1
|
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.
Collapse
Affiliation(s)
- Patrizia Spigaglia
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Roma, Italy
| |
Collapse
|
2
|
Wang Y, Hunt A, Danziger L, Drwiega EN. A Comparison of Currently Available and Investigational Fecal Microbiota Transplant Products for Recurrent Clostridioides difficile Infection. Antibiotics (Basel) 2024; 13:436. [PMID: 38786164 PMCID: PMC11117328 DOI: 10.3390/antibiotics13050436] [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: 04/17/2024] [Revised: 05/09/2024] [Accepted: 05/10/2024] [Indexed: 05/25/2024] Open
Abstract
Clostridioides difficile infection (CDI) is an intestinal infection that causes morbidity and mortality and places significant burden and cost on the healthcare system, especially in recurrent cases. Antibiotic overuse is well recognized as the leading cause of CDI in high-risk patients, and studies have demonstrated that even short-term antibiotic exposure can cause a large and persistent disturbance to human colonic microbiota. The recovery and sustainability of the gut microbiome after dysbiosis have been associated with fewer CDI recurrences. Fecal microbiota transplantation (FMT) refers to the procedure in which human donor stool is processed and transplanted to a patient with CDI. It has been historically used in patients with pseudomembranous colitis even before the discovery of Clostridioides difficile. More recent research supports the use of FMT as part of the standard therapy of recurrent CDI. This article will be an in-depth review of five microbiome therapeutic products that are either under investigation or currently commercially available: Rebyota (fecal microbiota, live-jslm, formerly RBX2660), Vowst (fecal microbiota spores, live-brpk, formerly SER109), VE303, CP101, and RBX7455. Included in this review is a comparison of the products' composition and dosage forms, available safety and efficacy data, and investigational status.
Collapse
Affiliation(s)
- Yifan Wang
- Department of Pharmacy Practice, University of Illinois at Chicago College of Pharmacy, Chicago, IL 60612, USA
| | - Aaron Hunt
- Department of Pharmacy Practice, University of Illinois at Chicago College of Pharmacy, Chicago, IL 60612, USA
| | - Larry Danziger
- Department of Pharmacy Practice, University of Illinois at Chicago College of Pharmacy, Chicago, IL 60612, USA
- Division of Infectious Diseases, University of Illinois at Chicago College of Medicine, Chicago, IL 60612, USA
| | - Emily N. Drwiega
- Department of Pharmacy Practice, University of Illinois at Chicago College of Pharmacy, Chicago, IL 60612, USA
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Lee SH, Park HK, Kang CD, Choi DH, Park SC, Park JM, Nam SJ, Chae GB, Lee KY, Cho H, Lee SJ. High Dose Intramuscular Vitamin D3 Supplementation Impacts the Gut Microbiota of Patients With Clostridioides Difficile Infection. Front Cell Infect Microbiol 2022; 12:904987. [PMID: 35774395 PMCID: PMC9239168 DOI: 10.3389/fcimb.2022.904987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 05/10/2022] [Indexed: 11/13/2022] Open
Abstract
Background and Aim Current therapeutic strategies for Clostridioides difficile infections (CDI), including oral vancomycin, metronidazole and fecal microbial transplantation, have limited efficacy and treatment failure may occur in as many as one- third of cases. Recent studies have reported that lower concentrations of 25-hydroxyvitamin D are associated with CDI severity and recurrence. However, there have been no studies on microbiota composition after the administration of vitamin D in patients with CDI. Therefore, our study aimed to compare the microbiota composition between the two groups, including eight CDI-positive patients with vitamin D supplementation and ten CDI-positive patients without vitamin D supplementation by using 16S rRNA microbial profiling. Methods Twenty subjects were enrolled in this prospective randomized controlled study. One subject dropped out due to lack of contact with the guardian after discharge and one subject dropped out due to withdrawal of consent. Thus, 18 patients with CDI and vitamin D insufficiency (vitamin D level < 17 ng/mL) were divided into two groups: CDI with vitamin D supplementation (n = 8) and CDI without vitamin D supplementation (control: n = 10). Subjects with vitamin D insufficiency were randomized to receive 200,000 IU intramuscular cholecalciferol whereas patients in the control group received only oral vancomycin. Stool samples were obtained twice before vancomycin was administered and eight weeks after treatment; the V3-V4 16S rRNA metagenomic sequencing was performed using EzBioCloud. Results The alpha diversity of the gut microbiota in the recovery state was significantly higher than that in the CDI state. Analysis of bacterial relative abundance showed significantly lower Proteobacteria and higher Lachnospiraceae, Ruminococcaceae, Akkermansiaceae, and Bifidobacteriaceae in the recovery state. When comparing the control and vitamin D treatment groups after eight weeks, increase in alpha diversity and, abundance of Lachnospiraceae, and Ruminococcaceae exhibited the same trend in both groups. A significant increase in Bifidobacteriaceae and Christensenellaceae was observed in the vitamin D group; Proteobacteria abundance was significantly lower in the vitamin D treatment group after eight weeks than that in the control group. Conclusion Our study confirmed that the increase in the abundance of beneficial bacteria such as Bifidobacteriaceae, and Christensenellaceae were prominently evident during recovery after administration of a high dose of cholecalciferol. These findings indicate that vitamin D administration may be useful in patients with CDI, and further studies with larger sample sizes are required.
Collapse
Affiliation(s)
- Sang Hoon Lee
- Department of Internal Medicine, Kangwon National University Hospital, Kangwon National University School of Medicine, Chuncheon, South Korea
| | - Han-Ki Park
- Division of Allergy and Clinical Immunology, Department of Internal Medicine, School of Medicine, Kyungpook National University Chilgok Hospital, Kyungpook National University, Daegu, South Korea
| | - Chang Don Kang
- Department of Internal Medicine, Kangwon National University Hospital, Kangwon National University School of Medicine, Chuncheon, South Korea
| | - Dae Hee Choi
- Department of Internal Medicine, Kangwon National University Hospital, Kangwon National University School of Medicine, Chuncheon, South Korea
| | - Sung Chul Park
- Department of Internal Medicine, Kangwon National University Hospital, Kangwon National University School of Medicine, Chuncheon, South Korea
| | - Jin Myung Park
- Department of Internal Medicine, Kangwon National University Hospital, Kangwon National University School of Medicine, Chuncheon, South Korea
| | - Seung-Joo Nam
- Department of Internal Medicine, Kangwon National University Hospital, Kangwon National University School of Medicine, Chuncheon, South Korea
| | - Gi Bong Chae
- Department of Surgery, Kangwon National University Hospital, Kangwon NationalUniversity School of Medicine, Chuncheon, South Korea
| | - Kyoung yul Lee
- Department of Pathology, Kangwon National University School of Medicine, Chuncheon, South Korea
| | - Hyunseok Cho
- Department of Hospital Medicine, Kangwon National University School of Medicine, Chuncheon, South Korea
| | - Sung Joon Lee
- Department of Internal Medicine, Kangwon National University Hospital, Kangwon National University School of Medicine, Chuncheon, South Korea
- *Correspondence: Sung Joon Lee, ; orcid.org/0000-0002-6451-0400
| |
Collapse
|
6
|
Abstract
The gastrointestinal ecosystem is formed from interactions between the host, indigenous gut microbiota, and external world. When colonizing the gut, bacteria must overcome barriers imposed by the intestinal environment, such as host immune responses and microbiota-mediated nutrient limitation. Thus, understanding bacterial colonization requires determining how the gut landscape interacts with microbes attempting to establish within the ecosystem. However, the complicated network of interactions between elements of the intestinal environment makes it challenging to uncover emergent properties of the system using only reductionist methods. A systems biology approach, which aims to investigate complex systems by examining the behavior and relationships of all elements of the system, may afford a more holistic perspective of the colonization process. Here, we examine the confluence between the gut landscape and bacterial colonization through the lens of systems biology. We offer an overview of the conceptual and methodological underpinnings of systems biology, followed by a discussion of key elements of the gut ecosystem as they pertain to bacterial establishment and growth. We conclude by reintegrating these elements to guide future comprehensive investigations of the ecosystem in the context of bacterial intestinal colonization.
Collapse
Affiliation(s)
- Madeline R. Barron
- Department of Microbiology & Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Vincent B. Young
- Department of Microbiology & Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan Medical School, Ann Arbor, Michigan, USA
| |
Collapse
|
7
|
Haran JP, Ward DV, Bhattarai SK, Loew E, Dutta P, Higgins A, McCormick BA, Bucci V. The high prevalence of Clostridioides difficile among nursing home elders associates with a dysbiotic microbiome. Gut Microbes 2022; 13:1-15. [PMID: 33764826 PMCID: PMC8007149 DOI: 10.1080/19490976.2021.1897209] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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 disproportionally affects the elderly living in nursing homes (NHs). Our objective was to explore the prevalence of C. difficile in NH elders, over time and to determine whether the microbiome or other clinical factors are associated with C. difficile colonization.We collected serial stool samples from NH residents. C. difficile prevalence was determined by quantitative polymerase-chain reaction detection of Toxin genes tcdA and tcdB; microbiome composition was determined by shotgun metagenomic sequencing. We used mixed-effect random forest modeling machine to determine bacterial taxa whose abundance is associated with C. difficile prevalence while controlling for clinical covariates including demographics, medications, and past medical history.We enrolled 167 NH elders who contributed 506 stool samples. Of the 123 elders providing multiple samples, 30 (24.4%) elders yielded multiple samples in which C. difficile was detected and 78 (46.7%) had at least one C. difficile positive sample. Elders with C. difficile positive samples were characterized by increased abundances of pathogenic or inflammatory-associated bacterial taxa and by lower abundances of taxa with anti-inflammatory or symbiotic properties. Proton pump inhibitor (PPI) use is associated with lower prevalence of C. difficile (Odds Ratio 0.46; 95%CI, 0.22-0.99) and the abundance of bacterial species with known beneficial effects was higher in PPI users and markedly lower in elders with high C. difficile prevalence.C. difficile is prevalent among NH elders and a dysbiotic gut microbiome associates with C. difficile colonization status. Manipulating the gut microbiome may prove to be a key strategy in the reduction of C. difficile in the NH.
Collapse
Affiliation(s)
- John P. Haran
- Department of Emergency Medicine, University of Massachusetts Medical School, Worcester, MA, USA,Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, USA,Program in Microbiome Dynamics, University of Massachusetts Medical School, Worcester, MA, USA,CONTACT John P. Haran Department of Emergency Medicine, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA01655
| | - Doyle V. Ward
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, USA,Program in Microbiome Dynamics, University of Massachusetts Medical School, Worcester, MA, USA
| | - Shakti K. Bhattarai
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, USA,Program in Microbiome Dynamics, University of Massachusetts Medical School, Worcester, MA, USA
| | - Ethan Loew
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, USA,Program in Microbiome Dynamics, University of Massachusetts Medical School, Worcester, MA, USA
| | - Protiva Dutta
- Department of Emergency Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Amanda Higgins
- Department of Emergency Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Beth A. McCormick
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, USA,Program in Microbiome Dynamics, University of Massachusetts Medical School, Worcester, MA, USA
| | - Vanni Bucci
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, USA,Program in Microbiome Dynamics, University of Massachusetts Medical School, Worcester, MA, USA
| |
Collapse
|
8
|
Machine Learning Approaches to Investigate Clostridioides difficile Infection and Outcomes: A Systematic Review. Int J Med Inform 2022; 160:104706. [DOI: 10.1016/j.ijmedinf.2022.104706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 12/21/2021] [Accepted: 01/22/2022] [Indexed: 11/20/2022]
|
9
|
Pellissery AJ, Vinayamohan PG, Kuttappan DA, Mishra N, Fragomeni BDO, Maas K, Mooyottu S, Venkitanarayanan K. Protective Effect of Baicalin against Clostridioides difficile Infection in Mice. Antibiotics (Basel) 2021; 10:antibiotics10080926. [PMID: 34438975 PMCID: PMC8388895 DOI: 10.3390/antibiotics10080926] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 07/26/2021] [Accepted: 07/27/2021] [Indexed: 12/17/2022] Open
Abstract
This study investigated the prophylactic and therapeutic efficacies of baicalin (BC), a plant-derived flavone glycoside, in reducing the severity of Clostridioides difficile infection (CDI) in a mouse model. In the prophylactic trial, C57BL/6 mice were provided with BC (0, 11, and 22 mg/L in drinking water) from 12 days before C. difficile challenge through the end of the experiment, whereas BC administration started day 1 post challenge in the therapeutic trial. Both challenge and control groups were infected with 106 CFU/mL of hypervirulent C. difficile BAA 1803 spores or sterile PBS, and the clinical and diarrheal scores were recorded for 10 days post challenge. On day 2 post challenge, fecal and tissue samples were collected from mice prophylactically administered with BC for microbiome and histopathologic analysis. Both prophylactic and therapeutic supplementation of BC significantly reduced the severity of colonic lesions and improved CDI clinical progression and outcome compared with control (p < 0.05). Microbiome analysis revealed a significant increase in Gammaproteobacteria and reduction in the abundance of protective microbiota (Firmicutes) in antibiotic-treated and C. difficile-infected mice compared with controls (p < 0.05). However, baicalin supplementation favorably altered the microbiome composition, as revealed by an increased abundance in beneficial bacteria, especially Lachnospiraceae and Akkermansia. Our results warrant follow-up investigations on the use of BC as an adjunct to antibiotic therapy to control gut dysbiosis and reduce C. difficile infection in humans.
Collapse
Affiliation(s)
- Abraham Joseph Pellissery
- Department of Animal Science, University of Connecticut, Storrs, CT 06269, USA; (A.J.P.); (D.A.K.); (B.O.F.)
| | | | - Deepa Ashwarya Kuttappan
- Department of Animal Science, University of Connecticut, Storrs, CT 06269, USA; (A.J.P.); (D.A.K.); (B.O.F.)
| | - Neha Mishra
- Department of Pathobiology and Veterinary Science, University of Connecticut, Storrs, CT 06269, USA;
| | - Breno de Oliveira Fragomeni
- Department of Animal Science, University of Connecticut, Storrs, CT 06269, USA; (A.J.P.); (D.A.K.); (B.O.F.)
| | - Kendra Maas
- Microbial Analysis, Resources, and Services, University of Connecticut, Storrs, CT 06269, USA;
| | - Shankumar Mooyottu
- Department of Veterinary Pathology, Iowa State University, Ames, IA 50011, USA;
| | - Kumar Venkitanarayanan
- Department of Animal Science, University of Connecticut, Storrs, CT 06269, USA; (A.J.P.); (D.A.K.); (B.O.F.)
- Correspondence: ; Tel.: +1-(860)-486-1957
| |
Collapse
|
10
|
Engevik MA, Engevik AC, Engevik KA, Auchtung JM, Chang-Graham AL, Ruan W, Luna RA, Hyser JM, Spinler JK, Versalovic J. Mucin-Degrading Microbes Release Monosaccharides That Chemoattract Clostridioides difficile and Facilitate Colonization of the Human Intestinal Mucus Layer. ACS Infect Dis 2021; 7:1126-1142. [PMID: 33176423 DOI: 10.1021/acsinfecdis.0c00634] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
It is widely accepted that the pathogen Clostridioides difficile exploits an intestinal environment with an altered microbiota, but the details of these microbe-microbe interactions are unclear. Adherence and colonization of mucus has been demonstrated for several enteric pathogens and it is possible that mucin-associated microbes may be working in concert with C. difficile. We showed that C. difficile ribotype-027 adheres to MUC2 glycans and using fecal bioreactors, we identified that C. difficile associates with several mucin-degrading microbes. C. difficile was found to chemotax toward intestinal mucus and its glycan components, demonstrating that C. difficile senses the mucus layer. Although C. difficile lacks the glycosyl hydrolases required to degrade mucin glycans, coculturing C. difficile with the mucin-degrading Akkermansia muciniphila, Bacteroides thetaiotaomicron, and Ruminococcus torques allowed C. difficile to grow in media that lacked glucose but contained purified MUC2. Collectively, these studies expand our knowledge on how intestinal microbes support C. difficile.
Collapse
Affiliation(s)
- Melinda A. Engevik
- Department of Pathology & Immunology, Baylor College of Medicine Houston Texas 77030, United States
- Department of Pathology, Texas Children’s Hospital Houston Texas 77030, United States
| | - Amy C. Engevik
- Department of Surgery, Vanderbilt University School of Medicine, Nashville Tennessee 37232, United States
- Epithelial Biology Center, Vanderbilt University School of Medicine, Nashville Tennessee 37232, United States
| | - Kristen A. Engevik
- Department of Molecular Virology and Microbiology, Baylor College of Medicine Houston Texas 77030, United States
| | - Jennifer M. Auchtung
- Department of Molecular Virology and Microbiology, Baylor College of Medicine Houston Texas 77030, United States
- Department of Food Science and Technology, University of Nebraska—Lincoln, Lincoln Nebraska 68588, United States
| | - Alexandra L. Chang-Graham
- Department of Molecular Virology and Microbiology, Baylor College of Medicine Houston Texas 77030, United States
| | - Wenly Ruan
- Department of Pathology & Immunology, Baylor College of Medicine Houston Texas 77030, United States
- Department of Pathology, Texas Children’s Hospital Houston Texas 77030, United States
| | - Ruth Ann Luna
- Department of Pathology & Immunology, Baylor College of Medicine Houston Texas 77030, United States
- Department of Pathology, Texas Children’s Hospital Houston Texas 77030, United States
| | - Joseph M. Hyser
- Department of Molecular Virology and Microbiology, Baylor College of Medicine Houston Texas 77030, United States
| | - Jennifer K. Spinler
- Department of Pathology & Immunology, Baylor College of Medicine Houston Texas 77030, United States
- Department of Pathology, Texas Children’s Hospital Houston Texas 77030, United States
| | - James Versalovic
- Department of Pathology & Immunology, Baylor College of Medicine Houston Texas 77030, United States
- Department of Pathology, Texas Children’s Hospital Houston Texas 77030, United States
| |
Collapse
|
11
|
Sehgal K, Khanna S. Gut microbiome and Clostridioides difficile infection: a closer look at the microscopic interface. Therap Adv Gastroenterol 2021; 14:1756284821994736. [PMID: 33747125 PMCID: PMC7905718 DOI: 10.1177/1756284821994736] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 01/19/2021] [Indexed: 02/06/2023] Open
Abstract
The pathogenesis of Clostridioides difficile infection (CDI) was recognized with its link to the use of antimicrobials. Antimicrobials significantly alter gut microbiota structure and composition, which led to the discovery of the association of this gut perturbation with the development of CDI. A number of factors implicated in its pathogenesis, such as advancing age, proton-pump inhibitors, and gastrointestinal diseases, are linked to gut microbiota perturbations. In an effort to better understand CDI, a multitude of studies have tried to ascertain protective and predictive microbial footprints linked with CDI. It has further been realized that CDI in itself can alter the gut microbiome. Its spore-forming capability poses as an impediment in the management of the infection and contributes to its recurrence. Antibiotic therapies used for its management have also been linked to gut microbiota changes, making its treatment a little more challenging. In an effort to exploit and utilize this association, gut microbial restoration therapies, particularly in the form of fecal microbial transplant, are increasingly being put to use and are proving to be beneficial. In this review, we summarize the association of the gut microbiome and microbial perturbation with initial and recurrent CDI.
Collapse
Affiliation(s)
- Kanika Sehgal
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First St SW, Rochester, MN 55905, USA
| | - Sahil Khanna
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| |
Collapse
|
12
|
Herrera G, Paredes-Sabja D, Patarroyo MA, Ramírez JD, Muñoz M. Updating changes in human gut microbial communities associated with Clostridioides difficile infection. Gut Microbes 2021; 13:1966277. [PMID: 34486488 PMCID: PMC8425690 DOI: 10.1080/19490976.2021.1966277] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 07/29/2021] [Accepted: 08/02/2021] [Indexed: 02/04/2023] Open
Abstract
Clostridioides difficile is the causative agent of antibiotic-associated diarrhea, a worldwide public health problem. Different factors can promote the progression of C. difficile infection (CDI), mainly altered intestinal microbiota composition. Microbial species belonging to different domains (i.e., bacteria, archaea, eukaryotes, and even viruses) are synergistically and antagonistically associated with CDI. This review was aimed at updating changes regarding CDI-related human microbiota composition using recent data and an integral approach that included the different microorganism domains. The three domains of life contribute to intestinal microbiota homeostasis at different levels in which relationships among microorganisms could explain the wide range of clinical manifestations. A holistic understanding of intestinal ecosystem functioning will facilitate identifying new predictive factors for infection and developing better treatment and new diagnostic tools, thereby reducing this disease's morbidity and mortality.
Collapse
Affiliation(s)
- Giovanny Herrera
- Centro de Investigaciones en Microbiología y Biotecnología – UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad Del Rosario, Bogotá, Colombia
| | - Daniel Paredes-Sabja
- ANID – Millennium Science Initiative Program – Millennium Nucleus in the Biology of the Intestinal Microbiota, Santiago, Chile
- Department of Biology, Texas A&M University, College Station, TX, 77843, USA
| | - Manuel Alfonso Patarroyo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
- Microbiology Department, Faculty of Medicine, Universidad Nacional de Colombia, Bogotá D.C. 111321, Colombia
- Health Sciences Division, Main Campus, Universidad Santo Tomás, Bogotá D.C. 110231, Colombia
| | - Juan David Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología – UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad Del Rosario, Bogotá, Colombia
| | - Marina Muñoz
- Centro de Investigaciones en Microbiología y Biotecnología – UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad Del Rosario, Bogotá, Colombia
- ANID – Millennium Science Initiative Program – Millennium Nucleus in the Biology of the Intestinal Microbiota, Santiago, Chile
| |
Collapse
|
13
|
Vakili B, Fateh A, Asadzadeh Aghdaei H, Sotoodehnejadnematalahi F, Siadat SD. Intestinal Microbiota in Elderly Inpatients with Clostridioides difficile Infection. Infect Drug Resist 2020; 13:2723-2731. [PMID: 32801806 PMCID: PMC7415437 DOI: 10.2147/idr.s262019] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 07/21/2020] [Indexed: 12/11/2022] Open
Abstract
Purpose The incidence of Clostridioides difficile infection (CDI) has been reported as 10-fold higher among the elderly population than in young adults. The aim of this study was to compare the targeted bacteria population in the fecal microbiota in two groups of hospitalized elderly, categorized according to CDI and non-CDI. Patient and Methods In this case–control study, 84 fecal samples of the 28 patients with CDI and 56 non-CDI patients (>65 years) were studied. C. difficile isolates were characterized by anaerobic culture and multiplex PCR. Quantitative PCR was used to analyze the bacterial elements. Results CDI group differed significantly for a prolonged hospital stay, previous surgery, residence in nursing home and exposure to a range of antibiotics including quinolone, clindamycin and cephalosporin. CDI group had significantly fewer members of Bacteroides spp., Clostridium cluster IV, Bifidobacterium spp., Faecalibacterium prausnitzii, and Prevotella spp. in their fecal microbiota than the control group (P < 0.05). The abundances of Akkermansia muciniphila, Lactobacillus spp., Escherichia coli and Klebsiella spp. were higher in group CDI compared with the control group (P < 0.05). Conclusion CDI status is associated with the abundance of some bacterial populations. In this study, an increase in Akkermansia muciniphila, Lactobacillus spp., and Enterobacteriaceae genus was highlighted in CDI patients. A reduction in butyrate-producing bacteria was found in CDI patients. The differences in the composition of fecal microbiota can help to understand how antimicrobial agents impact on gut homeostasis and lead to loss of colonization resistance to C. difficile.
Collapse
Affiliation(s)
- Bahareh Vakili
- Department of Biology, School of Basic Science, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Abolfazl Fateh
- Department of Mycobacteriology and Pulmonary Research, Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Hamid Asadzadeh Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Seyed Davar Siadat
- Department of Mycobacteriology and Pulmonary Research, Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| |
Collapse
|
14
|
Kinneman L, Zhu W, Wong WSW, Clemency N, Provenzano M, Vilboux T, Jane't K, Seo-Mayer P, Levorson R, Kou M, Ascher D, Niederhuber JE, Hourigan SK. Assessment of the Urinary Microbiome in Children Younger Than 48 Months. Pediatr Infect Dis J 2020; 39:565-570. [PMID: 32091499 DOI: 10.1097/inf.0000000000002622] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
BACKGROUND The urinary tract was once thought to be sterile, and little is known about the urinary microbiome in children. This study aimed to examine the urinary microbiome of young children across demographic and clinical factors. METHODS Children <48 months, undergoing a urinary catheterization for clinical purposes in the Pediatric Emergency Department were recruited and urine samples collected. Detailed demographic and clinical information were recorded. Urine samples underwent DNA extraction and 16S ribosomal RNA gene sequencing, urinalysis and urine culture. RESULTS Eighty-five children were included; a urinary microbiome was identified in every child. Nine children had Escherichia coli urinary tract infections (UTIs) identified. Those with UTIs had a significantly decreased alpha diversity (t test, P < 0.001) and the composition of the microbiome clustered separately (P = 0.001) compared with those without UTIs. CONCLUSIONS A urinary microbiome was identified in every child, even neonates. Differences in microbiome diversity and composition were observed in patients with a standard culture positive UTI. The urinary microbiome has just begun to be explored, and the implications on long-term disease processes deserve further investigation.
Collapse
Affiliation(s)
- Lauren Kinneman
- From the Department of Pediatrics and Department of Emergency Medicine, Inova Children's Hospital, Falls Church, VA.,Division of Emergency Medicine, Department of Pediatrics, University of Washington, Seattle, WA.,Seattle Children's Emergency Department, Seattle, WA
| | - Wei Zhu
- Seattle Children's Emergency Department, Seattle, WA
| | - Wendy S W Wong
- Inova Translational Medicine Institute, Falls Church, VA.,Seattle Children's Emergency Department, Seattle, WA
| | - Nicole Clemency
- Inova Translational Medicine Institute, Falls Church, VA.,Seattle Children's Emergency Department, Seattle, WA
| | - Marina Provenzano
- Inova Translational Medicine Institute, Falls Church, VA.,Seattle Children's Emergency Department, Seattle, WA
| | | | - Keary Jane't
- Inova Translational Medicine Institute, Falls Church, VA
| | - Patricia Seo-Mayer
- From the Department of Pediatrics and Department of Emergency Medicine, Inova Children's Hospital, Falls Church, VA.,Pediatric Specialists of Virginia, Falls Church, VA
| | - Rebecca Levorson
- From the Department of Pediatrics and Department of Emergency Medicine, Inova Children's Hospital, Falls Church, VA.,Pediatric Specialists of Virginia, Falls Church, VA
| | - Maybelle Kou
- From the Department of Pediatrics and Department of Emergency Medicine, Inova Children's Hospital, Falls Church, VA
| | - David Ascher
- From the Department of Pediatrics and Department of Emergency Medicine, Inova Children's Hospital, Falls Church, VA
| | - John E Niederhuber
- Inova Translational Medicine Institute, Falls Church, VA.,Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA
| | - Suchitra K Hourigan
- From the Department of Pediatrics and Department of Emergency Medicine, Inova Children's Hospital, Falls Church, VA.,Inova Translational Medicine Institute, Falls Church, VA.,Pediatric Specialists of Virginia, Falls Church, VA
| |
Collapse
|
15
|
Vakili B, Fateh A, Asadzadeh Aghdaei H, Sotoodehnejadnematalahi F, Siadat SD. Characterization of Gut Microbiota in Hospitalized Patients with Clostridioides difficile Infection. Curr Microbiol 2020; 77:1673-1680. [PMID: 32296918 DOI: 10.1007/s00284-020-01980-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 04/04/2020] [Indexed: 12/28/2022]
|
16
|
Characterization of Circulating Clostridium difficile Strains, Host Response and Intestinal Microbiome in Hospitalized Children With Diarrhea. Pediatr Infect Dis J 2020; 39:221-228. [PMID: 31876614 DOI: 10.1097/inf.0000000000002559] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
BACKGROUND Clostridium difficile is capable of causing severe enterocolitis in adults. The significance of toxin-producing C. difficile in children with diarrhea is unclear and practice differs on whether to institute treatment. We aimed to characterize the microbiome in relation to the presence of C. difficile and co-infection with other pathogens and to describe host response to infection. METHODS Participants were children with acute diarrhea, 0-16 years of age, from whom stool samples had been submitted to the hospital laboratory for routine microbiology/virology. Convenience sampling was used for 50 prospective and 150 retrospective samples. No participants were treated for C. difficile. Rates of culture positivity for C. difficile, presence of toxin and PCR-ribotype were compared between age groups. Presence of other potential pathogens, comorbidities and complications were recorded. Microbiotal diversity was measured by 16S profiling. RESULTS Nineteen of 77 (25%) children <2 years of age and 13 of 119 (11%) children >2 years of age were C. difficile positive, of whom 10 (53%) and 9 (69%), respectively, carried toxigenic strains. Increased Shannon diversity was seen in children carrying C. difficile, with altered milieu. Presence of C. difficile was not associated with adverse clinical outcomes. In stools containing both Norovirus and C. difficile, there was increased relative abundance of verrucomicrobia. CONCLUSIONS Children with diarrhea regularly carried toxigenic and non-toxigenic strains of C. difficile, demonstrating enhanced microbiotal diversity, and change in milieu, without apparent morbidity. This unexpected finding is contrary to that seen in adults with C. difficile disease.
Collapse
|
17
|
Jurburg SD, Cornelissen JJBWJ, de Boer P, Smits MA, Rebel JMJ. Successional Dynamics in the Gut Microbiome Determine the Success of Clostridium difficile Infection in Adult Pig Models. Front Cell Infect Microbiol 2019; 9:271. [PMID: 31448240 PMCID: PMC6691177 DOI: 10.3389/fcimb.2019.00271] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 07/15/2019] [Indexed: 01/27/2023] Open
Abstract
Clostridium difficile infections (CDI) are a major cause of antibiotic-associated diarrhea. It is hypothesized that CDI develops due to the antibiotic-induced disruption of the intestinal microbial community structure, which allows C. difficile to flourish. Here, we pre-treated weaned pigs with the antibiotics Clindamycin or Ciprofloxacin for 1 day, and subsequently inoculated them with a human and pig enteropathogenic C. difficile strain 078 spores. Body temperature, clinical signs of disease, and the fecal microbiome were monitored daily for 15 days. Clindamycin had a stronger effect on the pigs than Ciprofloxacin, resulting in drastic shifts in the fecal microbiome, decreases in microbial diversity and significant increases in body temperature, even in the absence of C. difficile. Fecal shedding of C. difficile was detectable for 3 and 9 days in Ciprofloxacin and Clindamycin treated pigs inoculated with C. difficile, respectively, and in both cases decreased cell proliferation rates were detected in colon tissue. The timing of C. difficile shedding coincided with the decrease in a large cluster of Firmicutes following Clindamycin treatment, a pattern which was also independent of C. difficile inoculation. The observed community patterns suggest that successional dynamics following antibiotic treatment facilitate C. difficile establishment. The similarities between the microbiome responses observed in our study and those previously reported in CDI-infected humans further support the utility of adult pigs as models for the study of CDI.
Collapse
Affiliation(s)
- Stephanie D Jurburg
- Wageningen Bioveterinary Research, Lelystad, Netherlands.,iDiv - German Centre for Integrative Biodiversity Research, Leipzig, Germany
| | | | | | - Mari A Smits
- Wageningen Bioveterinary Research, Lelystad, Netherlands
| | - Johanna M J Rebel
- Wageningen Bioveterinary Research, Lelystad, Netherlands.,Wageningen Livestock Research, Wageningen, Netherlands
| |
Collapse
|
18
|
Decreased Fecal Bacterial Diversity and Altered Microbiome in Children Colonized With Clostridium difficile. J Pediatr Gastroenterol Nutr 2019; 68:502-508. [PMID: 30540709 DOI: 10.1097/mpg.0000000000002210] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
OBJECTIVES The gut microbiome is believed to play a role in the susceptibility to and treatment of Clostridium difficile infections (CDIs). It is, however, unknown whether the gut microbiome is also affected by asymptomatic C difficile colonization. Our study aimed to evaluate the fecal microbiome of children based on C difficile colonization, and CDI risk factors, including antibiotic use and comorbid inflammatory bowel disease (IBD). METHODS Subjects with IBD and non-IBD controls were prospectively enrolled from pediatric clinics for a biobanking project (n = 113). A fecal sample was collected from each subject for research purposes only and was evaluated for asymptomatic toxigenic C difficile colonization. Fecal microbiome composition was determined by 16S rRNA sequencing. RESULTS We found reduced bacterial diversity and altered microbiome composition in subjects with C difficile colonization, concurrent antibiotic use, and/or concomitant IBD (all P < 0.05). Accounting for antibiotic use and IBD status, children colonized with C difficile had significant enrichment in taxa from the genera Ruminococcus, Eggerthella, and Clostridium. Children without C difficile had increased relative abundances of Faecalibacterium and Rikenellaceae. Imputed metagenomic functions of those colonized were enriched for genes in oxidative phosphorylation and beta-lactam resistance, whereas in the subjects without C difficile, several functions in translation and metabolism were over-represented. CONCLUSIONS In children, C difficile colonization, or factors that predispose to colonization such as antibiotic use and IBD status were associated with decreased gut bacterial diversity and altered microbiome composition. Averting such microbiome alterations may be a method to prevent or treat CDI.
Collapse
|
19
|
Tran MCN, Kullar R, Goldstein EJC. Investigational drug therapies currently in early-stage clinical development for the treatment of clostridioides (clostridium) difficile infection. Expert Opin Investig Drugs 2019; 28:323-335. [DOI: 10.1080/13543784.2019.1581763] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Mai-Chi N. Tran
- Department of Pharmacy, Providence St. John’s Health Center, Santa Monica,
CA, USA
- Department of Pharmacy, Clinica Juan Pablo Medical Group, Los Angeles,
CA, USA
| | | | - Ellie J. C. Goldstein
- R M Alden Research Laboratory, Santa Monica,
CA, USA
- David Geffen School of Medicine, Los Angeles,
CA, USA
| |
Collapse
|
20
|
Davidovics ZH, Michail S, Nicholson MR, Kociolek LK, Pai N, Hansen R, Schwerd T, Maspons A, Shamir R, Szajewska H, Thapar N, de Meij T, Mosca A, Vandenplas Y, Kahn SA, Kellermayer R. Fecal Microbiota Transplantation for Recurrent Clostridium difficile Infection and Other Conditions in Children: A Joint Position Paper From the North American Society for Pediatric Gastroenterology, Hepatology, and Nutrition and the European Society for Pediatric Gastroenterology, Hepatology, and Nutrition. J Pediatr Gastroenterol Nutr 2019; 68:130-143. [PMID: 30540704 PMCID: PMC6475090 DOI: 10.1097/mpg.0000000000002205] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Fecal microbiota transplantation (FMT) is becoming part of the treatment algorithms against recurrent Clostridium difficile infection (rCDI) both in adult and pediatric gastroenterology practice. With our increasing recognition of the critical role the microbiome plays in human health and disease, FMT is also being considered as a potential therapy for other disorders, including inflammatory bowel disease (Crohn disease, ulcerative colitis), graft versus host disease, neuropsychiatric diseases, and metabolic syndrome. Controlled trials with FMT for rCDI have not been performed in children, and numerous clinical and regulatory considerations have to be considered when using this untraditional therapy. This report is intended to provide guidance for FMT in the treatment of rCDI in pediatric patients.
Collapse
Affiliation(s)
- Zev H. Davidovics
- Department of Pediatric Gastroenterology, Digestive Diseases, Hepatology, and Nutrition, Connecticut Children’s Medical Center, University of Connecticut School of Medicine, Farmington, CT
| | - Sonia Michail
- Children’s Hospital Los Angeles, University of Southern California, Los Angeles, CA
| | - Maribeth R. Nicholson
- D. Brent Polk Division of Gastroenterology, Hepatology, and Nutrition, Vanderbilt University Medical Center, Nashville, TN
| | - Larry K. Kociolek
- Ann and Robert H. Lurie Children’s Hospital of Chicago, North-western University Feinberg School of Medicine, Chicago, IL
| | - Nikhil Pai
- Division of Pediatric Gastroenterology and Nutrition, McMaster Children’s Hospital, McMaster University, Hamilton, Ontario, Canada
| | - Richard Hansen
- Department of Paediatric Gastroenterology, Royal Hospital for Children, Glasgow, Scotland
| | - Tobias Schwerd
- Department of Pediatrics, Dr. von Hauner Children’s Hospital, University Hospital, LMU Munich, Munich, Germany
| | | | - Raanan Shamir
- Institute for Gastroenterology, Nutrition and Liver Disease, Schneider Children’s Medical Center, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Hania Szajewska
- Department of Paediatrics, The Medical University of Warsaw, Warsaw, Poland
| | - Nikhil Thapar
- Department of Paediatric Gastroenterology, Great Ormond Street Hospital NHS Foundation Trust, London, United Kingdom
| | - Tim de Meij
- Department of Paediatric Gastroenterology, VU University Medical Center, Amsterdam, The Netherlands
| | - Alexis Mosca
- Division of Pediatric Gastroenterology and Nutrition, Robert Debré Hospital (APHP)
- French Group of Fecal Transplantation, St Antoine Hospital (APHP), Paris, France
| | - Yvan Vandenplas
- KidZ Health Castle, Universitair Ziekenuis Brussel, Vrije Universiteit Brussel, Brussels, Belgium
| | - Stacy A. Kahn
- Division of Gastroetenterology and Nutrition, Inflammatory Bowel Disease Center, Boston Children’s Hospital, Harvard Medical School, 17 Boston, MA
| | - Richard Kellermayer
- Section of Pediatric Gastroenterology and Nutrition, Texas Children’s Hospital, Baylor College of Medicine, Children’s Nutrition and Research Center, Houston, TX
| | - FMT Special Interest Group of the North American Society of Pediatric Gastroenterology Hepatology, Nutrition, the European Society for Pediatric Gastroenterology Hepatology, Nutrition
- Department of Pediatric Gastroenterology, Digestive Diseases, Hepatology, and Nutrition, Connecticut Children’s Medical Center, University of Connecticut School of Medicine, Farmington, CT
- Children’s Hospital Los Angeles, University of Southern California, Los Angeles, CA
- D. Brent Polk Division of Gastroenterology, Hepatology, and Nutrition, Vanderbilt University Medical Center, Nashville, TN
- Ann and Robert H. Lurie Children’s Hospital of Chicago, North-western University Feinberg School of Medicine, Chicago, IL
- Division of Pediatric Gastroenterology and Nutrition, McMaster Children’s Hospital, McMaster University, Hamilton, Ontario, Canada
- Department of Paediatric Gastroenterology, Royal Hospital for Children, Glasgow, Scotland
- Department of Pediatrics, Dr. von Hauner Children’s Hospital, University Hospital, LMU Munich, Munich, Germany
- VeMiDoc, LLC, El Paso, TX
- Institute for Gastroenterology, Nutrition and Liver Disease, Schneider Children’s Medical Center, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Department of Paediatrics, The Medical University of Warsaw, Warsaw, Poland
- Department of Paediatric Gastroenterology, Great Ormond Street Hospital NHS Foundation Trust, London, United Kingdom
- Department of Paediatric Gastroenterology, VU University Medical Center, Amsterdam, The Netherlands
- Division of Pediatric Gastroenterology and Nutrition, Robert Debré Hospital (APHP)
- French Group of Fecal Transplantation, St Antoine Hospital (APHP), Paris, France
- KidZ Health Castle, Universitair Ziekenuis Brussel, Vrije Universiteit Brussel, Brussels, Belgium
- Division of Gastroetenterology and Nutrition, Inflammatory Bowel Disease Center, Boston Children’s Hospital, Harvard Medical School, 17 Boston, MA
- Section of Pediatric Gastroenterology and Nutrition, Texas Children’s Hospital, Baylor College of Medicine, Children’s Nutrition and Research Center, Houston, TX
| |
Collapse
|
21
|
Thorpe CM, Kane AV, Chang J, Tai A, Vickers RJ, Snydman DR. Enhanced preservation of the human intestinal microbiota by ridinilazole, a novel Clostridium difficile-targeting antibacterial, compared to vancomycin. PLoS One 2018; 13:e0199810. [PMID: 30071046 PMCID: PMC6071993 DOI: 10.1371/journal.pone.0199810] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 05/09/2018] [Indexed: 12/21/2022] Open
Abstract
Ridinilazole, a novel targeted antibacterial being developed for the treatment of C. difficile infection (CDI) and prevention of recurrence, was shown in a recent Phase 2 study to be superior to vancomycin with regard to the primary efficacy measure, sustained clinical response (SCR), with the superiority being driven primarily by marked reductions in the rates of CDI recurrence within 30 days. Tolerability of ridinilazole was comparable to that of vancomycin. The current nested cohort study compared the effects of ridinilazole and vancomycin on fecal microbiota during and after treatment among participants in the Phase 2 study. Changes in the microbiota were assessed using qPCR and high-throughput sequencing on participants' stools collected at multiple time-points (baseline [Day 1], Day 5, end-of-treatment [EOT; Day 10], Day 25, end-of-study [EOS; Day 40], and at CDI recurrence). qPCR analyses showed profound losses of Bacteroides, C. coccoides, C. leptum, and Prevotella groups at EOT with vancomycin treatment, while ridinilazole-treated participants had a modest decrease in C. leptum group levels at EOT, with levels recovering by Day 25. Vancomycin-treated participants had a significant increase in the Enterobacteriaceae group, with this increase persisting beyond EOT. At EOT, alpha diversity decreased with both antibiotics, though to a significantly lesser extent with ridinilazole (p <0.0001). Beta diversity analysis showed a significantly larger weighted Unifrac distance from baseline-to-EOT with vancomycin. Taxonomically, ridinilazole had a markedly narrower impact, with modest reductions in relative abundance in Firmicutes taxa. Microbiota composition returned to baseline sooner with ridinilazole than with vancomycin. Vancomycin treatment resulted in microbiome-wide changes, with significant reductions in relative abundances of Firmicutes, Bacteroidetes, Actinobacteria, and a profound increase in abundance of Proteobacteria. These findings demonstrate that ridinilazole is significantly less disruptive to microbiota than vancomycin, which may contribute to the reduced CDI recurrence observed in the Phase 2 study.
Collapse
Affiliation(s)
- Cheleste M. Thorpe
- Tufts Medical Center, Boston, MA, United States of America
- Tufts University School of Medicine, Boston, MA, United States of America
| | - Anne V. Kane
- Tufts Medical Center, Boston, MA, United States of America
| | - Justin Chang
- Tufts University School of Medicine, Boston, MA, United States of America
| | - Albert Tai
- Tufts University School of Medicine, Boston, MA, United States of America
| | | | - David R. Snydman
- Tufts Medical Center, Boston, MA, United States of America
- Tufts University School of Medicine, Boston, MA, United States of America
| |
Collapse
|
22
|
Horvat S, Rupnik M. Interactions Between Clostridioides difficile and Fecal Microbiota in in Vitro Batch Model: Growth, Sporulation, and Microbiota Changes. Front Microbiol 2018; 9:1633. [PMID: 30087660 PMCID: PMC6066498 DOI: 10.3389/fmicb.2018.01633] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 06/29/2018] [Indexed: 12/14/2022] Open
Abstract
Disturbance in gut microbiota is crucial for the development of Clostridioides difficile infection (CDI). Different mechanisms through which gut microbiota influences C. difficile colonization are known. However, C. difficile could also affect gut microbiota balance as previously demonstrated by cultivation of fecal microbiota in C. difficile conditioned medium. In current study, the interactions of C. difficile cells with gut microbiota were addressed. Three different strains (ribotypes 027, 014/020, and 010) were co-cultivated with two types of fecal microbiota (healthy and dysbiotic) using in vitro batch model. While all strains showed higher sporulation frequency in the presence of dysbiotic fecal microbiota, the growth was strain dependent. C. difficile either proliferated to comparable levels in the presence of dysbiotic and healthy fecal microbiota or grew better in co-culture with dysbiotic microbiota. In co-cultures with any C. difficile strain fecal microbiota showed decreased richness and diversity. Dysbiotic fecal microbiota was more affected after co-culture with C. difficile than healthy microbiota. Altogether, 62 OTUs were significantly changed in co-cultures of dysbiotic microbiota/C. difficile and 45 OTUs in co-cultures of healthy microbiota/C. difficile. However, the majority of significantly changed OTUs in both types of microbiota belonged to the phylum Firmicutes with Lachnospiraceae and Ruminococcaceae origin.
Collapse
Affiliation(s)
- Sabina Horvat
- Department of Microbiology, Faculty of Medicine, University of Maribor, Maribor, Slovenia
| | - Maja Rupnik
- Department of Microbiology, Faculty of Medicine, University of Maribor, Maribor, Slovenia.,Centre for Medical Microbiology, National Laboratory for Health, Environment and Food, Maribor, Slovenia
| |
Collapse
|
23
|
Chilton C, Pickering D, Freeman J. Microbiologic factors affecting Clostridium difficile recurrence. Clin Microbiol Infect 2018; 24:476-482. [DOI: 10.1016/j.cmi.2017.11.017] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 11/22/2017] [Accepted: 11/24/2017] [Indexed: 12/17/2022]
|
24
|
Samarkos M, Mastrogianni E, Kampouropoulou O. The role of gut microbiota in Clostridium difficile infection. Eur J Intern Med 2018; 50:28-32. [PMID: 29428498 DOI: 10.1016/j.ejim.2018.02.006] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Revised: 02/02/2018] [Accepted: 02/04/2018] [Indexed: 02/07/2023]
Abstract
Clostridium difficile infection has emerged as a major health problem. Because it is a spore-forming microorganism, C. difficile is difficult to eradicate and recurrences of the infection are frequent. The strong association of CDI with prior use of antibiotics led to the recognition that disturbances in the gut microbiota apparently plays a central role in CDI. Except for antibiotics, several other risk factors for CDI have been recognised, such as advanced age and use of proton pump inhibitors. The common characteristic of these factors is that they are associated with changes in the composition of gut microbiota. Data from human studies have shown that the presence of C. difficile, either as a colonizer or as a pathogen, is associated with reduced microbiota diversity. C. difficile infection per se seems to be associated with changes in the representation of specific microbial populations (e.g. taxa) which either may act protectively against C. difficile colonization of the gut or may increase susceptibility for C. difficile infection. Therapeutic gut microbiota manipulation can be achieved by faecal microbiota transplantation, which is highly effective for the treatment of CDI.
Collapse
Affiliation(s)
- Michael Samarkos
- 1st Department of Medicine, School of Medicine, National and Kapodistrian University of Athens, Greece.
| | - Elpida Mastrogianni
- 1st Department of Medicine, School of Medicine, National and Kapodistrian University of Athens, Greece
| | - Olga Kampouropoulou
- 1st Department of Medicine, School of Medicine, National and Kapodistrian University of Athens, Greece
| |
Collapse
|
25
|
Evaluating the effect of Clostridium difficile conditioned medium on fecal microbiota community structure. Sci Rep 2017; 7:16448. [PMID: 29180685 PMCID: PMC5703886 DOI: 10.1038/s41598-017-15434-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 10/26/2017] [Indexed: 01/05/2023] Open
Abstract
Clostridium difficile infection (CDI) is typically associated with disturbed gut microbiota and changes related to decreased colonization resistance against C. difficile are well described. However, nothing is known about possible effects of C. difficile on gut microbiota restoration during or after CDI. In this study, we have mimicked such a situation by using C. difficile conditioned medium of six different C. difficile strains belonging to PCR ribotypes 027 and 014/020 for cultivation of fecal microbiota. A marked decrease of microbial diversity was observed in conditioned medium of both tested ribotypes. The majority of differences occurred within the phylum Firmicutes, with a general decrease of gut commensals with putative protective functions (i.e. Lactobacillus, Clostridium_XIVa) and an increase in opportunistic pathogens (i.e. Enterococcus). Bacterial populations in conditioned medium differed between the two C. difficile ribotypes, 027 and 014/020 and are likely associated with nutrient availability. Fecal microbiota cultivated in medium conditioned by E. coli, Salmonella Enteritidis or Staphylococcus epidermidis grouped together and was clearly different from microbiota cultivated in C. difficile conditioned medium suggesting that C. difficile effects are specific. Our results show that the changes observed in microbiota of CDI patients are partially directly influenced by C. difficile.
Collapse
|
26
|
|
27
|
Vickers RJ, Tillotson G, Goldstein EJC, Citron DM, Garey KW, Wilcox MH. Ridinilazole: a novel therapy for Clostridium difficile infection. Int J Antimicrob Agents 2016; 48:137-43. [PMID: 27283730 DOI: 10.1016/j.ijantimicag.2016.04.026] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 04/22/2016] [Accepted: 04/23/2016] [Indexed: 12/15/2022]
Abstract
Clostridium difficile infection (CDI) is the leading cause of infectious healthcare-associated diarrhoea. Recurrent CDI increases disease morbidity and mortality, posing a high burden to patients and a growing economic burden to the healthcare system. Thus, there exists a significant unmet and increasing medical need for new therapies for CDI. This review aims to provide a concise summary of CDI in general and a specific update on ridinilazole (formerly SMT19969), a novel antibacterial currently under development for the treatment of CDI. Owing to its highly targeted spectrum of activity and ability to spare the normal gut microbiota, ridinilazole provides significant advantages over metronidazole and vancomycin, the mainstay antibiotics for CDI. Ridinilazole is bactericidal against C. difficile and exhibits a prolonged post-antibiotic effect. Furthermore, treatment with ridinilazole results in decreased toxin production. A phase 1 trial demonstrated that oral ridinilazole is well tolerated and specifically targets clostridia whilst sparing other faecal bacteria. Phase 2 and 3 trials will hopefully further our understanding of the clinical utility of ridinilazole for the treatment of CDI.
Collapse
Affiliation(s)
- Richard J Vickers
- Summit Therapeutics plc, 85b Park Drive, Milton Park, Abingdon, Oxford OX14 4RY, UK.
| | | | - Ellie J C Goldstein
- R.M. Alden Research Laboratory, Culver City, CA, USA; David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | | | - Kevin W Garey
- University of Houston College of Pharmacy, Houston, TX, USA
| | - Mark H Wilcox
- Microbiology, Leeds Teaching Hospitals and University of Leeds, Old Medical School, Leeds General Infirmary, Leeds, UK
| |
Collapse
|
28
|
Sangster W, Hegarty JP, Schieffer KM, Wright JR, Hackman J, Toole DR, Lamendella R, Stewart DB. Bacterial and Fungal Microbiota Changes Distinguish C. difficile Infection from Other Forms of Diarrhea: Results of a Prospective Inpatient Study. Front Microbiol 2016; 7:789. [PMID: 27252696 PMCID: PMC4879479 DOI: 10.3389/fmicb.2016.00789] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 05/09/2016] [Indexed: 12/15/2022] Open
Abstract
This study sought to characterize the bacterial and fungal microbiota changes associated with Clostridium difficile infection (CDI) among inpatients with diarrhea, in order to further explain the pathogenesis of this infection as well as to potentially guide new CDI therapies. Twenty-four inpatients with diarrhea were enrolled, 12 of whom had CDI. Each patient underwent stool testing for CDI prior to being treated with difficile-directed antibiotics, when appropriate. Clinical data was obtained from the medical record, while each stool sample underwent 16S rRNA and ITS sequencing for bacterial and fungal elements. An analysis of microbial community structures distinct to the CDI population was also performed. The results demonstrated no difference between the CDI and non-CDI cohorts with respect to any previously reported CDI risk factors. Butyrogenic bacteria were enriched in both CDI and non-CDI patients. A previously unreported finding of increased numbers of Akkermansia muciniphila in CDI patients was observed, an organism which degrades mucin and which therefore may provide a selective advantage toward CDI. Fungal elements of the genus Penicillium were predominant in CDI; these organisms produce antibacterial chemicals which may resist recovery of healthy microbiota. The most frequent CDI microbial community networks involved Peptostreptococcaceae and Enterococcus, with decreased population density of Bacteroides. These results suggest that the development of CDI is associated with microbiota changes which are consistently associated with CDI in human subjects. These gut taxa contribute to the intestinal dysbiosis associated with C. difficile infection.
Collapse
Affiliation(s)
- William Sangster
- Division of Colon and Rectal Surgery, Department of Surgery, College of Medicine, The Pennsylvania State University, Hershey PA, USA
| | - John P Hegarty
- Division of Colon and Rectal Surgery, Department of Surgery, College of Medicine, The Pennsylvania State University, Hershey PA, USA
| | - Kathleen M Schieffer
- Division of Colon and Rectal Surgery, Department of Surgery, College of Medicine, The Pennsylvania State University, Hershey PA, USA
| | - Justin R Wright
- Department of Biology, Juniata College, HuntingdonPA, USA; Wright Labs, LLC, HuntingdonPA, USA
| | - Jada Hackman
- Department of Biology, Juniata College, Huntingdon PA, USA
| | - David R Toole
- Department of Biology, Juniata College, Huntingdon PA, USA
| | - Regina Lamendella
- Department of Biology, Juniata College, HuntingdonPA, USA; Wright Labs, LLC, HuntingdonPA, USA
| | - David B Stewart
- Division of Colon and Rectal Surgery, Department of Surgery, College of Medicine, The Pennsylvania State University, Hershey PA, USA
| |
Collapse
|
29
|
Active and Secretory IgA-Coated Bacterial Fractions Elucidate Dysbiosis in Clostridium difficile Infection. mSphere 2016; 1:mSphere00101-16. [PMID: 27303742 PMCID: PMC4888886 DOI: 10.1128/msphere.00101-16] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 05/03/2016] [Indexed: 12/18/2022] Open
Abstract
C. difficile is a major enteric pathogen with worldwide distribution. Its expansion is associated with broad-spectrum antibiotics which disturb the normal gut microbiome. In this study, the DNA sequencing of highly active bacteria and bacteria opsonized by intestinal secretory immunoglobulin A (SIgA) separated from the whole bacterial community by FACS elucidated how the gut dysbiosis promotes C. difficile infection (CDI). Bacterial groups with inhibitory effects on C. difficile growth, such as Lactobacillales, were mostly inactive in the CDI patients. C. difficile was typical for the bacterial fraction opsonized by SIgA in patients with CDI, while Fusobacterium was characteristic for the SIgA-opsonized fraction of the controls. The study demonstrates that sequencing of specific bacterial fractions provides additional information about dysbiotic processes in the gut. The detected patterns have been confirmed with the whole patient cohort independently of the taxonomic differences detected in the nonfractionated microbiomes. The onset of Clostridium difficile infection (CDI) has been associated with treatment with wide-spectrum antibiotics. Antibiotic treatment alters the activity of gut commensals and may result in modified patterns of immune responses to pathogens. To study these mechanisms during CDI, we separated bacteria with high cellular RNA content (the active bacteria) and their inactive counterparts by fluorescence-activated cell sorting (FACS) of the fecal bacterial suspension. The gut dysbiosis due to the antibiotic treatment may result in modification of immune recognition of intestinal bacteria. The immune recognition patterns were assessed by FACS of bacterial fractions either coated or not with intestinal secretory immunoglobulin A (SIgA). We described the taxonomic distributions of these four bacterial fractions (active versus inactive and SIgA coated versus non-SIgA coated) by massive 16S rRNA gene amplicon sequencing and quantified the proportion of C. difficile toxin genes in the samples. The overall gut microbiome composition was more robustly influenced by antibiotics than by the C. difficile toxins. Bayesian networks revealed that the C. difficile cluster was preferentially SIgA coated during CDI. In contrast, in the CDI-negative group Fusobacterium was the characteristic genus of the SIgA-opsonized fraction. Lactobacillales and Clostridium cluster IV were mostly inactive in CDI-positive patients. In conclusion, although the proportion of C. difficile in the gut is very low, it is able to initiate infection during the gut dysbiosis caused by environmental stress (antibiotic treatment) as a consequence of decreased activity of the protective bacteria. IMPORTANCEC. difficile is a major enteric pathogen with worldwide distribution. Its expansion is associated with broad-spectrum antibiotics which disturb the normal gut microbiome. In this study, the DNA sequencing of highly active bacteria and bacteria opsonized by intestinal secretory immunoglobulin A (SIgA) separated from the whole bacterial community by FACS elucidated how the gut dysbiosis promotes C. difficile infection (CDI). Bacterial groups with inhibitory effects on C. difficile growth, such as Lactobacillales, were mostly inactive in the CDI patients. C. difficile was typical for the bacterial fraction opsonized by SIgA in patients with CDI, while Fusobacterium was characteristic for the SIgA-opsonized fraction of the controls. The study demonstrates that sequencing of specific bacterial fractions provides additional information about dysbiotic processes in the gut. The detected patterns have been confirmed with the whole patient cohort independently of the taxonomic differences detected in the nonfractionated microbiomes.
Collapse
|
30
|
Milani C, Ticinesi A, Gerritsen J, Nouvenne A, Lugli GA, Mancabelli L, Turroni F, Duranti S, Mangifesta M, Viappiani A, Ferrario C, Maggio M, Lauretani F, De Vos W, van Sinderen D, Meschi T, Ventura M. Gut microbiota composition and Clostridium difficile infection in hospitalized elderly individuals: a metagenomic study. Sci Rep 2016; 6:25945. [PMID: 27166072 PMCID: PMC4863157 DOI: 10.1038/srep25945] [Citation(s) in RCA: 155] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 04/22/2016] [Indexed: 12/17/2022] Open
Abstract
The gut microbiota composition of elderly hospitalized patients with Clostridium difficile infection (CDI) exposed to previous antibiotic treatment is still poorly investigated. The aim of this study was to compare the microbiota composition by means of 16S rRNA microbial profiling among three groups of hospitalized elderly patients (age ≥ 65) under standard diet including 25 CDI-positive (CDI group), 29 CDI-negative exposed to antibiotic treatment (AB+ group) and 30 CDI-negative subjects not on antibiotic treatment (AB− group). The functional properties of the gut microbiomes of CDI-positive vs CDI-negative subjects were also assessed by shotgun metagenomics. A significantly lower microbial diversity was detected in CDI samples, whose microbiomes clustered separately from CDI-negative specimens. CDI was associated with a significant under-representation of gut commensals with putative protective functionalities, including Bacteroides, Alistipes, Lachnospira and Barnesiella, and over-representation of opportunistic pathogens. These findings were confirmed by functional shotgun metagenomics analyses, including an in-depth profiling of the Peptostreptococcaceae family. In CDI-negative patients, antibiotic treatment was associated with significant depletion of few commensals like Alistipes, but not with a reduction in species richness. A better understanding of the correlations between CDI and the microbiota in high-risk elderly subjects may contribute to identify therapeutic targets for CDI.
Collapse
Affiliation(s)
- Christian Milani
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Italy
| | - Andrea Ticinesi
- Internal Medicine and Critical Subacute Care Unit, Parma University Hospital, Parma, Italy.,Department of Clinical and Experimental Medicine, University of Parma, Parma, Italy
| | - Jacoline Gerritsen
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB, Wageningen, The Netherlands
| | - Antonio Nouvenne
- Internal Medicine and Critical Subacute Care Unit, Parma University Hospital, Parma, Italy.,Department of Clinical and Experimental Medicine, University of Parma, Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Italy
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Italy
| | - Sabrina Duranti
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Italy
| | - Marta Mangifesta
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Italy
| | | | - Chiara Ferrario
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Italy
| | - Marcello Maggio
- Department of Clinical and Experimental Medicine, University of Parma, Parma, Italy.,Geriatric Unit, Parma University Hospital, Parma, Italy
| | - Fulvio Lauretani
- Internal Medicine and Critical Subacute Care Unit, Parma University Hospital, Parma, Italy
| | - Willem De Vos
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB, Wageningen, The Netherlands
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland
| | - Tiziana Meschi
- Internal Medicine and Critical Subacute Care Unit, Parma University Hospital, Parma, Italy.,Department of Clinical and Experimental Medicine, University of Parma, Parma, Italy
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Italy
| |
Collapse
|
31
|
Clostridium difficile infection: epidemiology, diagnosis and understanding transmission. Nat Rev Gastroenterol Hepatol 2016; 13:206-16. [PMID: 26956066 DOI: 10.1038/nrgastro.2016.25] [Citation(s) in RCA: 219] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Clostridium difficile infection (CDI) continues to affect patients in hospitals and communities worldwide. The spectrum of clinical disease ranges from mild diarrhoea to toxic megacolon, colonic perforation and death. However, this bacterium might also be carried asymptomatically in the gut, potentially leading to 'silent' onward transmission. Modern technologies, such as whole-genome sequencing and multi-locus variable-number tandem-repeat analysis, are helping to track C. difficile transmission across health-care facilities, countries and continents, offering the potential to illuminate previously under-recognized sources of infection. These typing strategies have also demonstrated heterogeneity in terms of CDI incidence and strain types reflecting different stages of epidemic spread. However, comparison of CDI epidemiology, particularly between countries, is challenging due to wide-ranging approaches to sampling and testing. Diagnostic strategies for C. difficile are complicated both by the wide range of bacterial targets and tests available and the need to differentiate between toxin-producing and non-toxigenic strains. Multistep diagnostic algorithms have been recommended to improve sensitivity and specificity. In this Review, we describe the latest advances in the understanding of C. difficile epidemiology, transmission and diagnosis, and discuss the effect of these developments on the clinical management of CDI.
Collapse
|
32
|
Trček J, Mahnič A, Rupnik M. Diversity of the microbiota involved in wine and organic apple cider submerged vinegar production as revealed by DHPLC analysis and next-generation sequencing. Int J Food Microbiol 2016; 223:57-62. [DOI: 10.1016/j.ijfoodmicro.2016.02.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 01/21/2016] [Accepted: 02/08/2016] [Indexed: 12/16/2022]
|
33
|
Bandelj P, Blagus R, Briski F, Frlic O, Vergles Rataj A, Rupnik M, Ocepek M, Vengust M. Identification of risk factors influencing Clostridium difficile prevalence in middle-size dairy farms. Vet Res 2016; 47:41. [PMID: 26968527 PMCID: PMC4788955 DOI: 10.1186/s13567-016-0326-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 01/25/2016] [Indexed: 12/22/2022] Open
Abstract
Farm animals have been suggested to play an important role in the epidemiology of Clostridium difficile infection (CDI) in the community. The purpose of this study was to evaluate risk factors associated with C. difficile dissemination in family dairy farms, which are the most common farming model in the European Union. Environmental samples and fecal samples from cows and calves were collected repeatedly over a 1 year period on 20 mid-size family dairy farms. Clostridium difficile was detected in cattle feces on all farms using qPCR. The average prevalence between farms was 10% (0–44.4%) and 35.7% (3.7–66.7%) in cows and calves, respectively. Bacterial culture yielded 103 C. difficile isolates from cattle and 61 from the environment. Most C. difficile isolates were PCR-ribotype 033. A univariate mixed effect model analysis of risk factors associated dietary changes with increasing C. difficile prevalence in cows (P = 0.0004); and dietary changes (P = 0.004), breeding Simmental cattle (P = 0.001), mastitis (P = 0.003) and antibiotic treatment (P = 0.003) in calves. Multivariate analysis of risk factors found that dietary changes in cows (P = 0.0001) and calves (P = 0.002) increase C. difficile prevalence; mastitis was identified as a risk factor in calves (P = 0.001). This study shows that C. difficile is common on dairy farms and that shedding is more influenced by farm management than environmental factors. Based on molecular typing of C. difficile isolates, it could also be concluded that family dairy farms are currently not contributing to increased CDI incidence.
Collapse
Affiliation(s)
- Petra Bandelj
- Veterinary faculty, University of Ljubljana, cesta v Mestni log 47, 1115, Ljubljana, Slovenia.
| | - Rok Blagus
- Institute for biostatistics and Medical informatics, University of Ljubljana, Vrazov trg 2, 1104, Ljubljana, Slovenia
| | | | - Olga Frlic
- , Vinharje 6, 4223, Poljane nad Skofjo Loko, Slovenia
| | | | - Maja Rupnik
- National Laboratory for Health, Environment and Food, Prvomajska ulica 1, 2000, Maribor, Slovenia.,Faculty of Medicine, University of Maribor, Taborska ulica 8, 2000, Maribor, Slovenia.,Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova cesta 39, 1000, Ljubljana, Slovenia
| | - Matjaz Ocepek
- Veterinary faculty, University of Ljubljana, cesta v Mestni log 47, 1115, Ljubljana, Slovenia
| | - Modest Vengust
- Veterinary faculty, University of Ljubljana, cesta v Mestni log 47, 1115, Ljubljana, Slovenia
| |
Collapse
|
34
|
Abstract
Exposure to antibiotics is the major risk factor for Clostridium difficile diarrhea (CDD), suggesting that impairment of colonization resistance due to depletion of the gut flora is a significant underlying disease susceptibility factor. Many properties of probiotic organisms indicate that they may be able to replenish the depleted gut flora and restore colonization resistance. However, despite numerous clinical trials, the evidence base for probiotics in the prevention of CDD remains weak. A recent large trial of a multistrain, high-dose probiotic did not show clear evidence of efficacy. The role of probiotics in the prevention of CDD remains unclear.
Collapse
Affiliation(s)
- Stephen J Allen
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK.
| |
Collapse
|
35
|
Hourigan SK, Chen LA, Grigoryan Z, Laroche G, Weidner M, Sears CL, Oliva-Hemker M. Microbiome changes associated with sustained eradication of Clostridium difficile after single faecal microbiota transplantation in children with and without inflammatory bowel disease. Aliment Pharmacol Ther 2015. [PMID: 26198180 DOI: 10.1111/apt.13326] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND Little data are available regarding the effectiveness and associated microbiome changes of faecal microbiota transplantation (FMT) for Clostridium difficile infection (CDI) in children, especially in those with inflammatory bowel disease (IBD) with presumed underlying dysbiosis. AIM To investigate C. difficile eradication and microbiome changes with FMT in children with and without IBD. METHODS Children with a history of recurrent CDI (≥3 recurrences) underwent FMT via colonoscopy. Stool samples were collected pre-FMT and post-FMT at 2-10 weeks, 10-20 weeks and 6 months. The v4 hypervariable region of the 16S rRNA gene was sequenced. C. difficile toxin B gene polymerase chain reaction was performed. RESULTS Eight children underwent FMT for CDI; five had IBD. All had resolution of CDI symptoms. All tested had eradication of C. difficile at 10-20 weeks and 6 months post-FMT. Pre-FMT patient samples had significantly decreased bacterial richness compared with donors (P = 0.01), in those with IBD (P = 0.02) and without IBD (P = 0.01). Post-FMT, bacterial diversity in patients increased. Six months post-FMT, there was no significant difference between bacterial diversity of donors and patients without IBD; however, bacterial diversity in those with IBD returned to pre-FMT baseline. Microbiome composition at 6 months in IBD-negative patients more closely approximated donor composition compared to IBD-positive patients. CONCLUSIONS FMT gives sustained C. difficile eradication in children with and without IBD. FMT-restored diversity is sustained in children without IBD. In those with IBD, bacterial diversity returns to pre-FMT baseline by 6 months, suggesting IBD host-related mechanisms modify faecal microbiome diversity.
Collapse
Affiliation(s)
- S K Hourigan
- Johns Hopkins School of Medicine, Baltimore, MD, USA.,Pediatric Specialists of Virginia, Fairfax, VA, USA
| | - L A Chen
- Johns Hopkins School of Medicine, Baltimore, MD, USA.,NYU School of Medicine, New York, NY, USA
| | | | - G Laroche
- Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - M Weidner
- Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - C L Sears
- Johns Hopkins School of Medicine, Baltimore, MD, USA
| | | |
Collapse
|
36
|
Novel riboswitch-binding flavin analog that protects mice against Clostridium difficile infection without inhibiting cecal flora. Antimicrob Agents Chemother 2015; 59:5736-46. [PMID: 26169403 DOI: 10.1128/aac.01282-15] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 07/03/2015] [Indexed: 01/08/2023] Open
Abstract
Novel mechanisms of action and new chemical scaffolds are needed to rejuvenate antibacterial drug discovery, and riboswitch regulators of bacterial gene expression are a promising class of targets for the discovery of new leads. Herein, we report the characterization of 5-(3-(4-fluorophenyl)butyl)-7,8-dimethylpyrido[3,4-b]quinoxaline-1,3(2H,5H)-dione (5FDQD)-an analog of riboflavin that was designed to bind riboswitches that naturally recognize the essential coenzyme flavin mononucleotide (FMN) and regulate FMN and riboflavin homeostasis. In vitro, 5FDQD and FMN bind to and trigger the function of an FMN riboswitch with equipotent activity. MIC and time-kill studies demonstrated that 5FDQD has potent and rapidly bactericidal activity against Clostridium difficile. In C57BL/6 mice, 5FDQD completely prevented the onset of lethal antibiotic-induced C. difficile infection (CDI). Against a panel of bacteria representative of healthy bowel flora, the antibacterial selectivity of 5FDQD was superior to currently marketed CDI therapeutics, with very little activity against representative strains from the Bacteroides, Lactobacillus, Bifidobacterium, Actinomyces, and Prevotella genera. Accordingly, a single oral dose of 5FDQD caused less alteration of culturable cecal flora in mice than the comparators. Collectively, these data suggest that 5FDQD or closely related analogs could potentially provide a high rate of CDI cure with a low likelihood of infection recurrence. Future studies will seek to assess the role of FMN riboswitch binding to the mechanism of 5FDQD antibacterial action. In aggregate, our results indicate that riboswitch-binding antibacterial compounds can be discovered and optimized to exhibit activity profiles that merit preclinical and clinical development as potential antibacterial therapeutic agents.
Collapse
|
37
|
Vincent C, Manges AR. Antimicrobial Use, Human Gut Microbiota and Clostridium difficile Colonization and Infection. Antibiotics (Basel) 2015; 4:230-53. [PMID: 27025623 PMCID: PMC4790283 DOI: 10.3390/antibiotics4030230] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 06/23/2015] [Accepted: 06/24/2015] [Indexed: 12/20/2022] Open
Abstract
Clostridium difficile infection (CDI) is the most important cause of nosocomial diarrhea. Broad-spectrum antimicrobials have profound detrimental effects on the structure and diversity of the indigenous intestinal microbiota. These alterations often impair colonization resistance, allowing the establishment and proliferation of C. difficile in the gut. Studies involving animal models have begun to decipher the precise mechanisms by which the intestinal microbiota mediates colonization resistance against C. difficile and numerous investigations have described gut microbiota alterations associated with C. difficile colonization or infection in human subjects. Fecal microbiota transplantation (FMT) is a highly effective approach for the treatment of recurrent CDI that allows the restoration of a healthy intestinal ecosystem via infusion of fecal material from a healthy donor. The recovery of the intestinal microbiota after FMT has been examined in a few reports and work is being done to develop custom bacterial community preparations that could be used as a replacement for fecal material.
Collapse
Affiliation(s)
- Caroline Vincent
- Department of Microbiology and Immunology, McGill University, Montréal, QC H3A 2B4, Canada.
| | - Amee R Manges
- School of Population and Public Health, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.
| |
Collapse
|
38
|
Zhang L, Dong D, Jiang C, Li Z, Wang X, Peng Y. Insight into alteration of gut microbiota in Clostridium difficile infection and asymptomatic C. difficile colonization. Anaerobe 2015; 34:1-7. [PMID: 25817005 DOI: 10.1016/j.anaerobe.2015.03.008] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Revised: 03/23/2015] [Accepted: 03/25/2015] [Indexed: 02/08/2023]
Abstract
Clostridium difficile is well recognized as the common pathogen of nosocomial diarrhea, meanwhile, asymptomatic colonization with C. difficile in part of the population has also drawn public attention. Although gut microbiota is known to play an important role in the pathogenesis of C. difficile infection (CDI), whether there is any alteration of gut microbial composition in asymptomatic C. difficile carriers hasn't been clearly described. The purpose of this study was to explore the differences in gut microbiome among CDI patients, asymptomatic C. difficile carriers and healthy individuals. We performed fecal microbiota analysis on the samples of eight CDI patients, eight asymptomatic C. difficile carriers and nine healthy subjects using 16S rRNA gene pyrosequencing. CDI patients and asymptomatic carriers showed reduced microbial richness and diversity compared with healthy subjects, accompanied with a paucity of phylum Bacteroidetes and Firmicutes as well as an overabundance of Proteobacteria. Some normally commensal bacteria, especially butyrate producers, were significantly depleted in CDI patients and asymptomatic carriers. Furthermore, the differences observed in microbial community structure between CDI patients and asymptomatic carriers suggested that the gut microbiota may be a potential factor of disease state for CDI. Our study demonstrates the characterization and diversity of gut microbiota in CDI and asymptomatic C. difficile colonization, which will provide new ideas for surveillance of the disease state and development of microbiota-targeted agents for CDI prevention and treatment.
Collapse
Affiliation(s)
- Lihua Zhang
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, 197 Ruijin No.2 Road, Shanghai 200025, China
| | - Danfeng Dong
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, 197 Ruijin No.2 Road, Shanghai 200025, China
| | - Cen Jiang
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, 197 Ruijin No.2 Road, Shanghai 200025, China
| | - Zhen Li
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, 197 Ruijin No.2 Road, Shanghai 200025, China
| | - Xuefeng Wang
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, 197 Ruijin No.2 Road, Shanghai 200025, China
| | - Yibing Peng
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, 197 Ruijin No.2 Road, Shanghai 200025, China.
| |
Collapse
|
39
|
Vickers R, Robinson N, Best E, Echols R, Tillotson G, Wilcox M. A randomised phase 1 study to investigate safety, pharmacokinetics and impact on gut microbiota following single and multiple oral doses in healthy male subjects of SMT19969, a novel agent for Clostridium difficile infections. BMC Infect Dis 2015; 15:91. [PMID: 25880933 PMCID: PMC4349307 DOI: 10.1186/s12879-015-0759-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 01/15/2015] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Clostridium difficile infection (CDI) is a leading cause of diarrhoea in health care settings with symptoms ranging from mild and self-limiting to life threatening. SMT19969 is a novel, non-absorbable antibiotic currently under development for the treatment of CDI. Here we report the results from a Phase I study. METHODS A double-blind, randomized, placebo-controlled study assessing safety and tolerability of single and multiple oral doses of SMT19969 in healthy volunteers. Pharmacokinetic assessments included blood and faecal sampling. The effect of food on systemic exposure and analysis of the gut microbiota were also included. RESULTS Fifty-six healthy male subjects were enrolled. Following single oral doses of up to 2,000 mg in the fasted state, plasma concentrations of SMT19969 were generally below the lower limit of quantification. In the fed state levels ranged from 0.102 to 0.296 ng/mL after single dosing and after repeat dosing at Day 10 from 0.105 to 0.305 ng/mL. Following single and multiple oral doses of SMT19969, mean daily faecal concentrations increased with increasing dose level and were significantly above the typical MIC range for C. difficile (0.06-0.5 μg/mL). At 200 mg BID, mean (± SD) faecal concentrations of 1,466 (±547) μg/g and 1,364 (±446) μg/g were determined on days 5 and 10 of dosing respectively. No notable metabolites were detected in faeces. Overall, all doses of SMT19969 were well tolerated both as single oral doses or BID oral doses for 10 days. The majority (88%) of adverse events (AEs) were classified as gastrointestinal disorders and were mild in severity, resolving without treatment. The gut microbiota was analysed in the multiple dose groups with minimal changes observed in the bacterial groups analysed except for total clostridia which were reduced to below the limit of detection by day 4 of dosing. CONCLUSIONS Oral administration of SMT19969 was considered safe and well tolerated and was associated with negligible plasma concentrations after single and multiple doses. In addition, minimal disruption of normal gut microbiota was noted, confirming the highly selective spectrum of the compound. These results support the further clinical development of SMT19969 as an oral therapy for CDI. TRIAL REGISTRATION Current Controlled Trials. ISRCTN10858225 .
Collapse
Affiliation(s)
- Richard Vickers
- Summit PLC, 85b Park Drive, Milton Park, Abingdon, Oxford, OX14 4RY, UK.
| | - Neil Robinson
- Summit PLC, 85b Park Drive, Milton Park, Abingdon, Oxford, OX14 4RY, UK.
| | - Emma Best
- Microbiology, Leeds Teaching Hospitals & University of Leeds, Old Medical School, Leeds General Infirmary, Leeds, LS1 3EX, UK.
| | | | | | - Mark Wilcox
- Microbiology, Leeds Teaching Hospitals & University of Leeds, Old Medical School, Leeds General Infirmary, Leeds, LS1 3EX, UK.
| |
Collapse
|
40
|
Martin J. The contribution of strains and hosts to outcomes in Clostridium difficile infection. Infect Dis Clin North Am 2015; 29:51-61. [PMID: 25582645 DOI: 10.1016/j.idc.2014.11.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Acquisition of Clostridium difficile spores can be followed by a spectrum of clinical outcomes ranging from asymptomatic transit through the bowel to severe colitis and death. This clinical variability is a product of bacterial virulence and host susceptibility to the pathogen. It is important to identify patients at high risk of poor outcome so that increased monitoring and optimal treatment strategies can be instigated. This article discusses the evidence linking strain type to clinical outcome, including the importance of toxin and nontoxin virulence factors. It reviews host factors and their relationship with C difficile infection susceptibility, recurrence, and mortality.
Collapse
Affiliation(s)
- Jessica Martin
- University of Leeds, Old Medical School, Leeds General Infirmary, Leeds LS1 3EX, UK.
| |
Collapse
|
41
|
Čitar M, Hacin B, Tompa G, Štempelj M, Rogelj I, Dolinšek J, Narat M, Matijašić BB. Human intestinal mucosa-associated Lactobacillus and Bifidobacterium strains with probiotic properties modulate IL-10, IL-6 and IL-12 gene expression in THP-1 cells. Benef Microbes 2015; 6:325-36. [DOI: 10.3920/bm2014.0081] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Lactobacilli and bifidobacteria are considered one of the permanent genera of the physiological human intestinal microbiota and represent an enormous pool of potential probiotic candidates. Approximately 450 isolates of presumptive Lactobacillus or Bifidobacterium strains were obtained from bioptic samples of colonic and ileal mucosa from 15 adolescents aged 12 to 18 years. On the basis of randomly amplified polymorphic DNA (RAPD)-PCR analysis, 20 strains were selected for further taxonomic classification and characterisation, as well as assessment of probiotic properties and safety. Importantly, selected strains showed the capability of colonising different parts of the intestine. The most frequently isolated species was Lactobacillus paracasei followed by Lactobacillus fermentum. The majority of isolates were susceptible to antimicrobials of human and veterinary importance, however, tetracycline and/or erythromycin resistance was observed in Lactobacillus plantarum and L. fermentum strains. Thirteen strains were able to ferment more than 19 different carbon sources and three out of five tested strains exerted antagonistic activity against several different indicator strains. Two Lactobacillus isolates (L. paracasei L350 and L. fermentum L930 bb) and one Bifidobacterium isolate (Bifidobacterium animalis subsp. animalis IM386) fulfilled in vitro selection criteria for probiotic strains and exhibited strong downregulation of pro-inflammatory cytokines IL-6 and IL-12 and upregulation of anti-inflammatory IL-10. The selected strains represent suitable candidates for further studies regarding their positive influence on host health and could play an important role in ameliorating the symptoms of inflammatory bowel diseases.
Collapse
Affiliation(s)
- M. Čitar
- Biotechnical Faculty, Department of Animal Science, Institute of Dairy Science and Probiotics, University of Ljubljana, Groblje 3, 1230 Domžale, Slovenia
- Medis, Pharmaceutical Company, d.o.o., Brnčičeva 1, 1231 Ljubljana, Slovenia
| | - B. Hacin
- Veterinary Faculty, National Veterinary Institute, Pri Hrastu 18, 5000 Nova Gorica, Slovenia
| | - G. Tompa
- Biotechnical Faculty, Department of Animal Science, Institute of Dairy Science and Probiotics, University of Ljubljana, Groblje 3, 1230 Domžale, Slovenia
| | - M. Štempelj
- Medis, Pharmaceutical Company, d.o.o., Brnčičeva 1, 1231 Ljubljana, Slovenia
| | - I. Rogelj
- Biotechnical Faculty, Department of Animal Science, Institute of Dairy Science and Probiotics, University of Ljubljana, Groblje 3, 1230 Domžale, Slovenia
| | - J. Dolinšek
- Department of Pediatrics, Gastroenterology, hepatology and nutrition Unit, University Medical Centre Maribor, Ljubljanska ulica 5, 2000 Maribor, Slovenia
| | - M. Narat
- Biotechnical Faculty, Department of Animal Science, Chair of Genetics, Animal Biotechnology and Immunology, University of Ljubljana, Groblje 3, 1230 Domžale, Slovenia
| | - B. Bogovič Matijašić
- Biotechnical Faculty, Department of Animal Science, Institute of Dairy Science and Probiotics, University of Ljubljana, Groblje 3, 1230 Domžale, Slovenia
| |
Collapse
|
42
|
Sangster W, Hegarty JP, Stewart DB. Phage therapy for Clostridium difficile infection: An alternative to antibiotics? SEMINARS IN COLON AND RECTAL SURGERY 2014. [DOI: 10.1053/j.scrs.2014.05.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
|
43
|
Zalig S, Rupnik M. Clostridium difficile infection and gut microbiota. SEMINARS IN COLON AND RECTAL SURGERY 2014. [DOI: 10.1053/j.scrs.2014.05.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
|
44
|
Abstract
Clostridium difficile-associated illness is an increasingly prevalent and morbid condition. The elderly population is at a disproportionate risk of developing symptomatic disease and associated complications, including progression to severe or fulminant disease, and development of recurrent infections. This article analyzes the factors that influence C difficile disease propensity and severity, with particular attention directed toward features relevant to the rapidly aging population.
Collapse
Affiliation(s)
- Jonathan M Keller
- Department of Medicine, University of Washington Medical Center, 1959 Northeast Pacific Street, Box 356421, Seattle, WA 98195, USA
| | | |
Collapse
|
45
|
Abstract
Clostridium difficile infection (CDI) is the leading health care-associated illness. Both human and animal models have demonstrated the importance of the gut microbiota's capability of providing colonization resistance against C. difficile. Risk factors for disease development include antibiotic use, which disrupts the gut microbiota, leading to the loss of colonization resistance and subsequent CDI. Identification of the specific microbes capable of restoring this function remains elusive. Future studies directed at how microbial communities influence the metabolic environment may help elucidate the role of the microbiota in disease development. These findings will improve current biotherapeutics for patients with CDI, particularly those with recurrent disease.
Collapse
|
46
|
Preclinical studies of amixicile, a systemic therapeutic developed for treatment of Clostridium difficile infections that also shows efficacy against Helicobacter pylori. Antimicrob Agents Chemother 2014; 58:4703-12. [PMID: 24890599 DOI: 10.1128/aac.03112-14] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Amixicile shows efficacy in the treatment of Clostridium difficile infections (CDI) in a mouse model, with no recurrence of CDI. Since amixicile selectively inhibits the action of a B vitamin (thiamine pyrophosphate) cofactor of pyruvate:ferredoxin oxidoreductase (PFOR), it may both escape mutation-based drug resistance and spare beneficial probiotic gut bacteria that do not express this enzyme. Amixicile is a water-soluble derivative of nitazoxanide (NTZ), an antiparasitic therapeutic that also shows efficacy against CDI in humans. In comparative studies, amixicile showed no toxicity to hepatocytes at 200 μM (NTZ was toxic above 10 μM); was not metabolized by human, dog, or rat liver microsomes; showed equivalence or superiority to NTZ in cytochrome P450 assays; and did not activate efflux pumps (breast cancer resistance protein, P glycoprotein). A maximum dose (300 mg/kg) of amixicile given by the oral or intraperitoneal route was well tolerated by mice and rats. Plasma exposure (rats) based on the area under the plasma concentration-time curve was 79.3 h · μg/ml (30 mg/kg dose) to 328 h · μg/ml (100 mg/kg dose), the maximum concentration of the drug in serum was 20 μg/ml, the time to the maximum concentration of the drug in serum was 0.5 to 1 h, and the half-life was 5.6 h. Amixicile did not concentrate in mouse feces or adversely affect gut populations of Bacteroides species, Firmicutes, segmented filamentous bacteria, or Lactobacillus species. Systemic bioavailability was demonstrated through eradication of Helicobacter pylori in a mouse infection model. In summary, the efficacy of amixicile in treating CDI and other infections, together with low toxicity, an absence of mutation-based drug resistance, and excellent drug metabolism and pharmacokinetic metrics, suggests a potential for broad application in the treatment of infections caused by PFOR-expressing microbial pathogens in addition to CDI.
Collapse
|
47
|
Variations in virulence and molecular biology among emerging strains of Clostridium difficile. Microbiol Mol Biol Rev 2014; 77:567-81. [PMID: 24296572 DOI: 10.1128/mmbr.00017-13] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Clostridium difficile is a Gram-positive, spore-forming organism which infects and colonizes the large intestine, produces potent toxins, triggers inflammation, and causes significant systemic complications. Treating C. difficile infection (CDI) has always been difficult, because the disease is both caused and resolved by antibiotic treatment. For three and a half decades, C. difficile has presented a treatment challenge to clinicians, and the situation took a turn for the worse about 10 years ago. An increase in epidemic outbreaks related to CDI was first noticed around 2003, and these outbreaks correlated with a sudden increase in the mortality rate of this illness. Further studies discovered that these changes in CDI epidemiology were associated with the rapid emergence of hypervirulent strains of C. difficile, now collectively referred to as NAP1/BI/027 strains. The discovery of new epidemic strains of C. difficile has provided a unique opportunity for retrospective and prospective studies that have sought to understand how these strains have essentially replaced more historical strains as a major cause of CDI. Moreover, detailed studies on the pathogenesis of NAP1/BI/027 strains are leading to new hypotheses on how this emerging strain causes severe disease and is more commonly associated with epidemics. In this review, we provide an overview of CDI, discuss critical mechanisms of C. difficile virulence, and explain how differences in virulence-associated factors between historical and newly emerging strains might explain the hypervirulence exhibited by this pathogen during the past decade.
Collapse
|
48
|
Bassis CM, Theriot CM, Young VB. Alteration of the murine gastrointestinal microbiota by tigecycline leads to increased susceptibility to Clostridium difficile infection. Antimicrob Agents Chemother 2014; 58:2767-74. [PMID: 24590475 PMCID: PMC3993203 DOI: 10.1128/aac.02262-13] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 02/23/2014] [Indexed: 12/29/2022] Open
Abstract
Antibiotics can play dual roles in Clostridium difficile infection (CDI); antibiotic treatment increases the risk of CDI, and antibiotics are used to treat CDI. The glycylcycline antibiotic tigecycline has broad antimicrobial activity, yet it is rarely associated with the development of CDI, presumably due to its activity against C. difficile. In this study, we investigated how tigecycline treatment affects the structure of the gut microbiota and susceptibility to CDI by treating mice with tigecycline (n = 20) or saline (n = 8) for 10 days. A sequence analysis of the bacterial 16S rRNA gene amplicons was used to monitor changes in the fecal microbiota. A subset of the mice was followed for 5 weeks after the end of treatment. The remaining mice were challenged with C. difficile strain VPI 10463 spores 2 days after the tigecycline treatment ended. Tigecycline treatment resulted in major shifts in the gut microbiota, including large decreases in Bacteroidetes levels and large increases in Proteobacteria levels. Mice with tigecycline-altered microbial communities were susceptible to challenge with C. difficile spores and developed clinical signs of severe CDI. Five weeks after the cessation of tigecycline treatment, the recovery of the bacterial community was incomplete and diversity was lower than in the untreated controls. Antibiotics with intrinsic activity against C. difficile can still alter the microbiota in a way that leads to susceptibility to CDI after discontinuation of the drug. These results indicate that microbiotic dynamics are key in the development of CDI, and a better understanding of these dynamics may lead to better strategies to prevent and treat this disease.
Collapse
Affiliation(s)
- Christine M. Bassis
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, Michigan, USA
| | - Casey M. Theriot
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, Michigan, USA
| | - Vincent B. Young
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, Michigan, USA
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| |
Collapse
|
49
|
Imirzalioglu C, Sethi S, Schneider C, Hain T, Chakraborty T, Mayser P, Domann E. Distinct polymicrobial populations in a chronic foot ulcer with implications for diagnostics and anti-infective therapy. BMC Res Notes 2014; 7:196. [PMID: 24679105 PMCID: PMC3974921 DOI: 10.1186/1756-0500-7-196] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Accepted: 03/27/2014] [Indexed: 11/27/2022] Open
Abstract
Background Polymicrobial infections caused by combinations of different bacteria are being detected with an increasing frequency. The evidence of such complex infections is being revealed through the use of novel molecular and culture-independent methods. Considerable progress has been made in the last decade regarding the diagnostic application of such molecular techniques. In particular, 16S rDNA-based sequencing and even metagenomic analyses have been successfully used to study the microbial diversity in ecosystems and human microbiota. Here, we utilized denaturing high-performance liquid chromatography (DHPLC) as a diagnostic tool for identifying different bacterial species in complex clinical samples of a patient with a chronic foot ulcer. Case presentation A 45-year-old female suffered from a chronic 5x5cm large plantar ulcer located in the posterior calcaneal area with subcutaneous tissue infection and osteomyelitis. The chronic ulcer developed over a period of 8 years. Culture and DHPLC revealed a distinct and location-dependent polymicrobial infection of the ulcer. The analysis of a superficial biopsy revealed a mixture of Staphylococcus aureus, Proteus vulgaris, and Fusobacterium nucleatum, whereas the tissue-deep biopsy harbored a mixture of four different bacterial species, namely Gemella morbillorum, Porphyromonas asaccharolytica, Bacteroides fragilis, and Arcanobacterium haemolyticum. Conclusions This clinical case highlights the difficulties in assessing polymicrobial infections where a mixture of fastidious, rapid and slow growing bacteria as well as anaerobes exists as structured communities within the tissue architecture of chronic wound infections. The diagnosis of this multilayered polymicrobial infection led to a microbe-adapted antibiotic therapy, targeting the polymicrobial nature of this infection in addition to a standard local wound treatment. However, a complete wound closure could not be achieved due to the long-lasting extensive destruction of tissue.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Eugen Domann
- Institute of Medical Microbiology, Justus-Liebig University Giessen, Schubertstrasse 81, D-35392 Giessen, Germany.
| |
Collapse
|
50
|
Abstract
PURPOSE OF REVIEW Clostridium difficile infection (CDI) is the leading cause of antibiotic-associated diarrhea and pseudomembranous colitis in the healthcare setting. An emerging consensus suggests that CDI is caused by pathogenic toxin production, gut microbial dysbiosis and altered host inflammatory responses. The aim of this review is to summarize and highlight recent advances focused on CDI pathogenic mechanisms. RECENT FINDINGS Potential paradigm shifts relating to the mechanisms of toxin action and inhibition have recently been reported, with new insights into spore germination and surface protein function also gaining traction. Multiomic analysis of microbiome dysbiosis has identified important CDI-associated microbial community shifts that may form the basis of future targeted bacteriotherapy, and functional metabolite biomarkers that require further characterization. Classical innate and adaptive immunity against CDI is rapidly being delineated, with novel innate S-nitrosylation signals also being identified. SUMMARY Studies in patients and animal disease models are shedding new light on the critical roles of the microbiota, metabolome and host responses in primary and recurrent CDI. An improved understanding of the CDI disease pathogenesis will provide the basis for developing new therapies for treating disease and preventing recurrence.
Collapse
|