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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 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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Tiwari A, Krolicka A, Tran TT, Räisänen K, Ásmundsdóttir ÁM, Wikmark OG, Lood R, Pitkänen T. Antibiotic resistance monitoring in wastewater in the Nordic countries: A systematic review. ENVIRONMENTAL RESEARCH 2024; 246:118052. [PMID: 38163547 DOI: 10.1016/j.envres.2023.118052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/23/2023] [Accepted: 12/25/2023] [Indexed: 01/03/2024]
Abstract
The Nordic countries (Denmark, Finland, Iceland, Norway, and Sweden) have effectively kept lower antibiotic-resistant bacterial (ARB) pathogen rates than many other countries. However, in recent years, these five countries have encountered a rise in ARB cases and challenges in treating infections due to the growing prevalence of ARB pathogens. Wastewater-based surveillance (WBS) is a valuable supplement to clinical methods for ARB surveillance, but there is a lack of comprehensive understanding of WBS application for ARB in the Nordic countries. This review aims to compile the latest state-of-the-art developments in WBS for ARB monitoring in the Nordic countries and compare them with clinical surveillance practices. After reviewing 1480 papers from the primary search, 54 were found relevant, and 15 additional WBS-related papers were included. Among 69 studies analyzed, 42 dedicated clinical epidemiology, while 27 focused on wastewater monitoring. The PRISMA review of the literature revealed that Nordic countries focus on four major WBS objectives of ARB: assessing ARB in the human population, identifying ARB evading wastewater treatment, quantifying removal rates, and evaluating potential ARB evolution during the treatment process. In both clinical and wastewater contexts, the most studied targets were pathogens producing carbapenemase and extended-spectrum beta-lactamase (ESBL), primarily Escherichia coli and Klebsiella spp. However, vancomycin-resistant Enterococcus (VRE) and methicillin-resistant Staphylococcus aureus (MRSA) have received more attention in clinical epidemiology than in wastewater studies, probably due to their lower detection rates in wastewater. Clinical surveillance has mostly used culturing, antibiotic susceptibility testing, and genotyping, but WBS employed PCR-based and metagenomics alongside culture-based techniques. Imported cases resulting from international travel and hospitalization abroad appear to have frequently contributed to the rise in ARB pathogen cases in these countries. The many similarities between the Nordic countries (e.g., knowledge exchange practices, antibiotic usage patterns, and the current ARB landscape) could facilitate collaborative efforts in developing and implementing WBS for ARB in population-level screening.
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Affiliation(s)
- Ananda Tiwari
- Expert Microbiology Unit, Finnish Institute for Health and Welfare, 70701, Kuopio, Finland.
| | - Adriana Krolicka
- Norwegian Research Centre AS (NORCE), Nygårdstangen, 5838, Bergen, Norway
| | - Tam T Tran
- Norwegian Research Centre AS (NORCE), Nygårdstangen, 5838, Bergen, Norway
| | - Kati Räisänen
- Expert Microbiology Unit, Finnish Institute for Health and Welfare, Helsinki, Finland
| | | | - Odd-Gunnar Wikmark
- Norwegian Research Centre AS (NORCE), Nygårdstangen, 5838, Bergen, Norway; Unit for Environmental Science and Management, North West University, Potchefstroom Campus, Private Bag X6001, Potchefstroom 2520, South Africa
| | - Rolf Lood
- Department of Clinical Sciences Lund, Division of Infection Medicine, Faculty of Medicine, Lund University, Lund, Sweden
| | - Tarja Pitkänen
- Expert Microbiology Unit, Finnish Institute for Health and Welfare, 70701, Kuopio, Finland; Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Finland.
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Rusconi B, Bard AK, McDonough R, Kindsvogel AM, Wang JD, Udayan S, McDonald KG, Newberry RD, Tarr PI. Intergenerational protective anti-gut commensal immunoglobulin G originates in early life. Proc Natl Acad Sci U S A 2024; 121:e2309994121. [PMID: 38517976 PMCID: PMC10990157 DOI: 10.1073/pnas.2309994121] [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: 06/15/2023] [Accepted: 02/16/2024] [Indexed: 03/24/2024] Open
Abstract
Maternal immunoglobulins of the class G (IgGs) protect offspring from enteric infection, but when, where, and how these antibodies are physiologically generated and confer protection remains enigmatic. We found that circulating IgGs in adult mice preferentially bind early-life gut commensal bacteria over their own adult gut commensal bacteria. IgG-secreting plasma cells specific for early-life gut bacteria appear in the intestine soon after weaning, where they remain into adulthood. Manipulating exposure to gut bacteria or plasma cell development before, but not after, weaning reduced IgG-secreting plasma cells targeting early-life gut bacteria throughout life. Further, the development of this anti-gut commensal IgG response coincides with the early-life interval in which goblet cell-associated antigen passages (GAPs) are present in the colon. Offspring of dams "perturbed" by B cell ablation or reduced bacterial exposure in early life were more susceptible to enteric pathogen challenge. In contrast to current concepts, protective maternal IgGs targeted translocating gut commensals in the offspring, not the enteric pathogen. These early-life events affecting anti-commensal IgG production have intergenerational effects for protection of the offspring.
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Affiliation(s)
- Brigida Rusconi
- Department of Pediatrics, Division of Gastroenterology, Hepatology and Nutrition, Washington University School of Medicine in St. Louis, St. Louis, MO63110
| | - Adina K. Bard
- Department of Pediatrics, Division of Gastroenterology, Hepatology and Nutrition, Washington University School of Medicine in St. Louis, St. Louis, MO63110
| | - Ryan McDonough
- Department of Pediatrics, Division of Gastroenterology, Hepatology and Nutrition, Washington University School of Medicine in St. Louis, St. Louis, MO63110
| | - Angel M. Kindsvogel
- Department of Pediatrics, Division of Gastroenterology, Hepatology and Nutrition, Washington University School of Medicine in St. Louis, St. Louis, MO63110
| | - Jacqueline D. Wang
- Department of Pediatrics, Division of Gastroenterology, Hepatology and Nutrition, Washington University School of Medicine in St. Louis, St. Louis, MO63110
| | - Sreeram Udayan
- Department of Internal Medicine, Division of Gastroenterology, Washington University School of Medicine in St. Louis, St. Louis, MO63110
| | - Keely G. McDonald
- Department of Internal Medicine, Division of Gastroenterology, Washington University School of Medicine in St. Louis, St. Louis, MO63110
| | - Rodney D. Newberry
- Department of Internal Medicine, Division of Gastroenterology, Washington University School of Medicine in St. Louis, St. Louis, MO63110
| | - Phillip I. Tarr
- Department of Pediatrics, Division of Gastroenterology, Hepatology and Nutrition, Washington University School of Medicine in St. Louis, St. Louis, MO63110
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, MO63110
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Knapple WL, Yoho DS, Sheh A, Thul J, Feuerstadt P. Retrospective subgroup analysis of fecal microbiota, live-jslm (REBYOTA ®) administered by colonoscopy under enforcement discretion for the prevention of recurrent Clostridioides difficile infection. Therap Adv Gastroenterol 2024; 17:17562848241239547. [PMID: 38529070 PMCID: PMC10962041 DOI: 10.1177/17562848241239547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 02/27/2024] [Indexed: 03/27/2024] Open
Abstract
Background Fecal microbiota, live-jslm (RBL; REBYOTA®), is the first Food and Drug Administration (FDA)-approved, single-dose, rectally administered, microbiota-based live biotherapeutic product for preventing Clostridioides difficile infection (CDI) recurrence. Alternative routes of administration are of clinical interest. Objectives Evaluate the safety and efficacy of RBL administration via colonoscopy. Design Retrospective analysis of electronic medical records of participants administered RBL via colonoscopy under FDA enforcement discretion. Methods The number of participants with treatment and/or procedure-emergent adverse events (TEAEs) was evaluated. Treatment success and sustained clinical response, defined as the absence of CDI recurrence within 8 weeks and 6 months, respectively, were evaluated. Results TEAEs were experienced by 75% (6/8) of participants; most were mild to moderate in severity, and none due to RBL or its administration. Most participants had treatment success (80%; 8/10); 75% (6/8) had sustained clinical response. Conclusion Real-world safety and efficacy of RBL administered via colonoscopy were consistent with clinical trials of rectally administered RBL. Graphical abstract
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Affiliation(s)
- Whitfield L. Knapple
- Arkansas Gastroenterology, 3401 Springhill Drive #400, North Little Rock, AR 72117, USA
| | - David S. Yoho
- Mid-Atlantic Permanente Medical Group, Springfield, VA, USA
| | | | - Joan Thul
- Ferring Pharmaceuticals, Inc., Parsippany, NJ, USA
| | - Paul Feuerstadt
- Yale University School of Medicine, New Haven, CT, USA
- PACT Gastroenterology Center, Hamden, CT, USA
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Nooij S, Vendrik KEW, Zwittink RD, Ducarmon QR, Keller JJ, Kuijper EJ, Terveer EM. Long-term beneficial effect of faecal microbiota transplantation on colonisation of multidrug-resistant bacteria and resistome abundance in patients with recurrent Clostridioides difficile infection. Genome Med 2024; 16:37. [PMID: 38419010 PMCID: PMC10902993 DOI: 10.1186/s13073-024-01306-7] [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: 08/23/2023] [Accepted: 02/13/2024] [Indexed: 03/02/2024] Open
Abstract
BACKGROUND Multidrug-resistant (MDR) bacteria are a growing global threat, especially in healthcare facilities. Faecal microbiota transplantation (FMT) is an effective prevention strategy for recurrences of Clostridioides difficile infections and can also be useful for other microbiota-related diseases. METHODS We study the effect of FMT in patients with multiple recurrent C. difficile infections on colonisation with MDR bacteria and antibiotic resistance genes (ARG) on the short (3 weeks) and long term (1-3 years), combining culture methods and faecal metagenomics. RESULTS Based on MDR culture (n = 87 patients), we notice a decrease of 11.5% in the colonisation rate of MDR bacteria after FMT (20/87 before FMT = 23%, 10/87 3 weeks after FMT). Metagenomic sequencing of patient stool samples (n = 63) shows a reduction in relative abundances of ARGs in faeces, while the number of different resistance genes in patients remained higher compared to stools of their corresponding healthy donors (n = 11). Furthermore, plasmid predictions in metagenomic data indicate that patients harboured increased levels of resistance plasmids, which appear unaffected by FMT. In the long term (n = 22 patients), the recipients' resistomes are still donor-like, suggesting the effect of FMT may last for years. CONCLUSIONS Taken together, we hypothesise that FMT restores the gut microbiota to a composition that is closer to the composition of healthy donors, and potential pathogens are either lost or decreased to very low abundances. This process, however, does not end in the days following FMT. It may take months for the gut microbiome to re-establish a balanced state. Even though a reservoir of resistance genes remains, a notable part of which on plasmids, FMT decreases the total load of resistance genes.
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Affiliation(s)
- Sam Nooij
- Netherlands Donor Feces Bank, Leiden University Center of Infectious Diseases (LUCID) Medical Microbiology and Infection Prevention, Leiden University Medical Center, PO Box 9600, Postzone E4-P, Leiden, 2300RC, Netherlands.
- Center for Microbiome Analyses and Therapeutics, LUCID Research, Leiden University Medical Center, Leiden, Netherlands.
| | - Karuna E W Vendrik
- Netherlands Donor Feces Bank, Leiden University Center of Infectious Diseases (LUCID) Medical Microbiology and Infection Prevention, Leiden University Medical Center, PO Box 9600, Postzone E4-P, Leiden, 2300RC, Netherlands
- Center for Microbiome Analyses and Therapeutics, LUCID Research, Leiden University Medical Center, Leiden, Netherlands
- Present address: Centre for Infectious Disease Control, Netherlands Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Romy D Zwittink
- Center for Microbiome Analyses and Therapeutics, LUCID Research, Leiden University Medical Center, Leiden, Netherlands
- Present address: Centre for Infectious Disease Control, Netherlands Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Quinten R Ducarmon
- Center for Microbiome Analyses and Therapeutics, LUCID Research, Leiden University Medical Center, Leiden, Netherlands
| | - Josbert J Keller
- Netherlands Donor Feces Bank, Leiden University Center of Infectious Diseases (LUCID) Medical Microbiology and Infection Prevention, Leiden University Medical Center, PO Box 9600, Postzone E4-P, Leiden, 2300RC, Netherlands
- Department of Gastroenterology, Haaglanden Medical Center, The Hague, Netherlands
| | - Ed J Kuijper
- Center for Microbiome Analyses and Therapeutics, LUCID Research, Leiden University Medical Center, Leiden, Netherlands
| | - Elisabeth M Terveer
- Netherlands Donor Feces Bank, Leiden University Center of Infectious Diseases (LUCID) Medical Microbiology and Infection Prevention, Leiden University Medical Center, PO Box 9600, Postzone E4-P, Leiden, 2300RC, Netherlands
- Center for Microbiome Analyses and Therapeutics, LUCID Research, Leiden University Medical Center, Leiden, Netherlands
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Sun Y, Wang X, Li L, Zhong C, Zhang Y, Yang X, Li M, Yang C. The role of gut microbiota in intestinal disease: from an oxidative stress perspective. Front Microbiol 2024; 15:1328324. [PMID: 38419631 PMCID: PMC10899708 DOI: 10.3389/fmicb.2024.1328324] [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: 10/27/2023] [Accepted: 01/30/2024] [Indexed: 03/02/2024] Open
Abstract
Recent studies have indicated that gut microbiota-mediated oxidative stress is significantly associated with intestinal diseases such as colorectal cancer, ulcerative colitis, and Crohn's disease. The level of reactive oxygen species (ROS) has been reported to increase when the gut microbiota is dysregulated, especially when several gut bacterial metabolites are present. Although healthy gut microbiota plays a vital role in defending against excessive oxidative stress, intestinal disease is significantly influenced by excessive ROS, and this process is controlled by gut microbiota-mediated immunological responses, DNA damage, and intestinal inflammation. In this review, we discuss the relationship between gut microbiota and intestinal disease from an oxidative stress perspective. In addition, we also provide a summary of the most recent therapeutic approaches for preventing or treating intestinal diseases by modifying gut microbiota.
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Affiliation(s)
- Yiqi Sun
- Surgery of Traditional Chinese Medicine Department, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Xurui Wang
- Surgery of Traditional Chinese Medicine Department, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Lei Li
- Department of Anorectal Surgery, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Chao Zhong
- Traditional Chinese Medicine Department of Orthopaedic and Traumatic, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Yu Zhang
- Colorectal and Anal Surgery, Chengdu Anorectal Hospital, Chengdu, China
| | - Xiangdong Yang
- Colorectal and Anal Surgery, Chengdu Anorectal Hospital, Chengdu, China
| | - Mingyue Li
- Special Needs Outpatient Department, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Chao Yang
- Surgery of Traditional Chinese Medicine Department, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
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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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Abstract
Antibiotics have benefitted human health since their introduction nearly a century ago. However, the rise of antibiotic resistance may portend the dawn of the "post-antibiotic age." With the narrow pipeline for novel antimicrobials, we need new approaches to deal with the rise of multidrug resistant organisms. In the last 2 decades, the role of the intestinal microbiota in human health has been acknowledged and studied widely. Of the various activities carried out by the gut microbiota, colonization resistance is a key function that helps maintain homeostasis. Therefore, re-establishing a healthy microbiota is a novel strategy for treating drug resistance organisms. Preliminary studies suggest that this is a viable approach. However, the extent of their success still needs to be examined. Herein, we will review work in this area and suggest where future studies can further investigate this method for dealing with the threat of antibiotic resistance.
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Affiliation(s)
- Nguyen T Q Nhu
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Vincent B Young
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
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Gonzales-Luna AJ, Carlson TJ, Garey KW. Review Article: Safety of Live Biotherapeutic Products Used for the Prevention of Clostridioides difficile Infection Recurrence. Clin Infect Dis 2023; 77:S487-S496. [PMID: 38051970 DOI: 10.1093/cid/ciad642] [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: 12/07/2023] Open
Abstract
Live biotherapeutic products (LBPs) represent a new class of therapeutics indicated to prevent the recurrence of Clostridioides difficile infection (CDI) in adults. However, microbiota-based therapies have been used in CDI management before the Food and Drug Administration (FDA) designated this new drug class. The regulation of these microbiome-based therapies has varied, and several safety concerns have arisen over time. Requirements established by the FDA regarding the development of LBPs minimizes many of these prior concerns, and phase III trials have proven the safety and efficacy of 2 stool donor-derived LBPs: fecal microbiota, live-jslm (Rebyota™; formerly RBX2660) and fecal microbiota spores, live-brpk (Vowst™; formerly SER-109). Mild gastrointestinal side effects are common, but no severe drug-related adverse events have been reported with their use to date. A third LBP entering phase III clinical trials, VE303, follows a novel approach by sourcing bacterial strains from clonal cell banks and has demonstrated a similarly favorable safety profile.
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Affiliation(s)
- Anne J Gonzales-Luna
- Department of Pharmacy and Translational Research, University of Houston College of Pharmacy, Houston, Texas, USA
| | - Travis J Carlson
- Pharmacotherapy Division, College of Pharmacy, The University of Texas at Austin, San Antonio, Texas, USA
- Pharmacotherapy Education and Research Center, Joe R. and Teresa Lozano Long School of Medicine, University of Texas Health San Antonio, San Antonio, Texas, USA
- University Hospital, University Health, San Antonio, Texas, USA
| | - Kevin W Garey
- Department of Pharmacy and Translational Research, University of Houston College of Pharmacy, Houston, Texas, USA
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Rooney AM, Cochrane K, Fedsin S, Yao S, Anwer S, Dehmiwal S, Hota S, Poutanen S, Allen-Vercoe E, Coburn B. A microbial consortium alters intestinal Pseudomonadota and antimicrobial resistance genes in individuals with recurrent Clostridioides difficile infection. mBio 2023; 14:e0348222. [PMID: 37404011 PMCID: PMC10506460 DOI: 10.1128/mbio.03482-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 05/23/2023] [Indexed: 07/06/2023] Open
Abstract
Intestinal colonization with pathogens and antimicrobial-resistant organisms (AROs) is associated with increased risk of infection. Fecal microbiota transplant (FMT) has successfully been used to cure recurrent Clostridioides difficile infection (rCDI) and to decolonize intestinal AROs. However, FMT has significant practical barriers to safe and broad implementation. Microbial consortia represent a novel strategy for ARO and pathogen decolonization, with practical and safety advantages over FMT. We undertook an investigator-initiated analysis of stool samples collected from previous interventional studies of a microbial consortium, microbial ecosystem therapeutic (MET-2), and FMT for rCDI before and after treatment. Our aim was to assess whether MET-2 was associated with decreased Pseudomonadota (Proteobacteria) and antimicrobial resistance gene (ARG) burden with similar effects to FMT. Participants were selected for inclusion if baseline stool had Pseudomonadota relative abundance ≥10%. Pre- and post-treatment Pseudomonadota relative abundance, total ARGs, and obligate anaerobe and butyrate-producer relative abundances were determined by shotgun metagenomic sequencing. MET-2 administration had similar effects to FMT on microbiome outcomes. The median Pseudomonadota relative abundance decreased by four logs after MET-2 treatment, a greater decrease than that observed after FMT. Total ARGs decreased, while beneficial obligate anaerobe and butyrate-producer relative abundances increased. The observed microbiome response remained stable over 4 months post-administration for all outcomes. IMPORTANCE Overgrowth of intestinal pathogens and AROs is associated with increased risk of infection. With the rise in antimicrobial resistance, new therapeutic strategies that decrease pathogen and ARO colonization in the gut are needed. We evaluated whether a microbial consortium had similar effects to FMT on Pseudomonadota abundances and ARGs as well as obligate anaerobes and beneficial butyrate producers in individuals with high Pseudomonadota relative abundance at baseline. This study provides support for a randomized, controlled clinical trial of microbial consortia (such as MET-2) for ARO decolonization and anaerobe repletion.
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Affiliation(s)
- Ashley M. Rooney
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- Toronto General Hospital Research Institute, University Health Network, Toronto, Canada
| | | | - Stephanie Fedsin
- Department of Microbiology, Sinai Health, Toronto, Canada
- Division of Infectious Diseases, University Health Network, Toronto, Canada
| | - Samantha Yao
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Shaista Anwer
- Department of Microbiology, Sinai Health, Toronto, Canada
- Division of Infectious Diseases, University Health Network, Toronto, Canada
| | - Satyender Dehmiwal
- Department of Microbiology, Sinai Health, Toronto, Canada
- Division of Infectious Diseases, University Health Network, Toronto, Canada
| | - Susy Hota
- Infection Prevention and Control Department, University Health Network, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
| | - Susan Poutanen
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- Department of Microbiology, Sinai Health, Toronto, Canada
- Division of Infectious Diseases, University Health Network, Toronto, Canada
| | - Emma Allen-Vercoe
- NuBiyota, University of Guelph, Guelph, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
| | - Bryan Coburn
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- Toronto General Hospital Research Institute, University Health Network, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
| | - MTOP Investigators
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- Toronto General Hospital Research Institute, University Health Network, Toronto, Canada
- NuBiyota, University of Guelph, Guelph, Canada
- Department of Microbiology, Sinai Health, Toronto, Canada
- Division of Infectious Diseases, University Health Network, Toronto, Canada
- Infection Prevention and Control Department, University Health Network, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
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11
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Olsen MA, Keller MR, Stwalley D, Yu H, Dubberke ER. Increased Incidence and Risk of Septicemia and Urinary Tract Infection After Clostridioides difficile Infection. Open Forum Infect Dis 2023; 10:ofad313. [PMID: 37547851 PMCID: PMC10403155 DOI: 10.1093/ofid/ofad313] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 06/13/2023] [Indexed: 08/08/2023] Open
Abstract
Background Although increased occurrence of septicemia in persons with Clostridioides difficile infection (CDI) has been reported, incidence rates and risk of septicemia and urinary tract infection (UTI) after CDI are unclear. Methods The first episode of CDI was identified using 2011-2017 MarketScan and CMS Medicare data and CDI cases categorized by standard surveillance definitions. Uninfected persons were frequency matched 4:1 to cases by the CDI case surveillance definition. Multivariable Cox proportional hazards models were used to identify risk factors for septicemia and UTI within 90 days of CDI onset, accounting for the competing risk of death in the Medicare population. Results The incidence of septicemia was highest after hospital-onset CDI in the Medicare, younger commercial, and younger Medicaid populations (25.5%, 15.7%, and 19.5%, respectively) and lowest in those with community-associated CDI (3.8%, 4.3%, and 8.3%, respectively). In contrast, the incidence of UTI was highest in those with other healthcare facility onset CDI in all 3 populations (32.1%, 24.2%, and 18.1%, respectively). Hospital-onset CDI was associated with highest risk of septicemia compared with uninfected controls in all 3 populations. In the younger populations, risk of septicemia was more uniform across the CDI surveillance definitions. The risk of UTI was significantly higher in all CDI surveillance categories compared to uninfected controls, and among CDI cases it was lowest in those with community-associated CDI. Conclusions The incidence of septicemia is high after CDI, particularly after hospital-onset infection. Additional preventive measures are needed to reduce infectious complications of CDI.
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Affiliation(s)
- Margaret A Olsen
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Matthew R Keller
- Institute for Informatics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Dustin Stwalley
- Institute for Informatics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Holly Yu
- Pfizer, Collegeville, Pennsylvania, USA
| | - Erik R Dubberke
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
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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: 22] [Impact Index Per Article: 22.0] [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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Liu L, Wang H, Chen X, Xie P. Gut microbiota: a new insight into neurological diseases. Chin Med J (Engl) 2023; 136:1261-1277. [PMID: 35830286 PMCID: PMC10309523 DOI: 10.1097/cm9.0000000000002212] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Indexed: 12/13/2022] Open
Abstract
ABSTRACT In the last decade, it has become increasingly recognized that a balanced gut microbiota plays an important role in maintaining the health of the host. Numerous clinical and preclinical studies have shown that changes in gut microbiota composition are associated with a variety of neurological diseases, e.g., Parkinson's disease, Alzheimer's disease, and myasthenia gravis. However, the underlying molecular mechanisms are complex and remain unclear. Behavioral phenotypes can be transmitted from humans to animals through gut microbiota transplantation, indicating that the gut microbiota may be an important regulator of neurological diseases. However, further research is required to determine whether animal-based findings can be extended to humans and to elucidate the relevant potential mechanisms by which the gut microbiota regulates neurological diseases. Such investigations may aid in the development of new microbiota-based strategies for diagnosis and treatment and improve the clinical management of neurological disorders. In this review, we describe the dysbiosis of gut microbiota and the corresponding mechanisms in common neurological diseases, and discuss the potential roles that the intestinal microbiome may play in the diagnosis and treatment of neurological disorders.
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Affiliation(s)
- Lanxiang Liu
- Department of Neurology, Yongchuan Hospital of Chongqing Medical University, Chongqing 402160, China
- National Health Commission Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Haiyang Wang
- National Health Commission Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Xueyi Chen
- National Health Commission Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Peng Xie
- Department of Neurology, Yongchuan Hospital of Chongqing Medical University, Chongqing 402160, China
- National Health Commission Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
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14
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Yadegar A, Pakpoor S, Ibrahim FF, Nabavi-Rad A, Cook L, Walter J, Seekatz AM, Wong K, Monaghan TM, Kao D. Beneficial effects of fecal microbiota transplantation in recurrent Clostridioides difficile infection. Cell Host Microbe 2023; 31:695-711. [PMID: 37167952 DOI: 10.1016/j.chom.2023.03.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Fecal microbiota transplantation (FMT) is highly effective in preventing recurrent Clostridioides difficile infection (rCDI). However, the mechanisms underpinning its clinical efficacy are incompletely understood. Herein, we provide an overview of rCDI pathogenesis followed by a discussion of potential mechanisms of action focusing on the current understanding of trans-kingdom microbial, metabolic, immunological, and epigenetic mechanisms. We then outline the current research gaps and offer methodological recommendations for future studies to elevate the quality of research and advance knowledge translation. By combining interventional trials with multiomics technology and host and environmental factors, analyzing longitudinally collected biospecimens will generate results that can be validated with animal and other models. Collectively, this will confirm causality and improve translation, ultimately to develop targeted therapies to replace FMT.
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Affiliation(s)
- Abbas Yadegar
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sepideh Pakpoor
- School of Engineering, University of British Columbia, Kelowna, BC, Canada
| | - Fathima F Ibrahim
- National Institute for Health Research Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, UK; Nottingham Digestive Diseases Centre, School of Medicine, University of Nottingham, Nottingham, UK
| | - Ali Nabavi-Rad
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Laura Cook
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Jens Walter
- School of Microbiology, Department of Medicine and APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Anna M Seekatz
- Department of Biological Sciences, Clemson University, Clemson, SC, USA
| | - Karen Wong
- Division of Gastroenterology, Department of Medicine, University of Alberta, Edmonton, AB, Canada
| | - Tanya M Monaghan
- National Institute for Health Research Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, UK; Nottingham Digestive Diseases Centre, School of Medicine, University of Nottingham, Nottingham, UK.
| | - Dina Kao
- Division of Gastroenterology, Department of Medicine, University of Alberta, Edmonton, AB, Canada.
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15
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Merrick B, Sergaki C, Edwards L, Moyes DL, Kertanegara M, Prossomariti D, Shawcross DL, Goldenberg SD. Modulation of the Gut Microbiota to Control Antimicrobial Resistance (AMR)-A Narrative Review with a Focus on Faecal Microbiota Transplantation (FMT). Infect Dis Rep 2023; 15:238-254. [PMID: 37218816 DOI: 10.3390/idr15030025] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 04/19/2023] [Accepted: 05/05/2023] [Indexed: 05/24/2023] Open
Abstract
Antimicrobial resistance (AMR) is one of the greatest challenges facing humanity, causing a substantial burden to the global healthcare system. AMR in Gram-negative organisms is particularly concerning due to a dramatic rise in infections caused by extended-spectrum beta-lactamase and carbapenemase-producing Enterobacterales (ESBL and CPE). These pathogens have limited treatment options and are associated with poor clinical outcomes, including high mortality rates. The microbiota of the gastrointestinal tract acts as a major reservoir of antibiotic resistance genes (the resistome), and the environment facilitates intra and inter-species transfer of mobile genetic elements carrying these resistance genes. As colonisation often precedes infection, strategies to manipulate the resistome to limit endogenous infections with AMR organisms, as well as prevent transmission to others, is a worthwhile pursuit. This narrative review presents existing evidence on how manipulation of the gut microbiota can be exploited to therapeutically restore colonisation resistance using a number of methods, including diet, probiotics, bacteriophages and faecal microbiota transplantation (FMT).
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Affiliation(s)
- Blair Merrick
- Centre for Clinical Infection and Diagnostics Research, Guy's and St Thomas' NHS Foundation Trust, King's College, London SE1 7EH, UK
| | - Chrysi Sergaki
- Diagnostics R&D, Medicines and Healthcare Products Regulatory Agency (MHRA), Potters Bar EN6 3QG, UK
| | - Lindsey Edwards
- School of Immunology and Microbial Sciences, Institute of Liver Studies, Faculty of Life Sciences and Medicine, King's College, London SE1 1UL, UK
- Institute of Liver Studies, King's College Hospital NHS Foundation Trust, London SE5 9RS, UK
| | - David L Moyes
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral and Craniofacial Sciences, King's College, London SE1 1UK, UK
| | - Michael Kertanegara
- Centre for Clinical Infection and Diagnostics Research, Guy's and St Thomas' NHS Foundation Trust, King's College, London SE1 7EH, UK
| | - Désirée Prossomariti
- Centre for Clinical Infection and Diagnostics Research, Guy's and St Thomas' NHS Foundation Trust, King's College, London SE1 7EH, UK
| | - Debbie L Shawcross
- School of Immunology and Microbial Sciences, Institute of Liver Studies, Faculty of Life Sciences and Medicine, King's College, London SE1 1UL, UK
- Institute of Liver Studies, King's College Hospital NHS Foundation Trust, London SE5 9RS, UK
| | - Simon D Goldenberg
- Centre for Clinical Infection and Diagnostics Research, Guy's and St Thomas' NHS Foundation Trust, King's College, London SE1 7EH, UK
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16
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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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17
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Barbu IC, Gheorghe-Barbu I, Grigore GA, Vrancianu CO, Chifiriuc MC. Antimicrobial Resistance in Romania: Updates on Gram-Negative ESCAPE Pathogens in the Clinical, Veterinary, and Aquatic Sectors. Int J Mol Sci 2023; 24:7892. [PMID: 37175597 PMCID: PMC10178704 DOI: 10.3390/ijms24097892] [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: 04/03/2023] [Revised: 04/20/2023] [Accepted: 04/21/2023] [Indexed: 05/15/2023] Open
Abstract
Multidrug-resistant Gram-negative bacteria such as Acinetobacter baumannii, Pseudomonas aeruginosa, and members of the Enterobacterales order are a challenging multi-sectorial and global threat, being listed by the WHO in the priority list of pathogens requiring the urgent discovery and development of therapeutic strategies. We present here an overview of the antibiotic resistance profiles and epidemiology of Gram-negative pathogens listed in the ESCAPE group circulating in Romania. The review starts with a discussion of the mechanisms and clinical significance of Gram-negative bacteria, the most frequent genetic determinants of resistance, and then summarizes and discusses the epidemiological studies reported for A. baumannii, P. aeruginosa, and Enterobacterales-resistant strains circulating in Romania, both in hospital and veterinary settings and mirrored in the aquatic environment. The Romanian landscape of Gram-negative pathogens included in the ESCAPE list reveals that all significant, clinically relevant, globally spread antibiotic resistance genes and carrying platforms are well established in different geographical areas of Romania and have already been disseminated beyond clinical settings.
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Affiliation(s)
- Ilda Czobor Barbu
- Microbiology-Immunology Department, Faculty of Biology, University of Bucharest, 050095 Bucharest, Romania
- The Research Institute of the University of Bucharest, 050095 Bucharest, Romania
| | - Irina Gheorghe-Barbu
- Microbiology-Immunology Department, Faculty of Biology, University of Bucharest, 050095 Bucharest, Romania
- The Research Institute of the University of Bucharest, 050095 Bucharest, Romania
| | - Georgiana Alexandra Grigore
- Microbiology-Immunology Department, Faculty of Biology, University of Bucharest, 050095 Bucharest, Romania
- The Research Institute of the University of Bucharest, 050095 Bucharest, Romania
- National Institute of Research and Development for Biological Sciences, 060031 Bucharest, Romania
| | - Corneliu Ovidiu Vrancianu
- Microbiology-Immunology Department, Faculty of Biology, University of Bucharest, 050095 Bucharest, Romania
- The Research Institute of the University of Bucharest, 050095 Bucharest, Romania
| | - Mariana Carmen Chifiriuc
- Microbiology-Immunology Department, Faculty of Biology, University of Bucharest, 050095 Bucharest, Romania
- The Research Institute of the University of Bucharest, 050095 Bucharest, Romania
- Academy of Romanian Scientists, 050044 Bucharest, Romania
- Romanian Academy, 010071 Bucharest, Romania
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18
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Ding D, Wang B, Zhang X, Zhang J, Zhang H, Liu X, Gao Z, Yu Z. The spread of antibiotic resistance to humans and potential protection strategies. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 254:114734. [PMID: 36950985 DOI: 10.1016/j.ecoenv.2023.114734] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 02/26/2023] [Accepted: 03/03/2023] [Indexed: 06/18/2023]
Abstract
Antibiotic resistance is currently one of the greatest threats to human health. Widespread use and residues of antibiotics in humans, animals, and the environment can exert selective pressure on antibiotic resistance bacteria (ARB) and antibiotic resistance gene (ARG), accelerating the flow of antibiotic resistance. As ARG spreads to the population, the burden of antibiotic resistance in humans increases, which may have potential health effects on people. Therefore, it is critical to mitigate the spread of antibiotic resistance to humans and reduce the load of antibiotic resistance in humans. This review briefly described the information of global antibiotic consumption information and national action plans (NAPs) to combat antibiotic resistance and provided a set of feasible control strategies for the transmission of ARB and ARG to humans in three areas including (a) Reducing the colonization capacity of exogenous ARB, (b) Enhancing human colonization resistance and mitigating the horizontal gene transfer (HGT) of ARG, (c) Reversing ARB antibiotic resistance. With the hope of achieving interdisciplinary one-health prevention and control of bacterial resistance.
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Affiliation(s)
- Dong Ding
- The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, China; College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Bin Wang
- College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Xiaoan Zhang
- The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Junxi Zhang
- NHC Key Laboratory of Birth Defects Prevention & Henan Key Laboratory of Population Defects Prevention, Zhengzhou, China
| | - Huanhuan Zhang
- College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Xinxin Liu
- College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Zhan Gao
- The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, China.
| | - Zengli Yu
- College of Public Health, Zhengzhou University, Zhengzhou, China; The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China.
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19
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Cerini P, Meduri FR, Tomassetti F, Polidori I, Brugneti M, Nicolai E, Bernardini S, Pieri M, Broccolo F. Trends in Antibiotic Resistance of Nosocomial and Community-Acquired Infections in Italy. Antibiotics (Basel) 2023; 12:antibiotics12040651. [PMID: 37107013 PMCID: PMC10135155 DOI: 10.3390/antibiotics12040651] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 03/20/2023] [Accepted: 03/22/2023] [Indexed: 03/29/2023] Open
Abstract
The World Health Organization has recently identified three categories of pathogens, namely: critical, high, and medium priority, according to the need for new antibiotics. Critical priority pathogens include carbapenem-resistant microorganism (CPO) such as A. baumannii and P. aeruginosa, K. pneumoniae, and Enterobacter spp., whereas vancomycin-resistant E. faecium (VRE), methicillin and vancomycin-resistant S. aureus (MRSA) are in the high priority list. We compared the trend of antimicrobial resistants (AMRs) in clinical isolates, divided by year and bacteria spp., of samples obtained from nosocomial and community patients. Patient records were collected, including age, sex, site of infection, isolated organisms, and drug susceptibility patterns. From 2019 to 2022, a total of 113,635 bacterial isolates were tested, of which 11,901 resulted in antimicrobial resistants. An increase in the prevalence of several antibiotics resistant bacteria was observed. Specifically, the percentage of CPO cases increased from 2.62% to 4.56%, the percentage of MRSA increased from 1.84% to 2.81%, and the percentage of VRE increased from 0.58% to 2.21%. AMRs trend resulted in increases in CPO and MRSA for both community and nosocomial. Our work aims to highlight the necessity of preventive and control measures to be adopted in order to reduce the spread of multidrug-resistant pathogens.
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20
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Gulati AS, Nicholson MR, Khoruts A, Kahn SA. Fecal Microbiota Transplantation Across the Lifespan: Balancing Efficacy, Safety, and Innovation. Am J Gastroenterol 2023; 118:435-439. [PMID: 36580630 PMCID: PMC9992015 DOI: 10.14309/ajg.0000000000002167] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 12/21/2022] [Indexed: 12/31/2022]
Abstract
Fecal microbiota transplantation (FMT) is a rapidly growing therapy aimed at reconstituting the dysbiotic microbiota of a patient with the beneficial stool microbiota of a healthy individual. The efficacy rates of FMT are very robust for recurrent Clostridioides difficile infection in both children and adults. Although complications of FMT have been reported, it is generally believed to be a safe procedure. Novel indications for FMT are being studied, with the hope that ultimately it may be useful for a variety of disorders. As this field continues to grow, however, it is necessary to consider efficacy, safety, and innovation across the lifespan. There are unique concerns regarding FMT as it pertains to children, adults, and the elderly. In this review, we seek to update clinicians, researchers, and regulators on how these factors must be balanced across the lifespan as we move forward with this innovative therapy.
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Affiliation(s)
- Ajay S. Gulati
- Department of Pediatrics, Division of Gastroenterology, Hepatology and Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Maribeth R. Nicholson
- Department of Pediatrics, Division of Gastroenterology, Hepatology and Nutrition, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Alexander Khoruts
- Department of Medicine, Division of Gastroenterology, Center for Immunology, University of Minnesota, Minneapolis, MN 55414, USA
| | - Stacy A. Kahn
- Department of Pediatrics, Division of Gastroenterology, Hepatology and Nutrition, Boston, MA 02115, USA
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21
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Capacity of a Microbial Synbiotic To Rescue the In Vitro Metabolic Activity of the Gut Microbiome following Perturbation with Alcohol or Antibiotics. Appl Environ Microbiol 2023; 89:e0188022. [PMID: 36840551 PMCID: PMC10056957 DOI: 10.1128/aem.01880-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
Abstract
The human gut microbiome contributes crucial bioactive metabolites that support human health and is sensitive to perturbations from the ingestion of alcohol and antibiotics. We interrogated the response and recovery of human gut microbes after acute alcohol or broad-spectrum antibiotic administration in a gut model simulating the luminal and mucosal colonic environment with an inoculated human microbiome. Both alcohol and antibiotic treatments reduced the production of major short-chain fatty acids (SCFAs) (acetate, propionate, and butyrate), which are established modulators of human health. Treatment with a microbial synbiotic restored and enhanced gut function. Butyrate and acetate production increased by up to 29.7% and 18.6%, respectively, relative to untreated, dysbiotic samples. In parallel, treatment led to increases in the relative abundances of beneficial commensal organisms not found in the synbiotic (e.g., Faecalibacterium prausnitzii and the urolithin-producing organism Gordonibacter pamelaeae) as well as species present in the synbiotic (e.g., Bifidobacterium infantis), suggesting synergistic interactions between supplemented and native microorganisms. These results lead us to conclude that functional shifts in the microbiome, evaluated by both metabolite production and specific taxonomic compositional changes, are an appropriate metric to assess microbiome "recovery" following a dysbiosis-inducing disruption. Overall, these findings support the execution of randomized clinical studies to determine whether a microbial synbiotic can help restore microbiome function after a disruption. IMPORTANCE The human gut microbiome is sensitive to disruptions by common stressors such as alcohol consumption and antibiotic treatment. In this study, we used an in vitro system modeling the gut microbiome to investigate whether treatment with a microbial synbiotic can help restore microbiome function after stress. We find that a complex gut community treated with alcohol or antibiotics showed reduced levels of production of short-chain fatty acids, which are critical beneficial molecules produced by a healthy gut microbiota. Treatment of stressed communities with a microbial synbiotic resulted in the recovery of SCFA production as well as an increase in the abundance of beneficial commensal organisms. Our results suggest that treatment with a microbial synbiotic has the potential to restore healthy gut microbiome function after stress and merits further investigation in clinical studies.
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22
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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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23
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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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24
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Tillotson G, Archbald-Pannone L, Johnson S, Ng S, Ando M, Harvey A, Bancke L, Feuerstadt P. Microbiota-Based Live Biotherapeutic RBX2660 for the Reduction of Recurrent Clostridioides difficile Infection in Older Adults With Underlying Comorbidities. Open Forum Infect Dis 2023; 10:ofac703. [PMID: 36686631 PMCID: PMC9846189 DOI: 10.1093/ofid/ofac703] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 12/29/2022] [Indexed: 12/31/2022] Open
Abstract
Background Advanced age and underlying comorbidities are associated with greater rates of recurrence in patients with Clostridioides difficile infection (CDI). Reducing the likelihood of recurrence through treatment with an antimicrobial followed by a microbiota replacement therapy can decrease the burden of this infection and improve patient outcomes. We report the efficacy and safety of RBX2660, a microbiota-based live biotherapeutic, in older adults with recurrent CDI, grouped by comorbidities. Methods In this post hoc subgroup analysis of the PUNCH CD3 trial, we assessed outcomes in older adults (age ≥65 years) grouped by Charlson Comorbidity Index severity scores at screening (moderate [3-4] and severe [≥5]) and by the presence of underlying cardiac, renal, or gastrointestinal disorders. Results RBX2660 treatment success rates in older adults with comorbidities were consistent across subgroups and similar to those in the total RBX2660-treated population. A greater percentage of RBX2660-treated older adults remained free of CDI recurrence through 8 weeks following treatment compared with placebo-treated participants in all but 2 subgroups assessed. Across all subgroups, most treatment-emergent adverse events (TEAEs) were mild or moderate in severity and related to a preexisting condition. None of the serious or life-threatening TEAEs that occurred were related to RBX2660 or its administration. Occurrence of TEAEs did not cluster in any subgroup. Conclusions RBX2660 is efficacious and safe in older adults with recurrent CDI and underlying comorbidities.
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Affiliation(s)
- Glenn Tillotson
- Correspondence: Glenn Tillotson, PhD, GST Micro, 327 Plantation Road, North, VA 23128, USA ()
| | - Laurie Archbald-Pannone
- Department of Internal Medicine and Infectious Diseases, University of Virginia Hospital, Charlottesville, Virginia, USA
| | - Stuart Johnson
- Department of Infectious Diseases, Edward Hines Jr Veterans Affairs Hospital, Hines, Illinois, USA
- Loyola University Medical Center, Maywood, Illinois, USA
| | - Samson Ng
- Medical Affairs, Ferring Pharmaceuticals, Parsippany, New Jersey, USA
| | | | - Adam Harvey
- Clinical Research Department, Rebiotix Inc, a Ferring Company, Roseville, Minnesota, USA
| | - Lindy Bancke
- Clinical Research Department, Rebiotix Inc, a Ferring Company, Roseville, Minnesota, USA
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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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Double-edged sword: impact of fecal microbiome transplants on the gut resistome. Curr Opin Gastroenterol 2023; 39:16-22. [PMID: 36504032 DOI: 10.1097/mog.0000000000000894] [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] [Indexed: 12/15/2022]
Abstract
PURPOSE OF REVIEW Fecal microbiome transplants (FMT) show promise in treating various diseases, such as Clostridioides difficile infections. FMT have also demonstrated the capacity to modulate the collection of antibiotic resistance genes (ARGs), termed the resistome, within the gut. The purpose of this review was to critically evaluate the literature regarding the interaction between FMT and the gut resistome and determine whether FMT could be used specifically to reduce ARG carriage in the gut. RECENT FINDINGS Several studies have demonstrated a decrease in ARG carriage post-FMT administration in various disease states, including recurrent C. difficile infection and after antibiotic usage. However, other studies have reported an expansion of the resistome following FMT. Most studies contained small patient cohorts regardless of the outcome and showed heterogeneity in responses. SUMMARY Research on resistome modulation by FMT is preliminary, and human studies currently lack consensus regarding benefits and risks. From a safety perspective, screening donor samples for ARGs in addition to antibiotic-resistant organisms may be advisable. Additional studies on the mechanisms underlying heterogeneity between studies and individuals are required before FMT is considered an efficient approach for resistome amelioration.
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Impact of international travel and diarrhea on gut microbiome and resistome dynamics. Nat Commun 2022; 13:7485. [PMID: 36470885 PMCID: PMC9722912 DOI: 10.1038/s41467-022-34862-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 11/08/2022] [Indexed: 12/11/2022] Open
Abstract
International travel contributes to the global spread of antimicrobial resistance. Travelers' diarrhea exacerbates the risk of acquiring multidrug-resistant organisms and can lead to persistent gastrointestinal disturbance post-travel. However, little is known about the impact of diarrhea on travelers' gut microbiomes, and the dynamics of these changes throughout travel. Here, we assembled a cohort of 159 international students visiting the Andean city of Cusco, Peru and applied next-generation sequencing techniques to 718 longitudinally-collected stool samples. We find that gut microbiome composition changed significantly throughout travel, but taxonomic diversity remained stable. However, diarrhea disrupted this stability and resulted in an increased abundance of antimicrobial resistance genes that can remain high for weeks. We also identified taxa differentially abundant between diarrheal and non-diarrheal samples, which were used to develop a classification model that distinguishes between these disease states. Additionally, we sequenced the genomes of 212 diarrheagenic Escherichia coli isolates and found those from travelers who experienced diarrhea encoded more antimicrobial resistance genes than those who did not. In this work, we find the gut microbiomes of international travelers' are resilient to dysbiosis; however, they are also susceptible to colonization by multidrug-resistant bacteria, a risk that is more pronounced in travelers with diarrhea.
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Seekatz AM, Safdar N, Khanna S. The role of the gut microbiome in colonization resistance and recurrent Clostridioides difficile infection. Therap Adv Gastroenterol 2022; 15:17562848221134396. [PMID: 36425405 PMCID: PMC9679343 DOI: 10.1177/17562848221134396] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 10/04/2022] [Indexed: 11/21/2022] Open
Abstract
The species composition of the human gut microbiota is related to overall health, and a healthy gut microbiome is crucial in maintaining colonization resistance against pathogens. Disruption of gut microbiome composition and functionality reduces colonization resistance and has been associated with several gastrointestinal and non-gastrointestinal diseases. One prime example is Clostridioides difficile infection (CDI) and subsequent recurrent infections that occur after the development of systemic antibiotic-related dysbiosis. Standard-of-care antibiotics used for both acute and recurrent infections do not address dysbiosis and often worsen the condition. Moreover, monoclonal antibodies, recommended in conjunction with standard-of-care antibiotics for the prevention of recurrent CDI in patients at high risk of recurrence, reduce recurrences but do not address the underlying dysbiosis. Fecal microbiota transplantation (FMT) is an evolving therapeutic strategy in which microbes are harvested from healthy donor stool and transplanted into the gut of a recipient to restore the gut microbiome. Although effective in the prevention of recurrent CDI, some existing challenges include screening and the standardization of stool acquisition and processing. Recent safety alerts by the US Food and Drug Administration raised concern about the possibility of transmission of multidrug-resistant organisms or severe acute respiratory syndrome coronavirus 2 via FMT. Increased knowledge that microbes are beneficial in restoring the gut microbiome has led to the clinical development of several newer biotherapeutic formulations that are more regulated than FMT, which may allow for improved restoration of the gut microbiome and prevention of CDI recurrence. This review focuses on mechanisms by which gut microbiome restoration could influence colonization resistance against the pathogen C. difficile. Plain language summary The Role of the Gut Microbiome in Clostridioides difficile Infection Introduction: A rich and diverse gut microbiome is key to immune system regulation and colonization resistance against pathogens.A disruption in the gut microbiome composition can make the gut more vulnerable to diseases such as Clostridioides difficile infection (CDI), caused by the bacterium C. difficile.CDI management presents a therapeutic dilemma, as it is usually treated with antibiotics that can treat the infection but also can damage the microbiome.Treatment of CDI using antibiotics can further reduce microbial diversity and deplete beneficial bacteria from the gut leading to a condition called dysbiosis.Antibiotic treatment can be followed by therapies that restore the gut microbiota, boost colonization resistance, and prevent the development of antimicrobial resistance.It is important to evaluate treatment options to determine their safety and effectiveness. Methods: The researchers provided an overview of the mechanisms that the gut microbiome uses to prevent colonization of the gut by pathogens.They subsequently reviewed the efficacy and shortcomings of the following treatments for CDI: - Antibiotics- Monoclonal antibodies- Fecal microbiota transplantation (FMT) Results: Commensal intestinal bacteria prevent colonization of the gut by pathogens using mechanisms such as: - Competition for key nutrients- Production of inhibitory bile acids- Short-chain fatty acid production- Lowering the luminal pH- Production of bacteriocinsAntibiotic therapy is recommended as a standard treatment for CDI. However, patients are vulnerable to recurrent CDI after discontinuation of the therapy.Monoclonal antibodies that inactivate C. difficile toxins may be recommended along with antibiotics to prevent recurrent CDI. However, this approach does not restore the microbiome.FMT is one method of microbial restoration, where stool is harvested from a healthy donor and transplanted into a patient's colon.Although FMT has shown some efficacy in the treatment of recurrent CDI, the procedure is not standardized.Safety concerns have been raised about the possibility of transmission of multidrug-resistant pathogens via FMT. Conclusion: Treatment methods that can efficiently restore the diversity of the gut microbiome are crucial in preventing recurrence of CDI.
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Affiliation(s)
| | - Nasia Safdar
- University of Wisconsin, Madison, WI, USA
- William S. Middleton Memorial VA Hospital, Madison, WI, USA
| | - Sahil Khanna
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA
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Pan X, Zhou Z, Liu B, Wu Z. A novel therapeutic concern: Antibiotic resistance genes in common chronic diseases. Front Microbiol 2022; 13:1037389. [DOI: 10.3389/fmicb.2022.1037389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 09/26/2022] [Indexed: 11/13/2022] Open
Abstract
Infections caused by multidrug-resistant bacteria carrying antibiotic resistance genes pose a severe threat to global public health and human health. In clinical practice, it has been found that human gut microbiota act as a “reservoir” of antibiotic resistance genes (ARGs) since gut microbiota contain a wide variety of ARGs, and that the structure of the gut microbiome is influenced by the profile of the drug resistance genes present. In addition, ARGs can spread within and between species of the gut microbiome in multiple ways. To better understand gut microbiota ARGs and their effects on patients with chronic diseases, this article reviews the generation of ARGs, common vectors that transmit ARGs, the characteristics of gut microbiota ARGs in common chronic diseases, their impact on prognosis, the current state of treatment for ARGs, and what should be addressed in future research.
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Boeriu A, Roman A, Fofiu C, Dobru D. The Current Knowledge on Clostridioides difficile Infection in Patients with Inflammatory Bowel Diseases. Pathogens 2022; 11:pathogens11070819. [PMID: 35890064 PMCID: PMC9323231 DOI: 10.3390/pathogens11070819] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/17/2022] [Accepted: 07/18/2022] [Indexed: 11/17/2022] Open
Abstract
Clostridioides difficile (C. difficile) represents a major health burden with substantial economic and clinical impact. Patients with inflammatory bowel diseases (IBD) were identified as a risk category for Clostridioides difficile infection (CDI). In addition to traditional risk factors for C. difficile acquisition, IBD-specific risk factors such as immunosuppression, severity and extension of the inflammatory disease were identified. C. difficile virulence factors, represented by both toxins A and B, induce the damage of the intestinal mucosa and vascular changes, and promote the inflammatory host response. Given the potential life-threatening complications, early diagnostic and therapeutic interventions are required. The screening for CDI is recommended in IBD exacerbations, and the diagnostic algorithm consists of clinical evaluation, enzyme immunoassays (EIAs) or nucleic acid amplification tests (NAATs). An increased length of hospitalization, increased colectomy rate and mortality are the consequences of concurrent CDI in IBD patients. Selection of CD strains of higher virulence, antibiotic resistance, and the increasing rate of recurrent infections make the management of CDI in IBD more challenging. An individualized therapeutic approach is recommended to control CDI as well as IBD flare. Novel therapeutic strategies have been developed in recent years in order to manage severe, refractory or recurrent CDI. In this article, we aim to review the current evidence in the field of CDI in patients with underlying IBD, pointing to pathogenic mechanisms, risk factors for infection, diagnostic steps, clinical impact and outcomes, and specific management.
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Affiliation(s)
- Alina Boeriu
- Gastroenterology Department, University of Medicine Pharmacy, Sciences, and Technology “George Emil Palade” Targu Mures, 540142 Targu Mures, Romania; (A.B.); (C.F.); (D.D.)
- Gastroenterology Department, Mures County Clinical Hospital, 540103 Targu Mures, Romania
| | - Adina Roman
- Gastroenterology Department, University of Medicine Pharmacy, Sciences, and Technology “George Emil Palade” Targu Mures, 540142 Targu Mures, Romania; (A.B.); (C.F.); (D.D.)
- Gastroenterology Department, Mures County Clinical Hospital, 540103 Targu Mures, Romania
- Correspondence: ; Tel.: +40-752934465
| | - Crina Fofiu
- Gastroenterology Department, University of Medicine Pharmacy, Sciences, and Technology “George Emil Palade” Targu Mures, 540142 Targu Mures, Romania; (A.B.); (C.F.); (D.D.)
| | - Daniela Dobru
- Gastroenterology Department, University of Medicine Pharmacy, Sciences, and Technology “George Emil Palade” Targu Mures, 540142 Targu Mures, Romania; (A.B.); (C.F.); (D.D.)
- Gastroenterology Department, Mures County Clinical Hospital, 540103 Targu Mures, Romania
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Performance Characteristics of Next-Generation Sequencing for the Detection of Antimicrobial Resistance Determinants in Escherichia coli Genomes and Metagenomes. mSystems 2022; 7:e0002222. [PMID: 35642524 PMCID: PMC9238399 DOI: 10.1128/msystems.00022-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Short-read sequencing can provide detection of multiple genomic determinants of antimicrobial resistance from single bacterial genomes and metagenomic samples. Despite its increasing application in human, animal, and environmental microbiology, including human clinical trials, the performance of short-read Illumina sequencing for antimicrobial resistance gene (ARG) detection, including resistance-conferring single nucleotide polymorphisms (SNPs), has not been systematically characterized. Using paired-end 2 × 150 bp (base pair) Illumina sequencing and an assembly-based method for ARG prediction, we determined sensitivity, positive predictive value (PPV), and sequencing depths required for ARG detection in an Escherichia coli isolate of sequence type (ST) 38 spiked into a synthetic microbial community at varying abundances. Approximately 300,000 reads or 15× genome coverage was sufficient to detect ARGs in E. coli ST38, with comparable sensitivity and PPV to ~100× genome coverage. Using metagenome assembly of mixed microbial communities, ARG detection at E. coli relative abundances of 1% would require assembly of approximately 30 million reads to achieve 15× target coverage. The minimum sequencing depths were validated using public data sets of 948 E. coli genomes and 10 metagenomic rectal swab samples. A read-based approach using k-mer alignment (KMA) for ARG prediction did not substantially improve minimum sequencing depths for ARG detection compared to assembly of the E. coli ST38 genome or the combined metagenomic samples. Analysis of sequencing depths from recent studies assessing ARG content in metagenomic samples demonstrated that sequencing depths had a median estimated detection frequency of 84% (interquartile range: 30%-92%) for a relative abundance of 1%. IMPORTANCE Systematically determining Illumina sequencing performance characteristics for detection of ARGs in metagenomic samples is essential to inform study design and appraisal of human, animal, and environmental metagenomic antimicrobial resistance studies. In this study, we quantified the performance characteristics of ARG detection in E. coli genomes and metagenomes and established a benchmark of ~15× coverage for ARG detection for E. coli in metagenomes. We demonstrate that for low relative abundances, sequencing depths of ~30 million reads or more may be required for adequate sensitivity for many applications.
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Trunfio M, Scabini S, Rugge W, Bonora S, Di Perri G, Calcagno A. Concurrent and Subsequent Co-Infections of Clostridioides difficile Colitis in the Era of Gut Microbiota and Expanding Treatment Options. Microorganisms 2022; 10:microorganisms10071275. [PMID: 35888994 PMCID: PMC9317215 DOI: 10.3390/microorganisms10071275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 06/19/2022] [Accepted: 06/22/2022] [Indexed: 02/01/2023] Open
Abstract
We narratively reviewed the physiopathology, epidemiology, and management of co-infections in Clostridioides difficile colitis (CDI) by searching the following keywords in Embase, MedLine, and PubMed: “Clostridium/Clostridioides difficile”, “co-infection”, “blood-stream infection” (BSI), “fungemia”, “Candida”, “Cytomegalovirus”, “probiotics”, “microbial translocation” (MT). Bacterial BSIs (mainly by Enterobacteriaceae and Enterococcus) and fungemia (mainly by Candida albicans) may occur in up to 20% and 9% of CDI, increasing mortality and length of hospitalization. Up to 68% of the isolates are multi-drug-resistant bacteria. A pivotal role is played by gut dysbiosis, intestinal barrier leakage, and MT. Specific risk factors are represented by CDI-inducing broad-spectrum antibiotics, oral vancomycin use, and CDI severity. Probiotics administration (mainly Saccharomyces and Lactobacillus) during moderate/severe CDI may favor probiotics superinfection. Other co-infections (such as Cytomegalovirus or protozoa) can complicate limited and specific cases. There is mounting evidence that fidaxomicin, bezlotoxumab, and fecal microbiota transplantation can significantly reduce the rate of co-infections compared to historical therapies by interrupting the vicious circle between CDI, treatments, and MT. Bacterial BSIs and candidemia represent the most common co-infections in CDI. Physicians should be aware of this complication to promptly diagnose and treat it and enforce preventive strategies that include a more comprehensive consideration of newer treatment options.
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Affiliation(s)
- Mattia Trunfio
- Unit of Infectious Diseases, Amedeo di Savoia Hospital, Department of Medical Sciences, University of Turin, 10149 Torino, Italy; (W.R.); (S.B.); (G.D.P.); (A.C.)
- Correspondence: ; Tel.: +39-0114393884
| | - Silvia Scabini
- Unit of Infectious Diseases, AOU “Città della Salute e della Scienza”, Department of Medical Sciences, University of Turin, 10149 Torino, Italy;
| | - Walter Rugge
- Unit of Infectious Diseases, Amedeo di Savoia Hospital, Department of Medical Sciences, University of Turin, 10149 Torino, Italy; (W.R.); (S.B.); (G.D.P.); (A.C.)
| | - Stefano Bonora
- Unit of Infectious Diseases, Amedeo di Savoia Hospital, Department of Medical Sciences, University of Turin, 10149 Torino, Italy; (W.R.); (S.B.); (G.D.P.); (A.C.)
| | - Giovanni Di Perri
- Unit of Infectious Diseases, Amedeo di Savoia Hospital, Department of Medical Sciences, University of Turin, 10149 Torino, Italy; (W.R.); (S.B.); (G.D.P.); (A.C.)
| | - Andrea Calcagno
- Unit of Infectious Diseases, Amedeo di Savoia Hospital, Department of Medical Sciences, University of Turin, 10149 Torino, Italy; (W.R.); (S.B.); (G.D.P.); (A.C.)
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Liu Y, Zhang F. Changes of antibiotic resistance genes and gut microbiota after the ingestion of goat milk. J Dairy Sci 2022; 105:4804-4817. [PMID: 35346469 DOI: 10.3168/jds.2021-21325] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 01/28/2022] [Indexed: 11/19/2022]
Abstract
Antibiotic resistance genes, as newly emerging contaminants, have become a serious challenge to public health through the food chain. The gut of humans and animals is an important reservoir for the development and dissemination of antibiotic resistance genes because of the great abundance and diversity of intestinal microbiota. In the present study, we evaluated the influence of goat milk on the diversity and abundance of antibiotic resistance genes and gut microbial communities, especially pathogenic bacteria. Male mice were used, 12 for each of the 2 groups: a control group that received sterile distilled water and a treated group that received goat milk, and gut microbiota and antibiotic resistance genes were compared in these groups using metagenomic analysis. The results revealed that ingestion of goat milk decreased the diversity and abundance of antibiotic resistance genes in the mice gut. The relative abundance of fluoroquinolone, peptide, macrolide, and β-lactam resistance genes in the total microbial genes significantly decreased after the intervention. Goat milk intake also significantly reduced the abundance of pathogenic bacteria, such as Clostridium bolteae, Clostridium symbiosum, Helicobacter cinaedi, and Helicobacter bilis. Therefore, goat milk intake might decrease the transfer potential of antibiotic resistance gene to pathogenic bacteria in the gut. In addition, bacteria with multiple resistance mechanisms accounted for approximately 4.5% of total microbial communities in the control group, whereas it was not detectable in the goat milk group, indicating the total inhibition by goat milk intake. This study highlights the influence of goat milk on antibiotic resistome and microbial communities in the gut, and provides a new insight into the function of goat milk for further study.
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Affiliation(s)
- Yufang Liu
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an 710119, China
| | - Fuxin Zhang
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an 710119, China.
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Crits-Christoph A, Hallowell HA, Koutouvalis K, Suez J. Good microbes, bad genes? The dissemination of antimicrobial resistance in the human microbiome. Gut Microbes 2022; 14:2055944. [PMID: 35332832 PMCID: PMC8959533 DOI: 10.1080/19490976.2022.2055944] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
A global rise in antimicrobial resistance among pathogenic bacteria has proved to be a major public health threat, with the rate of multidrug-resistant bacterial infections increasing over time. The gut microbiome has been studied as a reservoir of antibiotic resistance genes (ARGs) that can be transferred to bacterial pathogens via horizontal gene transfer (HGT) of conjugative plasmids and mobile genetic elements (the gut resistome). Advances in metagenomic sequencing have facilitated the identification of resistome modulators, including live microbial therapeutics such as probiotics and fecal microbiome transplantation that can either expand or reduce the abundances of ARG-carrying bacteria in the gut. While many different gut microbes encode for ARGs, they are not uniformly distributed across, or transmitted by, various members of the microbiome, and not all are of equal clinical relevance. Both experimental and theoretical approaches in microbial ecology have been applied to understand differing frequencies of ARG horizontal transfer between commensal microbes as well as between commensals and pathogens. In this commentary, we assess the evidence for the role of commensal gut microbes in encoding antimicrobial resistance genes, the degree to which they are shared both with other commensals and with pathogens, and the host and environmental factors that can impact resistome dynamics. We further discuss novel sequencing-based approaches for identifying ARGs and predicting future transfer events of clinically relevant ARGs from commensals to pathogens.
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Affiliation(s)
- Alexander Crits-Christoph
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Haley Anne Hallowell
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Kalia Koutouvalis
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Jotham Suez
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA,CONTACT Jotham Suez Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, 615 N Wolfe St, Baltimore, Maryland, USA, 21205
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35
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Zhang Y, Saint Fleur A, Feng H. The development of live biotherapeutics against Clostridioides difficile infection towards reconstituting gut microbiota. Gut Microbes 2022; 14:2052698. [PMID: 35319337 PMCID: PMC8959509 DOI: 10.1080/19490976.2022.2052698] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Clostridioides difficile is the most prevalent pathogen of nosocomial diarrhea. In the United States, over 450,000 cases of C. difficile infection (CDI), responsible for more than 29,000 deaths, are reported annually in recent years. Because of the emergence of hypervirulent strains and strains less susceptible to vancomycin and fidaxomicin, new therapeutics other than antibiotics are urgently needed. The gut microbiome serves as one of the first-line defenses against C. difficile colonization. The use of antibiotics causes gut microbiota dysbiosis and shifts the status from colonization resistance to infection. Hence, novel CDI biotherapeutics capable of reconstituting normal gut microbiota have become a focus of drug development in this field.
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Affiliation(s)
- Yongrong Zhang
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, MD21201, United States
| | - Ashley Saint Fleur
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, MD21201, United States
| | - Hanping Feng
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, MD21201, United States,CONTACT Hanping Feng Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, MD21201United States
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36
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Ni Q, Zhang P, Li Q, Han Z. Oxidative Stress and Gut Microbiome in Inflammatory Skin Diseases. Front Cell Dev Biol 2022; 10:849985. [PMID: 35321240 PMCID: PMC8937033 DOI: 10.3389/fcell.2022.849985] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 02/18/2022] [Indexed: 12/12/2022] Open
Abstract
Oxidative stress plays a dominant role in inflammatory skin diseases. Emerging evidence has shown that the close interaction occurred between oxidative stress and the gut microbiome. Overall, in this review, we have summarized the impact of oxidative stress and gut microbiome during the progression and treatment for inflammatory skin diseases, the interactions between gut dysbiosis and redox imbalance, and discussed the potential possible role of oxidative stress in the gut-skin axis. In addition, we have also elucidated the promising gut microbiome/redox-targeted therapeutic strategies for inflammatory skin diseases.
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Affiliation(s)
- Qingrong Ni
- Department of Dermatology, Air Force Medical Center, Fourth Military Medical University, Beijing, China
| | - Ping Zhang
- Department of Dermatology, Air Force Medical Center, Fourth Military Medical University, Beijing, China
| | - Qiang Li
- Department of Dermatology, Air Force Medical Center, Fourth Military Medical University, Beijing, China
| | - Zheyi Han
- Department of Gastroenterology, Air Force Medical Center, Fourth Military Medical University, Beijing, China
- *Correspondence: Zheyi Han,
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37
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Analysis of the clinical pipeline of treatments for drug resistant bacterial infections: despite progress, more action is needed. Antimicrob Agents Chemother 2022; 66:e0199121. [PMID: 35007139 PMCID: PMC8923189 DOI: 10.1128/aac.01991-21] [Citation(s) in RCA: 97] [Impact Index Per Article: 48.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
There is an urgent global need for new strategies and drugs to control and treat multidrug-resistant bacterial infections. In 2017, the World Health Organization (WHO) released a list of 12 antibiotic-resistant priority pathogens and began to critically analyze the antibacterial clinical pipeline. This review analyzes “traditional” and “nontraditional” antibacterial agents and modulators in clinical development current on 30 June 2021 with activity against the WHO priority pathogens mycobacteria and Clostridioides difficile. Since 2017, 12 new antibacterial drugs have been approved globally, but only vaborbactam belongs to a new antibacterial class. Also innovative is the cephalosporin derivative cefiderocol, which incorporates an iron-chelating siderophore that facilitates Gram-negative bacteria cell entry. Overall, there were 76 antibacterial agents in clinical development (45 traditional and 31 nontraditional), with 28 in phase 1, 32 in phase 2, 12 in phase 3, and 4 under regulatory evaluation. Forty-one out of 76 (54%) targeted WHO priority pathogens, 16 (21%) were against mycobacteria, 15 (20%) were against C. difficile, and 4 (5%) were nontraditional agents with broad-spectrum effects. Nineteen of the 76 antibacterial agents have new pharmacophores, and 4 of these have new modes of actions not previously exploited by marketed antibacterial drugs. Despite there being 76 antibacterial clinical candidates, this analysis indicated that there were still relatively few clinically differentiated antibacterial agents in late-stage clinical development, especially against critical-priority pathogens. We believe that future antibacterial research and development (R&D) should focus on the development of innovative and clinically differentiated candidates that have clear and feasible progression pathways to the market.
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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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Rao K, Dubberke ER. Can prediction scores be used to identify patients at risk of Clostridioides difficile infection? Curr Opin Gastroenterol 2022; 38:7-14. [PMID: 34628418 DOI: 10.1097/mog.0000000000000793] [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] [Indexed: 12/10/2022]
Abstract
PURPOSE OF REVIEW To describe the current state of literature on modeling risk of incident and recurrent Clostridioides difficile infection (iCDI and rCDI), to underscore limitations, and to propose a path forward for future research. RECENT FINDINGS There are many published risk factors and models for both iCDI and rCDI. The approaches include scores with a limited list of variables designed to be used at the bedside, but more recently have also included automated tools that take advantage of the entire electronic health record. Recent attempts to externally validate scores have met with mixed success. SUMMARY For iCDI, the performance largely hinges on the incidence, which even for hospitalized patients can be low (often <1%). Most scores fail to achieve high accuracy and/or are not externally validated. A challenge in predicting rCDI is the significant overlap with risk factors for iCDI, reducing the discriminatory ability of models. Automated electronic health record-based tools show promise but portability to other centers is challenging. Future studies should include external validation and consider biomarkers to augment performance.
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Affiliation(s)
- Krishna Rao
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Erik R Dubberke
- Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
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Ma X, Xu T, Qian M, Zhang Y, Yang Z, Han X. Faecal microbiota transplantation alleviates early-life antibiotic-induced gut microbiota dysbiosis and mucosa injuries in a neonatal piglet model. Microbiol Res 2021; 255:126942. [PMID: 34915267 DOI: 10.1016/j.micres.2021.126942] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 12/04/2021] [Accepted: 12/07/2021] [Indexed: 12/16/2022]
Abstract
Faecal microbiota transplantation (FMT) is a promising approach to modulate the gut microbiota. Gut microbiota dysbiosis caused by antibiotic administration is a universal problem. This study aimed to evaluate the effect of FMT on the dysbiosis of gut microbiota and metabolic profiles and injury of the intestinal barrier induced by antibiotics and used a neonatal piglet model. Neonatal piglets were administered ampicillin for 3 days, and antibiotic-induced dysbiosis was evaluated by the occurrence of diarrhoea and alteration of gut microbiota. Then, FMT was conducted for 3 days to rebuild the gut microbiota. High-throughput sequencing and a mass spectrometry platform were used for integrated microbiome-metabolome analysis. The results showed that antibiotics led to a decline in the diversity of gut microbiota. Furthermore, there was an increase in the relative abundance of potential pathogenic bacteria, such as Oscillibacter, Pseudomonas and Eubacterium, and an increase in the relative abundance of tetracycline resistance genes (tet genes). FMT restored the diversity and promoted the relative abundance of beneficial bacteria, such as Parabacteroides, Dorea and Parasutterella, while decreasing the relative abundance of tet genes. Untargeted metabolomics analysis found that alpha linolenic acid and linoleic acid metabolism were the key metabolic pathways utilized in the FMT group, and targeted metabolomics analysis further verified the variation in the associated metabolites arachidonic acid and conjugated linoleic acid. FMT also significantly enhanced the relative expression of tight junction (ZO-1, claudin-1 and occludin) and adherens junction (β-catenin, E-cadherin) proteins and anti-inflammatory cytokines (IL-10, TGF-β1) and reduced the production of proinflammatory cytokines (IL-6, IL-1β, TNF-α and IFN-γ) in the colon. FMT not only modulated the gut microbiota composition and microbial metabolism but also reduced the relative abundance of tet genes, improving the intestinal barrier function and inflammatory responses in antibiotic-treated piglets.
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Affiliation(s)
- Xin Ma
- Key Laboratory of Animal Nutrition and Feed Science in East China, Ministry of Agriculture, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Tingting Xu
- Key Laboratory of Animal Nutrition and Feed Science in East China, Ministry of Agriculture, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Mengqi Qian
- Key Laboratory of Animal Nutrition and Feed Science in East China, Ministry of Agriculture, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yuchen Zhang
- Key Laboratory of Animal Nutrition and Feed Science in East China, Ministry of Agriculture, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zhiren Yang
- Key Laboratory of Animal Nutrition and Feed Science in East China, Ministry of Agriculture, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; Hainan Institute of Zhejiang University, Yazhou Bay Science and Technology City, Yazhou District, Sanya 572025, China
| | - Xinyan Han
- Key Laboratory of Animal Nutrition and Feed Science in East China, Ministry of Agriculture, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; Hainan Institute of Zhejiang University, Yazhou Bay Science and Technology City, Yazhou District, Sanya 572025, China.
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Abstract
Microbes in the 21st century are understood as symbionts ‘completing’ the human ‘superorganism’ (Homo sapiens plus microbial partners-in-health). This paper addresses a significant paradox: despite the vast majority of our genes being microbial, the lack of routine safety testing for the microbiome has led to unintended collateral side effects from pharmaceuticals that can damage the microbiome and inhibit innate ‘colonization resistance’ against pathobionts. Examples are discussed in which a Microbiome First Medicine approach provides opportunities to ‘manage our microbes’ holistically, repair dysbiotic superorganisms, and restore health and resilience in the gut and throughout the body: namely, managing nosocomial infections for Clostridioides difficile and Staphylococcus aureus and managing the gut and neural systems (gut–brain axis) in autism spectrum disorder. We then introduce a risk analysis tool: the evidence map. This ‘mapping’ tool was recently applied by us to evaluate evidence for benefits, risks, and uncertainties pertaining to the breastmilk ecosystem. Here, we discuss the potential role of the evidence map as a risk analysis methodology to guide scientific and societal efforts to: (1) enhance ecosystem resilience, (2) ‘manage our microbes’, and (3) minimize the adverse effects of both acute and chronic diseases.
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Le Guern R, Stabler S, Gosset P, Pichavant M, Grandjean T, Faure E, Karaca Y, Faure K, Kipnis E, Dessein R. Colonization resistance against multi-drug-resistant bacteria: a narrative review. J Hosp Infect 2021; 118:48-58. [PMID: 34492304 DOI: 10.1016/j.jhin.2021.09.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 09/01/2021] [Accepted: 09/01/2021] [Indexed: 12/15/2022]
Abstract
Colonization resistance by gut microbiota is a fundamental phenomenon in infection prevention and control. Hospitalized patients may be exposed to multi-drug-resistant bacteria when hand hygiene compliance among healthcare workers is not adequate. An additional layer of defence is provided by the healthy gut microbiota, which helps clear the exogenous bacteria and acts as a safety net when hand hygiene procedures are not followed. This narrative review focuses on the role of the gut microbiota in colonization resistance against multi-drug-resistant bacteria, and its implications for infection control. The review discusses the underlying mechanisms of colonization resistance (direct or indirect), the concept of resilience of the gut microbiota, the link between the antimicrobial spectrum and gut dysbiosis, and possible therapeutic strategies. Antimicrobial stewardship is crucial to maximize the effects of colonization resistance. Avoiding unnecessary antimicrobial therapy, shortening the antimicrobial duration as much as possible, and favouring antibiotics with low anti-anaerobe activity may decrease the acquisition and expansion of multi-drug-resistant bacteria. Even after antimicrobial therapy, the resilience of the gut microbiota often occurs spontaneously. Spontaneous resilience explains the existence of a window of opportunity for colonization of multi-drug-resistant bacteria during or just after antimicrobial therapy. Strategies favouring resilience of the gut microbiota, such as high-fibre diets or precision probiotics, should be evaluated.
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Affiliation(s)
- R Le Guern
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, Centre for Infection and Immunity of Lille, Lille, France; Laboratoire de Bactériologie-Hygiène, CHU Lille, Lille, France.
| | - S Stabler
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, Centre for Infection and Immunity of Lille, Lille, France; Service de Maladies Infectieuses, CHU Lille, Lille, France
| | - P Gosset
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, Centre for Infection and Immunity of Lille, Lille, France
| | - M Pichavant
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, Centre for Infection and Immunity of Lille, Lille, France
| | - T Grandjean
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, Centre for Infection and Immunity of Lille, Lille, France
| | - E Faure
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, Centre for Infection and Immunity of Lille, Lille, France; Service de Maladies Infectieuses, CHU Lille, Lille, France
| | - Y Karaca
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, Centre for Infection and Immunity of Lille, Lille, France
| | - K Faure
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, Centre for Infection and Immunity of Lille, Lille, France; Service de Maladies Infectieuses, CHU Lille, Lille, France
| | - E Kipnis
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, Centre for Infection and Immunity of Lille, Lille, France; Service de Réanimation Chirurgicale, CHU Lille, Lille, France
| | - R Dessein
- Univ. Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, Centre for Infection and Immunity of Lille, Lille, France; Laboratoire de Bactériologie-Hygiène, CHU Lille, Lille, France
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Chiu CW, Tsai PJ, Lee CC, Ko WC, Hung YP. Application of Microbiome Management in Therapy for Clostridioides difficile Infections: From Fecal Microbiota Transplantation to Probiotics to Microbiota-Preserving Antimicrobial Agents. Pathogens 2021; 10:pathogens10060649. [PMID: 34073695 PMCID: PMC8225043 DOI: 10.3390/pathogens10060649] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 05/02/2021] [Accepted: 05/19/2021] [Indexed: 02/07/2023] Open
Abstract
Oral vancomycin and metronidazole, though they are the therapeutic choice for Clostridioides difficile infections (CDIs), also markedly disturb microbiota, leading to a prolonged loss of colonization resistance to C. difficile after therapy; as a result, their use is associated with a high treatment failure rate and high recurrent rate. An alternative for CDIs therapy contains the delivery of beneficial (probiotic) microorganisms into the intestinal tract to restore the microbial balance. Recently, mixture regimens containing Lactobacillus species, Saccharomyces boulardii, or Clostridium butyricum have been extensively studied for the prophylaxis of CDIs. Fecal microbiota transplantation (FMT), the transfer of (processed) fecal material from healthy donors to patients for treating CDIs, combined with vancomycin was recommended as the primary therapy for multiple recurrent CDIs (rCDIs). Either probiotics or FMT have been utilized extensively in preventing or treating CDIs, aiming at less disturbance in the microbiota to prevent rCDIs after therapy cessation. Otherwise, many newly developed therapeutic agents have been developed and aim to preserve microbiota during CDI treatment to prevent disease recurrence and might be useful in clinical patients with rCDIs in the future.
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Affiliation(s)
- Chun-Wei Chiu
- Department of Internal Medicine, Tainan Hospital, Ministry of Health and Welfare, Tainan 700, Taiwan;
| | - Pei-Jane Tsai
- Department of Medical Laboratory Science and Biotechnology, National Cheng Kung University, Medical College, Tainan 704, Taiwan;
| | - Ching-Chi Lee
- Clinical Medicine Research Center, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan;
- Department of Internal Medicine, College of Medicine, National Cheng Kung University Hospital, Tainan 704, Taiwan
| | - Wen-Chien Ko
- Department of Internal Medicine, College of Medicine, National Cheng Kung University Hospital, Tainan 704, Taiwan
- Department of Medicine, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan
- Correspondence: (W.-C.K.); (Y.-P.H.)
| | - Yuan-Pin Hung
- Department of Internal Medicine, Tainan Hospital, Ministry of Health and Welfare, Tainan 700, Taiwan;
- Department of Internal Medicine, College of Medicine, National Cheng Kung University Hospital, Tainan 704, Taiwan
- Department of Medicine, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan
- Correspondence: (W.-C.K.); (Y.-P.H.)
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Su F, Luo Y, Yu J, Shi J, Zhao Y, Yan M, Huang H, Tan Y. Tandem fecal microbiota transplantation cycles in an allogeneic hematopoietic stem cell transplant recipient targeting carbapenem-resistant Enterobacteriaceae colonization: a case report and literature review. Eur J Med Res 2021; 26:37. [PMID: 33910622 PMCID: PMC8080403 DOI: 10.1186/s40001-021-00508-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 04/13/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Due to limited antibiotic options, carbapenem-resistant Enterobacteriaceae (CRE) infections are associated with high non-relapse mortality after allogeneic hematopoietic stem cell transplantation (allo-HSCT). Also, intestinal CRE colonization is a risk factor for subsequent CRE infection. Several clinical studies have reported successful fecal microbiota transplantation (FMT) for the gut decontamination of a variety of multidrug-resistant bacteria (MDRB), even in immunosuppressed patients. Similarly, other studies have also indicated that multiple FMTs may increase or lead to successful therapeutic outcomes. CASE PRESENTATION We report CRE colonization in an allo-HSCT patient with recurrent CRE infections, and its successful eradication using tandem FMT cycles at 488 days after allo-HSCT. We also performed a comprehensive microbiota analysis. No acute or delayed adverse events (AEs) were observed. The patient remained clinically stable with CRE-negative stool culture at 26-month follow-up. Our analyses also showed some gut microbiota reconstruction. We also reviewed the current literature on decolonization strategies for CRE. CONCLUSIONS CRE colonization led to a high no-relapse mortality after allo-HSCT; however, well-established decolonization strategies are currently lacking. The successful decolonization of this patient suggests that multiple FMT cycles may be potential options for CRE decolonization.
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Affiliation(s)
- Fengqin Su
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Road, Hangzhou, 310003, China.,Institute of Hematology, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Yi Luo
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Road, Hangzhou, 310003, China.,Institute of Hematology, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Jian Yu
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Road, Hangzhou, 310003, China.,Institute of Hematology, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Jimin Shi
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Road, Hangzhou, 310003, China.,Institute of Hematology, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Yanmin Zhao
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Road, Hangzhou, 310003, China.,Institute of Hematology, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Mengni Yan
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Road, Hangzhou, 310003, China.,Institute of Hematology, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - He Huang
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Road, Hangzhou, 310003, China.,Institute of Hematology, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Yamin Tan
- Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Road, Hangzhou, 310003, China. .,Hematology Department, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, 1 Banshan East Road, Hangzhou, 310022, Zhejiang, China.
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45
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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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