive measures and treatment, cardiovascular disease (CVD) remains associated with a high burden of morbidity and mortality. The protracted nature of the development and progression of CVD motivates the identification of early and complementary targets that might explain and alleviate any residual risk in treated patients. The gut microbiota has emerged as a sentinel between our inner milieu and outer environment and relays a modified risk associated with these factors to the host. Accordingly, numerous mechanistic studies in animal models support a causal role of the gut microbiome in CVD via specific microbial or shared microbiota-host metabolites and have identified converging mammalian targets for these signals. Similarly, large-scale cohort studies have repeatedly reported perturbations of the gut microbial community in CVD, supporting the translational potential of targeting this ecological niche, but the move from bench to bedside has not been smooth. In this Review, we provide an overview of the current evidence on the interconnectedness of the gut microbiome and CVD against the noisy backdrop of highly prevalent confounders in advanced CVD, such as increased metabolic burden and polypharmacy. We further aim to conceptualize the molecular mechanisms at the centre of these associations and identify actionable gut microbiome-based targets, while contextualizing the current knowledge within the clinical scenario and emphasizing the limitations of the field that need to be overcome.
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Affiliation(s)
- Rima Mohsen Chakaroun
- The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
| | - Lisa M Olsson
- The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Fredrik Bäckhed
- The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
- Region Västra Götaland, Sahlgrenska University Hospital, Department of Clinical Physiology, Gothenburg, Sweden.
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
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16
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Chopra T. A profile of the live biotherapeutic product RBX2660 and its role in preventing recurrent Clostridioides difficile infection. Expert Rev Anti Infect Ther 2023; 21:243-253. [PMID: 36756869 DOI: 10.1080/14787210.2023.2171986] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
INTRODUCTION Clostridiodes difficile infection (CDI) is a life-threatening illness that has been labelled as an urgent threat by the Centers for Disease prevention (CDC). AREAS COVERED RBX2660, a live biotherapeutic product offers a very promising treatment option for patients with recurrent Clostridiodes difficile infection(rCDI). RBX2660 restores the healthy gut microbiome and shows clinically meaningful benefits for patients suffering from rCDI. Safety, efficacy, and tolerability of RBX2660 have been thoroughly assessed . EXPERT OPINION An FDA-approved, standardized, and accessible microbiota restoration product like RBX2660 would provide a new option for patients in need of treatment for rCDI by breaking the cycle of disease recurrence.
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Affiliation(s)
- Teena Chopra
- Division of Infectious Diseases. Corporate Medical Director, Infection Prevention, Epidemiology, and Antibiotic Stewardship, Detroit Medical Center and Wayne State University, Detroit, Michigan, USA
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17
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Emerging Options for the Prevention and Management of Clostridioides difficile Infection. Drugs 2023; 83:105-116. [PMID: 36645620 PMCID: PMC9841950 DOI: 10.1007/s40265-022-01832-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/20/2022] [Indexed: 01/17/2023]
Abstract
Agents in development for the prevention or treatment of Clostridioides difficile infection can be split into three broad categories: antibiotics, microbiome restoration, and vaccines. Given the extensive list of agents currently in development, this narrative review will focus on agents that have progressed into late-stage clinical trials, defined as having a Phase III clinical trial registered on ClinicalTrials.gov. These agents include one antibiotic (ridinilazole), three live biotherapeutic products (LBPs) (CP101, RBX2660, and SER109), and two toxoid vaccines (PF06425090 and a second toxoid vaccine). As new prevention and treatment strategies enter the market, clinicians and administrators will need knowledge of these products to make rational decisions on how best to adopt them into clinical practice.
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18
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Human Fecal Bile Acid Analysis after Investigational Microbiota-Based Live Biotherapeutic Delivery for Recurrent Clostridioides difficile Infection. Microorganisms 2023; 11:microorganisms11010135. [PMID: 36677428 PMCID: PMC9865816 DOI: 10.3390/microorganisms11010135] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/28/2022] [Accepted: 12/29/2022] [Indexed: 01/06/2023] Open
Abstract
Microbiome-based therapeutics are increasingly evaluated as a strategy to reduce recurrent Clostridioides difficile infection (rCDI), with proposed mechanisms including restoration of the microbiota and microbiota-mediated functions, such as bile acid (BA) metabolism. This study reports a quantitative and sensitive assay for targeted metabolomic assessment, and the application of the assay to profile BA composition in a Phase 2 trial of the investigational microbiota-based live biotherapeutic RBX2660 for reduction of rCDI. A liquid chromatography tandem mass spectrometry method was developed to extract and quantify 35 BAs from 113 participant stool samples from 27 RBX2660-treated rCDI participants in the double-blinded, placebo-controlled clinical trial. The results demonstrate a high-confidence assay as represented by sensitivity, linearity, accuracy, and precision. Furthermore, the assay enabled the observation of primary BAs as the dominant BA species at baseline in stool samples from clinical trial participants, consistent with the expected loss of commensals after broad-spectrum antibiotic treatment. After RBX2660 administration, there was a significant drop in primary BAs concurrent with increased secondary BAs that sustained through 24 months post-RBX2660. Taken together, we describe a robust assay that demonstrates altered BA metabolism in rCDI patients treated with RBX2660 administration.
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19
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Gonzales-Luna AJ, Carlson TJ, Garey KW. Gut microbiota changes associated with Clostridioides difficile infection and its various treatment strategies. Gut Microbes 2023; 15:2223345. [PMID: 37318134 DOI: 10.1080/19490976.2023.2223345] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 06/01/2023] [Accepted: 06/05/2023] [Indexed: 06/16/2023] Open
Abstract
Human gut microbiota are critical to both the development of and recovery from Clostridioides difficile infection (CDI). Antibiotics are the mainstay of CDI treatment, yet inherently cause further imbalances in the gut microbiota, termed dysbiosis, complicating recovery. A variety of microbiota-based therapeutic approaches are in use or in development to limit disease- and treatment-associated dysbiosis and improve rates of sustained cure. These include the recently FDA-approved fecal microbiota, live-jslm (formerly RBX2660) and fecal microbiota spores, live-brpk (formerly SER-109), which represent a new class of live biotherapeutic products (LBPs), traditional fecal microbiota transplantation (FMT), and ultra-narrow-spectrum antibiotics. Here, we aim to review the microbiome changes associated with CDI as well as a variety of microbiota-based treatment approaches.
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Affiliation(s)
- Anne J Gonzales-Luna
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, TX, USA
| | - Travis J Carlson
- Department of Clinical Sciences, High Point University Fred Wilson School of Pharmacy, High Point, NC, USA
| | - Kevin W Garey
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, TX, USA
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20
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SER-109: An Oral Investigational Microbiome Therapeutic for Patients with Recurrent Clostridioides difficile Infection (rCDI). Antibiotics (Basel) 2022; 11:antibiotics11091234. [PMID: 36140013 PMCID: PMC9495252 DOI: 10.3390/antibiotics11091234] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/07/2022] [Accepted: 09/08/2022] [Indexed: 11/16/2022] Open
Abstract
Clostridioides difficile infection (CDI) is classified as an urgent health threat by the Centers for Disease Control and Prevention (CDC), and affects nearly 500,000 Americans annually. Approximately 20−25% of patients with a primary infection experience a recurrence, and the risk of recurrence increases with subsequent episodes to greater than 40%. The leading risk factor for CDI is broad-spectrum antibiotics, which leads to a loss of microbial diversity and impaired colonization resistance. Current FDA-approved CDI treatment strategies target toxin or toxin-producing bacteria, but do not address microbiome disruption, which is key to the pathogenesis of recurrent CDI. Fecal microbiota transplantation (FMT) reduces the risk of recurrent CDI through the restoration of microbial diversity. However, FDA safety alerts describing hospitalizations and deaths related to pathogen transmission have raised safety concerns with the use of unregulated and unstandardized donor-derived products. SER-109 is an investigational oral microbiome therapeutic composed of purified spore-forming Firmicutes. SER-109 was superior to a placebo in reducing CDI recurrence at Week 8 (12% vs. 40%, respectively; p < 0.001) in adults with a history of recurrent CDI with a favorable observed safety profile. Here, we discuss the role of the microbiome in CDI pathogenesis and the clinical development of SER-109, including its rigorous manufacturing process, which mitigates the risk of pathogen transmission. Additionally, we discuss compositional and functional changes in the gastrointestinal microbiome in patients with recurrent CDI following treatment with SER-109 that are critical to a sustained clinical response.
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21
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Rakotonirina A, Galperine T, Allémann E. Fecal microbiota transplantation: a review on current formulations in Clostridioides difficile infection and future outlooks. Expert Opin Biol Ther 2022; 22:929-944. [PMID: 35763604 DOI: 10.1080/14712598.2022.2095901] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION The role of the gut microbiota in health and the pathogenesis of several diseases has been highlighted in recent years. Even though the precise mechanisms involving the microbiome in these ailments are still unclear, microbiota-modulating therapies have been developed. Fecal microbiota transplantation (FMT) has shown significant results against Clostridioides difficile infection (CDI), and its potential has been investigated for other diseases. Unfortunately, the technical aspects of the treatment make it difficult to implement. Pharmaceutical technology approaches to encapsulate microorganisms could play an important role in providing this treatment and render the treatment modalities easier to handle. AREAS COVERED After an overview of CDI, this narrative review aims to discuss the current formulations for FMT and specifically addresses the technical aspects of the treatment. This review also distinguishes itself by focusing on the hurdles and emphasizing the possible improvements using pharmaceutical technologies. EXPERT OPINION FMT is an efficient treatment for recurrent CDI. However, its standardization is overlooked. The approach of industrial and hospital preparations of FMT are different, but both show promise in their respective methodologies. Novel FMT formulations could enable further research on dysbiotic diseases in the future.
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Affiliation(s)
- Adèle Rakotonirina
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland.,Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
| | - Tatiana Galperine
- Infectious Diseases Service, Department of Medicine, University Hospital and University of Lausanne, Lausanne, Switzerland.,French Group of Faecal Microbiota Transplantation
| | - Eric Allémann
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland.,Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
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22
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Wensel CR, Pluznick JL, Salzberg SL, Sears CL. Next-generation sequencing: insights to advance clinical investigations of the microbiome. J Clin Invest 2022; 132:e154944. [PMID: 35362479 PMCID: PMC8970668 DOI: 10.1172/jci154944] [Citation(s) in RCA: 135] [Impact Index Per Article: 67.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Next-generation sequencing (NGS) technology has advanced our understanding of the human microbiome by allowing for the discovery and characterization of unculturable microbes with prediction of their function. Key NGS methods include 16S rRNA gene sequencing, shotgun metagenomic sequencing, and RNA sequencing. The choice of which NGS methodology to pursue for a given purpose is often unclear for clinicians and researchers. In this Review, we describe the fundamentals of NGS, with a focus on 16S rRNA and shotgun metagenomic sequencing. We also discuss pros and cons of each methodology as well as important concepts in data variability, study design, and clinical metadata collection. We further present examples of how NGS studies of the human microbiome have advanced our understanding of human disease pathophysiology across diverse clinical contexts, including the development of diagnostics and therapeutics. Finally, we share insights as to how NGS might further be integrated into and advance microbiome research and clinical care in the coming years.
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Affiliation(s)
| | - Jennifer L. Pluznick
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Steven L. Salzberg
- Department of Biomedical Engineering
- Department of Computer Science, and
- Department of Biostatistics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Cynthia L. Sears
- Department of Medicine and
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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23
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Orenstein R, Dubberke ER, Khanna S, Lee CH, Yoho D, Johnson S, Hecht G, DuPont HL, Gerding DN, Blount KF, Mische S, Harvey A. Durable reduction of Clostridioides difficile infection recurrence and microbiome restoration after treatment with RBX2660: results from an open-label phase 2 clinical trial. BMC Infect Dis 2022; 22:245. [PMID: 35279084 PMCID: PMC8917640 DOI: 10.1186/s12879-022-07256-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 02/14/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Effective treatment options for recurrent Clostridioides difficile infection (rCDI) are limited, with high recurrence rates associated with the current standard of care. Herein we report results from an open-label Phase 2 trial to evaluate the safety, efficacy, and durability of RBX2660—a standardized microbiota-based investigational live biotherapeutic—and a closely-matched historical control cohort.
Methods
This prospective, multicenter, open-label Phase 2 study enrolled patients who had experienced either ≥ 2 recurrences of CDI, treated by standard-of-care antibiotic therapy, after a primary CDI episode, or ≥ 2 episodes of severe CDI requiring hospitalization. Participants received up to 2 doses of RBX2660 rectally administered with doses 7 days apart. Treatment success was defined as the absence of CDI diarrhea without the need for retreatment for 8 weeks after completing study treatment. A historical control group with matched inclusion and exclusion criteria was identified from a retrospective chart review of participants treated with standard-of-care antibiotics for recurrent CDI who matched key criteria for the study. The primary objective was to compare treatment success of RBX2660 to the historical control group. A key secondary outcome was the safety profile of RBX2660, including adverse events and CDI occurrence through 24 months after treatment. In addition, fecal samples from RBX2660-treated participants were sequenced to evaluate microbiome composition and functional changes from before to after treatment.
Results
In this Phase 2 open-label clinical trial, RBX2660 demonstrated a 78.9% (112/142) treatment success rate compared to a 30.7% (23/75) for the historical control group (p < 0.0001; Chi-square test). Post-hoc analysis indicated that 91% (88/97) of evaluable RBX2660 responders remained CDI occurrence-free to 24 months after treatment demonstrating durability. RBX2660 was well-tolerated with mostly mild to moderate adverse events. The composition and diversity of RBX2660 responders’ fecal microbiome significantly changed from before to after treatment to become more similar to RBX2660, and these changes were durable to 24 months after treatment.
Conclusions
In this Phase 2 trial, RBX2660 was safe and effective for reducing rCDI recurrence as compared to a historical control group. Microbiome changes are consistent with restorative changes implicated in resisting C. difficile recurrence.
Clinical Trials Registration NCT02589847 (10/28/2015)
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24
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Current clinical translation of microbiome medicines. Trends Pharmacol Sci 2022; 43:281-292. [DOI: 10.1016/j.tips.2022.02.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 02/01/2022] [Accepted: 02/02/2022] [Indexed: 12/17/2022]
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25
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Blount K, Jones C, Walsh D, Gonzalez C, Shannon WD. Development and Validation of a Novel Microbiome-Based Biomarker of Post-antibiotic Dysbiosis and Subsequent Restoration. Front Microbiol 2022; 12:781275. [PMID: 35058900 PMCID: PMC8764365 DOI: 10.3389/fmicb.2021.781275] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 11/18/2021] [Indexed: 11/23/2022] Open
Abstract
Background: The human gut microbiota are important to health and wellness, and disrupted microbiota homeostasis, or “dysbiosis,” can cause or contribute to many gastrointestinal disease states. Dysbiosis can be caused by many factors, most notably antibiotic treatment. To correct dysbiosis and restore healthier microbiota, several investigational microbiota-based live biotherapeutic products (LBPs) are in formal clinical development. To better guide and refine LBP development and to better understand and manage the risks of antibiotic administration, biomarkers that distinguish post-antibiotic dysbiosis from healthy microbiota are needed. Here we report the development of a prototype Microbiome Health Index for post-Antibiotic dysbiosis (MHI-A). Methods: MHI-A was developed and validated using longitudinal gut microbiome data from participants in clinical trials of RBX2660 and RBX7455 – investigational LBPs in development for reducing recurrent Clostridioides difficile infections (rCDI). The MHI-A algorithm relates the relative abundances of microbiome taxonomic classes that changed the most after RBX2660 or RBX7455 treatment, that strongly correlated with clinical response, and that reflect biological mechanisms believed important to rCDI. The diagnostic utility of MHI-A was reinforced using publicly available microbiome data from healthy or antibiotic-treated populations. Results: MHI-A has high accuracy to distinguish post-antibiotic dysbiosis from healthy microbiota. MHI-A values were consistent across multiple healthy populations and were significantly shifted by antibiotic treatments known to alter microbiota compositions, shifted less by microbiota-sparing antibiotics. Clinical response to RBX2660 and RBX7455 correlated with a shift of MHI-A from dysbiotic to healthy values. Conclusion: MHI-A is a promising biomarker of post-antibiotic dysbiosis and subsequent restoration. MHI-A may be useful for rank-ordering the microbiota-disrupting effects of antibiotics and as a pharmacodynamic measure of microbiota restoration.
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Affiliation(s)
- Ken Blount
- Rebiotix Inc., a Ferring Company, Roseville, MN, United States
| | - Courtney Jones
- Rebiotix Inc., a Ferring Company, Roseville, MN, United States
| | - Dana Walsh
- Rebiotix Inc., a Ferring Company, Roseville, MN, United States
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26
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Abstract
Symbiotic microorganisms inhabiting the gastrointestinal tract promote health by decreasing susceptibility to infection and enhancing resistance to a range of diseases. In this Review, we discuss our increasing understanding of the impact of the microbiome on the mammalian host and recent efforts to culture and characterize intestinal symbiotic microorganisms that produce or modify metabolites that impact disease pathology. Manipulation of the intestinal microbiome has great potential to reduce the incidence and/or severity of a wide range of human conditions and diseases, and the biomedical research community now faces the challenge of translating our understanding of the microbiome into beneficial medical therapies. Our increasing understanding of symbiotic microbial species and the application of ecological principles and machine learning are providing exciting opportunities for microbiome-based therapeutics to progress from faecal microbiota transplantation to the administration of precisely defined and clinically validated symbiotic microbial consortia that optimize disease resistance.
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27
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Schupack DA, Mars RAT, Voelker DH, Abeykoon JP, Kashyap PC. The promise of the gut microbiome as part of individualized treatment strategies. Nat Rev Gastroenterol Hepatol 2022; 19:7-25. [PMID: 34453142 PMCID: PMC8712374 DOI: 10.1038/s41575-021-00499-1] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/14/2021] [Indexed: 02/07/2023]
Abstract
Variability in disease presentation, progression and treatment response has been a central challenge in medicine. Although variability in host factors and genetics are important, it has become evident that the gut microbiome, with its vast genetic and metabolic diversity, must be considered in moving towards individualized treatment. In this Review, we discuss six broad disease groups: infectious disease, cancer, metabolic disease, cardiovascular disease, autoimmune or inflammatory disease, and allergic and atopic diseases. We highlight current knowledge on the gut microbiome in disease pathogenesis and prognosis, efficacy, and treatment-related adverse events and its promise for stratifying existing treatments and as a source of novel therapies. The Review is not meant to be comprehensive for each disease state but rather highlights the potential implications of the microbiome as a tool to individualize treatment strategies in clinical practice. Although early, the outlook is optimistic but challenges need to be overcome before clinical implementation, including improved understanding of underlying mechanisms, longitudinal studies with multiple data layers reflecting gut microbiome and host response, standardized approaches to testing and reporting, and validation in larger cohorts. Given progress in the microbiome field with concurrent basic and clinical studies, the microbiome will likely become an integral part of clinical care within the next decade.
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Affiliation(s)
- Daniel A Schupack
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Ruben A T Mars
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Dayne H Voelker
- Division of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Jithma P Abeykoon
- Division of Hematology and Oncology, Mayo Clinic, Rochester, MN, USA
| | - Purna C Kashyap
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA.
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA.
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28
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Jones-Freeman B, Chonwerawong M, Marcelino VR, Deshpande AV, Forster SC, Starkey MR. The microbiome and host mucosal interactions in urinary tract diseases. Mucosal Immunol 2021; 14:779-792. [PMID: 33542492 DOI: 10.1038/s41385-020-00372-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 12/03/2020] [Indexed: 02/06/2023]
Abstract
The urinary tract consists of the bladder, ureters, and kidneys, and is an essential organ system for filtration and excretion of waste products and maintaining systemic homeostasis. In this capacity, the urinary tract is impacted by its interactions with other mucosal sites, including the genitourinary and gastrointestinal systems. Each of these sites harbors diverse ecosystems of microbes termed the microbiota, that regulates complex interactions with the local and systemic immune system. It remains unclear whether changes in the microbiota and associated metabolites may be a consequence or a driver of urinary tract diseases. Here, we review the current literature, investigating the impact of the microbiota on the urinary tract in homeostasis and disease including urinary stones, acute kidney injury, chronic kidney disease, and urinary tract infection. We propose new avenues for exploration of the urinary microbiome using emerging technology and discuss the potential of microbiome-based medicine for urinary tract conditions.
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Affiliation(s)
- Bernadette Jones-Freeman
- Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Michelle Chonwerawong
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia.,Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, Australia
| | - Vanessa R Marcelino
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia.,Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, Australia
| | - Aniruddh V Deshpande
- Priority Research Centre GrowUpWell, Faculty of Health and Medicine, The University of Newcastle, Callaghan, NSW, Australia.,Department of Pediatric Urology and Surgery, John Hunter Children's Hospital, New Lambton Heights, NSW, Australia.,Urology Unit, Department of Pediatric Surgery, Children's Hospital at Westmead, Sydney Children's Hospital Network, Westmead, NSW, Australia
| | - Samuel C Forster
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia.,Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, Australia
| | - Malcolm R Starkey
- Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, VIC, Australia. .,Priority Research Centre GrowUpWell, Faculty of Health and Medicine, The University of Newcastle, Callaghan, NSW, Australia.
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29
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Tortajada-Girbés M, Rivas A, Hernández M, González A, Ferrús MA, Pina-Pérez MC. Alimentary and Pharmaceutical Approach to Natural Antimicrobials against Clostridioides difficile Gastrointestinal Infection. Foods 2021; 10:foods10051124. [PMID: 34069413 PMCID: PMC8159093 DOI: 10.3390/foods10051124] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 05/08/2021] [Accepted: 05/16/2021] [Indexed: 02/07/2023] Open
Abstract
Incidence of Clostridioides difficile infection (CDI) has been increasing in recent decades due to different factors, namely (i) extended use of broad-spectrum antibiotics, (ii) transmission within asymptomatic and susceptible patients, and (iii) unbalanced gastrointestinal microbiome and collateral diseases that favor C. difficile gastrointestinal domination and toxin production. Although antibiotic therapies have resulted in successful control of CDI in the last 20 years, the development of novel strategies is urged in order to combat the capability of C. difficile to generate and acquire resistance to conventional treatments and its consequent proliferation. In this regard, vegetable and marine bioactives have emerged as alternative and effective molecules to fight against this concerning pathogen. The present review examines the effectiveness of natural antimicrobials from vegetable and algae origin that have been used experimentally in in vitro and in vivo settings to prevent and combat CDI. The aim of the present work is to contribute to accurately describe the prospective use of emerging antimicrobials as future nutraceuticals and preventive therapies, namely (i) as dietary supplement to prevent CDI and reduce CDI recurrence by means of microbiota modulation and (ii) administering them complementarily to other treatments requiring antibiotics to prevent C. difficile gut invasion and infection progression.
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Affiliation(s)
- Miguel Tortajada-Girbés
- Department of Pediatrics, University Dr. Peset Hospital, Avda, de Gaspar Aguilar, 90, 46017 Valencia, Spain;
| | - Alejandro Rivas
- Departmento Tecnología de Alimentos, Escuela Técnica Superior de Ingeniería Agronómica y del Medio Natural (ETSIAMN), Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain;
| | - Manuel Hernández
- Departmento Biotecnología, Escuela Técnica Superior de Ingeniería Agronómica y del Medio Natural (ETSIAMN), Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain; (M.H.); (A.G.); (M.A.F.)
| | - Ana González
- Departmento Biotecnología, Escuela Técnica Superior de Ingeniería Agronómica y del Medio Natural (ETSIAMN), Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain; (M.H.); (A.G.); (M.A.F.)
| | - Maria A. Ferrús
- Departmento Biotecnología, Escuela Técnica Superior de Ingeniería Agronómica y del Medio Natural (ETSIAMN), Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain; (M.H.); (A.G.); (M.A.F.)
| | - Maria C. Pina-Pérez
- Departmento Microbiologia y Ecología, Facultad Ciencias Biológicas, Universitat de València, C/Dr. Moliner, 50, 46100 Burjassot, Spain
- Correspondence:
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Wang LL, Janes ME, Kumbhojkar N, Kapate N, Clegg JR, Prakash S, Heavey MK, Zhao Z, Anselmo AC, Mitragotri S. Cell therapies in the clinic. Bioeng Transl Med 2021; 6:e10214. [PMID: 34027097 PMCID: PMC8126820 DOI: 10.1002/btm2.10214] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/30/2021] [Accepted: 02/09/2021] [Indexed: 12/16/2022] Open
Abstract
Cell therapies have emerged as a promising therapeutic modality with the potential to treat and even cure a diverse array of diseases. Cell therapies offer unique clinical and therapeutic advantages over conventional small molecules and the growing number of biologics. Particularly, living cells can simultaneously and dynamically perform complex biological functions in ways that conventional drugs cannot; cell therapies have expanded the spectrum of available therapeutic options to include key cellular functions and processes. As such, cell therapies are currently one of the most investigated therapeutic modalities in both preclinical and clinical settings, with many products having been approved and many more under active clinical investigation. Here, we highlight the diversity and key advantages of cell therapies and discuss their current clinical advances. In particular, we review 28 globally approved cell therapy products and their clinical use. We also analyze >1700 current active clinical trials of cell therapies, with an emphasis on discussing their therapeutic applications. Finally, we critically discuss the major biological, manufacturing, and regulatory challenges associated with the clinical translation of cell therapies.
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Affiliation(s)
- Lily Li‐Wen Wang
- John A. Paulson School of Engineering & Applied SciencesHarvard UniversityCambridgeMassachusettsUSA
- Wyss Institute for Biologically Inspired EngineeringBostonMassachusettsUSA
- Harvard‐MIT Division of Health Sciences and Technology, Massachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Morgan E. Janes
- John A. Paulson School of Engineering & Applied SciencesHarvard UniversityCambridgeMassachusettsUSA
- Wyss Institute for Biologically Inspired EngineeringBostonMassachusettsUSA
- Harvard‐MIT Division of Health Sciences and Technology, Massachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Ninad Kumbhojkar
- John A. Paulson School of Engineering & Applied SciencesHarvard UniversityCambridgeMassachusettsUSA
- Wyss Institute for Biologically Inspired EngineeringBostonMassachusettsUSA
| | - Neha Kapate
- John A. Paulson School of Engineering & Applied SciencesHarvard UniversityCambridgeMassachusettsUSA
- Wyss Institute for Biologically Inspired EngineeringBostonMassachusettsUSA
- Harvard‐MIT Division of Health Sciences and Technology, Massachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - John R. Clegg
- John A. Paulson School of Engineering & Applied SciencesHarvard UniversityCambridgeMassachusettsUSA
- Wyss Institute for Biologically Inspired EngineeringBostonMassachusettsUSA
| | - Supriya Prakash
- John A. Paulson School of Engineering & Applied SciencesHarvard UniversityCambridgeMassachusettsUSA
- Wyss Institute for Biologically Inspired EngineeringBostonMassachusettsUSA
| | - Mairead K. Heavey
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of PharmacyUniversity of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
| | - Zongmin Zhao
- John A. Paulson School of Engineering & Applied SciencesHarvard UniversityCambridgeMassachusettsUSA
- Wyss Institute for Biologically Inspired EngineeringBostonMassachusettsUSA
| | - Aaron C. Anselmo
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of PharmacyUniversity of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
| | - Samir Mitragotri
- John A. Paulson School of Engineering & Applied SciencesHarvard UniversityCambridgeMassachusettsUSA
- Wyss Institute for Biologically Inspired EngineeringBostonMassachusettsUSA
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Mehta SR, Yen EF. Microbiota-based Therapies Clostridioides difficile infection that is refractory to antibiotic therapy. Transl Res 2021; 230:197-207. [PMID: 33278650 DOI: 10.1016/j.trsl.2020.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 11/05/2020] [Accepted: 11/29/2020] [Indexed: 11/27/2022]
Abstract
Clostridioides difficile infection (CDI) has had a devastating impact worldwide with significant rates of mortality, especially among the elderly. Despite effective antibiotics, the incidence of recurrent CDI (rCDI) is increasing and more difficult to treat with antibiotics alone. Fecal Microbiota Transplantation (FMT) has emerged as a consistently effective treatment for rCDI. Mechanisms for FMT are not entirely understood, but remain an area of active investigation. There have been recent safety reports with the use of FMT regarding transmission of pathogens in a few patients that have led to serious illness. With appropriate screening, FMT can be safely administered and continue to have a significant impact on eradication of rCDI and improve the lives of patients suffering from this disease. In this review, we summarize current treatments for CDI with a focus on microbiota-based therapies used for antibiotic refractory disease.
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Affiliation(s)
- Shama R Mehta
- NorthShore University HealthSystem, Division of Gastroenterology, 2650 Ridge Avenue, Suite G221, Evanston, IL 60201
| | - Eugene F Yen
- NorthShore University HealthSystem, Division of Gastroenterology, 2650 Ridge Avenue, Suite G221, Evanston, IL 60201.
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Lamousé-Smith E, Kelly D, De Cremoux I. Designing bugs as drugs: exploiting the gut microbiome. Am J Physiol Gastrointest Liver Physiol 2021; 320:G295-G303. [PMID: 33264062 PMCID: PMC8609565 DOI: 10.1152/ajpgi.00381.2019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The extensive investigation of the human microbiome and the accumulating evidence regarding its critical relationship to human health and disease has advanced recognition of its potential as the next frontier of drug development. The rapid development of technologies, directed at understanding the compositional and functional dynamics of the human microbiome, and the ability to mine for novel therapeutic targets and biomarkers are leading innovative efforts to develop microbe-derived drugs that can prevent and treat autoimmune, metabolic, and infectious diseases. Increasingly, academics, biotechs, investors, and large pharmaceutical companies are partnering to collectively advance various therapeutic modalities ranging from live bacteria to small molecules. We review the leading platforms in current development focusing on live microbial consortia, engineered microbes, and microbial-derived metabolites. We will also touch on how the field is addressing and challenging the traditional definitions of pharmacokinetics and pharmacodynamics, dosing, toxicity, and safety to advance the development of these novel and cutting-edge therapeutics into the clinic.
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Langdon A, Schwartz DJ, Bulow C, Sun X, Hink T, Reske KA, Jones C, Burnham CAD, Dubberke ER, Dantas G. Microbiota restoration reduces antibiotic-resistant bacteria gut colonization in patients with recurrent Clostridioides difficile infection from the open-label PUNCH CD study. Genome Med 2021; 13:28. [PMID: 33593430 PMCID: PMC7888090 DOI: 10.1186/s13073-021-00843-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 02/03/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Once antibiotic-resistant bacteria become established within the gut microbiota, they can cause infections in the host and be transmitted to other people and the environment. Currently, there are no effective modalities for decreasing or preventing colonization by antibiotic-resistant bacteria. Intestinal microbiota restoration can prevent Clostridioides difficile infection (CDI) recurrences. Another potential application of microbiota restoration is suppression of non-C. difficile multidrug-resistant bacteria and overall decrease in the abundance of antibiotic resistance genes (the resistome) within the gut microbiota. This study characterizes the effects of RBX2660, a microbiota-based investigational therapeutic, on the composition and abundance of the gut microbiota and resistome, as well as multidrug-resistant organism carriage, after delivery to patients suffering from recurrent CDI. METHODS An open-label, multi-center clinical trial in 11 centers in the USA for the safety and efficacy of RBX2660 on recurrent CDI was conducted. Fecal specimens from 29 of these subjects with recurrent CDI who received either one (N = 16) or two doses of RBX2660 (N = 13) were analyzed secondarily. Stool samples were collected prior to and at intervals up to 6 months post-therapy and analyzed in three ways: (1) 16S rRNA gene sequencing for microbiota taxonomic composition, (2) whole metagenome shotgun sequencing for functional pathways and antibiotic resistome content, and (3) selective and differential bacterial culturing followed by isolate genome sequencing to longitudinally track multidrug-resistant organisms. RESULTS Successful prevention of CDI recurrence with RBX2660 correlated with taxonomic convergence of patient microbiota to the donor microbiota as measured by weighted UniFrac distance. RBX2660 dramatically reduced the abundance of antibiotic-resistant Enterobacteriaceae in the 2 months after administration. Fecal antibiotic resistance gene carriage decreased in direct relationship to the degree to which donor microbiota engrafted. CONCLUSIONS Microbiota-based therapeutics reduce resistance gene abundance and resistant organisms in the recipient gut microbiome. This approach could potentially reduce the risk of infections caused by resistant organisms within the patient and the transfer of resistance genes or pathogens to others. TRIAL REGISTRATION ClinicalTrials.gov, NCT01925417 ; registered on August 19, 2013.
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Affiliation(s)
- Amy Langdon
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO USA
- Clinical Research Training Center, Washington University School of Medicine in St. Louis, St. Louis, MO USA
| | - Drew J. Schwartz
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO USA
- Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, MO USA
| | - Christopher Bulow
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO USA
| | - Xiaoqing Sun
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
| | - Tiffany Hink
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
| | - Kimberly A. Reske
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
| | | | - Carey-Ann D. Burnham
- Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, MO USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
| | - Erik R. Dubberke
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
- Department of Biomedical Engineering, Washington University in St Louis, St. Louis, MO USA
| | - for the CDC Prevention Epicenter Program
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO USA
- Clinical Research Training Center, Washington University School of Medicine in St. Louis, St. Louis, MO USA
- Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, MO USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
- Rebiotix, Inc., Minneapolis, MN USA
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
- Department of Biomedical Engineering, Washington University in St Louis, St. Louis, MO USA
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Henson MA. Computational modeling of the gut microbiota reveals putative metabolic mechanisms of recurrent Clostridioides difficile infection. PLoS Comput Biol 2021; 17:e1008782. [PMID: 33617526 PMCID: PMC7932513 DOI: 10.1371/journal.pcbi.1008782] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 03/04/2021] [Accepted: 02/05/2021] [Indexed: 12/16/2022] Open
Abstract
Approximately 30% of patients who have Clostridioides difficile infection (CDI) will suffer at least one incident of reinfection. While the underlying causes of CDI recurrence are poorly understood, interactions between C. difficile and commensal gut bacteria are thought to play an important role. In this study, an in silico pipeline was used to process 16S rRNA gene amplicon sequence data of 225 stool samples from 93 CDI patients into sample-specific models of bacterial community metabolism. Clustered metabolite production rates generated from post-diagnosis samples generated a high Enterobacteriaceae abundance cluster containing disproportionately large numbers of recurrent samples and patients. This cluster was predicted to have significantly reduced capabilities for secondary bile acid synthesis but elevated capabilities for aromatic amino acid catabolism. When applied to 16S sequence data of 40 samples from fecal microbiota transplantation (FMT) patients suffering from recurrent CDI and their stool donors, the community modeling method generated a high Enterobacteriaceae abundance cluster with a disproportionate large number of pre-FMT samples. This cluster also was predicted to exhibit reduced secondary bile acid synthesis and elevated aromatic amino acid catabolism. Collectively, these in silico predictions suggest that Enterobacteriaceae may create a gut environment favorable for C. difficile spore germination and/or toxin synthesis.
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Affiliation(s)
- Michael A. Henson
- Department of Chemical Engineering and Institute for Applied Life Sciences, University of Massachusetts, Amherst, Massachusetts, United States of America
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Ross CN, Reveles KR. Feasibility of fecal microbiota transplantation via oral gavage to safely alter gut microbiome composition in marmosets. Am J Primatol 2020; 82:e23196. [PMID: 32970852 PMCID: PMC7679041 DOI: 10.1002/ajp.23196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 08/17/2020] [Accepted: 08/22/2020] [Indexed: 11/10/2022]
Abstract
Disruption of microbial communities within human hosts has been associated with infection, obesity, cognitive decline, cancer risk and frailty, suggesting that microbiome-targeted therapies may be an option for improving healthspan and lifespan. The objectives of this study were to determine the feasibility of delivering fecal microbiota transplants (FMTs) to marmosets via oral gavage and to evaluate if alteration of the gut microbiome post-FMT could be achieved. This was a prospective study of marmosets housed at the Barshop Institute for Longevity and Aging Studies in San Antonio, Texas. Eligible animals included healthy young adult males (age 2-5 years) with no recent medication use. Stool from two donors was combined and administered in 0.5 ml doses to five young recipients once weekly for 3 weeks. Safety outcomes and alterations in the gut microbiome composition via 16S ribosomal RNA sequencing were compared at baseline and monthly up to 6 months post-FMT. Overall, significant differences in the percent relative abundance was seen in FMT recipients at the phylum and family levels from baseline to 1 month and baseline to 6 months post-FMT. In permutational multivariate analysis of variance analyses, treatment status (donor vs. recipient) (p = .056) and time course (p = .019) predicted β diversity (p = .056). The FMT recipients did not experience any negative health outcomes over the course of the treatment. FMT via oral gavage was safe to administer to young adult marmosets. The marmoset microbiome may be altered by FMT; however, progressive changes in the microbiome are strongly driven by the host and its baseline microbiome composition.
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Affiliation(s)
- Corinna N Ross
- Department of Science and Mathematics, Texas A&M University San Antonio, San Antonio, Texas, USA
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA
- Barshop Institute for Longevity and Aging Research, University of Texas Health San Antonio, San Antonio, Texas, USA
| | - Kelly R Reveles
- College of Pharmacy, The University of Texas at Austin, Austin, Texas, USA
- Pharmacotherapy Education & Research Center, University of Texas Health San Antonio, San Antonio, Texas, USA
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Khanna S, Pardi DS, Jones C, Shannon WD, Gonzalez C, Blount K. RBX7455, a Non-frozen, Orally Administered Investigational Live Biotherapeutic, Is Safe, Effective, and Shifts Patients' Microbiomes in a Phase 1 Study for Recurrent Clostridioides difficile Infections. Clin Infect Dis 2020; 73:e1613-e1620. [PMID: 32966574 PMCID: PMC8492147 DOI: 10.1093/cid/ciaa1430] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Indexed: 12/15/2022] Open
Abstract
Background Recurrent Clostridioides difficile infections (rCDI) are a global public health threat. To reduce rCDI, microbiota-restoring therapies are needed, particularly standardized, easy-to-administer formulations. Methods This phase I open-label trial assessed the safety, efficacy in preventing rCDI recurrence, and intestinal microbiome effects of RBX7455, a room temperature-stable, orally administered investigational live biotherapeutic. Adult participants with 1 or more prior episodes of rCDI received: 4 RBX7455 capsules twice daily for 4 days (group 1); 4 RBX7455 capsules twice daily for 2 days (group 2); or 2 RBX7455 capsules twice daily for 2 days (group 3). For all groups, the first dose was administered in clinic, with remaining doses self-administered at home. Adverse events were monitored during and for 6 months after treatment. Treatment success was defined as rCDI prevention through 8 weeks after treatment. Participants’ microbiome composition was assessed prior to and for 6 months after treatment. Results Nine of 10 group 1 patients (90%), 8 of 10 group 2 patients (80%), and 10 of 10 group 3 patients (100%) were recurrence-free at the 8-week endpoint with durability to 6 months. Seventy-five treatment-emergent adverse events were observed in 27 participants with no serious investigational product-related events. Prior to treatment, participants’ microbiomes were dissimilar from the RBX7455 composition with decreased Bacteroidia- and Clostridia-class bacteria, whereas after treatment, responders’ microbiomes showed increased Bacteroidia and Clostridia. Conclusions Three dosing regimens of RBX7455 were safe and effective at preventing rCDI. Responders’ microbiomes converged toward the composition of RBX7455. These results support its continued clinical evaluation. Clinical Trials Registration NCT02981316.
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Affiliation(s)
- Sahil Khanna
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA
| | - Darrell S Pardi
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA
| | - Courtney Jones
- Rebiotix Inc, a Ferring Company, Roseville, Minnesota, USA
| | | | | | - Ken Blount
- Rebiotix Inc, a Ferring Company, Roseville, Minnesota, USA
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Kwak S, Choi J, Hink T, Reske KA, Blount K, Jones C, Bost MH, Sun X, Burnham CAD, Dubberke ER, Dantas G. Impact of investigational microbiota therapeutic RBX2660 on the gut microbiome and resistome revealed by a placebo-controlled clinical trial. MICROBIOME 2020; 8:125. [PMID: 32862830 PMCID: PMC7457799 DOI: 10.1186/s40168-020-00907-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 08/11/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Intestinal microbiota restoration can be achieved by complementing a subject's perturbed microbiota with that of a healthy donor. Recurrent Clostridioides difficile infection (rCDI) is one key application of such treatment. Another emerging application of interest is reducing antibiotic-resistant genes (ARGs) and organisms (AROs). In this study, we investigated fecal specimens from a multicenter, randomized, double-blind, placebo-controlled phase 2b study of microbiota-based investigational drug RBX2660. Patients were administered either placebo, 1 dose of RBX2660 and 1 placebo, or 2 doses of RBX2660 via enema and longitudinally tracked for changes in their microbiome and antibiotic resistome. RESULTS All patients exhibited significant recovery of gut microbiome diversity and a decrease of ARG relative abundance during the first 7 days post-treatment. However, the microbiome and resistome shifts toward average configurations from unperturbed individuals were more significant and longer-lasting in RBX2660 recipients compared to placebo. We quantified microbiome and resistome modification by RBX2660 using a novel "transplantation index" metric. We identified taxonomic and metabolic features distinguishing the baseline microbiome of non-transplanted patients and taxa specifically enriched during the process of transplantation. We elucidated the correlation between resistome and taxonomic transplantations and post-treatment dynamics of patient-specific and RBX2660-specific ARGs. Whole genome sequencing of AROs cultured from RBX2660 product and patient samples indicate ARO eradication in patients via RBX2660 administration, but also, to a lesser extent, introduction of RBX2660-derived AROs. CONCLUSIONS Through shotgun metagenomic sequencing, we elucidated the effects of RBX2660 in the microbiome and resistome. Antibiotic discontinuation alone resulted in significant recovery of gut microbial diversity and reduced ARG relative abundance, but RBX2660 administration more rapidly and completely changed the composition of patients' microbiome, resistome, and ARO colonization by transplanting RBX2660 microbiota into the recipients. Although ARGs and AROs were transmitted through RBX2660, the resistome post-RBX2660 more closely resembled that of the administered product-a proxy for the donor-than an antibiotic perturbed state. TRIAL REGISTRATION ClinicalTrials.gov, NCT02299570 . Registered 19 November 2014 Video Abstract.
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Affiliation(s)
- Suryang Kwak
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
| | - JooHee Choi
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
| | - Tiffany Hink
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
| | - Kimberly A. Reske
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
| | - Kenneth Blount
- Rebiotix Inc. a Ferring Company, Minneapolis, MN 55113 USA
| | - Courtney Jones
- Rebiotix Inc. a Ferring Company, Minneapolis, MN 55113 USA
| | - Margaret H. Bost
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
| | - Xiaoqing Sun
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
| | - Carey-Ann D. Burnham
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
| | - Erik R. Dubberke
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63110 USA
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
| | - for the CDC Prevention Epicenter Program
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
- Rebiotix Inc. a Ferring Company, Minneapolis, MN 55113 USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63110 USA
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110 USA
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Follow your Gut: Microbiome-Based Approaches in the Developmental Pipeline for the Prevention and Adjunctive Treatment of Clostridioides difficile Infection (CDI). Curr Infect Dis Rep 2020. [DOI: 10.1007/s11908-020-00729-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Vargason AM, Santhosh S, Anselmo AC. Surface Modifications for Improved Delivery and Function of Therapeutic Bacteria. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e2001705. [PMID: 32410314 DOI: 10.1002/smll.202001705] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 04/08/2020] [Accepted: 04/09/2020] [Indexed: 06/11/2023]
Abstract
Live therapeutic bacteria (LTBs) hold promise to treat microbiome-related diseases. However, few approaches to improve the colonization of LTBs in the gastrointestinal tract exist, despite colonization being a prerequisite for efficacy of many LTBs. Here, a modular platform to rapidly modify the surface of LTBs to enable receptor-specific interactions with target surfaces is reported. Inspired by bacterial adhesins that facilitate colonization, synthetic adhesins (SAs) are developed for LTBs in the form of antibodies conjugated to their surface. The SA platform is nontoxic, does not alter LTB growth kinetics, and can be used with any antibody or bacterial strain combination. By improving adhesion, SA-modified bacteria demonstrate enhanced in vitro pathogen exclusion from cell monolayers. In vivo kinetics of SA-modified LTBs is tracked in the feces and intestines of treated mice, demonstrating that SA-modified bacteria alter short-term intestinal transit and improve LTB colonization and pharmacokinetics. This platform enables rapid formation of an intestinal niche, leading to an increased maximum concentration and a 20% improvement in total LTB exposure. This work is the first application of traditional pharmacokinetic analysis to design and evaluate LTB drug delivery systems and provides a platform toward controlling adhesion, colonization, and efficacy of LTBs.
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Affiliation(s)
- Ava M Vargason
- Division of Pharmacoengineering and Molecular Pharmaceutics, University of North Carolina at Chapel Hill, Eshelman School of Pharmacy, Chapel Hill, NC, 27599, USA
| | - Shruti Santhosh
- Division of Pharmacoengineering and Molecular Pharmaceutics, University of North Carolina at Chapel Hill, Eshelman School of Pharmacy, Chapel Hill, NC, 27599, USA
| | - Aaron C Anselmo
- Division of Pharmacoengineering and Molecular Pharmaceutics, University of North Carolina at Chapel Hill, Eshelman School of Pharmacy, Chapel Hill, NC, 27599, USA
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40
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Fadda HM. The Route to Palatable Fecal Microbiota Transplantation. AAPS PharmSciTech 2020; 21:114. [PMID: 32296975 DOI: 10.1208/s12249-020-1637-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 02/05/2020] [Indexed: 12/16/2022] Open
Abstract
The community of symbiotic microorganisms that reside in our gastrointestinal tract is integral to human health. Fecal microbiota transplantation (FMT) has been shown to be highly effective in treating recurrent Clostridioides difficile infection (rCDI) and is now recommended by medical societies for patients suffering from rCDI who have failed to respond to conventional therapy. The main challenges with FMT are its accessibility, acceptability, lack of standardization, and regulatory complexity, which will be discussed in this review. Access to FMT is being addressed through the development of frozen and lyophilized FMT preparations that can be prepared at stool banks and shipped to the point of care. Both access and patient acceptance would be enhanced by oral FMT capsules, and there is potential to reduce capsule burden by utilizing colonic release capsules, targeting the site of disease. This review compares the efficacy of different FMT routes of administration: capsules, nasal feeding tubes, enemas, and colonoscopic infusions. FMT is considered investigational by the Food and Drug Administration. In effort to improve access to FMT, physicians may perform FMT outside of an investigational new drug application for treating CDI infections not responsive to standard therapies. The majority of FMT studies report only minor adverse effects; however, there is risk of transmission of infections.
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Reed H, Begun J. The future of faecal microbiota transplantation in gastrointestinal illness. MICROBIOLOGY AUSTRALIA 2020. [DOI: 10.1071/ma20027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The gut microbiome is made up of hundreds of trillions of microorganisms that reside in a state of homeostatic balance within the healthy individual. Next generation sequencing has provided insight into the diversity of these microorganisms that reside within our gastrointestinal tract; despite developments in metabolomics and culturing techniques, the functions of many of these bacteria remain largely elusive. As such, research into the capacity of the gut microbiome to regulate immune homeostasis has revealed the importance of bacteria in human health, with the potential for exploiting these bacteria only now coming into focus.
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Majid M, Andleeb S. Designing a multi-epitopic vaccine against the enterotoxigenic Bacteroides fragilis based on immunoinformatics approach. Sci Rep 2019; 9:19780. [PMID: 31874963 PMCID: PMC6930219 DOI: 10.1038/s41598-019-55613-w] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 10/23/2019] [Indexed: 12/14/2022] Open
Abstract
Enterotoxigenic Bacteroides fragilis is an enteric pathogen which is described as a causative agent of various intestinal infections and inflammatory diseases. Moreover, various research studies have reported it to be a leading factor in the development of colorectal cancer. As a part of the normal human microbiome, its treatment has become quite a challenge due to the alarming resistance against the available antibiotics. Although, this particular strain of B. fragilis shows susceptibility to few antibiotics, it is pertinent to devise an effective vaccine strategy for its elimination. There is no vaccine available against this pathogen up to date; therefore, we systematically ventured the outer membrane toxin producing proteins found exclusively in the toxigenic B. fragilis through the in-silico approaches to predict a multi-epitopic chimeric vaccine construct. The designed protein constitutes of epitopes which are predicted for linear B cells, Helper and T cells of outer membrane proteins expected to be putative vaccine candidates. The finalized proteins are only expressed in the enterotoxigenic B. fragilis, thus proving them to be exclusive. The 3D structure of the protein was first predicted followed by its refinement and validation via utilizing the bioinformatic approaches. Docking of the designed protein with the TLR2 receptor forecasted apt binding. Upon immune simulation, notable levels were observed in the expression of the immune cells.
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Affiliation(s)
- Mahnoor Majid
- Department of Industrial Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences & Technology (NUST), Islamabad, 44000, Pakistan
| | - Saadia Andleeb
- Department of Industrial Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences & Technology (NUST), Islamabad, 44000, Pakistan.
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