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Dowrick JM, Roy NC, Bayer S, Frampton CMA, Talley NJ, Gearry RB, Angeli-Gordon TR. Unsupervised machine learning highlights the challenges of subtyping disorders of gut-brain interaction. Neurogastroenterol Motil 2024:e14898. [PMID: 39119757 DOI: 10.1111/nmo.14898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 07/17/2024] [Accepted: 07/31/2024] [Indexed: 08/10/2024]
Abstract
BACKGROUND Unsupervised machine learning describes a collection of powerful techniques that seek to identify hidden patterns in unlabeled data. These techniques can be broadly categorized into dimension reduction, which transforms and combines the original set of measurements to simplify data, and cluster analysis, which seeks to group subjects based on some measure of similarity. Unsupervised machine learning can be used to explore alternative subtyping of disorders of gut-brain interaction (DGBI) compared to the existing gastrointestinal symptom-based definitions of Rome IV. PURPOSE This present review aims to familiarize the reader with fundamental concepts of unsupervised machine learning using accessible definitions and provide a critical summary of their application to the evaluation of DGBI subtyping. By considering the overlap between Rome IV clinical definitions and identified clusters, along with clinical and physiological insights, this paper speculates on the possible implications for DGBI. Also considered are algorithmic developments in the unsupervised machine learning community that may help leverage increasingly available omics data to explore biologically informed definitions. Unsupervised machine learning challenges the modern subtyping of DGBI and, with the necessary clinical validation, has the potential to enhance future iterations of the Rome criteria to identify more homogeneous, diagnosable, and treatable patient populations.
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Affiliation(s)
- Jarrah M Dowrick
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
- High-Value Nutrition National Science Challenge, Auckland, New Zealand
| | - Nicole C Roy
- High-Value Nutrition National Science Challenge, Auckland, New Zealand
- Department of Human Nutrition, University of Otago, Dunedin, New Zealand
- Riddet Institute, Massey University, Palmerston North, New Zealand
| | - Simone Bayer
- High-Value Nutrition National Science Challenge, Auckland, New Zealand
- Department of Medicine, University of Otago, Christchurch, New Zealand
| | - Chris M A Frampton
- High-Value Nutrition National Science Challenge, Auckland, New Zealand
- Department of Medicine, University of Otago, Christchurch, New Zealand
- Department of Psychological Medicine, University of Otago, Christchurch, New Zealand
| | - Nicholas J Talley
- High-Value Nutrition National Science Challenge, Auckland, New Zealand
- School of Medicine and Public Health, University of Newcastle, Callaghan, New South Wales, Australia
| | - Richard B Gearry
- High-Value Nutrition National Science Challenge, Auckland, New Zealand
- Department of Medicine, University of Otago, Christchurch, New Zealand
| | - Timothy R Angeli-Gordon
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
- High-Value Nutrition National Science Challenge, Auckland, New Zealand
- Riddet Institute, Massey University, Palmerston North, New Zealand
- Department of Surgery, University of Auckland, Auckland, New Zealand
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Chen Y, Feng S, Li Y, Zhang C, Chao G, Zhang S. Gut microbiota and intestinal immunity-A crosstalk in irritable bowel syndrome. Immunology 2024; 172:1-20. [PMID: 38174581 DOI: 10.1111/imm.13749] [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: 08/21/2023] [Accepted: 12/20/2023] [Indexed: 01/05/2024] Open
Abstract
Irritable bowel syndrome (IBS), one of the most prevalent functional gastrointestinal disorders, is characterized by recurrent abdominal pain and abnormal defecation habits, resulting in a severe healthcare burden worldwide. The pathophysiological mechanisms of IBS are multi-factorially involved, including food antigens, visceral hypersensitivity reactions, and the brain-gut axis. Numerous studies have found that gut microbiota and intestinal mucosal immunity play an important role in the development of IBS in crosstalk with multiple mechanisms. Therefore, based on existing evidence, this paper elaborates that the damage and activation of intestinal mucosal immunity and the disturbance of gut microbiota are closely related to the progression of IBS. Combined with the application prospect, it also provides references for further in-depth exploration and clinical practice.
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Affiliation(s)
- Yuxuan Chen
- The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China
| | - Shuyan Feng
- The First Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China
| | - Ying Li
- The First Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China
| | - Chi Zhang
- Sir Run Run Shaw Hospital of Zhejiang University, Hangzhou, China
| | - Guanqun Chao
- Department of General Practice, Sir Run Run Shaw Hospital of Zhejiang University, Hangzhou, China
| | - Shuo Zhang
- The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China
- Department of Gastroenterology, The Second Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
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Clusters of community-dwelling individuals empirically derived from stool diaries correspond with clinically meaningful outcomes. Eur J Gastroenterol Hepatol 2021; 33:e740-e745. [PMID: 34138762 DOI: 10.1097/meg.0000000000002236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
BACKGROUND Functional gastrointestinal disorders (FGIDs) are diagnosed according to expert consensus criteria based on recall of symptoms over periods of 3 months or longer. Whether the expert opinion concords with underlying disease process and whether individual recall is accurate are both in doubt. This study aimed to identify naturally occurring clusters of individuals with respect to symptom pattern, evaluate their significance, compare cluster profiles with expert opinion and evaluate their temporal stability. METHODS As part of a random population study of FGID-related symptoms, we first explored the use of prospective stool and symptom diaries combined with empirical grouping of individuals into clusters using nonhierarchical cluster analysis. RESULTS The analysis identified two clusters of individuals, one of which was characterized by elevated scores on all domains of symptoms (26% of the sample) and one that was low to average on all domains (74% of the sample). Cluster membership was found to be stable over a long interval. Clusters were found to differ on most domains of quality-of-life (d = 0.46-0.74), self-rated health (d = -0.42) and depression (d = -0.42) but not anxiety. Prevalence of clinically diagnosed irritable bowel syndrome (IBS) was higher in the more impacted cluster (33%) compared with the healthy cluster (13%; P < 0.0001). CONCLUSION A naturalistic classification of individuals challenges consensus criteria in showing that some IBS individuals have a symptom experience not unlike health. The proposed approach has demonstrated temporal stability over time, unlike consensus criteria. A naturalistic disease classification system may have practical advantages over consensus criteria when supported by a decision-analytic system.
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Schmulson M, Frati-Munari A. Bowel symptoms in patients that receive proton pump inhibitors. Results of a multicenter survey in Mexico. REVISTA DE GASTROENTEROLOGÍA DE MÉXICO (ENGLISH EDITION) 2019. [DOI: 10.1016/j.rgmxen.2018.05.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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Barbara G, Grover M, Bercik P, Corsetti M, Ghoshal UC, Ohman L, Rajilić-Stojanović M. Rome Foundation Working Team Report on Post-Infection Irritable Bowel Syndrome. Gastroenterology 2019; 156:46-58.e7. [PMID: 30009817 PMCID: PMC6309514 DOI: 10.1053/j.gastro.2018.07.011] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 07/03/2018] [Accepted: 07/05/2018] [Indexed: 02/06/2023]
Abstract
BACKGROUND & AIMS The existence of postinfection irritable bowel syndrome (PI-IBS) has been substantiated by epidemiology studies conducted in diverse geographic and clinical settings. However, the available evidence has not been well summarized, and there is little guidance for diagnosis and treatment of PI-IBS. The ROME Foundation has produced a working team report to summarize the available evidence on the pathophysiology of PI-IBS and provide guidance for diagnosis and treatment, based on findings reported in the literature and clinical experience. METHODS The working team conducted an evidence-based review of publication databases for articles describing the clinical features (diagnosis), pathophysiology (intestinal sensorimotor function, microbiota, immune dysregulation, barrier dysfunction, enteroendocrine pathways, and genetics), and animal models of PI-IBS. We used a Delphi-based consensus system to create guidelines for management of PI-IBS and a developed treatment algorithm based on published findings and experiences of team members. RESULTS PI-IBS develops in about 10% of patients with infectious enteritis. Risk factors include female sex, younger age, psychological distress during or before acute gastroenteritis, and severity of the acute episode. The pathogenesis of PI-PBS appears to involve changes in the intestinal microbiome as well as epithelial, serotonergic, and immune system factors. However, these mechanisms are incompletely understood. There are no evidence-based, effective pharmacologic strategies for treatment of PI-IBS. We provide a consensus-based treatment algorithm, based on clinical presentation and potential disease mechanisms. CONCLUSIONS Based on a systematic review of the literature and team experience, we summarize the clinical features, pathophysiology (from animal models and human studies), and progression of PI-IBS. Based on these findings, we present an algorithm for diagnosis and treatment of PI-IBS based on team consensus. We also propose areas for future investigation.
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Affiliation(s)
- Giovanni Barbara
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy.
| | - Madhusudan Grover
- Enteric NeuroScience Program, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Premysl Bercik
- Department of Medicine, Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Maura Corsetti
- Nottingham Digestive Diseases Biomedical Research Centre, National Institute for Health Research, Nottingham University Hospitals NHS Trust, University of Nottingham, UK
| | - Uday C Ghoshal
- Department of Gastroenterology, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, India
| | - Lena Ohman
- Department of Microbiology and Immunology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Mirjana Rajilić-Stojanović
- Department of Biochemical Engineering and Biotechnology, Faculty of Technology and Metallurgy, University of Belgrade, Belgrade, Serbia
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Schmulson MJ, Frati-Munari AC. Bowel symptoms in patients that receive proton pump inhibitors. Results of a multicenter survey in Mexico. REVISTA DE GASTROENTEROLOGÍA DE MÉXICO 2018; 84:44-51. [PMID: 29678362 DOI: 10.1016/j.rgmx.2018.02.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Revised: 02/20/2018] [Accepted: 02/23/2018] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Proton pump inhibitors (PPIs) have been associated with small intestinal bacterial overgrowth (SIBO), which increases with prolonged PPI use, and SIBO has been associated with irritable bowel syndrome (IBS). OBJECTIVE The aim of the present study was to study the prevalence of bowel symptoms in patients treated with PPIs in Mexico. METHODS Gastroenterologists in 36 cities surveyed patients treated with PPIs, utilizing an ad hoc questionnaire to determine the presence of bowel symptoms and IBS. RESULTS Two hundred and fifteen physicians interviewed 1,851 patients. PPI indications were gastritis (48.8%), gastroesophageal reflux (38.5%), peptic ulcer (6.2%), and others (6.5%). A total of 77.5% of the patients received treatment for ≤6 months and 11.9% for ≥1 year. Symptoms were reported in 92.3% of the patients: abnormal bowel habits (90%), bloating (82%), abdominal pain (63%), flatulence (58%), and abdominal discomfort (53%). A total of 67.5% of the patients fit the Rome III criteria for IBS. Symptoms presented in 55.9% of the patients before PPI intake and in 44.1% of the patients after PPI use (P<.005). Constipation (63.8%) predominated in the former, and diarrhea (56.5%) in the latter (P<.0001). The treatments prescribed for managing those symptoms were antispasmodics, antibiotics, prokinetics, and antiflatulents, but patients stated greater satisfaction with antibiotics (mainly rifaximin) (P<.0001). CONCLUSION The association of PPIs with bowel symptoms and IBS is frequent in Mexico. Diarrhea and bloating predominate, and antibiotics produce the greatest treatment satisfaction, suggesting that SIBO or dysbiosis is the cause of the PPI-related bowel symptoms. However, that remains to be confirmed.
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Affiliation(s)
- M J Schmulson
- Laboratorio de Hígado, Páncreas y Motilidad (HIPAM)-Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Hospital General de México, Ciudad de México, México; Gastroenterología y Motilidad Gastrointestinal, Clínica Lomas Altas SC, Ciudad de México, México; Gastroenterología y Endoscopía en Práctica Médica-Centro Médico ABC, Ciudad de México, México.
| | - A C Frati-Munari
- Alfa Wassermann S.A. de C.V., Ciudad de México, México; Medicina interna, Hospital Médica Sur, Ciudad de México, México
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Abstract
Irritable bowel syndrome (IBS) is one of the most common gastrointestinal disorders worldwide. The economic impact of IBS on the health care system is substantial, as is the personal impact on patients. Patients with diarrhea-predominant IBS (IBS-D) comprise a substantial proportion of the overall IBS population. Primary care providers are often the first point of contact for patients with IBS-D and can accurately diagnose IBS after a careful history and examination without extensive diagnostic tests. Several pharmacologic treatments (eg, loperamide, alosetron, and antidepressants) and non-pharmacologic treatments (eg, dietary modification and probiotics) are available for IBS-D, but restrictions on use (eg, alosetron) or the lack of controlled trial data showing reductions in both global and individual IBS-D symptoms (eg, bloating, pain and stool frequency) emphasize the need for alternative treatment options. Two newer medications (eluxadoline and rifaximin) were approved in May 2015 for the treatment of IBS-D, and represent new treatment options for this common gastrointestinal condition.
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Affiliation(s)
- Brian E Lacy
- Division of Gastroenterology and Hepatology, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
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Abstract
Irritable bowel syndrome (IBS) is one of the most common gastrointestinal disorders worldwide. The economic impact of IBS on the health care system is substantial, as is the personal impact on patients. Patients with diarrhea-predominant IBS (IBS-D) comprise a substantial proportion of the overall IBS population. Primary care providers are often the first point of contact for patients with IBS-D and can accurately diagnose IBS after a careful history and examination without extensive diagnostic tests. Several pharmacologic treatments (eg, loperamide, alosetron, and antidepressants) and non-pharmacologic treatments (eg, dietary modification and probiotics) are available for IBS-D, but restrictions on use (eg, alosetron) or the lack of controlled trial data showing reductions in both global and individual IBS-D symptoms (eg, bloating, pain and stool frequency) emphasize the need for alternative treatment options. Two newer medications (eluxadoline and rifaximin) were approved in May 2015 for the treatment of IBS-D, and represent new treatment options for this common gastrointestinal condition.
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Affiliation(s)
- Brian E Lacy
- Division of Gastroenterology and Hepatology, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
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Schwille-Kiuntke J, Enck P, Polster AV, Gaile M, Kremsner PG, Zanger P. Postinfectious irritable bowel syndrome after travelers' diarrhea--a cohort study. Neurogastroenterol Motil 2015; 27:1147-55. [PMID: 26009981 DOI: 10.1111/nmo.12601] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 04/24/2015] [Indexed: 12/19/2022]
Abstract
BACKGROUND There is sound evidence for the role of gastrointestinal infections in the development of postinfectious irritable bowel syndrome (PI-IBS), but understanding the interaction between mental factors and the infection remains incomplete. This study aims to (i) assess the occurrence of PI-IBS in a cohort of patients with self-reported travelers' diarrhea (TD), (ii) assess risk factors for PI-IBS development, and (iii) investigate the prognosis of PI-IBS after 1 year. METHODS Patients consulting the travel clinic at the University Hospital Tuebingen, Germany (in 2009 and 2010) were identified from records and questioned in follow-ups in 2011 and 2012. We used the Rome III modular questionnaire to assess IBS, the Hospital Anxiety and Depression Scale to assess anxiety and depression, and the Patient Health Questionnaire to assess somatization. KEY RESULTS We identified 529 eligible subjects from the clinical records. Of 135 subjects (age: 36.6 ± 14.6 years, 58.5% female) included in the study sample 6.7% (95% CI 3.0-11.1) had PI-IBS. We found more females (88.9% vs 56.3%, p = 0.08) and younger age subjects (mean 29.3 vs 37.1 years, p = 0.02) among the PI-IBS subjects. A multivariable regression model revealed vomiting at baseline and high somatization scores as strong and independent PI-IBS risk factors. One year later PI-IBS occurrence decreased to 3.3% (three cases of 90). CONCLUSIONS & INFERENCES Our findings underline the close linkage of mental and somatic processes for the manifestation of PI-IBS. Screening for psychiatric comorbidities in patients with severe gastrointestinal infections may allow identifying groups at high risk for PI-IBS.
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Affiliation(s)
- J Schwille-Kiuntke
- Department of Internal Medicine VI: Psychosomatic Medicine and Psychotherapy, University Hospital Tübingen, Tübingen, Germany
| | - P Enck
- Department of Internal Medicine VI: Psychosomatic Medicine and Psychotherapy, University Hospital Tübingen, Tübingen, Germany
| | - A V Polster
- Department of Internal Medicine VI: Psychosomatic Medicine and Psychotherapy, University Hospital Tübingen, Tübingen, Germany.,Department of Internal Medicine, University of Gothenburg, Gothenburg, Sweden
| | - M Gaile
- Department of Internal Medicine VII: Institute of Tropical Medicine, University Hospital Tübingen, Tübingen, Germany
| | - P G Kremsner
- Department of Internal Medicine VII: Institute of Tropical Medicine, University Hospital Tübingen, Tübingen, Germany
| | - P Zanger
- Department of Internal Medicine VII: Institute of Tropical Medicine, University Hospital Tübingen, Tübingen, Germany.,Institute of Public Health, University Hospital Heidelberg, Heidelberg, Germany
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