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Romero-Rodríguez A, Ruíz-Villafán B, Sánchez S, Paredes-Sabja D. Is there a role for intestinal sporobiota in the antimicrobial resistance crisis? Microbiol Res 2024; 288:127870. [PMID: 39173554 DOI: 10.1016/j.micres.2024.127870] [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: 06/04/2024] [Revised: 07/23/2024] [Accepted: 08/06/2024] [Indexed: 08/24/2024]
Abstract
Antimicrobial resistance (AMR) is a complex issue requiring specific, multi-sectoral measures to slow its spread. When people are exposed to antimicrobial agents, it can cause resistant bacteria to increase. This means that the use, misuse, and excessive use of antimicrobial agents exert selective pressure on bacteria, which can lead to the development of "silent" reservoirs of antimicrobial resistance genes. These genes can later be mobilized into pathogenic bacteria and contribute to the spread of AMR. Many socioeconomic and environmental factors influence the transmission and dissemination of resistance genes, such as the quality of healthcare systems, water sanitation, hygiene infrastructure, and pollution. The sporobiota is an essential part of the gut microbiota that plays a role in maintaining gut homeostasis. However, because spores are highly transmissible and can spread easily, they can be a vector for AMR. The sporobiota resistome, particularly the mobile resistome, is important for tracking, managing, and limiting the spread of antimicrobial resistance genes among pathogenic and commensal bacterial species.
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Affiliation(s)
- A Romero-Rodríguez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, Ciudad de México 04510, Mexico.
| | - B Ruíz-Villafán
- Laboratorio de Microbiología Industrial. Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - S Sánchez
- Laboratorio de Microbiología Industrial. Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico
| | - D Paredes-Sabja
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
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2
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Lin S, Han S, Wang X, Wang X, Shi X, He Z, Sun M, Sun J. Oral Microto-Nano Genome-Editing System Enabling Targeted Delivery and Conditional Activation of CRISPR-Cas9 for Gene Therapy of Inflammatory Bowel Disease. ACS NANO 2024; 18:25657-25670. [PMID: 39215751 DOI: 10.1021/acsnano.4c07750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
The potent CRISPR-Cas9 technology can correct genes in human mutated cells to achieve the treatment of multiple diseases, but it lacks safe and effective delivery systems. Herein, we proposed an oral microto-nano genome-editing system aiming at the enteric excessive level of TNF-α for specific gene therapy of inflammatory bowel disease (IBD). This editing system facilitated the assembly of Cas9/sgRNA ribonucleoprotein (RNP) into nanoclusters (NCs) through the bridging of disulfide bonds. RNP-NCs were subsequently encapsulated within inflammatory cell-targeted lipopolysaccharide-deleted outer membrane vesicles (dOMVs) sourced from Escherichia coli Nissle 1917, which were further shielded by an outer layer of calcium alginate microspheres (CAMs). By leveraging the protection effect of CAMs, the oral administration system withstood gastric acid degradation upon entry into the stomach, achieving targeted delivery to the intestines with high efficiency. As the pH gradually rose, the microscale CAMs swelled and disintegrated, releasing nanoscale RNP-NCs encapsulated in dOMVs into the intestines. These RNP-NCs@dOMVs could traverse the mucosal barrier and target inflammatory macrophages where conditionally activated Cas9/sgRNA RNPs effectively perform genomic editing of TNF-α within the nucleus. Such oral microto-nano genome-editing systems represent a promising translational platform for the treatment of IBD.
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Affiliation(s)
- Sicen Lin
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China
| | - Shuwen Han
- Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, Huzhou, Zhejiang313000, China
| | - Xu Wang
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China
| | - Xinyue Wang
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China
| | - Xianbao Shi
- Department of Pharmacy, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, Liaoning 121001, China
| | - Zhonggui He
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China
- Joint International Research Laboratory of Intelligent Drug Delivery Systems, Ministry of Education, Shenyang, Liaoning 110016, China
| | - Mengchi Sun
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China
- Joint International Research Laboratory of Intelligent Drug Delivery Systems, Ministry of Education, Shenyang, Liaoning 110016, China
| | - Jin Sun
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China
- Joint International Research Laboratory of Intelligent Drug Delivery Systems, Ministry of Education, Shenyang, Liaoning 110016, China
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3
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Li X, Xiao F, Wang X, Ye L, Xiao Y, Li D, Zhang T, Wang Y. Gut Microbial and Metabolic Features Associated With Clostridioides difficile Infection Recurrence in Children. Open Forum Infect Dis 2024; 11:ofae506. [PMID: 39319090 PMCID: PMC11420671 DOI: 10.1093/ofid/ofae506] [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] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Accepted: 09/02/2024] [Indexed: 09/26/2024] Open
Abstract
Background Recurrent Clostridioides difficile infection (CDI) is a critical clinical issue due to the increase in incidence and difficulty in treatment. We aimed to identify gut microbial and metabolic features associated with disease recurrence in a group of pediatric CDI patients. Methods A total of 84 children with primary CDI were prospectively enrolled in the study. Fecal samples collected at the initial diagnosis were subjected to 16S rRNA gene sequencing and targeted metabolomics analysis to profile the bacterial composition and metabolome. Results Twenty-six of 84 (31.0%) pediatric CDI patients experienced recurrence. The alpha diversity of the fecal microbiota was significantly lower in the recurrent group than in the nonrecurrent group, and the beta diversity was different from that of the nonrecurrent group. Taxonomic profiles revealed that the relative abundances of multiple bacterial taxa significantly differed between the recurrent and nonrecurrent groups. Linear discriminant analysis effect size analysis identified several bacterial genera that discriminated between recurrent and nonrecurrent groups, including Parabacteroides, Coprococcus, Dialister, and Clostridium. Recurrent bacteria presented lower abundances of several short-chain fatty acid (SCFA)-producing bacteria (Faecalibacterium, Butyricicoccus, Clostridium, Roseburia, and Ruminococcus), which were correlated with reduced fecal SCFA levels. In addition, several bile acids, including lithocholic acid (LCA), 12-ketoLCA, trihydroxycholestanoic acid, and deoxycholic acid, were decreased in recurrent patients. Conclusions Our study suggests that the differing gut microbiota profiles in pediatric CDI patients may contribute to disease recurrence by modulating SCFA concentrations and bile acid profiles. The gut microbiota and metabolite signatures may be used to predict disease recurrence in children with CDI.
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Affiliation(s)
- Xiaolu Li
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Fangfei Xiao
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xufei Wang
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Lin Ye
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yongmei Xiao
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Dan Li
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ting Zhang
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Gut Microbiota and Metabolic Research Center, Institute of Pediatric Infection, Immunity and Critical Care Medicine, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yizhong Wang
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Gut Microbiota and Metabolic Research Center, Institute of Pediatric Infection, Immunity and Critical Care Medicine, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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Bilska A, Wochna K, Habiera M, Serwańska-Leja K. Health Hazard Associated with the Presence of Clostridium Bacteria in Food Products. Foods 2024; 13:2578. [PMID: 39200505 PMCID: PMC11353352 DOI: 10.3390/foods13162578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Revised: 07/28/2024] [Accepted: 08/16/2024] [Indexed: 09/02/2024] Open
Abstract
Clostridium bacteria were already known to Hippocrates many years before Christ. The name of the Clostridium species is owed to the Polish microbiologist, Adam Prażmowski. It is now known that these Clostridium bacteria are widespread in the natural environment, and their presence in food products is a threat to human health and life. According to European Food Safety Authority (EFSA) reports, every year, there are poisonings or deaths due to ingestion of bacterial toxins, including those of the Clostridium spp. The strengthening of consumer health awareness has increased interest in consuming products with minimal processing in recent years, which has led to a need to develop new techniques to ensure the safety of microbiological food, including elimination of bacteria from the Clostridium genera. On the other hand, the high biochemical activity of Clostridium bacteria allows them to be used in the chemical, pharmaceutical, and medical industries. Awareness of microbiological food safety is very important for our health. Unfortunately, in 2022, an increase in infections with Clostridium bacteria found in food was recorded. Knowledge about food contamination should thus be widely disseminated.
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Affiliation(s)
- Agnieszka Bilska
- Department of Food and Nutrition, Poznan University of Physical Education, Krolowej Jadwigi 27/39, 61-871 Poznan, Poland;
| | - Krystian Wochna
- Department of Swimming and Water Lifesaving, Poznan University of Physical Education, Krolowej Jadwigi 27/39, 61-871 Poznan, Poland; (K.W.)
| | - Małgorzata Habiera
- Department of Swimming and Water Lifesaving, Poznan University of Physical Education, Krolowej Jadwigi 27/39, 61-871 Poznan, Poland; (K.W.)
| | - Katarzyna Serwańska-Leja
- Department of Sports Dietetics, Poznan University of Physical Education, 61-871 Poznan, Poland
- Department of Animal Anatomy, Faculty of Veterinary Medicine and Animal Sciences, Poznan University of Life Sciences, Wojska Polskiego 71c, 60-625 Poznan, Poland
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5
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Spigaglia P. Clostridioides difficile and Gut Microbiota: From Colonization to Infection and Treatment. Pathogens 2024; 13:646. [PMID: 39204246 PMCID: PMC11357127 DOI: 10.3390/pathogens13080646] [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: 07/08/2024] [Revised: 07/23/2024] [Accepted: 07/29/2024] [Indexed: 09/03/2024] Open
Abstract
Clostridioides difficile is the main causative agent of antibiotic-associated diarrhea (AAD) in hospitals in the developed world. Both infected patients and asymptomatic colonized individuals represent important transmission sources of C. difficile. C. difficile infection (CDI) shows a large range of symptoms, from mild diarrhea to severe manifestations such as pseudomembranous colitis. Epidemiological changes in CDIs have been observed in the last two decades, with the emergence of highly virulent types and more numerous and severe CDI cases in the community. C. difficile interacts with the gut microbiota throughout its entire life cycle, and the C. difficile's role as colonizer or invader largely depends on alterations in the gut microbiota, which C. difficile itself can promote and maintain. The restoration of the gut microbiota to a healthy state is considered potentially effective for the prevention and treatment of CDI. Besides a fecal microbiota transplantation (FMT), many other approaches to re-establishing intestinal eubiosis are currently under investigation. This review aims to explore current data on C. difficile and gut microbiota changes in colonized individuals and infected patients with a consideration of the recent emergence of highly virulent C. difficile types, with an overview of the microbial interventions used to restore the human gut microbiota.
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Affiliation(s)
- Patrizia Spigaglia
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Roma, Italy
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Furtado KL, Plott L, Markovetz M, Powers D, Wang H, Hill DB, Papin J, Allbritton NL, Tamayo R. Clostridioides difficile-mucus interactions encompass shifts in gene expression, metabolism, and biofilm formation. mSphere 2024; 9:e0008124. [PMID: 38837404 PMCID: PMC11332178 DOI: 10.1128/msphere.00081-24] [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: 02/01/2024] [Accepted: 04/28/2024] [Indexed: 06/07/2024] Open
Abstract
In a healthy colon, the stratified mucus layer serves as a crucial innate immune barrier to protect the epithelium from microbes. Mucins are complex glycoproteins that serve as a nutrient source for resident microflora and can be exploited by pathogens. We aimed to understand how the intestinal pathogen, Clostridioides difficile, independently uses or manipulates mucus to its benefit, without contributions from members of the microbiota. Using a 2-D primary human intestinal epithelial cell model to generate physiologic mucus, we assessed C. difficile-mucus interactions through growth assays, RNA-Seq, biophysical characterization of mucus, and contextualized metabolic modeling. We found that host-derived mucus promotes C. difficile growth both in vitro and in an infection model. RNA-Seq revealed significant upregulation of genes related to central metabolism in response to mucus, including genes involved in sugar uptake, the Wood-Ljungdahl pathway, and the glycine cleavage system. In addition, we identified differential expression of genes related to sensing and transcriptional control. Analysis of mutants with deletions in highly upregulated genes reflected the complexity of C. difficile-mucus interactions, with potential interplay between sensing and growth. Mucus also stimulated biofilm formation in vitro, which may in turn alter the viscoelastic properties of mucus. Context-specific metabolic modeling confirmed differential metabolism and the predicted importance of enzymes related to serine and glycine catabolism with mucus. Subsequent growth experiments supported these findings, indicating mucus is an important source of serine. Our results better define responses of C. difficile to human gastrointestinal mucus and highlight flexibility in metabolism that may influence pathogenesis. IMPORTANCE Clostridioides difficile results in upward of 250,000 infections and 12,000 deaths annually in the United States. Community-acquired infections continue to rise, and recurrent disease is common, emphasizing a vital need to understand C. difficile pathogenesis. C. difficile undoubtedly interacts with colonic mucus, but the extent to which the pathogen can independently respond to and take advantage of this niche has not been explored extensively. Moreover, the metabolic complexity of C. difficile remains poorly understood but likely impacts its capacity to grow and persist in the host. Here, we demonstrate that C. difficile uses native colonic mucus for growth, indicating C. difficile possesses mechanisms to exploit the mucosal niche. Furthermore, mucus induces metabolic shifts and biofilm formation in C. difficile, which has potential ramifications for intestinal colonization. Overall, our work is crucial to better understand the dynamics of C. difficile-mucus interactions in the context of the human gut.
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Affiliation(s)
- Kathleen L. Furtado
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| | - Lucas Plott
- Marsico Lung Institute, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| | - Matthew Markovetz
- Marsico Lung Institute, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| | - Deborah Powers
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, USA
| | - Hao Wang
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | - David B. Hill
- Marsico Lung Institute, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Physics and Astronomy, College of Arts and Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jason Papin
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, USA
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia, USA
- Department of Medicine, Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | - Nancy L. Allbritton
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | - Rita Tamayo
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
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Okhuysen PC, Ramesh MS, Louie T, Kiknadze N, Torre-Cisneros J, de Oliveira CM, Van Steenkiste C, Stychneuskaya A, Garey KW, Garcia-Diaz J, Li J, Duperchy E, Chang BY, Sukbuntherng J, Montoya JG, Styles L, Clow F, James D, Dubberke ER, Wilcox M. A Randomized, Double-Blind, Phase 3 Safety and Efficacy Study of Ridinilazole Versus Vancomycin for Treatment of Clostridioides difficile Infection: Clinical Outcomes With Microbiome and Metabolome Correlates of Response. Clin Infect Dis 2024; 78:1462-1472. [PMID: 38305378 PMCID: PMC11175683 DOI: 10.1093/cid/ciad792] [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: 10/02/2023] [Indexed: 02/03/2024] Open
Abstract
BACKGROUND Exposure to antibiotics predisposes to dysbiosis and Clostridioides difficile infection (CDI) that can be severe, recurrent (rCDI), and life-threatening. Nonselective drugs that treat CDI and perpetuate dysbiosis are associated with rCDI, in part due to loss of microbiome-derived secondary bile acid (SBA) production. Ridinilazole is a highly selective drug designed to treat CDI and prevent rCDI. METHODS In this phase 3 superiority trial, adults with CDI, confirmed with a stool toxin test, were randomized to receive 10 days of ridinilazole (200 mg twice daily) or vancomycin (125 mg 4 times daily). The primary endpoint was sustained clinical response (SCR), defined as clinical response and no rCDI through 30 days after end of treatment. Secondary endpoints included rCDI and change in relative abundance of SBAs. RESULTS Ridinilazole and vancomycin achieved an SCR rate of 73% versus 70.7%, respectively, a treatment difference of 2.2% (95% CI: -4.2%, 8.6%). Ridinilazole resulted in a 53% reduction in recurrence compared with vancomycin (8.1% vs 17.3%; 95% CI: -14.1%, -4.5%; P = .0002). Subgroup analyses revealed consistent ridinilazole benefit for reduction in rCDI across subgroups. Ridinilazole preserved microbiota diversity, increased SBAs, and did not increase the resistome. Conversely, vancomycin worsened CDI-associated dysbiosis, decreased SBAs, increased Proteobacteria abundance (∼3.5-fold), and increased the resistome. CONCLUSIONS Although ridinilazole did not meet superiority in SCR, ridinilazole greatly reduced rCDI and preserved microbiome diversity and SBAs compared with vancomycin. These findings suggest that treatment of CDI with ridinilazole results in an earlier recovery of gut microbiome health. Clinical Trials Registration.Ri-CoDIFy 1 and 2: NCT03595553 and NCT03595566.
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Affiliation(s)
- Pablo C Okhuysen
- Department of Infectious Diseases, Infection Control, and Employee Heatlh, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | - Thomas Louie
- Foothills Medical Center and University of Calgary, Calgary, Canada
| | | | - Julian Torre-Cisneros
- Reina Sofia University Hospital-IMIBIC, University of Córdoba, CIBERINFEC, Cordoba, Spain
| | | | | | | | - Kevin W Garey
- University of Houston College of Pharmacy, Houston, Texas, USA
| | | | - Jianling Li
- Summit Therapeutics, Menlo Park, California, USA
| | | | | | | | - Jose G Montoya
- Summit Therapeutics, Menlo Park, California, USA
- Dr. Jack S. Remington Laboratory for Specialty Diagnostics, Palo Alto Medical Foundation, Palo Alto, California, USA
| | - Lori Styles
- Summit Therapeutics, Menlo Park, California, USA
| | - Fong Clow
- Summit Therapeutics, Menlo Park, California, USA
| | | | - Erik R Dubberke
- Washington University School of Medicine, St.Louis, Missouri, USA
| | - Mark Wilcox
- Leeds Teaching Hospitals and University of Leeds, School of Medicine, Leeds, United Kingdom
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Tang M, Wang C, Xia Y, Tang J, Wang J, Shen L. Clostridioides difficile infection in inflammatory bowel disease: a clinical review. Expert Rev Anti Infect Ther 2024; 22:297-306. [PMID: 38676422 DOI: 10.1080/14787210.2024.2347955] [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: 03/14/2023] [Accepted: 04/23/2024] [Indexed: 04/28/2024]
Abstract
INTRODUCTION Strong clinical data demonstrate that inflammatory bowel disease (IBD) is an independent risk factor for Clostridiodes difficile infection (CDI) and suggest a globally increased prevalence and severity of C. difficile coinfection in IBD patients (CDI-IBD). In addition to elderly individuals, children are also at higher risk of CDI-IBD. Rapid diagnosis is essential since the clinical manifestations of active IBD and CDI-IBD are indistinguishable. Antibiotics have been well established in the treatment of CDI-IBD, but they do not prevent recurrence. AREAS COVERED Herein, the authors focus on reviewing recent research advances on the new therapies of CDI-IBD. The novel therapies include gut microbiota restoration therapies (such as prebiotics, probiotics and FMT), immunotherapy (such as vaccines and monoclonal antibodies) and diet strategies (such as groningen anti-inflammatory diet and mediterranean diet). Future extensive prospective and placebo-controlled studies are required to evaluate their efficacy and long-term safety. EXPERT OPINION Available studies show that the prevalence of CDI-IBD is not optimistic. Currently, potential treatment options for CDI-IBD include a number of probiotics and novel antibiotics. This review updates the knowledge on the management of CDI in IBD patients, which is timely and important for GI doctors and scientists.
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Affiliation(s)
- Mengjun Tang
- Central Laboratory, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, China
| | - Chunhua Wang
- Central Laboratory, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, China
| | - Ying Xia
- Central Laboratory, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, China
| | - Jian Tang
- Central Laboratory, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, China
| | - Jiao Wang
- Central Laboratory, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, China
- School of Basic Medicine, Hubei University of Arts and Science, Xiangyang, China
| | - Liang Shen
- Central Laboratory, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, China
- Department of Clinical Laboratory, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, China
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9
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Monday L, Tillotson G, Chopra T. Microbiota-Based Live Biotherapeutic Products for Clostridioides Difficile Infection- The Devil is in the Details. Infect Drug Resist 2024; 17:623-639. [PMID: 38375101 PMCID: PMC10876012 DOI: 10.2147/idr.s419243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 02/12/2024] [Indexed: 02/21/2024] Open
Abstract
Clostridioides difficile infection (CDI) remains a significant contributor to healthcare costs and morbidity due to high rates of recurrence. Currently, available antibiotic treatment strategies further disrupt the fecal microbiome and do not address the alterations in commensal flora (dysbiosis) that set the stage for CDI. Advances in microbiome-based research have resulted in the development of new agents, classified as live biotherapeutic products (LBPs), for preventing recurrent CDI (rCDI) by restoring eubiosis. Prior to the LBPs, fecal microbiota transplantation (FMT) was available for this purpose; however, lack of large-scale availability and safety concerns have remained barriers to its widespread use. The LBPs are an exciting development, but questions remain. Some are derived directly from human stool while other developmental products contain a defined microbial consortium manufactured ex vivo, and they may be composed of either living bacteria or their spores, making it difficult to compare members of this heterogenous drug class to one another. None have been studied head-to head or against FMT in preventing rCDI. As a class, they have considerable variability in their biologic composition, biopharmaceutic science, route of administration, stages of development, and clinical trial data. This review will start by explaining the role of dysbiosis in CDI, then give the details of the biopharmaceutical components for the LBPs which are approved or in development including how they differ from FMT and from one another. We then discuss the clinical trials of the LBPs currently approved for rCDI and end with the future clinical directions of LBPs beyond C. difficile.
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Affiliation(s)
- Lea Monday
- Division of Infectious Diseases, Wayne State University School of Medicine, Detroit, MI, USA
| | | | - Teena Chopra
- Division of Infectious Diseases, Wayne State University School of Medicine, Detroit, MI, USA
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10
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Furtado KL, Plott L, Markovetz M, Powers D, Wang H, Hill DB, Papin J, Allbritton NL, Tamayo R. Clostridioides difficile-mucus interactions encompass shifts in gene expression, metabolism, and biofilm formation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.01.578425. [PMID: 38352512 PMCID: PMC10862863 DOI: 10.1101/2024.02.01.578425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/25/2024]
Abstract
In a healthy colon, the stratified mucus layer serves as a crucial innate immune barrier to protect the epithelium from microbes. Mucins are complex glycoproteins that serve as a nutrient source for resident microflora and can be exploited by pathogens. We aimed to understand how the intestinal pathogen, Clostridioides diffiicile, independently uses or manipulates mucus to its benefit, without contributions from members of the microbiota. Using a 2-D primary human intestinal epithelial cell model to generate physiologic mucus, we assessed C. difficile-mucus interactions through growth assays, RNA-Seq, biophysical characterization of mucus, and contextualized metabolic modeling. We found that host-derived mucus promotes C. difficile growth both in vitro and in an infection model. RNA-Seq revealed significant upregulation of genes related to central metabolism in response to mucus, including genes involved in sugar uptake, the Wood-Ljungdahl pathway, and the glycine cleavage system. In addition, we identified differential expression of genes related to sensing and transcriptional control. Analysis of mutants with deletions in highly upregulated genes reflected the complexity of C. difficile-mucus interactions, with potential interplay between sensing and growth. Mucus also stimulated biofilm formation in vitro, which may in turn alter viscoelastic properties of mucus. Context-specific metabolic modeling confirmed differential metabolism and predicted importance of enzymes related to serine and glycine catabolism with mucus. Subsequent growth experiments supported these findings, indicating mucus is an important source of serine. Our results better define responses of C. difficile to human gastrointestinal mucus and highlight a flexibility in metabolism that may influence pathogenesis.
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Affiliation(s)
- Kathleen L. Furtado
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Lucas Plott
- Marsico Lung Institute, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Matthew Markovetz
- Marsico Lung Institute, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Deborah Powers
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Hao Wang
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - David B. Hill
- Marsico Lung Institute, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Physics and Astronomy, College of Arts and Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jason Papin
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA
- Department of Medicine, Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | | | - Rita Tamayo
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
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11
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Shin JH, Tillotson G, MacKenzie TN, Warren CA, Wexler HM, Goldstein EJC. Bacteroides and related species: The keystone taxa of the human gut microbiota. Anaerobe 2024; 85:102819. [PMID: 38215933 DOI: 10.1016/j.anaerobe.2024.102819] [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: 09/06/2023] [Revised: 01/08/2024] [Accepted: 01/09/2024] [Indexed: 01/14/2024]
Abstract
Microbial communities play a significant role in maintaining ecosystems in a healthy homeostasis. Presently, in the human gastrointestinal tract, there are certain taxonomic groups of importance, though there is no single species that plays a keystone role. Bacteroides spp. are known to be major players in the maintenance of eubiosis in the human gastrointestinal tract. Here we review the critical role that Bacteroides play in the human gut, their potential pathogenic role outside of the gut, and their various methods of adapting to the environment, with a focus on data for B. fragilis and B. thetaiotaomicron. Bacteroides are anaerobic non-sporing Gram negative organisms that are also resistant to bile acids, generally thriving in the gut and having a beneficial relationship with the host. While they are generally commensal organisms, some Bacteroides spp. can be opportunistic pathogens in scenarios of GI disease, trauma, cancer, or GI surgery, and cause infection, most commonly intra-abdominal infection. B. fragilis can develop antimicrobial resistance through multiple mechanisms in large part due to its plasticity and fluid genome. Bacteroidota (formerly, Bacteroidetes) have a very broad metabolic potential in the GI microbiota and can rapidly adapt their carbohydrate metabolism to the available nutrients. Gastrointestinal Bacteroidota species produce short-chain fatty acids such as succinate, acetate, butyrate, and occasionally propionate, as the major end-products, which have wide-ranging and many beneficial influences on the host. Bacteroidota, via bile acid metabolism, also play a role in in colonization-resistance of other organisms, including Clostridioides difficile, and maintenance of gut integrity.
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Affiliation(s)
- Jae Hyun Shin
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA.
| | | | | | - Cirle A Warren
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA.
| | - Hannah M Wexler
- GLAVAHCS, Los Angeles, CA, USA; David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
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12
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Gurung B, Stricklin M, Wang S. Gut Microbiota-Gut Metabolites and Clostridioides difficile Infection: Approaching Sustainable Solutions for Therapy. Metabolites 2024; 14:74. [PMID: 38276309 PMCID: PMC10819375 DOI: 10.3390/metabo14010074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 01/06/2024] [Accepted: 01/19/2024] [Indexed: 01/27/2024] Open
Abstract
Clostridioides difficile (C. difficile) infection (CDI) is the most common hospital-acquired infection. With the combination of a high rate of antibiotic resistance and recurrence, it has proven to be a debilitating public health threat. Current treatments for CDI include antibiotics and fecal microbiota transplantation, which contribute to recurrent CDIs and potential risks. Therefore, there is an ongoing need to develop new preventative treatment strategies for CDI. Notably, gut microbiota dysbiosis is the primary risk factor for CDI and provides a promising target for developing novel CDI therapy approaches. Along with gut microbiota dysbiosis, a reduction in important gut metabolites like secondary bile acids and short-chain fatty acids (SCFAs) were also seen in patients suffering from CDI. In this review study, we investigated the roles and mechanisms of gut microbiota and gut microbiota-derived gut metabolites, especially secondary bile acids and SCFAs in CDI pathogenesis. Moreover, specific signatures of gut microbiota and gut metabolites, as well as different factors that can modulate the gut microbiota, were also discussed, indicating that gut microbiota modulators like probiotics and prebiotics can be a potential therapeutic strategy for CDI as they can help restore gut microbiota and produce gut metabolites necessary for a healthy gut. The understanding of the associations between gut microbiota-gut metabolites and CDI will allow for developing precise and sustainable approaches, distinct from antibiotics and fecal transplant, for mitigating CDI and other gut microbiota dysbiosis-related diseases.
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Affiliation(s)
- Bijay Gurung
- Department of Biomedical Sciences, Ohio University Heritage College of Osteopathic Medicine, Ohio University, Athens, OH 45701, USA; (B.G.); (M.S.)
- Infectious and Tropical Disease Institute, Ohio University, Athens, OH 45701, USA
- Interdisciplinary Molecular and Cellular Biology Program, Ohio University, Athens, OH 45701, USA
| | - Maranda Stricklin
- Department of Biomedical Sciences, Ohio University Heritage College of Osteopathic Medicine, Ohio University, Athens, OH 45701, USA; (B.G.); (M.S.)
- Infectious and Tropical Disease Institute, Ohio University, Athens, OH 45701, USA
| | - Shaohua Wang
- Department of Biomedical Sciences, Ohio University Heritage College of Osteopathic Medicine, Ohio University, Athens, OH 45701, USA; (B.G.); (M.S.)
- Infectious and Tropical Disease Institute, Ohio University, Athens, OH 45701, USA
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13
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Henderickx JG, Crobach MJ, Terveer EM, Smits WK, Kuijper EJ, Zwittink RD. Fungal and bacterial gut microbiota differ between Clostridioides difficile colonization and infection. MICROBIOME RESEARCH REPORTS 2023; 3:8. [PMID: 38455084 PMCID: PMC10917615 DOI: 10.20517/mrr.2023.52] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 11/21/2023] [Accepted: 11/30/2023] [Indexed: 03/09/2024]
Abstract
Aim: The bacterial microbiota is well-recognized for its role in Clostridioides difficile colonization and infection, while fungi and yeasts remain understudied. The aim of this study was to analyze the predictive value of the mycobiota and its interactions with the bacterial microbiota in light of C. difficile colonization and infection. Methods: The mycobiota was profiled by ITS2 sequencing of fecal DNA from C. difficile infection (CDI) patients (n = 29), asymptomatically C. difficile colonization (CDC) patients (n = 38), and hospitalized controls with C. difficile negative stool culture (controls; n = 38). Previously published 16S rRNA gene sequencing data of the same cohort were used additionally for machine learning and fungal-bacterial network analysis. Results: CDI patients were characterized by a significantly higher abundance of Candida spp. (MD 0.270 ± 0.089, P = 0.002) and Candida albicans (MD 0.165 ± 0.082, P = 0.023) compared to controls. Additionally, they were deprived of Aspergillus spp. (MD -0.067 ± 0.026, P = 0.000) and Penicillium spp. (MD -0.118 ± 0.043, P = 0.000) compared to CDC patients. Network analysis revealed a positive association between several fungi and bacteria in CDI and CDC, although the analysis did not reveal a direct association between Clostridioides spp. and fungi. Furthermore, the microbiota machine learning model outperformed the models based on the mycobiota and the joint microbiota-mycobiota model. The microbiota classifier successfully distinguished CDI from CDC [Area Under the Receiver Operating Characteristic (AUROC) = 0.884] and CDI from controls (AUROC = 0.905). Blautia and Bifidobacterium were marker genera associated with CDC patients and controls. Conclusion: The gut mycobiota differs between CDI, CDC, and controls and may affect Clostridioides spp. through indirect interactions. The mycobiota data alone could not successfully discriminate CDC from controls or CDI patients and did not have additional predictive value to the bacterial microbiota data. The identification of bacterial marker genera associated with CDC and controls warrants further investigation.
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Affiliation(s)
- Jannie G.E. Henderickx
- Center for Microbiome Analyses and Therapeutics, Department of Medical Microbiology, Leiden University Medical Center, Leiden 2333 ZA, the Netherlands
- Department of Medical Microbiology and Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden 2333 ZA, the Netherlands
| | - Monique J.T. Crobach
- Department of Medical Microbiology and Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden 2333 ZA, the Netherlands
| | - Elisabeth M. Terveer
- Department of Medical Microbiology and Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden 2333 ZA, the Netherlands
- Netherlands Donor Feces Bank, Department of Medical Microbiology, Leiden University Medical Center, Leiden 2333 ZA, the Netherlands
| | - Wiep Klaas Smits
- Center for Microbiome Analyses and Therapeutics, Department of Medical Microbiology, Leiden University Medical Center, Leiden 2333 ZA, the Netherlands
- Department of Medical Microbiology and Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden 2333 ZA, the Netherlands
| | - Ed J. Kuijper
- Center for Microbiome Analyses and Therapeutics, Department of Medical Microbiology, Leiden University Medical Center, Leiden 2333 ZA, the Netherlands
- Department of Medical Microbiology and Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden 2333 ZA, the Netherlands
- Netherlands Donor Feces Bank, Department of Medical Microbiology, Leiden University Medical Center, Leiden 2333 ZA, the Netherlands
| | - Romy D. Zwittink
- Center for Microbiome Analyses and Therapeutics, Department of Medical Microbiology, Leiden University Medical Center, Leiden 2333 ZA, the Netherlands
- Department of Medical Microbiology and Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden 2333 ZA, the Netherlands
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14
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Yang J, Li Y, Meng L. Combination of Bifidobacterium breve and antibiotics against Clostridioides difficile: effect of the time interval of combination on antagonistic activity. Int Microbiol 2023; 26:833-840. [PMID: 36808573 DOI: 10.1007/s10123-023-00340-6] [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: 10/19/2022] [Revised: 02/06/2023] [Accepted: 02/13/2023] [Indexed: 02/21/2023]
Abstract
Co-administration of probiotics and antibiotics has been used to prevent or treat primary Clostridioides difficile (pCDI), and the closer the interval between the combination, the more effective it is, but the reason behind this is unknown. In this study, the cell-free culture supernatant (CFCS) of Bifidobacterium breve YH68 was used in combination with vancomycin (VAN) and metronidazole (MTR) to treat C. difficile cells. The growth and biofilm production of C. difficile under different co-administration time interval treatments were determined by optical density and crystalline violet staining, respectively. The toxin production of C. difficile was determined by enzyme immunoassay, and the relative expressions of C. difficile virulence genes tcdA and tcdB were determined by real-time qPCR method. Meanwhile, the types and contents of organic acids in YH68-CFCS were investigated by LC-MS/MS. The results showed that YH68-CFCS in combination with VAN or MTR significantly inhibited the growth, biofilm production, and toxin production of C. difficile in the effective time interval range (0-12 h) but did not affect the expression level of C. difficile virulence genes. In addition, the effective antibacterial component of YH68-CFCS is lactic acid (LA).
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Affiliation(s)
- Jingpeng Yang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China.
| | - Yanan Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Lingtong Meng
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China.
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15
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Auria E, Hunault L, England P, Monot M, Pipoli Da Fonseca J, Matondo M, Duchateau M, Tremblay YDN, Dupuy B. The cell wall lipoprotein CD1687 acts as a DNA binding protein during deoxycholate-induced biofilm formation in Clostridioides difficile. NPJ Biofilms Microbiomes 2023; 9:24. [PMID: 37169797 PMCID: PMC10175255 DOI: 10.1038/s41522-023-00393-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 04/27/2023] [Indexed: 05/13/2023] Open
Abstract
The ability of bacterial pathogens to establish recurrent and persistent infections is frequently associated with their ability to form biofilms. Clostridioides difficile infections have a high rate of recurrence and relapses and it is hypothesized that biofilms are involved in its pathogenicity and persistence. Biofilm formation by C. difficile is still poorly understood. It has been shown that specific molecules such as deoxycholate (DCA) or metronidazole induce biofilm formation, but the mechanisms involved remain elusive. In this study, we describe the role of the C. difficile lipoprotein CD1687 during DCA-induced biofilm formation. We showed that the expression of CD1687, which is part of an operon within the CD1685-CD1689 gene cluster, is controlled by multiple transcription starting sites and some are induced in response to DCA. Only CD1687 is required for biofilm formation and the overexpression of CD1687 is sufficient to induce biofilm formation. Using RNAseq analysis, we showed that CD1687 affects the expression of transporters and metabolic pathways and we identified several potential binding partners by pull-down assay, including transport-associated extracellular proteins. We then demonstrated that CD1687 is surface exposed in C. difficile, and that this localization is required for DCA-induced biofilm formation. Given this localization and the fact that C. difficile forms eDNA-rich biofilms, we confirmed that CD1687 binds DNA in a non-specific manner. We thus hypothesize that CD1687 is a component of the downstream response to DCA leading to biofilm formation by promoting interaction between the cells and the biofilm matrix by binding eDNA.
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Affiliation(s)
- Emile Auria
- Institut Pasteur, Université Paris-Cité, UMR-CNRS 6047, Laboratoire Pathogenèse des Bactéries Anaérobies, F-75015, Paris, France
| | - Lise Hunault
- Institut Pasteur, Université Paris-Cité, INSERM UMR1222, Unit of Antibodies in Therapy and Pathology, Paris, France
- Sorbonne Université, INSERM, CNRS, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), F-75013, Paris, France
| | - Patrick England
- Plateforme de Biophysique Moléculaire, Institut Pasteur, CNRS UMR3528, Paris, France
| | - Marc Monot
- Plateforme Technologique Biomics, Institut Pasteur, Paris, France
| | | | | | | | - Yannick D N Tremblay
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Bruno Dupuy
- Institut Pasteur, Université Paris-Cité, UMR-CNRS 6047, Laboratoire Pathogenèse des Bactéries Anaérobies, F-75015, Paris, France.
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16
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Chopra T, Hecht G, Tillotson G. Gut microbiota and microbiota-based therapies for Clostridioides difficile infection. Front Med (Lausanne) 2023; 9:1093329. [PMID: 36698844 PMCID: PMC9868170 DOI: 10.3389/fmed.2022.1093329] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 12/15/2022] [Indexed: 01/10/2023] Open
Abstract
Clostridioides difficile infection poses significant clinical challenges due to its recurrent nature. Current antibiotic management does not address the underlying issue, that of a disturbed gastrointestinal microbiome, called dysbiosis. This provides a supportive environment for the germination of C. difficile spores which lead to infection and toxin production as well as an array of other health conditions. The use of microbiome restoration therapies such as live biotherapeutics can reverse dysbiosis and lead to good clinical outcomes. Several such therapies are under clinical investigation.
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Affiliation(s)
- Teena Chopra
- Division of Infectious Diseases, Wayne State University, Detroit, MI, United States,*Correspondence: Teena Chopra,
| | - Gail Hecht
- Department of Medicine, Loyola University Chicago Stritch School of Medicine, Maywood, IL, United States
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17
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Mullish BH, Martinez-Gili L, Allegretti JR. Editorial: the acid test-can bile acids predict recurrence of Clostridioides difficile infection? Authors' reply. Aliment Pharmacol Ther 2023; 57:169-170. [PMID: 36480711 DOI: 10.1111/apt.17303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Benjamin H Mullish
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, St Mary's Hospital Campus, Imperial College London, London, UK.,Departments of Gastroenterology and Hepatology, St Mary's Hospital, Imperial College Healthcare NHS Trust, London, UK
| | - Laura Martinez-Gili
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, St Mary's Hospital Campus, Imperial College London, London, UK.,Section of Bioinformatics, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | - Jessica R Allegretti
- Division of Gastroenterology, Hepatology, and Endoscopy, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
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