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Li H, Hong L, Szymczak W, Orner E, Garber AI, Cooper VS, Chen W, De A, Tang JX, Mani S. Protocol for isolating single species of bacteria with swarming ability from human feces. STAR Protoc 2024; 5:102961. [PMID: 38573864 PMCID: PMC10999858 DOI: 10.1016/j.xpro.2024.102961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 11/20/2023] [Accepted: 03/01/2024] [Indexed: 04/06/2024] Open
Abstract
Understanding the specific movements of bacteria isolated from human feces can serve as a novel diagnostic and therapeutic tool for inflammatory bowel disease. Here, we present a protocol for a microbial swarming assay and to isolate the bacteria responsible for swarming activity. We describe steps for identifying bacteria using MALDI-TOF mass spectrometry and whole-genome sequencing. We then detail procedures for validating findings by observing the same swarming phenotype upon reperforming the swarming assay. For complete details on the use and execution of this protocol, please refer to De et al.1.
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Affiliation(s)
- Hao Li
- Department of Medicine, Genetics and Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Lilli Hong
- Department of Medicine, Genetics and Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Wendy Szymczak
- Montefiore Medical Center, Bronx, NY 10467, USA; Department of Pathology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Erika Orner
- Montefiore Medical Center, Bronx, NY 10467, USA; Department of Pathology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | | | - Vaughn S Cooper
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, School of Medicine, Pittsburgh, PA 15213, USA; Center for Evolutionary Biology and Medicine, University of Pittsburgh, School of Medicine, Pittsburgh, PA 15213, USA; Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA
| | - Weijie Chen
- Department of Medicine, Genetics and Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Intelligent Medicine Institute, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Arpan De
- Department of Medicine, Genetics and Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Jay X Tang
- Brown University, Physics Department, Providence, RI 02912, USA
| | - Sridhar Mani
- Department of Medicine, Genetics and Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
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Syed S, Boland BS, Bourke LT, Chen LA, Churchill L, Dobes A, Greene A, Heller C, Jayson C, Kostiuk B, Moss A, Najdawi F, Plung L, Rioux JD, Rosen MJ, Torres J, Zulqarnain F, Satsangi J. Challenges in IBD Research 2024: Precision Medicine. Inflamm Bowel Dis 2024; 30:S39-S54. [PMID: 38778628 DOI: 10.1093/ibd/izae084] [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: 03/15/2024] [Indexed: 05/25/2024]
Abstract
Precision medicine is part of 5 focus areas of the Challenges in IBD Research 2024 research document, which also includes preclinical human IBD mechanisms, environmental triggers, novel technologies, and pragmatic clinical research. Building on Challenges in IBD Research 2019, the current Challenges aims to provide a comprehensive overview of current gaps in inflammatory bowel diseases (IBDs) research and deliver actionable approaches to address them with a focus on how these gaps can lead to advancements in interception, remission, and restoration for these diseases. The document is the result of multidisciplinary input from scientists, clinicians, patients, and funders, and represents a valuable resource for patient-centric research prioritization. In particular, the precision medicine section is focused on the main research gaps in elucidating how to bring the best care to the individual patient in IBD. Research gaps were identified in biomarker discovery and validation for predicting disease progression and choosing the most appropriate treatment for each patient. Other gaps were identified in making the best use of existing patient biosamples and clinical data, developing new technologies to analyze large datasets, and overcoming regulatory and payer hurdles to enable clinical use of biomarkers. To address these gaps, the Workgroup suggests focusing on thoroughly validating existing candidate biomarkers, using best-in-class data generation and analysis tools, and establishing cross-disciplinary teams to tackle regulatory hurdles as early as possible. Altogether, the precision medicine group recognizes the importance of bringing basic scientific biomarker discovery and translating it into the clinic to help improve the lives of IBD patients.
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Affiliation(s)
- Sana Syed
- Department of Pediatrics, University of Virginia, Charlottesville, VA, USA
- Patient representative for Crohn's & Colitis Foundation, New York, NY, USA
| | - Brigid S Boland
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Lauren T Bourke
- Precision Medicine Drug Development, Early Respiratory and Immunology, AstraZeneca, Boston, MA, USA
| | - Lea Ann Chen
- Division of Gastroenterology, Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Laurie Churchill
- Leona M. and Harry B. Helmsley Charitable Trust, New York, NY, USA
| | | | - Adam Greene
- Department of Pediatrics, University of Virginia, Charlottesville, VA, USA
| | | | | | | | - Alan Moss
- Crohn's & Colitis Foundation, New York, NY, USA
| | | | - Lori Plung
- Patient representative for Crohn's & Colitis Foundation, New York, NY, USA
| | - John D Rioux
- Research Center, Montreal Heart Institute, Université de Montréal, Montréal, Québec, Canada
| | - Michael J Rosen
- Division of Pediatric Gastroenterology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Joana Torres
- Division of Gastroenterology, Hospital Beatriz Ângelo, Hospital da Luz, Lisbon, Portugal
- Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Fatima Zulqarnain
- Department of Pediatrics, University of Virginia, Charlottesville, VA, USA
| | - Jack Satsangi
- Translational Gastroenterology Unit, Experimental Medicine Division, Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
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3
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Ciorba MA, Konnikova L, Hirota SA, Lucchetta EM, Turner JR, Slavin A, Johnson K, Condray CD, Hong S, Cressall BK, Pizarro TT, Hurtado-Lorenzo A, Heller CA, Moss AC, Swantek JL, Garrett WS. Challenges in IBD Research 2024: Preclinical Human IBD Mechanisms. Inflamm Bowel Dis 2024; 30:S5-S18. [PMID: 38778627 DOI: 10.1093/ibd/izae081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Indexed: 05/25/2024]
Abstract
Preclinical human inflammatory bowel disease (IBD) mechanisms is one of 5 focus areas of the Challenges in IBD Research 2024 document, which also includes environmental triggers, novel technologies, precision medicine, and pragmatic clinical research. Herein, we provide a comprehensive overview of current gaps in inflammatory bowel diseases research that relate to preclinical research and deliver actionable approaches to address them with a focus on how these gaps can lead to advancements in IBD interception, remission, and restoration. The document is the result of multidisciplinary input from scientists, clinicians, patients, and funders and represents a valuable resource for patient-centric research prioritization. This preclinical human IBD mechanisms section identifies major research gaps whose investigation will elucidate pathways and mechanisms that can be targeted to address unmet medical needs in IBD. Research gaps were identified in the following areas: genetics, risk alleles, and epigenetics; the microbiome; cell states and interactions; barrier function; IBD complications (specifically fibrosis and stricturing); and extraintestinal manifestations. To address these gaps, we share specific opportunities for investigation for basic and translational scientists and identify priority actions.
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Affiliation(s)
- Matthew A Ciorba
- Inflammatory Bowel Diseases Center, Division of Gastroenterology, Washington University in St. Louis, Saint Louis, MO, USA
| | - Liza Konnikova
- Departments of Pediatrics, Immunobiology, and Obstetric, Gynecology and Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA
| | - Simon A Hirota
- Snyder Institute for Chronic Diseases, Dept. of Physiology and Pharmacology, University of Calgary, Calgary, Alberta, Canada
| | - Elena M Lucchetta
- The Leona M. and Harry B. Helmsley Charitable Trust, New York, NY, USA
| | - Jerrold R Turner
- Departments of Pathology and Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | | | - Cass D Condray
- Patient Representative for the Crohn's & Colitis Foundation, New York, NY, USA
| | - Sungmo Hong
- Patient Representative for the Crohn's & Colitis Foundation, New York, NY, USA
| | - Brandon K Cressall
- Patient Representative for the Crohn's & Colitis Foundation, New York, NY, USA
| | - Theresa T Pizarro
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | | | - Caren A Heller
- Research Department, Crohn's & Colitis Foundation, New York, NY, USA
| | - Alan C Moss
- Research Department, Crohn's & Colitis Foundation, New York, NY, USA
| | | | - Wendy S Garrett
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- The Harvard T. H. Chan Microbiome in Public Health Center, Boston, MA, USA
- Kymera Therapeutics, Watertown, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
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4
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Lewis JD, Daniel SG, Li H, Hao F, Patterson AD, Hecht AL, Brensinger CM, Wu GD, Bittinger K. Surgery for Crohn's Disease Is Associated With a Dysbiotic Microbiome and Metabolome: Results From Two Prospective Cohorts. Cell Mol Gastroenterol Hepatol 2024; 18:101357. [PMID: 38750900 PMCID: PMC11278594 DOI: 10.1016/j.jcmgh.2024.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 05/05/2024] [Accepted: 05/07/2024] [Indexed: 06/19/2024]
Abstract
BACKGROUND & AIMS Crohn's disease is associated with alterations in the gut microbiome and metabolome described as dysbiosis. We characterized the microbial and metabolic consequences of ileal resection, the most common Crohn's disease surgery. METHODS Patients with and without intestinal resection were identified from the Diet to Induce Remission in Crohn's Disease and Study of a Prospective Adult Research Cohort with Inflammatory Bowel Disease studies. Stool samples were analyzed with shotgun metagenomics sequencing. Fecal butyrate was measured with 1H nuclear magnetic resonance spectroscopy. Fecal bile acids and plasma 7α-hydroxy-4-cholesten-3-one (C4) was measured with mass spectrometry. RESULTS Intestinal resection was associated with reduced alpha diversity and altered beta diversity with increased Proteobacteria and reduced Bacteroidetes and Firmicutes. Surgery was associated with higher representation of genes in the KEGG pathway for ABC transporters and reduction in genes related to bacterial metabolism. Surgery was associated with reduced concentration of the But gene but this did not translate to reduced fecal butyrate concentration. Surgery was associated with decreased abundance of bai operon genes, with increased plasma C4 concentration, increased primary bile acids and reduced secondary bile acids, including isoLCA. Additionally, Egerthella lenta, Adlercreutzia equalofaciens, and Gordonibacter pamelaeae were lower in abundance among patients with prior surgery in both cohorts. CONCLUSIONS In 2 different populations, prior surgery in Crohn's disease is associated with altered fecal microbiome. Patients who had undergone ileal resection had reduction in the potentially beneficial bacteria E lenta and related actinobacteria and secondary bile acids, including isoLCA, suggesting that these could be biomarkers of patients at higher risk for disease progression.
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Affiliation(s)
- James D Lewis
- Division of Gastroenterology and Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
| | - Scott G Daniel
- Division of Gastroenterology, Hepatology and Nutrition, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Hongzhe Li
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Fuhua Hao
- Center for Molecular Toxicology and Carcinogenesis, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, State College, Pennsylvania
| | - Andrew D Patterson
- Center for Molecular Toxicology and Carcinogenesis, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, State College, Pennsylvania
| | - Aaron L Hecht
- Division of Gastroenterology and Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Colleen M Brensinger
- Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Gary D Wu
- Division of Gastroenterology and Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology and Nutrition, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
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Jangi S, Hsia K, Zhao N, Kumamoto CA, Friedman S, Singh S, Michaud DS. Dynamics of the Gut Mycobiome in Patients With Ulcerative Colitis. Clin Gastroenterol Hepatol 2024; 22:821-830.e7. [PMID: 37802272 PMCID: PMC10960711 DOI: 10.1016/j.cgh.2023.09.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 09/10/2023] [Accepted: 09/19/2023] [Indexed: 10/08/2023]
Abstract
BACKGROUND & AIMS Intestinal fungi have been implicated in the pathogenesis of ulcerative colitis (UC). However, it remains unclear if fungal composition is altered during active versus quiescent disease. METHODS We analyzed clinical and metagenomic data from the Study of a Prospective Adult Research Cohort with Inflammatory Bowel Disease (SPARC IBD), available via the IBD Plexus Program of the Crohn's & Colitis Foundation. We evaluated the fungal composition of fecal samples from 421 patients with UC during clinical activity and remission. Within a longitudinal subcohort (n = 52), we assessed for dynamic taxonomic changes across alterations in clinical activity over time. We examined if fungal amplicon sequence variants and fungal-bacterial relationships were altered during activity versus remission. Finally, we classified activity in UC using a supervised machine learning random forest model trained on fungal abundance data. RESULTS During clinical activity, the relative abundance of genus Candida was increased 3.5-fold (P-adj < 1 × 10-4) compared with during remission. Patients with longitudinal reductions in clinical activity demonstrated parallel reductions in Candida relative abundance (P < .05). Candida relative abundance correlated with Parabacteroides diastonis, Faecalibacterium prausnitzii, and Bacteroides dorei relative abundance (P < .05) during remission; however, these correlations were disrupted during activity. Fungal abundance data successfully classified patients with active or quiescent UC (area under the curve ∼0.80), with Candida relative abundance critical to the success of the model. CONCLUSIONS Clinical activity in UC is associated with an increased relative abundance of Candida, cross-sectionally and dynamically over time. The role of fecal Candida as a target for therapeutics in UC should be evaluated.
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Affiliation(s)
- Sushrut Jangi
- Department of Medicine, Tufts Medical Center, Boston, Massachusetts.
| | - Katie Hsia
- Department of Medicine, Tufts Medical Center, Boston, Massachusetts
| | - Naisi Zhao
- Public Health and Community Medicine, Tufts University School of Medicine, Boston, Massachusetts
| | - Carol A Kumamoto
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts
| | - Sonia Friedman
- Department of Medicine, Tufts Medical Center, Boston, Massachusetts
| | - Siddharth Singh
- Division of Gastroenterology, Department of Medicine, University of California, San Diego, California
| | - Dominique S Michaud
- Public Health and Community Medicine, Tufts University School of Medicine, Boston, Massachusetts
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6
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Lapp SL, Bewtra M, Lewis JD. Yield of Serial Testing for Tuberculosis Exposure in Patients With Inflammatory Bowel Diseases: One Test is Not Enough. Clin Gastroenterol Hepatol 2024; 22:420-422.e2. [PMID: 37331412 PMCID: PMC10725512 DOI: 10.1016/j.cgh.2023.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 05/19/2023] [Accepted: 06/02/2023] [Indexed: 06/20/2023]
Affiliation(s)
- Sean L Lapp
- Messiah University, New Holland, Pennsylvania
| | - Meenakshi Bewtra
- Division of Gastroenterology and Hepatology, Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - James D Lewis
- Division of Gastroenterology and Hepatology, Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania..
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7
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Hsia K, Zhao N, Chung M, Algarrahi K, Montaser Kouhsari L, Fu M, Chen H, Singh S, Michaud DS, Jangi S. Alterations in the Fungal Microbiome in Ulcerative Colitis. Inflamm Bowel Dis 2023; 29:1613-1621. [PMID: 37221272 PMCID: PMC10547232 DOI: 10.1093/ibd/izad082] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Indexed: 05/25/2023]
Abstract
BACKGROUND Although gut fungi have been implicated in the immunopathogenesis of inflammatory bowel disease, the fungal microbiome has not been deeply explored across endohistologic activity and treatment exposure in ulcerative colitis. METHODS We analyzed data from the SPARC IBD (Study of a Prospective Adult Research Cohort with Inflammatory Bowel Disease) registry. We evaluated the fungal composition of fecal samples from 98 patients with ulcerative colitis across endoscopic activity (n = 43), endohistologic activity (n = 41), and biologic exposure (n = 82). Across all subgroups, we assessed fungal diversity and differential abundance of taxonomic groups. RESULTS We identified 500 unique fungal amplicon sequence variants across the cohort of 82 patients, dominated by phylum Ascomycota. Compared with endoscopic remission, patients with endoscopic activity had increased Saccharomyces (log2 fold change = 4.54; adjusted P < 5 × 10-5) and increased Candida (log2 fold change = 2.56; adjusted P < .03). After adjusting for age, sex, and biologic exposure among patients with endoscopic activity, Saccharomyces (log2 fold change = 7.76; adjusted P < 1 × 10-15) and Candida (log2 fold change = 7.28; adjusted P< 1 × 10-8) remained enriched during endoscopic activity compared with quiescence. CONCLUSIONS Endoscopic inflammation in ulcerative colitis is associated with an expansion of Saccharomyces and Candida compared with remission. The role of these fungal taxa as potential biomarkers and targets for personalized approaches to therapeutics in ulcerative colitis should be evaluated.
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Affiliation(s)
- Katie Hsia
- Department of Medicine, Tufts Medical Center, Boston, MA, USA
| | - Naisi Zhao
- Department of Public Health and Community Medicine, Tufts University School of Medicine, Boston, MA, USA
| | - Mei Chung
- Friedman School of Nutrition and Science Policy, Tufts University, Boston, MA, USA
| | - Khalid Algarrahi
- Department of Pathology and Laboratory Medicine, Tufts Medical Center, Boston, MA, USA
| | | | - May Fu
- Department of Pathology and Laboratory Medicine, Tufts Medical Center, Boston, MA, USA
| | - Hannah Chen
- Department of Pathology and Laboratory Medicine, Tufts Medical Center, Boston, MA, USA
| | - Siddharth Singh
- Division of Gastroenterology, Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Dominique S Michaud
- Department of Public Health and Community Medicine, Tufts University School of Medicine, Boston, MA, USA
| | - Sushrut Jangi
- Division of Gastroenterology, Department of Medicine, Tufts Medical Center, Boston, MA, USA
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Coates MD, Clarke K, Williams E, Jeganathan N, Yadav S, Giampetro D, Gordin V, Smith S, Vrana K, Bobb A, Gazzio TT, Tressler H, Dalessio S. Abdominal Pain in Inflammatory Bowel Disease: An Evidence-Based, Multidisciplinary Review. CROHN'S & COLITIS 360 2023; 5:otad055. [PMID: 37867930 PMCID: PMC10588456 DOI: 10.1093/crocol/otad055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Indexed: 10/24/2023] Open
Abstract
Abdominal pain is one of the most common and impactful symptoms associated with inflammatory bowel disease (IBD), including both Crohn's disease and ulcerative colitis. A great deal of research has been undertaken over the past several years to improve our understanding and to optimize management of this issue. Unfortunately, there is still significant confusion about the underlying pathophysiology of abdominal pain in these conditions and the evidence underlying treatment options in this context. There is also a relative paucity of comprehensive reviews on this topic, including those that simultaneously evaluate pharmacological and nonpharmacological therapeutic options. In this review, our multidisciplinary team examines evidence for various currently available medical, surgical, and other analgesic options to manage abdominal pain in IBD.
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Affiliation(s)
- Matthew D Coates
- Department of Medicine, Division of Gastroenterology & Hepatology, Penn State College of Medicine, Hershey, PA, USA
- Department of Pharmacology, Penn State College of Medicine, Hershey, PA, USA
| | - Kofi Clarke
- Department of Medicine, Division of Gastroenterology & Hepatology, Penn State College of Medicine, Hershey, PA, USA
| | - Emmanuelle Williams
- Department of Medicine, Division of Gastroenterology & Hepatology, Penn State College of Medicine, Hershey, PA, USA
| | - Nimalan Jeganathan
- Department of Surgery, Division of Colorectal Surgery, Penn State College of Medicine, Hershey, PA, USA
| | - Sanjay Yadav
- Department of Psychiatry, Penn State College of Medicine, Hershey, PA, USA
| | - David Giampetro
- Department of Anesthesia & Perioperative Medicine, Penn State College of Medicine, Hershey, PA, USA
| | - Vitaly Gordin
- Department of Anesthesia & Perioperative Medicine, Penn State College of Medicine, Hershey, PA, USA
| | - Sadie Smith
- Department of Anesthesia & Perioperative Medicine, Penn State College of Medicine, Hershey, PA, USA
| | - Kent Vrana
- Department of Pharmacology, Penn State College of Medicine, Hershey, PA, USA
| | - Anne Bobb
- Department of Surgery, Division of Colorectal Surgery, Penn State College of Medicine, Hershey, PA, USA
| | - Thu Thi Gazzio
- Department of Surgery, Division of Colorectal Surgery, Penn State College of Medicine, Hershey, PA, USA
| | - Heather Tressler
- Department of Medicine, Division of Gastroenterology & Hepatology, Penn State College of Medicine, Hershey, PA, USA
| | - Shannon Dalessio
- Department of Medicine, Division of Gastroenterology & Hepatology, Penn State College of Medicine, Hershey, PA, USA
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9
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Yang JY, Lund JL, Funk MJ, Hudgens MG, Lewis JD, Kappelman MD. Utilization of Treat-to-Target Monitoring Colonoscopy After Treatment Initiation in the US-Based Study of a Prospective Adult Research Cohort With Inflammatory Bowel Disease. Am J Gastroenterol 2023; 118:1638-1647. [PMID: 37053548 DOI: 10.14309/ajg.0000000000002294] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 04/04/2023] [Indexed: 04/15/2023]
Abstract
INTRODUCTION Endoscopic healing has been associated with improved long-term clinical outcomes in inflammatory bowel disease (IBD) and is a recommended target for treatment. Evidence is limited regarding real-world uptake and patterns of treat-to-target monitoring to assess endoscopic healing after treatment initiation. We aimed to estimate the proportion of patients in the Study of a Prospective Adult Research Cohort with IBD (SPARC IBD) who received colonoscopy in the 3-15 months after starting a new IBD treatment. METHODS We identified SPARC IBD patients who initiated a new biologic (infliximab, adalimumab, certolizumab pegol, golimumab, vedolizumab, and ustekinumab) or tofacitinib. We estimated the proportion of patients who received colonoscopies in the 3-15 months after IBD treatment initiation and described use by patient subgroups. RESULTS Among 1,708 eligible initiations from 2017 to 2022, the most common medications were ustekinumab (32%), infliximab (22%), vedolizumab (20%), and adalimumab (16%). The median patient age was 38 years, with 66% Crohn's disease; 55% were female, and 12% were non-White. In the 3-15 months after medication initiation, 49.3% (95% confidence interval 46.2%-52.5%) of initiations were followed by a colonoscopy. Colonoscopy use was similar between ulcerative colitis and Crohn's disease, but was higher among male patients, those older than 40 years, and those who received colonoscopy within 3 months of initiation. Colonoscopy use varied between study sites, from 26.6% (15.0%-38.3%) to 63.2% (54.5%-72.0%). DISCUSSION Approximately half of SPARC IBD patients received colonoscopy in the 3-15 months after initiation to a new IBD treatment, suggesting a low uptake of treat-to-target colonoscopy for the assessment of mucosal healing in real-world clinical practice. The variation in colonoscopy use between study sites suggests a lack of consensus and a need for more robust evidence around whether or not the practice of routine monitoring colonoscopy is associated with improved patient outcomes.
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Affiliation(s)
- Jeff Y Yang
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jennifer L Lund
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Michele Jonsson Funk
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Michael G Hudgens
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - James D Lewis
- Division of Gastroenterology, Center for Clinical Epidemiology and Biostatistics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Michael D Kappelman
- Division of Pediatric Gastroenterology, Department of Pediatrics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
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10
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Ibing S, Cho JH, Böttinger EP, Ungaro RC. Second-Line Biologic Therapy Following Tumor Necrosis Factor Antagonist Failure: A Real-World Propensity Score-Weighted Analysis. Clin Gastroenterol Hepatol 2023; 21:2629-2638. [PMID: 36787837 DOI: 10.1016/j.cgh.2023.01.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 01/05/2023] [Accepted: 01/31/2023] [Indexed: 02/16/2023]
Abstract
BACKGROUND& AIMS Tumor necrosis factor (TNF) antagonists often are used as first-line medications to treat moderate to severe inflammatory bowel disease (IBD), but many patients do not achieve or maintain response. Our aim was to compare the effectiveness of second-line treatments (ustekinumab, vedolizumab, or a second TNF antagonist) after TNF antagonist exposure in patients with Crohn's disease (CD) and ulcerative colitis (UC) from 2 electronic health records-based cohorts. METHODS We identified patients with prior TNF antagonist exposure who switched to a different biologic in the Mount Sinai Health System (MSHS) electronic health records (CD, n = 527; UC, n = 165) and the Study of a Prospective Adult Research Cohort (SPARC) from the Inflammatory Bowel Disease Plexus Program of the Crohn's & Colitis Foundation (CD, n = 412; UC, n = 129). Treatment failure was defined as the composite of any IBD-related surgery, IBD-related hospitalization, new prescription of oral/intravenous corticosteroids, or need to switch to a third biologic agent. Time-to-event analysis was conducted with inverse probability of treatment-weighted data. RESULTS Overall, treatment failure occurred in 85% of MSHS and 72% of SPARC CD patients. In SPARC, the likelihood of treatment failure was significantly lower with ustekinumab compared with vedolizumab as second-line treatment (adjusted hazard ratio, 0.66; 95% CI, 0.54-0.82; P < .001), a trend confirmed in MSHS (adjusted hazard ratio, 0.89; 95% CI, 0.77-1.04; P = .15). In both cohorts, the superiority of ustekinumab compared with vedolizumab was shown when considering treatment failure as prescription of steroids or a third biologic agent. In UC, no differences between second-line treatment groups were identified. CONCLUSIONS In 2 independent real-world cohort settings, second-line therapy in CD with ustekinumab after TNF antagonist treatment failure was associated with a lower likelihood of treatment failure than second-line vedolizumab.
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Affiliation(s)
- Susanne Ibing
- Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, New York; Digital Health Center, Hasso Plattner Institute, University of Potsdam, Potsdam, Germany
| | - Judy H Cho
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Erwin P Böttinger
- Hasso Plattner Institute for Digital Health at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, New York; Digital Health Center, Hasso Plattner Institute, University of Potsdam, Potsdam, Germany
| | - Ryan C Ungaro
- The Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, New York.
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Golob J, Rao K, Berinstein J, Chey W, Owyang C, Kamada N, Higgins P, Young V, Bishu S, Lee A. The Fecal Microbiome in Quiescent Crohn's Disease with Persistent Gastrointestinal Symptoms Show Enrichment of Oral Microbes But Depletion of Butyrate and Indole Producers. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.05.16.23290065. [PMID: 37292648 PMCID: PMC10246066 DOI: 10.1101/2023.05.16.23290065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Background and Aims Even in the absence of inflammation, persistent symptoms in Crohn's disease (CD) are prevalent and negatively impact quality of life. We aimed to determine whether quiescent CD patients with persistent symptoms ( qCD+symptoms ) have changes in microbial structure and functional potential compared to those without symptoms ( qCD-symptoms ). Methods We performed a prospective multi-center observational study nested within the SPARC IBD study. CD patients were included if they had evidence of quiescent disease as defined by fecal calprotectin level < 150 mcg/g. Persistent symptoms were defined by the CD-PRO2 questionnaire. Active CD ( aCD ), diarrhea-predominant irritable bowel syndrome ( IBS-D ), and healthy controls ( HC ) were included as controls. Stool samples underwent whole genome shotgun metagenomic sequencing. Results A total of 424 patients were analyzed, including 39 qCD+symptoms, 274 qCD-symptoms, 21 aCD, 40 IBS-D, and 50 HC. Patients with qCD+symptoms had a less diverse microbiome, including significant reductions in Shannon diversity ( P <.001) and significant differences in microbial community structure ( P <.0001), compared with qCD-symptoms, IBS-D, and HC. Further, patients with qCD+symptoms showed significant enrichment of bacterial species that are normal inhabitants of the oral microbiome, including Klebsiella pneumoniae (q=.003) as well as depletion of important butyrate and indole producers, such as Eubacterium rectale (q=.001), Lachnospiraceae spp . (q<.0001), and Faecalibacterium prausnitzii (q<.0001), compared with qCD-symptoms. Finally, qCD+symptoms showed significant reductions in bacterial tnaA genes, which mediate tryptophan metabolism, as well as significant tnaA allelic variation, compared with qCD-symptoms. Conclusion The microbiome in patients with qCD+symptoms show significant changes in diversity, community profile, and composition compared with qCD-symptoms. Future studies will focus on the functional significance of these changes. What You Need to Know Background: Persistent symptoms in quiescent Crohn's disease (CD) are prevalent and lead to worse outcomes. While changes in the microbial community have been implicated, the mechanisms by which altered microbiota may lead to qCD+symptoms remain unclear.Findings: Quiescent CD patients with persistent symptoms demonstrated significant differences in microbial diversity and composition compared to those without persistent symptoms. Specifically, quiescent CD patients with persistent symptoms were enriched in bacterial species that are normal inhabitants of the oral microbiome but depleted in important butyrate and indole producers compared to those without persistent symptoms.Implications for Patient Care: Alterations in the gut microbiome may be a potential mediator of persistent symptoms in quiescent CD. Future studies will determine whether targeting these microbial changes may improve symptoms in quiescent CD.
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12
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Mehta RS, Mayers JR, Zhang Y, Bhosle A, Glasser NR, Nguyen LH, Ma W, Bae S, Branck T, Song K, Sebastian L, Pacheco JA, Seo HS, Clish C, Dhe-Paganon S, Ananthakrishnan AN, Franzosa EA, Balskus EP, Chan AT, Huttenhower C. Gut microbial metabolism of 5-ASA diminishes its clinical efficacy in inflammatory bowel disease. Nat Med 2023; 29:700-709. [PMID: 36823301 PMCID: PMC10928503 DOI: 10.1038/s41591-023-02217-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 01/10/2023] [Indexed: 02/25/2023]
Abstract
For decades, variability in clinical efficacy of the widely used inflammatory bowel disease (IBD) drug 5-aminosalicylic acid (5-ASA) has been attributed, in part, to its acetylation and inactivation by gut microbes. Identification of the responsible microbes and enzyme(s), however, has proved elusive. To uncover the source of this metabolism, we developed a multi-omics workflow combining gut microbiome metagenomics, metatranscriptomics and metabolomics from the longitudinal IBDMDB cohort of 132 controls and patients with IBD. This associated 12 previously uncharacterized microbial acetyltransferases with 5-ASA inactivation, belonging to two protein superfamilies: thiolases and acyl-CoA N-acyltransferases. In vitro characterization of representatives from both families confirmed the ability of these enzymes to acetylate 5-ASA. A cross-sectional analysis within the discovery cohort and subsequent prospective validation within the independent SPARC IBD cohort (n = 208) found three of these microbial thiolases and one acyl-CoA N-acyltransferase to be epidemiologically associated with an increased risk of treatment failure among 5-ASA users. Together, these data address a longstanding challenge in IBD management, outline a method for the discovery of previously uncharacterized gut microbial activities and advance the possibility of microbiome-based personalized medicine.
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Affiliation(s)
- Raaj S Mehta
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Clinical & Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Jared R Mayers
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Yancong Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biostatistics, T. H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Harvard Chan Microbiome in Public Health Center, T. H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Amrisha Bhosle
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biostatistics, T. H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Harvard Chan Microbiome in Public Health Center, T. H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Nathaniel R Glasser
- Resnick Sustainability Institute, California Institute of Technology, Pasadena, CA, USA
| | - Long H Nguyen
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Clinical & Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Wenjie Ma
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Clinical & Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Sena Bae
- Department of Immunology & Infectious Disease, T. H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Tobyn Branck
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biostatistics, T. H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Kijun Song
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Luke Sebastian
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | | | - Hyuk-Soo Seo
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Clary Clish
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sirano Dhe-Paganon
- Department of Cancer Biology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Ashwin N Ananthakrishnan
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Clinical & Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Eric A Franzosa
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biostatistics, T. H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Emily P Balskus
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Andrew T Chan
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Clinical & Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Immunology & Infectious Disease, T. H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Curtis Huttenhower
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Biostatistics, T. H. Chan School of Public Health, Harvard University, Boston, MA, USA.
- Harvard Chan Microbiome in Public Health Center, T. H. Chan School of Public Health, Harvard University, Boston, MA, USA.
- Department of Immunology & Infectious Disease, T. H. Chan School of Public Health, Harvard University, Boston, MA, USA.
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13
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Fan Y, Zhang L, Omidakhsh N, Bohn RL, Thompson JS, Brodovicz KG, Deepak P. Patients With Stricturing or Penetrating Crohn's Disease Phenotypes Report High Disease Burden and Treatment Needs. Inflamm Bowel Dis 2022:6650080. [PMID: 35880838 DOI: 10.1093/ibd/izac162] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Indexed: 12/09/2022]
Abstract
BACKGROUND Crohn's disease (CD) is a chronic autoimmune disease in which inflammation can progress to complications of stricturing and/or penetrating disease. Real-world data on burden of complicated CD phenotypes are limited. METHODS We analyzed cross-sectional data from the SPARC IBD (Study of a Prospective Adult Research Cohort with Inflammatory Bowel Disease) registry from 2016 to 2020. Four mutually exclusive phenotype cohorts were created: inflammatory CD (CD-I), complicated CD (stricturing CD, penetrating CD, and stricturing and penetrating CD [CD-SP]). Statistical analyses were performed using CD-I as the reference. RESULTS A total of 1557 patients were identified: CD-I (n = 674, 43.3%), stricturing CD (n = 457, 29.4%), penetrating CD (n = 166, 10.7%), and CD-SP (n = 260, 16.7%). Patients with complicated phenotypes reported significantly greater use of tumor necrosis factor inhibitors (84.2%-86.7% vs 66.0%; P < .001) and corticosteroids (75.3%-82.7% vs 68.0%; P < .001). Patients with CD-SP reported significantly more aphthous ulcer (15.4% vs 10.5%; P < .05), erythema nodosum (6.5% vs 3.6%; P < .05), inflammatory bowel disease-related arthropathy (25.8% vs 17.2%; P < .01), liquid stools (24.2% vs 9.3%; P < .001), nocturnal fecal incontinence (10.8% vs 2.5%; P < .001), and CD-related surgery (77.7% vs 12.2%; P < .001). CONCLUSIONS Patients with complicated CD phenotypes reported higher rates of active CD-related luminal and extraintestinal manifestations, and underwent more surgeries, despite being more likely to have received biologics than those with CD-I. The potential for early recognition and management of CD-I to prevent progression to complicated phenotypes should be explored in longitudinal studies.
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Affiliation(s)
- Yanni Fan
- Boehringer Ingelheim Corporation, Ridgefield, CT, USA
| | - Ling Zhang
- Boehringer Ingelheim Corporation, Ridgefield, CT, USA
| | | | | | | | | | - Parakkal Deepak
- Inflammatory Bowel Diseases Center, Washington University School of Medicine in St Louis, St Louis, MO, USA
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14
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Long MD, Zhang X, Lewis JD, Melmed GY, Siegel CA, Cerciello E, Dobes A, Weaver A, Weisbein L, Kappelman MD. Risks of Development of COVID-19 Among Patients With Inflammatory Bowel Disease: A Comparative Assessment of Risk Factors for Incident Infection. CROHN'S & COLITIS 360 2022; 4:otac011. [PMID: 36777042 PMCID: PMC9037404 DOI: 10.1093/crocol/otac011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Indexed: 11/12/2022] Open
Abstract
Background Patients with inflammatory bowel disease (IBD) may be at risk for development of COVID-19 infection due to innate immune dysfunction and/or immunosuppressive medication use. Methods In a prospective cohort of adult IBD patients, we captured data on clinical risk factors and IBD medication utilization. The outcome of interest was development of patient-reported laboratory confirmed COVID-19. We calculated incidence rate and performed bivariate analyses to describe the effects of risk factors (age, immunosuppression use, obesity, and race) on development of COVID-19. We utilized logistic regression models to determine the independent risks associated with each factor. Results A total of 3953 patients with IBD were followed for a mean duration of 212 days (SD 157). A total of 103 individuals developed COVID-19 during follow-up (2.6%, rate of 45 per 1000 person-years). Severity of infection was generally mild. Clinical characteristics were similar among those who developed COVID-19 as compared to not. African American race was associated with incident COVID-19 infection (OR 3.37, 95% CI 1.18-9.59). Immunosuppression use was not associated with development of COVID-19 (OR 1.19, 95% CI 0.72-1.75), nor was age (OR 1.00, 95% CI 0.99-1.02), nor obesity (OR 1.01, 95% CI 0.61-1.66). Conclusions Immunosuppression use did not increase the risk of development of COVID-19. Therapeutic management of IBD should not be altered to prevent a risk of developing COVID-19.
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Affiliation(s)
- Millie D Long
- University of North Carolina, Department of Medicine, Division of Gastroenterology and Hepatology, Chapel Hill, North Carolina, USA
- Center for Gastrointestinal Biology and Disease, University of North Carolina, Chapel Hill, North Carolina, USA
- Address correspondence to: Millie D. Long, MD, MPH, Gastroenterology and Hepatology Fellowship Program, University of North Carolina at Chapel Hill, Division of Gastroenterology and Hepatology, Campus Box #7080, Chapel Hill, NC 27599-7080, USA ()
| | - Xian Zhang
- Center for Gastrointestinal Biology and Disease, University of North Carolina, Chapel Hill, North Carolina, USA
| | - James D Lewis
- University of Pennsylvania, Department of Medicine, Division of Gastroenterology and Hepatology, Philadelphia, Pennsylvania, USA
| | - Gil Y Melmed
- Cedar Sinai Medical Center, Los Angeles, California, USA
| | - Corey A Siegel
- Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire, USA
| | | | - Angela Dobes
- Crohn’s & Colitis Foundation, New York, New York, USA
| | | | - Laura Weisbein
- Center for Gastrointestinal Biology and Disease, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Michael D Kappelman
- Center for Gastrointestinal Biology and Disease, University of North Carolina, Chapel Hill, North Carolina, USA
- University of North Carolina, Department of Pediatrics, Division of Gastroenterology and Hepatology, Chapel Hill, North Carolina, USA
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