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Saxena A, Mitchell C, Bogdon R, Roark K, Wilson K, Staley S, Hailey M, Williams MC, Rutkovsky A, Nagarkatti P, Nagarkatti M, Busbee PB. Aryl Hydrocarbon Receptor Regulates Muc2 Production Independently of IL-22 during Colitis. Int J Mol Sci 2024; 25:2404. [PMID: 38397081 PMCID: PMC10888603 DOI: 10.3390/ijms25042404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/09/2024] [Accepted: 02/15/2024] [Indexed: 02/25/2024] Open
Abstract
We previously reported that an aryl hydrocarbon receptor (AhR) ligand, indole-3-carbinol (I3C), was effective at reducing colitis severity through immune cell-mediated interleukin-22 (IL-22) production. Intestinal epithelial cells (IECs) are also involved in regulating colitis, so we investigated their AhR-mediated mechanisms in the current report. A transcriptome analysis of IECs in wildtype (WT) mice revealed that during colitis, I3C regulated select mucin proteins, which could be attributed to goblet cell development. To address this, experiments under in vivo colitis (mice) or in vitro colon organoid conditions were undertaken to determine how select mucin proteins were altered in the absence or presence of AhR in IECs during I3C treatment. Comparing WT to IEC-specific AhR knockout mice (AhRΔIEC), the results showed that AhR expression was essential in IECs for I3C-mediated protection during colitis. AhR-deficiency also impaired mucin protein expression, particularly mucin 2 (Muc2), independently of IL-22. Collectively, this report highlights the important role of AhR in direct regulation of Muc2. These results provide justification for future studies aimed at determining how AhR might regulate select mucins through mechanisms such as direct transcription binding to enhance production.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Philip Brandon Busbee
- Department of Pathology, Microbiology, and Immunology, School of Medicine, University of South Carolina, Columbia, SC 29209, USA; (A.S.); (C.M.); (R.B.); (K.R.); (K.W.); (S.S.); (M.H.); (A.R.); (P.N.); (M.N.)
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Porcari S, Severino A, Rondinella D, Bibbò S, Quaranta G, Masucci L, Maida M, Scaldaferri F, Sanguinetti M, Gasbarrini A, Cammarota G, Ianiro G. Fecal microbiota transplantation for recurrent Clostridioides difficile infection in patients with concurrent ulcerative colitis. J Autoimmun 2023; 141:103033. [PMID: 37085337 DOI: 10.1016/j.jaut.2023.103033] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 03/05/2023] [Accepted: 03/17/2023] [Indexed: 04/23/2023]
Abstract
AIMS Clostridioides difficile infection (CDI) is a major challenge for healthcare systems. Inflammatory bowel disease (IBD), including ulcerative colitis (UC) and Crohn's disease, is a risk factor for primary and recurrent CDI (rCDI). Moreover, CDI itself often worsens the clinical picture of IBD, increasing the risk of complications. Fecal microbiota transplantation (FMT) is a highly effective treatment for rCDI, but data from patients with IBD and CDI are limited and often referred to mixed cohorts. We aimed to report outcomes from a cohort of patients with UC treated with FMT for rCDI superinfection. METHODS AND RESULTS In a retrospective, single-centre cohort study we evaluated characteristics and outcomes of patients with UC who received FMT for rCDI. The primary outcome was negative C. difficile toxin 8 weeks after FMT. Thirty-five patients were included in the analysis. Sixteen patients were cured after single FMT, while 19 patients received repeat FMT. Overall, FMT cured rCDI in 32 patients (91%), and repeat FMT was significantly associated with sustained cure of CDI compared with single FMT (84% vs 50%, p = 0.018). Twenty-four patients (69%) experienced remission or an amelioration of UC activity. Serious adverse events were not observed. CONCLUSIONS In our cohort of patients with UC, FMT was highly effective in curing rCDI without severe adverse events and repeat FMT was significantly associated with CDI cure. Most patients also experienced remission or amelioration of UC activity after FMT. Our findings suggest that a sequential FMT protocol may be used routinely in patients with UC and rCDI.
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Affiliation(s)
- Serena Porcari
- Digestive Disease Center, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy; Dipartimento Universitario di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Andrea Severino
- Digestive Disease Center, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy; Dipartimento Universitario di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Debora Rondinella
- Digestive Disease Center, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy; Dipartimento Universitario di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Stefano Bibbò
- Digestive Disease Center, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy; Dipartimento Universitario di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Gianluca Quaranta
- Microbiology Unit, Fondazione Policlinico Universitario "A. Gemelli" IRCCS, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Luca Masucci
- Microbiology Unit, Fondazione Policlinico Universitario "A. Gemelli" IRCCS, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Marcello Maida
- Gastroenterology and Endoscopy Unit, S. Elia-Raimondi Hospital, Caltanissetta, Italy
| | - Franco Scaldaferri
- Digestive Disease Center, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy; Dipartimento Universitario di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Maurizio Sanguinetti
- Microbiology Unit, Fondazione Policlinico Universitario "A. Gemelli" IRCCS, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Antonio Gasbarrini
- Digestive Disease Center, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy; Dipartimento Universitario di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Giovanni Cammarota
- Digestive Disease Center, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy; Dipartimento Universitario di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Gianluca Ianiro
- Digestive Disease Center, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy; Dipartimento Universitario di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Rome, Italy.
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3
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Koop AH, Travers PM, Khanna S, Pardi DS, Farraye FA, Hashash JG. Fidaxomicin treatment for Clostridioides difficile infection in patients with inflammatory bowel disease. J Gastroenterol Hepatol 2023; 38:1910-1916. [PMID: 37337469 DOI: 10.1111/jgh.16265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 05/23/2023] [Accepted: 06/06/2023] [Indexed: 06/21/2023]
Abstract
BACKGROUND AND AIM Although fidaxomicin is an effective first-line treatment for Clostridioides difficile infection, it has not been well studied in patients with inflammatory bowel disease. We aimed to assess the effectiveness of fidaxomicin for the treatment of C. difficile infection in patients with inflammatory bowel disease. METHODS This was a multicenter retrospective study of adults with inflammatory bowel disease and C. difficile infection treated with fidaxomicin with at least 3 months of follow up. The primary outcomes were treatment response, defined as resolution of C. difficile infection-attributed diarrhea and/or negative C. difficile infection stool test, and time to C. difficile infection recurrence after fidaxomicin. RESULTS Thirty-three patients (median age 42 years; 60.6% female) were included. Most patients had ulcerative colitis (26, 78.8%), were receiving treatment with a biologic or small molecule medication (19, 57.6%), and had a prior episode of C. difficile infection (26, 78.8%, median 2 episodes, range 0-15). Fidaxomicin led to resolution of C. difficile infection in 20 (60.6%) patients, with 6/20 (30.0%) developing a recurrence at a median of 55 days. Most patients who failed to respond to fidaxomicin underwent fecal microbiota transplantation (10/13, 76.9%) with resolution. CONCLUSIONS In this cohort of patients with inflammatory bowel disease and C. difficile infection, 60.6% responded to treatment with fidaxomicin. Of those who did not respond, fecal microbiota transplantation was an effective therapy.
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Affiliation(s)
- Andree H Koop
- Division of Gastroenterology and Hepatology, Mayo Clinic, Jacksonville, Florida, USA
| | - Paul M Travers
- Division of Community Internal Medicine, Mayo Clinic, Jacksonville, Florida, USA
| | - Sahil Khanna
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA
| | - Darrell S Pardi
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA
| | - Francis A Farraye
- Division of Gastroenterology and Hepatology, Mayo Clinic, Jacksonville, Florida, USA
| | - Jana G Hashash
- Division of Gastroenterology and Hepatology, Mayo Clinic, Jacksonville, Florida, USA
- Division of Gastroenterology and Hepatology, American University of Beirut, Beirut, Lebanon
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Sebastian S, Segal JP, Hedin C, Pellino G, Kotze PG, Adamina M, Campmans-Kuijpers M, Davies J, de Vries AC, Casbas AG, El-Hussuna A, Juillerat P, Meade S, Millán M, Spinelli A. ECCO Topical Review: Roadmap to Optimal Peri-Operative Care in IBD. J Crohns Colitis 2023; 17:153-169. [PMID: 36055337 DOI: 10.1093/ecco-jcc/jjac129] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Indexed: 12/12/2022]
Abstract
BACKGROUND AND AIMS Despite the advances in medical therapies, a significant proportion of patients with inflammatory bowel diseases [IBD] require surgical intervention. This Topical Review aims to offer expert consensus practice recommendations for peri-operative care to optimize outcomes of IBD patients who undergo surgery. METHODS A multidisciplinary panel of IBD healthcare providers systematically reviewed aspects relevant to peri-operative care in IBD. Consensus statements were developed using Delphi methodology. RESULTS A total of 20 current practice positions were developed following systematic review of the current literature covering use of medication in the peri-operative period, nutritional assessment and intervention, physical and psychological rehabilitation and prehabilitation, and immediate postoperative care. CONCLUSION Peri-operative planning and optimization of the patient are imperative to ensure favourable outcomes and reduced morbidity. This Topical Review provides practice recommendations applicable in the peri-operative period in IBD patients undergoing surgery.
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Affiliation(s)
- Shaji Sebastian
- IBD Unit, Hull University Teaching Hospitals, Hull, UK
- Hull York Medical School, University of Hull, Hull, UK
| | - Jonathan P Segal
- Northern Hospital Epping, Melbourne, Australia
- University of Melbourne, Parkville, Melbourne, Australia
| | - Charlotte Hedin
- Department of Medicine, Karolinska Institutet, Solna, Stockholm, Sweden
- Gastroenterology Unit, Department of Gastroenterology, Dermatovenereology and Rheumatology, Karolinska University Hospital, Stockholm, Sweden
| | - Gianluca Pellino
- Department of Advanced Medical and Surgical Sciences, Universitá degli Studi della Campania 'Luigi Vanvitelli', Naples, Italy
| | - Paulo Gustavo Kotze
- Colorectal Surgery Unit, Pontificia Universidade Católica do Paraná [PUCPR], Curitiba, Brazil
| | - Michel Adamina
- Department of Surgery, Cantonal Hospital Winterthur, Winterthur, Switzerland
- Faculty of Medicine, University of Basel, Basel, Switzerland
| | - Marjo Campmans-Kuijpers
- Department of Gastroenterology and Hepatology, University Medical Centre Groningen, Groningen, the Netherlands
| | - Justin Davies
- Cambridge Colorectal Unit, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Annemarie C de Vries
- Department of Gastroenterology and Hepatology, Erasmus MC University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Ana Gutiérrez Casbas
- Gastroenterology Department, Hospital General Universitario de Alicante, ISABIAL and CIBERehd, Alicante, Spain
| | - Alaa El-Hussuna
- OpenSourceResearch organisation (osrc.network), Aalborg, Denmark
| | - Pascal Juillerat
- Clinic for Visceral Surgery and Medicine, Inselspital, University Hospital of Bern, Bern, Switzerland
| | - Susanna Meade
- Department of Gastroenterology, Guy's and Saint Thomas' Hospitals NHS Trust, London, UK
| | - Monica Millán
- General Surgery, Colorectal Unit, Hospital Universitari i Politecnic La Fe, Valencia, Spain
| | - Antonino Spinelli
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
- IRCCS Humanitas Research Hospital, Milan, Italy
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Xu D, Xu H, Zhang Y, Gao R. Novel Collaborative Weighted Non-negative Matrix Factorization Improves Prediction of Disease-Associated Human Microbes. Front Microbiol 2022; 13:834982. [PMID: 35369503 PMCID: PMC8965656 DOI: 10.3389/fmicb.2022.834982] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 01/19/2022] [Indexed: 12/14/2022] Open
Abstract
Extensive clinical and biomedical studies have shown that microbiome plays a prominent role in human health. Identifying potential microbe–disease associations (MDAs) can help reveal the pathological mechanism of human diseases and be useful for the prevention, diagnosis, and treatment of human diseases. Therefore, it is necessary to develop effective computational models and reduce the cost and time of biological experiments. Here, we developed a novel machine learning-based joint framework called CWNMF-GLapRLS for human MDA prediction using the proposed collaborative weighted non-negative matrix factorization (CWNMF) technique and graph Laplacian regularized least squares. Especially, to fuse more similarity information, we calculated the functional similarity of microbes. To deal with missing values and effectively overcome the data sparsity problem, we proposed a collaborative weighted NMF technique to reconstruct the original association matrix. In addition, we developed a graph Laplacian regularized least-squares method for prediction. The experimental results of fivefold and leave-one-out cross-validation demonstrated that our method achieved the best performance by comparing it with 5 state-of-the-art methods on the benchmark dataset. Case studies further showed that the proposed method is an effective tool to predict potential MDAs and can provide more help for biomedical researchers.
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Affiliation(s)
- Da Xu
- School of Mathematics and Statistics, Shandong University, Weihai, China
| | - Hanxiao Xu
- School of Mathematics and Statistics, Shandong University, Weihai, China
| | - Yusen Zhang
- School of Mathematics and Statistics, Shandong University, Weihai, China
- *Correspondence: Yusen Zhang,
| | - Rui Gao
- School of Control Science and Engineering, Shandong University, Jinan, China
- Rui Gao,
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Palacios Argueta P, Salazar M, Attar B, Simons-Linares R, Shen B. 90-Day Specific Readmission for Clostridium difficile Infection After Hospitalization With an Inflammatory Bowel Disease Flare: Outcomes and Risk Factors. Inflamm Bowel Dis 2021; 27:530-537. [PMID: 32812037 DOI: 10.1093/ibd/izaa224] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Indexed: 12/11/2022]
Abstract
BACKGROUND Patients with inflammatory bowel disease (IBD) have an increased risk for Clostridium difficile infection (CDI) and carry significantly higher morbidities and mortality than those without IBD. We aimed to investigate disease-specific readmission rates and independent risk factors for CDI within 90 days of an index hospitalization for an IBD flare. METHODS The Nationwide Readmission Database was queried for the year 2016. We collected data on hospital readmissions of 50,799 adults who were hospitalized for urgent IBD flare and discharged. The primary outcome was disease-specific readmission rate for CDI within 90 days of discharge. The secondary outcomes were readmission rate of colonoscopic procedures, morbidities (including mechanical ventilation and shock), and hospital economic burden. The risk factors for readmission were identified using Cox regression analysis. RESULTS The 90-day specific readmission rate was 0.1% (N = 477). A total of 3,005 days were associated with readmission, and the total health care in-hospital economic burden of readmission was $19.1 million (in charges) and $4.79 million (in costs). Independent predictors during index admission for readmission were mechanical ventilation for >24 hours (hazard ratio [HR], 6.62, 95% confidence interval [CI], 0.80-54.57); history of previous CDI (HR, 5.48; 95% CI, 3.66-8.19); HIV-positive status (HR, 4.60; 95% CI, 1.03-20.50); alcohol abuse disorders (HR, 2.06; 95% CI, 1.15-3.70); Parkinson's disease (HR, 4.68; 95% CI, 1.65-13.31); index admission for noncomplicated ulcerative colitis (HR, 4.72; 95% CI, 2.99-7.45]-), complicated ulcerative colitis (HR, 4.49; 95% CI, 2.80- 7.18), or noncomplicated Crohn disease (HR, 2.54; 95% CI, 2.80-4.04); and hospital length of stay (HR, 1.01; 95% CI, 1.01-1.02). CONCLUSIONS The 90-day CDI-specific readmission rate after the index admission of IBD flares was 0.1%. We found risk factors for CDI-associated readmissions such as history of Parkinson's disease, prior CDI, HIV-positive status, and alcohol abuse disorder. Finally, our study also revealed a high health care cost, charges, and burden.
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Affiliation(s)
| | - Miguel Salazar
- Internal Medicine, Cook County Health, Rush University, Chicago, Illinois, USA
| | - Bashar Attar
- Department of Gastroenterology and Hepatology, Cook County Health, Chicago, Illinois, USA
| | - Roberto Simons-Linares
- Gastroenterology and Hepatology Department, Digestive Disease Institute, Cleveland Clinic Foundation, Cleveland, Ohio, USA
| | - Bo Shen
- Surgery Department, Columbia University, New York Presbyterian Hospital, New York, New York, USA
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Xu D, Xu H, Zhang Y, Wang M, Chen W, Gao R. MDAKRLS: Predicting human microbe-disease association based on Kronecker regularized least squares and similarities. J Transl Med 2021; 19:66. [PMID: 33579301 PMCID: PMC7881563 DOI: 10.1186/s12967-021-02732-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 02/01/2021] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Microbes are closely related to human health and diseases. Identification of disease-related microbes is of great significance for revealing the pathological mechanism of human diseases and understanding the interaction mechanisms between microbes and humans, which is also useful for the prevention, diagnosis and treatment of human diseases. Considering the known disease-related microbes are still insufficient, it is necessary to develop effective computational methods and reduce the time and cost of biological experiments. METHODS In this work, we developed a novel computational method called MDAKRLS to discover potential microbe-disease associations (MDAs) based on the Kronecker regularized least squares. Specifically, we introduced the Hamming interaction profile similarity to measure the similarities of microbes and diseases besides Gaussian interaction profile kernel similarity. In addition, we introduced the Kronecker product to construct two kinds of Kronecker similarities between microbe-disease pairs. Then, we designed the Kronecker regularized least squares with different Kronecker similarities to obtain prediction scores, respectively, and calculated the final prediction scores by integrating the contributions of different similarities. RESULTS The AUCs value of global leave-one-out cross-validation and 5-fold cross-validation achieved by MDAKRLS were 0.9327 and 0.9023 ± 0.0015, which were significantly higher than five state-of-the-art methods used for comparison. Comparison results demonstrate that MDAKRLS has faster computing speed under two kinds of frameworks. In addition, case studies of inflammatory bowel disease (IBD) and asthma further showed 19 (IBD), 19 (asthma) of the top 20 prediction disease-related microbes could be verified by previously published biological or medical literature. CONCLUSIONS All the evaluation results adequately demonstrated that MDAKRLS has an effective and reliable prediction performance. It may be a useful tool to seek disease-related new microbes and help biomedical researchers to carry out follow-up studies.
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Affiliation(s)
- Da Xu
- School of Mathematics and Statistics, Shandong University, Weihai, 264209, China
| | - Hanxiao Xu
- School of Mathematics and Statistics, Shandong University, Weihai, 264209, China
| | - Yusen Zhang
- School of Mathematics and Statistics, Shandong University, Weihai, 264209, China.
| | - Mingyi Wang
- Department of Central Lab, Weihai Municipal Hospital, Cheeloo College of Medicine, Shandong University, Weihai, Shandong, China.
| | - Wei Chen
- School of Mathematics and Statistics, Shandong University, Weihai, 264209, China
| | - Rui Gao
- School of Control Science and Engineering, Shandong University, Jinan, 250061, China
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Lei X, Wang Y. Predicting Microbe-Disease Association by Learning Graph Representations and Rule-Based Inference on the Heterogeneous Network. Front Microbiol 2020; 11:579. [PMID: 32351464 PMCID: PMC7174569 DOI: 10.3389/fmicb.2020.00579] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 03/17/2020] [Indexed: 12/18/2022] Open
Abstract
More and more clinical observations have implied that microbes have great effects on human diseases. Understanding the relations between microbes and diseases are of profound significance for disease prevention and therapy. In this paper, we propose a predictive model based on the known microbe-disease associations to discover potential microbe-disease associations through integrating Learning Graph Representations and a modified Scoring mechanism on the Heterogeneous network (called LGRSH). Firstly, the similarity networks for microbe and disease are obtained based on the similarity of Gaussian interaction profile kernel. Then, we construct a heterogeneous network including these two similarity networks and microbe-disease associations' network. After that, the embedding algorithm Node2vec is implemented to learn representations of nodes in the heterogeneous network. Finally, according to these low-dimensional vector representations, we calculate the relevance between each microbe and disease by utilizing a modified rule-based inference method. By comparison with three other methods including LRLSHMDA, KATZHMDA and BiRWHMDA, LGRSH performs better than others. Moreover, in case studies of asthma, Chronic Obstructive Pulmonary Disease and Inflammatory Bowel Disease, there are 8, 8, and 10 out of the top-10 discovered disease-related microbes were validated respectively, demonstrating that LGRSH performs well in predicting potential microbe-disease associations.
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Affiliation(s)
- Xiujuan Lei
- School of Computer Science, Shaanxi Normal University, Xi'an, China
| | - Yueyue Wang
- School of Computer Science, Shaanxi Normal University, Xi'an, China
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Osaka T, Moriyama E, Arai S, Date Y, Yagi J, Kikuchi J, Tsuneda S. Meta-Analysis of Fecal Microbiota and Metabolites in Experimental Colitic Mice during the Inflammatory and Healing Phases. Nutrients 2017; 9:nu9121329. [PMID: 29211010 PMCID: PMC5748779 DOI: 10.3390/nu9121329] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 11/28/2017] [Accepted: 12/03/2017] [Indexed: 01/10/2023] Open
Abstract
The imbalance of gut microbiota is known to be associated with inflammatory bowel disease, but it remains unknown whether dysbiosis is a cause or consequence of chronic gut inflammation. In order to investigate the effects of gut inflammation on microbiota and metabolome, the sequential changes in gut microbiota and metabolites from the onset of colitis to the recovery in dextran sulfate sodium-induced colitic mice were characterized by using meta 16S rRNA sequencing and proton nuclear magnetic resonance (1H-NMR) analysis. Mice in the colitis progression phase showed the transient expansions of two bacterial families including Bacteroidaceae and Enterobacteriaceae and the depletion of major gut commensal bacteria belonging to the uncultured Bacteroidales family S24-7, Rikenellaceae, Lachnospiraceae, and Ruminococcaceae. After the initiation of the recovery, commensal Lactobacillus members promptly predominated in gut while other normally abundant bacteria excluding the Erysipelotrichaceae remained diminished. Furthermore, 1H-NMR analysis revealed characteristic fluctuations in fecal levels of organic acids (lactate and succinate) associated with the disease states. In conclusion, acute intestinal inflammation is a perturbation factor of gut microbiota but alters the intestinal environments suitable for Lactobacillus members.
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Affiliation(s)
- Toshifumi Osaka
- Department of Microbiology and Immunology, Tokyo Women's Medical University, 8-1, Kawada-cho, Shinjuku-ku, Tokyo 162-8666, Japan.
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.
| | - Eri Moriyama
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.
| | - Shunichi Arai
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.
| | - Yasuhiro Date
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehirocho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehirocho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Junji Yagi
- Department of Microbiology and Immunology, Tokyo Women's Medical University, 8-1, Kawada-cho, Shinjuku-ku, Tokyo 162-8666, Japan.
| | - Jun Kikuchi
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehirocho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehirocho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
- Graduate School of Bioagricultural Sciences, Nagoya University, 1 Furo-cho, Chikusa-ku, Nagoya, Aichi 464-0810, Japan.
| | - Satoshi Tsuneda
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.
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The Current Landscape and Lessons from Fecal Microbiota Transplantation for Inflammatory Bowel Disease: Past, Present, and Future. Inflamm Bowel Dis 2017; 23:1710-1717. [PMID: 28858073 DOI: 10.1097/mib.0000000000001247] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Fecal microbiota transplantation (FMT) has changed the standard of care for Clostridium difficile infection. However, there is limited data focusing on efficacy and safety profile of FMT in patients with C. difficile infection with underlying inflammatory bowel disease (IBD), including the risk of IBD flare. Recently, there is also emerging evidence supporting the role of FMT to treat IBD including promising randomized trials in ulcerative colitis. However, with heterogeneity across these studies, the clinical application of this emerging therapy has yet to be fully elucidated. Here, we aim to review the current landscape of this rapidly developing field, mapping the efficacy and safety of FMT (1) to treat C. difficile infection in patients with IBD, (2) to treat underlying IBD, and (3) outline ongoing clinical trials and the future of the microbiome space.
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Razik R, Rumman A, Bahreini Z, McGeer A, Nguyen GC. Recurrence of Clostridium difficile Infection in Patients with Inflammatory Bowel Disease: The RECIDIVISM Study. Am J Gastroenterol 2016; 111:1141-6. [PMID: 27215924 DOI: 10.1038/ajg.2016.187] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 04/02/2016] [Indexed: 12/11/2022]
Abstract
OBJECTIVES Recurrent Clostridium difficile infection (rCDI) contributes to a significant burden of disease in patients with inflammatory bowel disease (IBD). In this study, we seek to identify risk factors for rCDI in a population of IBD patients at the Mount Sinai Hospital IBD Centre. METHODS In this retrospective cohort study, IBD patients with rCDI diagnosed between 2010 and 2013 were identified and compared with IBD patients with single-episode CDI. Multivariate regression was used to identify predictors of rCDI in IBD. Outcome analysis was performed for hospitalizations due to CDI, colectomy, and CDI-attributable mortality. RESULTS A total of 503 patients were included, 110 (22%) of whom had IBD (49% CD, 51% ulcerative colitis). Recurrent CDI occurred in 32% of IBD patients compared with 24% of non-IBD patients (P<0.01). IBD patients with rCDI were more likely than those without rCDI to report recent antibiotic therapy (42.9 vs. 30.7%, P<0.01), 5-aminosalicylic acid (5-ASA) use (51.5 vs. 30.7%, P<0.001), steroid use (51.4 vs. 33.3%, P<0.001), and biologic therapy (48.6 vs. 40.0%, P<0.01). Infliximab (34.3 vs. 17.3%, P<0.01) but not adalimumab was associated with more rCDI events. Using a Cox model of predictors of rCDI in IBD, significant predictors included non-ileal Crohn's disease (hazard ratio (HR) 2.85, 95% confidence interval (CI) 1.30-6.30) and the use of 5-ASA (HR 2.15, 95% CI 1.11-4.18). CONCLUSIONS Compared with the general population, IBD patients are 33% more likely to experience rCDI. Within the IBD cohort, exposure to certain drug classes (antibiotics, 5-ASA, steroids, certain biologics) and non-ileal Crohn's disease were found to be the predictors of rCDI.
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Affiliation(s)
- Roshan Razik
- Department of Medicine, Division of Gastroenterology, University of Toronto, Toronto, Ontario, Canada.,Division of Gastroenterology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.,Department of Health Policy and Management, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Amir Rumman
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Zoya Bahreini
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Allison McGeer
- Department of Medicine, Division of Infectious Diseases, University of Toronto, Toronto, Ontario, Canada
| | - Geoffrey C Nguyen
- Department of Medicine, Division of Gastroenterology, University of Toronto, Toronto, Ontario, Canada
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Nitzan O, Elias M, Peretz A, Saliba W. Role of antibiotics for treatment of inflammatory bowel disease. World J Gastroenterol 2016; 22:1078-1087. [PMID: 26811648 PMCID: PMC4716021 DOI: 10.3748/wjg.v22.i3.1078] [Citation(s) in RCA: 162] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 07/06/2015] [Accepted: 11/13/2015] [Indexed: 02/06/2023] Open
Abstract
Inflammatory bowel disease is thought to be caused by an aberrant immune response to gut bacteria in a genetically susceptible host. The gut microbiota plays an important role in the pathogenesis and complications of the two main inflammatory bowel diseases: Crohn’s disease (CD) and ulcerative colitis. Alterations in gut microbiota, and specifically reduced intestinal microbial diversity, have been found to be associated with chronic gut inflammation in these disorders. Specific bacterial pathogens, such as virulent Escherichia coli strains, Bacteroides spp, and Mycobacterium avium subspecies paratuberculosis, have been linked to the pathogenesis of inflammatory bowel disease. Antibiotics may influence the course of these diseases by decreasing concentrations of bacteria in the gut lumen and altering the composition of intestinal microbiota. Different antibiotics, including ciprofloxacin, metronidazole, the combination of both, rifaximin, and anti-tuberculous regimens have been evaluated in clinical trials for the treatment of inflammatory bowel disease. For the treatment of active luminal CD, antibiotics may have a modest effect in decreasing disease activity and achieving remission, and are more effective in patients with disease involving the colon. Rifamixin, a non absorbable rifamycin has shown promising results. Treatment of suppurative complications of CD such as abscesses and fistulas, includes drainage and antibiotic therapy, most often ciprofloxacin, metronidazole, or a combination of both. Antibiotics might also play a role in maintenance of remission and prevention of post operative recurrence of CD. Data is more sparse for ulcerative colitis, and mostly consists of small trials evaluating ciprofloxacin, metronidazole and rifaximin. Most trials did not show a benefit for the treatment of active ulcerative colitis with antibiotics, though 2 meta-analyses concluded that antibiotic therapy is associated with a modest improvement in clinical symptoms. Antibiotics show a clinical benefit when used for the treatment of pouchitis. The downsides of antibiotic treatment, especially with recurrent or prolonged courses such as used in inflammatory bowel disease, are significant side effects that often cause intolerance to treatment, Clostridium dificile infection, and increasing antibiotic resistance. More studies are needed to define the exact role of antibiotics in inflammatory bowel diseases.
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Shields K, Araujo-Castillo RV, Theethira TG, Alonso CD, Kelly CP. Recurrent Clostridium difficile infection: From colonization to cure. Anaerobe 2015; 34:59-73. [PMID: 25930686 PMCID: PMC4492812 DOI: 10.1016/j.anaerobe.2015.04.012] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 04/22/2015] [Accepted: 04/23/2015] [Indexed: 12/16/2022]
Abstract
Clostridium difficile infection (CDI) is increasingly prevalent, dangerous and challenging to prevent and manage. Despite intense national and international attention the incidence of primary and of recurrent CDI (PCDI and RCDI, respectively) have risen rapidly throughout the past decade. Of major concern is the increase in cases of RCDI resulting in substantial morbidity, morality and economic burden. RCDI management remains challenging as there is no uniformly effective therapy, no firm consensus on optimal treatment, and reliable data regarding RCDI-specific treatment options is scant. Novel therapeutic strategies are critically needed to rapidly, accurately, and effectively identify and treat patients with, or at-risk for, RCDI. In this review we consider the factors implicated in the epidemiology, pathogenesis and clinical presentation of RCDI, evaluate current management options for RCDI and explore novel and emerging therapies.
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Affiliation(s)
- Kelsey Shields
- Division of Gastroenterology, Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Ave., Boston, MA 02215, United States.
| | - Roger V Araujo-Castillo
- Division of Infectious Diseases, Beth Israel Deaconess Medical Center, Harvard Medical School, Lowry Medical Office Building, Suite GB 110 Francis Street, Boston, MA 02215, United States.
| | - Thimmaiah G Theethira
- Division of Gastroenterology, Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Ave., Boston, MA 02215, United States.
| | - Carolyn D Alonso
- Division of Infectious Diseases, Beth Israel Deaconess Medical Center, Harvard Medical School, Lowry Medical Office Building, Suite GB 110 Francis Street, Boston, MA 02215, United States.
| | - Ciaran P Kelly
- Division of Gastroenterology, Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Ave., Boston, MA 02215, United States.
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Kaiser AM, Hogen R, Bordeianou L, Alavi K, Wise PE, Sudan R. Clostridium Difficile Infection from a Surgical Perspective. J Gastrointest Surg 2015; 19:1363-77. [PMID: 25917533 DOI: 10.1007/s11605-015-2785-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 02/18/2015] [Indexed: 01/31/2023]
Abstract
BACKGROUND The incidence and the severity of Clostridium difficile infection (CDI) have increased significantly over the last decade, especially in high-risk populations such as patients with inflammatory bowel disease (IBD). Surgeons must be able to both identify and minimize the risk of CDI in their own surgical patients and determine which CDI patients will benefit from surgery. PURPOSE We sought to define the risk factors, compare the treatment options, define the surgical indications, and identify factors that affect surgical outcomes for CDI based on the currently available literature. RESULTS Antibiotic use, exposure to the C. difficile bacteria, IBD, and higher levels of co-morbidity are all risk factors for CDI. The majority of CDI can be treated with antibiotics. Severe or fulminant colitis, however, has a high potential for poor outcome, but experience and some data suggest a lower mortality rate with colectomy rather than with continued medical treatment. Open total abdominal colectomy with end ileostomy is typically the preferred surgical strategy. It is often difficult to determine which patients will fail medical management as some may not manifest clinical signs of severe infection. Surrogate parameters of failure of medical therapy include respiratory and/or renal insufficiency, age greater than 60 years, peripheral vascular disease, congestive heart failure, and coagulopathy, all of which have been associated with worse surgical outcomes. Evidence suggests that in appropriately selected patients, colectomy performed before the development of shock requiring vasopressors, respiratory failure, renal failure, multi-organ dysfunction, and mental status changes may reduce mortality of the most severe forms of colitis. For less severe or recurrent presentations, creation of a loop ileostomy with intra-operative colonic lavage, fecal microbiota transfer, and C. difficile vaccinations are being discussed but have only been studied in small case-controlled series. CONCLUSIONS Prevention, containment, and non-surgical treatment are the cornerstone of management for CDI. However, the most severe forms with toxic colitis benefit from involvement of a surgical team. Swift open total abdominal colectomy with end ileostomy in patients with severe or fulminant C. difficile colitis has the best chance to reduce mortality if it is not delayed until shock, end organ damage, vasopressor requirement, mental status changes develop. Less aggressive approaches may be appropriate for milder and refractory forms but require further study before their applicability can be determined.
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Affiliation(s)
- Andreas M Kaiser
- Department of Surgery, Division of Colorectal Surgery, Keck School of Medicine, University of Southern California, 1441 Eastlake Avenue, Suite 7418, Los Angeles, 90033, CA, USA,
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