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Liu Y, Fachrul M, Inouye M, Méric G. Harnessing human microbiomes for disease prediction. Trends Microbiol 2024; 32:707-719. [PMID: 38246848 DOI: 10.1016/j.tim.2023.12.004] [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: 09/12/2023] [Revised: 12/12/2023] [Accepted: 12/12/2023] [Indexed: 01/23/2024]
Abstract
The human microbiome has been increasingly recognized as having potential use for disease prediction. Predicting the risk, progression, and severity of diseases holds promise to transform clinical practice, empower patient decisions, and reduce the burden of various common diseases, as has been demonstrated for cardiovascular disease or breast cancer. Combining multiple modifiable and non-modifiable risk factors, including high-dimensional genomic data, has been traditionally favored, but few studies have incorporated the human microbiome into models for predicting the prospective risk of disease. Here, we review research into the use of the human microbiome for disease prediction with a particular focus on prospective studies as well as the modulation and engineering of the microbiome as a therapeutic strategy.
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Affiliation(s)
- Yang Liu
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK; Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia; Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Melbourne, Victoria, Australia; Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK; British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Muhamad Fachrul
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia; Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Melbourne, Victoria, Australia; Human Genomics and Evolution Unit, St Vincent's Institute of Medical Research, Victoria, Australia; Melbourne Integrative Genomics, University of Melbourne, Parkville, Victoria, Australia; School of BioSciences, University of Melbourne, Parkville, Victoria, Australia
| | - Michael Inouye
- Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK; Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia; Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK; British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK; Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK; British Heart Foundation Cambridge Centre of Research Excellence, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Guillaume Méric
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia; Department of Cardiometabolic Health, University of Melbourne, Melbourne, Victoria, Australia; Central Clinical School, Monash University, Melbourne, Victoria, Australia; Department of Medical Science, Molecular Epidemiology, Uppsala University, Uppsala, Sweden; Department of Cardiovascular Research, Translation, and Implementation, La Trobe University, Melbourne, Victoria, Australia.
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Perea L, Faner R, Chalmers JD, Sibila O. Pathophysiology and genomics of bronchiectasis. Eur Respir Rev 2024; 33:240055. [PMID: 38960613 DOI: 10.1183/16000617.0055-2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 05/02/2024] [Indexed: 07/05/2024] Open
Abstract
Bronchiectasis is a complex and heterogeneous inflammatory chronic respiratory disease with an unknown cause in around 30-40% of patients. The presence of airway infection together with chronic inflammation, airway mucociliary dysfunction and lung damage are key components of the vicious vortex model that better describes its pathophysiology. Although bronchiectasis research has significantly increased over the past years and different endotypes have been identified, there are still major gaps in the understanding of the pathophysiology. Genomic approaches may help to identify new endotypes, as has been shown in other chronic airway diseases, such as COPD.Different studies have started to work in this direction, and significant contributions to the understanding of the microbiome and proteome diversity have been made in bronchiectasis in recent years. However, the systematic application of omics approaches to identify new molecular insights into the pathophysiology of bronchiectasis (endotypes) is still limited compared with other respiratory diseases.Given the complexity and diversity of these technologies, this review describes the key components of the pathophysiology of bronchiectasis and how genomics can be applied to increase our knowledge, including the study of new techniques such as proteomics, metabolomics and epigenomics. Furthermore, we propose that the novel concept of trained innate immunity, which is driven by microbiome exposures leading to epigenetic modifications, can complement our current understanding of the vicious vortex. Finally, we discuss the challenges, opportunities and implications of genomics application in clinical practice for better patient stratification into new therapies.
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Affiliation(s)
- Lidia Perea
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Rosa Faner
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias M.P. (CIBERES), Barcelona, Spain
| | - James D Chalmers
- Division of Molecular and Clinical Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Oriol Sibila
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias M.P. (CIBERES), Barcelona, Spain
- Respiratory Department, Hospital Clínic, University of Barcelona, Barcelona, Spain
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3
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Gao Y, Richardson H, Dicker AJ, Barton A, Kuzmanova E, Shteinberg M, Perea L, Goeminne PC, Cant E, Hennayake C, Pollock J, Abo Leyah H, Choi H, Polverino E, Blasi F, Welte T, Aliberti S, Long M, Shoemark A, Sibila O, Huang JTJ, Chalmers JD. Endotypes of Exacerbation in Bronchiectasis: An Observational Cohort Study. Am J Respir Crit Care Med 2024; 210:77-86. [PMID: 38717347 DOI: 10.1164/rccm.202310-1729oc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 05/07/2024] [Indexed: 07/02/2024] Open
Abstract
Rationale: Bronchiectasis is characterized by acute exacerbations, but the biological mechanisms underlying these events are poorly characterized. Objectives: To investigate the inflammatory and microbial characteristics of exacerbations of bronchiectasis. Methods: A total of 120 patients with bronchiectasis were enrolled and presented with acute exacerbations within 12 months. Spontaneous sputum samples were obtained during a period of clinical stability and again at exacerbation before receipt of antibiotic treatment. A validated rapid PCR assay for bacteria and viruses was used to classify exacerbations as bacterial, viral, or both. Sputum inflammatory assessments included label-free liquid chromatography-tandem mass spectrometry and measurement of sputum cytokines and neutrophil elastase activity. 16 s rRNA sequencing was used to characterize the microbiome. Measurements and Main Results: Bronchiectasis exacerbations showed profound molecular heterogeneity. At least one bacterium was identified in 103 samples (86%), and a high bacterial load (total bacterial load > 107 copies/g) was observed in 81 patients (68%). Respiratory viruses were identified in 55 (46%) patients, with rhinovirus being the most common virus (31%). PCR testing was more sensitive than culture. No consistent change in the microbiome was observed at exacerbation. Exacerbations were associated with increased neutrophil elastase, proteinase-3, IL-1β, and CXCL8. These markers were particularly associated with bacterial and bacterial plus viral exacerbations. Distinct inflammatory and microbiome profiles were seen between different exacerbation subtypes, including bacterial, viral, and eosinophilic events in both hypothesis-led and hypothesis-free analysis using integrated microbiome and proteomics, demonstrating four subtypes of exacerbation. Conclusions: Bronchiectasis exacerbations are heterogeneous events with contributions from bacteria, viruses, and inflammatory dysregulation.
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Affiliation(s)
- Yonghua Gao
- Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Hollian Richardson
- Division of Molecular and Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, Scotland, United Kingdom
| | - Alison J Dicker
- Division of Molecular and Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, Scotland, United Kingdom
| | - Alun Barton
- Division of Molecular and Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, Scotland, United Kingdom
| | - Elena Kuzmanova
- Division of Molecular and Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, Scotland, United Kingdom
| | - Michal Shteinberg
- Pulmonology Institute and Cystic Fibrosis Center, Carmel Medical Center, Haifa, Israel
| | - Lidia Perea
- Respiratory Institute, Hospital Clínic, Institute of Biomedical Research August Pi i Sunyer, University of Barcelona, Barcelona, Spain
| | - Pieter C Goeminne
- Department of Respiratory Disease, AZ Nikolaas, Sint-Niklaas, Belgium
| | - Erin Cant
- Division of Molecular and Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, Scotland, United Kingdom
| | - Chandani Hennayake
- Division of Molecular and Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, Scotland, United Kingdom
| | - Jennifer Pollock
- Division of Molecular and Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, Scotland, United Kingdom
| | - Hani Abo Leyah
- Department of Respiratory Medicine, Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, United Kingdom
| | - Hayoung Choi
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Internal Medicine, Hallym University Kangnam Sacred Heart Hospital, Seoul, Republic of Korea
| | - Eva Polverino
- Pneumology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, CIBERES, Barcelona, Spain
| | - Francesco Blasi
- Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Tobias Welte
- Department of Respiratory Medicine, Hannover Medical School, Hannover, Germany; and
| | - Stefano Aliberti
- Istituto di Ricovero e Cura a Carattere Scientifico di natura pubblica Humanitas Research Hospital, Rozzano, Milan, Italy
| | - Merete Long
- Division of Molecular and Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, Scotland, United Kingdom
| | - Amelia Shoemark
- Division of Molecular and Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, Scotland, United Kingdom
| | - Oriol Sibila
- Respiratory Institute, Hospital Clínic, Institute of Biomedical Research August Pi i Sunyer, University of Barcelona, Barcelona, Spain
| | - Jeffrey T J Huang
- Division of Molecular and Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, Scotland, United Kingdom
| | - James D Chalmers
- Division of Molecular and Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, Scotland, United Kingdom
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Mac Aogáin M, Dicker AJ, Mertsch P, Chotirmall SH. Infection and the microbiome in bronchiectasis. Eur Respir Rev 2024; 33:240038. [PMID: 38960615 DOI: 10.1183/16000617.0038-2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 05/02/2024] [Indexed: 07/05/2024] Open
Abstract
Bronchiectasis is marked by bronchial dilatation, recurrent infections and significant morbidity, underpinned by a complex interplay between microbial dysbiosis and immune dysregulation. The identification of distinct endophenotypes have refined our understanding of its pathogenesis, including its heterogeneous disease mechanisms that influence treatment and prognosis responses. Next-generation sequencing (NGS) has revolutionised the way we view airway microbiology, allowing insights into the "unculturable". Understanding the bronchiectasis microbiome through targeted amplicon sequencing and/or shotgun metagenomics has provided key information on the interplay of the microbiome and host immunity, a central feature of disease progression. The rapid increase in translational and clinical studies in bronchiectasis now provides scope for the application of precision medicine and a better understanding of the efficacy of interventions aimed at restoring microbial balance and/or modulating immune responses. Holistic integration of these insights is driving an evolving paradigm shift in our understanding of bronchiectasis, which includes the critical role of the microbiome and its unique interplay with clinical, inflammatory, immunological and metabolic factors. Here, we review the current state of infection and the microbiome in bronchiectasis and provide views on the future directions in this field.
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Affiliation(s)
- Micheál Mac Aogáin
- Biochemical Genetics Laboratory, Department of Biochemistry, St. James's Hospital, Dublin, Ireland
- Clinical Biochemistry Unit, School of Medicine, Trinity College Dublin, Dublin, Ireland
| | - Alison J Dicker
- Respiratory Research Group, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Pontus Mertsch
- Department of Medicine V, LMU University Hospital, LMU Munich, Comprehensive Pneumology Center (CPC), Member of the German Center of Lung Research (DZL), Munich, Germany
| | - Sanjay H Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Department of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore, Singapore
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5
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Johnson E, Long MB, Chalmers JD. Biomarkers in bronchiectasis. Eur Respir Rev 2024; 33:230234. [PMID: 38960612 DOI: 10.1183/16000617.0234-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 03/09/2024] [Indexed: 07/05/2024] Open
Abstract
Bronchiectasis is a heterogeneous disease with multiple aetiologies and diverse clinical features. There is a general consensus that optimal treatment requires precision medicine approaches focused on specific treatable disease characteristics, known as treatable traits. Identifying subtypes of conditions with distinct underlying biology (endotypes) depends on the identification of biomarkers that are associated with disease features, prognosis or treatment response and which can be applied in clinical practice. Bronchiectasis is a disease characterised by inflammation, infection, structural lung damage and impaired mucociliary clearance. Increasingly there are available methods to measure each of these components of the disease, revealing heterogeneous inflammatory profiles, microbiota, radiology and mucus and epithelial biology in patients with bronchiectasis. Using emerging biomarkers and omics technologies to guide treatment in bronchiectasis is a promising field of research. Here we review the most recent data on biomarkers in bronchiectasis.
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Affiliation(s)
- Emma Johnson
- Division of Molecular and Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Merete B Long
- Division of Molecular and Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - James D Chalmers
- Division of Molecular and Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
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6
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Chotirmall SH, Chalmers JD. The Precision Medicine Era of Bronchiectasis. Am J Respir Crit Care Med 2024; 210:24-34. [PMID: 38949497 PMCID: PMC11197062 DOI: 10.1164/rccm.202403-0473pp] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 04/10/2024] [Indexed: 07/02/2024] Open
Affiliation(s)
- Sanjay H. Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Department of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore, Singapore; and
| | - James D. Chalmers
- Division of Molecular and Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, United Kingdom
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7
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Brown GD, Ballou ER, Bates S, Bignell EM, Borman AM, Brand AC, Brown AJP, Coelho C, Cook PC, Farrer RA, Govender NP, Gow NAR, Hope W, Hoving JC, Dangarembizi R, Harrison TS, Johnson EM, Mukaremera L, Ramsdale M, Thornton CR, Usher J, Warris A, Wilson D. The pathobiology of human fungal infections. Nat Rev Microbiol 2024:10.1038/s41579-024-01062-w. [PMID: 38918447 DOI: 10.1038/s41579-024-01062-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/14/2024] [Indexed: 06/27/2024]
Abstract
Human fungal infections are a historically neglected area of disease research, yet they cause more than 1.5 million deaths every year. Our understanding of the pathophysiology of these infections has increased considerably over the past decade, through major insights into both the host and pathogen factors that contribute to the phenotype and severity of these diseases. Recent studies are revealing multiple mechanisms by which fungi modify and manipulate the host, escape immune surveillance and generate complex comorbidities. Although the emergence of fungal strains that are less susceptible to antifungal drugs or that rapidly evolve drug resistance is posing new threats, greater understanding of immune mechanisms and host susceptibility factors is beginning to offer novel immunotherapeutic options for the future. In this Review, we provide a broad and comprehensive overview of the pathobiology of human fungal infections, focusing specifically on pathogens that can cause invasive life-threatening infections, highlighting recent discoveries from the pathogen, host and clinical perspectives. We conclude by discussing key future challenges including antifungal drug resistance, the emergence of new pathogens and new developments in modern medicine that are promoting susceptibility to infection.
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Affiliation(s)
- Gordon D Brown
- Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter, UK.
| | - Elizabeth R Ballou
- Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter, UK
| | - Steven Bates
- Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter, UK
| | - Elaine M Bignell
- Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter, UK
| | - Andrew M Borman
- Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter, UK
| | - Alexandra C Brand
- Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter, UK
| | - Alistair J P Brown
- Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter, UK
| | - Carolina Coelho
- Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter, UK
| | - Peter C Cook
- Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter, UK
| | - Rhys A Farrer
- Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter, UK
| | - Nelesh P Govender
- Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter, UK
| | - Neil A R Gow
- Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter, UK
| | - William Hope
- Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter, UK
| | - J Claire Hoving
- Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter, UK
| | - Rachael Dangarembizi
- Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter, UK
| | - Thomas S Harrison
- Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter, UK
| | - Elizabeth M Johnson
- Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter, UK
| | - Liliane Mukaremera
- Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter, UK
| | - Mark Ramsdale
- Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter, UK
| | | | - Jane Usher
- Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter, UK
| | - Adilia Warris
- Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter, UK
| | - Duncan Wilson
- Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter, UK
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Hagiwara A, Shuto H, Kudoh R, Omori S, Hiramatsu K, Kadota JI, Fushimi K, Komiya K. Medical Causes of Hospitalisation among Patients with Bronchiectasis: A Nationwide Study in Japan. Pathogens 2024; 13:492. [PMID: 38921790 PMCID: PMC11206607 DOI: 10.3390/pathogens13060492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 05/30/2024] [Accepted: 06/07/2024] [Indexed: 06/27/2024] Open
Abstract
PURPOSE Although the international guidelines for managing bronchiectasis are centred on preventing the exacerbation of bronchiectasis, the medical causes of admissions to hospital among patients with bronchiectasis have not been fully investigated. METHODS This study targeted patients with bronchiectasis who were admitted to hospitals between April 2018 and March 2020 using the national inpatient database in Japan. The causes of hospitalisation and types of antibiotics used for hospitalised patients were recorded. RESULTS In total, 21,300 hospitalisations of 16,723 patients with bronchiectasis were analysed. The most common cause was respiratory diseases in 15,145 (71.1%) admissions, including bacterial pneumonia and the exacerbation of bronchiectasis in 6238 (41.2%) and 3151 (20.8%), respectively. Antipseudomonal antibiotics were used in approximately 60% of patients with bacterial pneumonia who were administered antibiotic treatments and in approximately 50% of patients with the exacerbation of bronchiectasis. CONCLUSIONS Bacterial pneumonia was the most frequent cause of hospitalisation, followed by the exacerbation of bronchiectasis, among patients with bronchiectasis. Physicians need to focus on the prevention of bacterial pneumonia in addition to the exacerbation of bronchiectasis in patients with bronchiectasis.
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Affiliation(s)
- Akihiko Hagiwara
- Respiratory Medicine and Infectious Diseases, Oita University Faculty of Medicine, 1-1 Idaigaoka, Hasama-machi, Yufu 879-5593, Oita, Japan
| | - Hisayuki Shuto
- Respiratory Medicine and Infectious Diseases, Oita University Faculty of Medicine, 1-1 Idaigaoka, Hasama-machi, Yufu 879-5593, Oita, Japan
| | - Ryohei Kudoh
- Respiratory Medicine and Infectious Diseases, Oita University Faculty of Medicine, 1-1 Idaigaoka, Hasama-machi, Yufu 879-5593, Oita, Japan
| | - Shota Omori
- Respiratory Medicine and Infectious Diseases, Oita University Faculty of Medicine, 1-1 Idaigaoka, Hasama-machi, Yufu 879-5593, Oita, Japan
| | - Kazufumi Hiramatsu
- Respiratory Medicine and Infectious Diseases, Oita University Faculty of Medicine, 1-1 Idaigaoka, Hasama-machi, Yufu 879-5593, Oita, Japan
| | - Jun-ichi Kadota
- Respiratory Medicine and Infectious Diseases, Oita University Faculty of Medicine, 1-1 Idaigaoka, Hasama-machi, Yufu 879-5593, Oita, Japan
| | - Kiyohide Fushimi
- Department of Health Policy and Informatics, Tokyo Medical and Dental University Graduate School, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
| | - Kosaku Komiya
- Respiratory Medicine and Infectious Diseases, Oita University Faculty of Medicine, 1-1 Idaigaoka, Hasama-machi, Yufu 879-5593, Oita, Japan
- Research Center for GLOBAL and LOCAL Infectious Diseases, Oita University Faculty of Medicine, 1-1 Idaigaoka, Hasama-machi, Yufu 879-5593, Oita, Japan
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He ZF, Lin SZ, Pan CX, Chen ZM, Cen LJ, Zhang XX, Huang Y, Chen CL, Zha SS, Li HM, Lin ZH, Shi MX, Zhong NS, Guan WJ. The roles of bacteria and viruses in COPD-Bronchiectasis association: A prospective cohort study. Respir Med 2024; 231:107692. [PMID: 38852923 DOI: 10.1016/j.rmed.2024.107692] [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: 02/29/2024] [Revised: 04/21/2024] [Accepted: 06/03/2024] [Indexed: 06/11/2024]
Abstract
BACKGROUND Exacerbations are implicated in bronchiectasis and COPD, which frequently co-exist [COPD-Bronchiectasis association (CBA)]. We aimed to determine the bacterial and viral spectrum at stable-state and exacerbation onset of CBA, and their association with exacerbations and clinical outcomes of CBA as compared with bronchiectasis. METHODS We prospectively collected spontaneous sputum from adults with CBA, bronchiectasis with (BO) and without airflow obstruction (BNO) for bacterial culture and viral detection at stable-state and exacerbations. RESULTS We enrolled 76 patients with CBA, 58 with BO, and 138 with BNO (711 stable and 207 exacerbation visits). Bacterial detection rate increased from BNO, CBA to BO at steady-state (P = 0.02), but not at AE onset (P = 0.91). No significant differences in viral detection rate were found among BNO, CBA and BO. Compared with steady-state, viral isolations occurred more frequently at exacerbation in BNO (15.8 % vs 32.1 %, P = 0.001) and CBA (19.5 % vs 30.6 %, P = 0.036) only. In CBA, isolation of viruses, human metapneumovirus and bacteria plus viruses was associated with exacerbation. Repeated detection of Pseudomonas aeruginosa (PA) correlated with higher modified Reiff score (P = 0.032) in CBA but not in BO (P = 0.178). Repeated detection of PA yielded a shorter time to the first exacerbation in CBA [median: 4.3 vs 11.1 months, P = 0.006] but not in BO (median: 8.4 vs 7.6 months, P = 0.47). CONCLUSIONS Isolation of any viruses, human metapneumovirus and bacterialplus viruses was associated with CBA exacerbations. Repeated detection of PA confers greater impact of future exacerbations on CBA than on BO.
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Affiliation(s)
- Zhen-Feng He
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Department of Respiratory and Critical Care Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Sheng-Zhu Lin
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Department of Respiratory and Critical Care Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Cui-Xia Pan
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Department of Respiratory and Critical Care Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Zhao-Ming Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Department of Respiratory and Critical Care Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Lai-Jian Cen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Department of Respiratory and Critical Care Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Xiao-Xian Zhang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Department of Respiratory and Critical Care Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Yan Huang
- Department of Geriatrics, National Key Clinical Specialty, Guangzhou First People's Hospital, South China University of Technology, Guangzhou, China
| | - Chun-Lan Chen
- Department of Respiratory and Critical Care Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Shan-Shan Zha
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Department of Respiratory and Critical Care Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Hui-Min Li
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Department of Respiratory and Critical Care Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Zhen-Hong Lin
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Department of Respiratory and Critical Care Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Ming-Xin Shi
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Department of Respiratory and Critical Care Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Nan-Shan Zhong
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Department of Respiratory and Critical Care Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China; Guangzhou National Laboratory, Guangzhou, China
| | - Wei-Jie Guan
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Department of Respiratory and Critical Care Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China; Guangzhou National Laboratory, Guangzhou, China.
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Azoicai A, Lupu A, Alexoae MM, Starcea IM, Mocanu A, Lupu VV, Mitrofan EC, Nedelcu AH, Tepordei RT, Munteanu D, Mitrofan C, Salaru DL, Ioniuc I. Lung microbiome: new insights into bronchiectasis' outcome. Front Cell Infect Microbiol 2024; 14:1405399. [PMID: 38895737 PMCID: PMC11183332 DOI: 10.3389/fcimb.2024.1405399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 05/15/2024] [Indexed: 06/21/2024] Open
Abstract
The present treatments for bronchiectasis, which is defined by pathological dilatation of the airways, are confined to symptom relief and minimizing exacerbations. The condition is becoming more common worldwide. Since the disease's pathophysiology is not entirely well understood, developing novel treatments is critically important. The interplay of chronic infection, inflammation, and compromised mucociliary clearance, which results in structural alterations and the emergence of new infection, is most likely responsible for the progression of bronchiectasis. Other than treating bronchiectasis caused by cystic fibrosis, there are no approved treatments. Understanding the involvement of the microbiome in this disease is crucial, the microbiome is defined as the collective genetic material of all bacteria in an environment. In clinical practice, bacteria in the lungs have been studied using cultures; however, in recent years, researchers use next-generation sequencing methods, such as 16S rRNA sequencing. Although the microbiome in bronchiectasis has not been entirely investigated, what is known about it suggests that Haemophilus, Pseudomonas and Streptococcus dominate the lung bacterial ecosystems, they present significant intraindividual stability and interindividual heterogeneity. Pseudomonas and Haemophilus-dominated microbiomes have been linked to more severe diseases and frequent exacerbations, however additional research is required to fully comprehend the role of microbiome in the evolution of bronchiectasis. This review discusses recent findings on the lung microbiota and its association with bronchiectasis.
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Affiliation(s)
- Alice Azoicai
- Mother and Child Medicine Department, “Grigore T. Popa” University of Medicine and Pharmacy, Iasi, Romania
| | - Ancuta Lupu
- Mother and Child Medicine Department, “Grigore T. Popa” University of Medicine and Pharmacy, Iasi, Romania
| | - Monica Mihaela Alexoae
- Mother and Child Medicine Department, “Grigore T. Popa” University of Medicine and Pharmacy, Iasi, Romania
| | - Iuliana Magdalena Starcea
- Mother and Child Medicine Department, “Grigore T. Popa” University of Medicine and Pharmacy, Iasi, Romania
| | - Adriana Mocanu
- Mother and Child Medicine Department, “Grigore T. Popa” University of Medicine and Pharmacy, Iasi, Romania
| | - Vasile Valeriu Lupu
- Mother and Child Medicine Department, “Grigore T. Popa” University of Medicine and Pharmacy, Iasi, Romania
| | | | - Alin Horatiu Nedelcu
- Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, Iasi, Romania
| | - Razvan Tudor Tepordei
- Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, Iasi, Romania
| | - Dragos Munteanu
- Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, Iasi, Romania
| | - Costica Mitrofan
- Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, Iasi, Romania
| | - Delia Lidia Salaru
- Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, Iasi, Romania
| | - Ileana Ioniuc
- Mother and Child Medicine Department, “Grigore T. Popa” University of Medicine and Pharmacy, Iasi, Romania
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11
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Choi H, McShane PJ, Aliberti S, Chalmers JD. Bronchiectasis management in adults: state of the art and future directions. Eur Respir J 2024; 63:2400518. [PMID: 38782469 PMCID: PMC11211698 DOI: 10.1183/13993003.00518-2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024]
Abstract
Formerly regarded as a rare disease, bronchiectasis is increasingly recognised. A renewed interest in this disease has led to significant progress in bronchiectasis research. Randomised clinical trials (RCTs) have demonstrated the benefits of airway clearance techniques, inhaled antibiotics and long-term macrolide therapy in bronchiectasis patients. However, the heterogeneity of bronchiectasis remains one of the most challenging aspects of management. Phenotypes and endotypes of bronchiectasis have been identified to help find "treatable traits" and partially overcome disease complexity. The goals of therapy for bronchiectasis are to reduce the symptom burden, improve quality of life, reduce exacerbations and prevent disease progression. We review the pharmacological and non-pharmacological treatments that can improve mucociliary clearance, reduce airway inflammation and tackle airway infection, the key pathophysiological features of bronchiectasis. There are also promising treatments in development for the management of bronchiectasis, including novel anti-inflammatory therapies. This review provides a critical update on the management of bronchiectasis focusing on treatable traits and recent RCTs.
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Affiliation(s)
- Hayoung Choi
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Internal Medicine, Hallym University Kangnam Sacred Heart Hospital, Hallym University College of Medicine, Seoul, Republic of Korea
| | - Pamela J McShane
- Division of Pulmonary and Critical Care, University of Texas Health Science Center at Tyler, Tyler, TX, USA
| | - Stefano Aliberti
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
- Respiratory Unit, IRCCS Humanitas Research Hospital, Milan, Italy
| | - James D Chalmers
- Division of Molecular and Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
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12
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Yang J, Li J, Zhang L, Shen Z, Xiao Y, Zhang G, Chen M, Chen F, Liu L, Wang Y, Chen L, Wang X, Zhang L, Wang L, Wang Z, Wang J, Li M, Ren L. Highly diverse sputum microbiota correlates with the disease severity in patients with community-acquired pneumonia: a longitudinal cohort study. Respir Res 2024; 25:223. [PMID: 38811936 PMCID: PMC11137881 DOI: 10.1186/s12931-024-02821-2] [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: 01/17/2024] [Accepted: 04/24/2024] [Indexed: 05/31/2024] Open
Abstract
BACKGROUND Community-acquired pneumonia (CAP) is a common and serious condition that can be caused by a variety of pathogens. However, much remains unknown about how these pathogens interact with the lower respiratory commensals, and whether any correlation exists between the dysbiosis of the lower respiratory microbiota and disease severity and prognosis. METHODS We conducted a retrospective cohort study to investigate the composition and dynamics of sputum microbiota in patients diagnosed with CAP. In total, 917 sputum specimens were collected consecutively from 350 CAP inpatients enrolled in six hospitals following admission. The V3-V4 region of the 16 S rRNA gene was then sequenced. RESULTS The sputum microbiota in 71% of the samples were predominately composed of respiratory commensals. Conversely, 15% of the samples demonstrated dominance by five opportunistic pathogens. Additionally, 5% of the samples exhibited sterility, resembling the composition of negative controls. Compared to non-severe CAP patients, severe cases exhibited a more disrupted sputum microbiota, characterized by the highly dominant presence of potential pathogens, greater deviation from a healthy state, more significant alterations during hospitalization, and sparser bacterial interactions. The sputum microbiota on admission demonstrated a moderate prediction of disease severity (AUC = 0.74). Furthermore, different pathogenic infections were associated with specific microbiota alterations. Acinetobacter and Pseudomonas were more abundant in influenza A infections, with Acinetobacter was also enriched in Klebsiella pneumoniae infections. CONCLUSION Collectively, our study demonstrated that pneumonia may not consistently correlate with severe dysbiosis of the respiratory microbiota. Instead, the degree of microbiota dysbiosis was correlated with disease severity in CAP patients.
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Affiliation(s)
- Jing Yang
- Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Changping Laboratory, Beijing, 102206, China
| | - Jinman Li
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Linfeng Zhang
- Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zijie Shen
- Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yan Xiao
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
- State Key Laboratory of Respiratory Health and Multimorbidity, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Guoliang Zhang
- Shenzhen Third People's Hospital, Shenzhen, 518112, China
| | - Mingwei Chen
- The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Fuhui Chen
- The Second Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
| | - Ling Liu
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, School of Medicine, Zhongda Hospital, Southeast University, Nanjing, 210009, China
| | - Ying Wang
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Lan Chen
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Xinming Wang
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Li Zhang
- Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing, 100101, China
| | - Lu Wang
- Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing, 100101, China
| | - Zhang Wang
- Institute of Ecological Sciences, South China Normal University, Guangzhou, 510631, China
| | - Jianwei Wang
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
| | - Mingkun Li
- Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Lili Ren
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
- State Key Laboratory of Respiratory Health and Multimorbidity, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
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13
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Su Q, Lau RI, Liu Q, Li MKT, Yan Mak JW, Lu W, Lau ISF, Lau LHS, Yeung GTY, Cheung CP, Tang W, Liu C, Ching JYL, Cheong PK, Chan FKL, Ng SC. The gut microbiome associates with phenotypic manifestations of post-acute COVID-19 syndrome. Cell Host Microbe 2024; 32:651-660.e4. [PMID: 38657605 DOI: 10.1016/j.chom.2024.04.005] [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: 11/29/2023] [Revised: 02/28/2024] [Accepted: 04/01/2024] [Indexed: 04/26/2024]
Abstract
The mechanisms underlying the many phenotypic manifestations of post-acute COVID-19 syndrome (PACS) are poorly understood. Herein, we characterized the gut microbiome in heterogeneous cohorts of subjects with PACS and developed a multi-label machine learning model for using the microbiome to predict specific symptoms. Our processed data covered 585 bacterial species and 500 microbial pathways, explaining 12.7% of the inter-individual variability in PACS. Three gut-microbiome-based enterotypes were identified in subjects with PACS and associated with different phenotypic manifestations. The trained model showed an accuracy of 0.89 in predicting individual symptoms of PACS in the test set and maintained a sensitivity of 86% and a specificity of 82% in predicting upcoming symptoms in an independent longitudinal cohort of subjects before they developed PACS. This study demonstrates that the gut microbiome is associated with phenotypic manifestations of PACS, which has potential clinical utility for the prediction and diagnosis of PACS.
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Affiliation(s)
- Qi Su
- Microbiota I-Center (MagIC), Hong Kong SAR, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Raphaela I Lau
- Microbiota I-Center (MagIC), Hong Kong SAR, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Qin Liu
- Microbiota I-Center (MagIC), Hong Kong SAR, China
| | - Moses K T Li
- Microbiota I-Center (MagIC), Hong Kong SAR, China
| | - Joyce Wing Yan Mak
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Wenqi Lu
- Microbiota I-Center (MagIC), Hong Kong SAR, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Ivan S F Lau
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Louis H S Lau
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Giann T Y Yeung
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Chun Pan Cheung
- Microbiota I-Center (MagIC), Hong Kong SAR, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Whitney Tang
- Microbiota I-Center (MagIC), Hong Kong SAR, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Chengyu Liu
- Microbiota I-Center (MagIC), Hong Kong SAR, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Jessica Y L Ching
- Microbiota I-Center (MagIC), Hong Kong SAR, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Pui Kuan Cheong
- Microbiota I-Center (MagIC), Hong Kong SAR, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Francis K L Chan
- Microbiota I-Center (MagIC), Hong Kong SAR, China; Centre for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Siew C Ng
- Microbiota I-Center (MagIC), Hong Kong SAR, China; Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China.
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14
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Shteinberg M, Chalmers JD, Narayana JK, Dicker AJ, Rahat MA, Simanovitch E, Bidgood L, Cohen S, Stein N, Abo-Hilu N, Abbott J, Avital S, Fireman-Klein E, Richardson H, Muhammad E, Jrbashyan J, Schneer S, Nasrallah N, Eisenberg I, Chotirmall SH, Adir Y. Bronchiectasis with Chronic Rhinosinusitis Is Associated with Eosinophilic Airway Inflammation and Is Distinct from Asthma. Ann Am Thorac Soc 2024; 21:748-758. [PMID: 38194593 DOI: 10.1513/annalsats.202306-551oc] [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: 06/20/2023] [Accepted: 01/09/2024] [Indexed: 01/11/2024] Open
Abstract
Rationale: Bronchiectasis is an airway inflammatory disease that is frequently associated with chronic rhinosinusitis (CRS). An eosinophilic endotype of bronchiectasis has recently been described, but detailed testing to differentiate eosinophilic bronchiectasis from asthma has not been performed. Objectives: This prospective observational study aimed to test the hypotheses that bronchiectasis with CRS is enriched for the eosinophilic phenotype in comparison with bronchiectasis alone and that the eosinophilic bronchiectasis phenotype exists as a separate entity from bronchiectasis associated with asthma. Methods: People with idiopathic or postinfectious bronchiectasis were assessed for concomitant CRS. We excluded people with asthma or primary ciliary dyskinesia and smokers. We assessed sputum and blood cell counts, nasal NO and fractional excreted NO, methacholine reactivity, skin allergy testing and total and specific immunoglobulin (Ig) E, cytokines in the sputum and serum, and the microbiome in the sputum and nasopharynx. Results: A total of 22 people with CRS (BE + CRS) and 17 without CRS (BE - CRS) were included. Sex, age, Reiff score, and bronchiectasis severity were similar. Median sputum eosinophil percentages were 0% (IQR, 0-1.5%) in BE - CRS and 3% (1-12%) in BE + CRS (P = 0.012). Blood eosinophil counts were predictive of sputum eosinophilia (counts ⩾3%; area under the receiver operating characteristic curve, 0.68; 95% confidence interval, 0.50-0.85). Inclusion of CRS improved the prediction of sputum eosinophilia by blood eosinophil counts (area under the receiver operating characteristic curve, 0.79; 95% confidence interval, 0.65-0.94). Methacholine tests were negative in 85.7% of patients in the BE - CRS group and 85.2% of patients in the BE + CRS group (P > 0.99). Specific IgE and skin testing were similar between the groups, but total IgE levels were increased in people with increased sputum eosinophils. Microbiome analysis demonstrated distinct microbiota in nasopharyngeal and airway samples in the BE + CRS and BE - CRS groups, without significant differences between groups. However, interactome analysis revealed altered interactomes in individuals with high sputum eosinophil counts and CRS. Conclusions: Bronchiectasis with CRS is associated with an eosinophilic airway inflammation that is distinct from asthma.
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Affiliation(s)
- Michal Shteinberg
- Pulmonology Institute and CF Center
- Technion-Israel Institute of Technology, The B. Rappoport Faculty of Medicine, Haifa, Israel
| | - James D Chalmers
- Division of Molecular and Clinical Medicine, Ninewells Hospital, University of Dundee, Dundee, United Kingdom
| | - Jayanth K Narayana
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore; and
| | - Alison J Dicker
- Division of Molecular and Clinical Medicine, Ninewells Hospital, University of Dundee, Dundee, United Kingdom
| | - Michal A Rahat
- Immunotherapy Laboratory
- Technion-Israel Institute of Technology, The B. Rappoport Faculty of Medicine, Haifa, Israel
| | | | - Lucy Bidgood
- Division of Molecular and Clinical Medicine, Ninewells Hospital, University of Dundee, Dundee, United Kingdom
| | - Shai Cohen
- Allergy and Immunology Unit
- Technion-Israel Institute of Technology, The B. Rappoport Faculty of Medicine, Haifa, Israel
| | - Nili Stein
- Community Medicine and Epidemiology Department
| | | | - James Abbott
- Division of Molecular and Clinical Medicine, Ninewells Hospital, University of Dundee, Dundee, United Kingdom
| | | | - Einat Fireman-Klein
- Pulmonology Institute and CF Center
- Technion-Israel Institute of Technology, The B. Rappoport Faculty of Medicine, Haifa, Israel
| | - Hollian Richardson
- Division of Molecular and Clinical Medicine, Ninewells Hospital, University of Dundee, Dundee, United Kingdom
| | | | | | - Sonia Schneer
- Pulmonology Institute and CF Center
- Technion-Israel Institute of Technology, The B. Rappoport Faculty of Medicine, Haifa, Israel
| | | | - Iya Eisenberg
- Radiology Department, Carmel Medical Center, Haifa, Israel
| | - Sanjay H Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore; and
- Department of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore
| | - Yochai Adir
- Pulmonology Institute and CF Center
- Technion-Israel Institute of Technology, The B. Rappoport Faculty of Medicine, Haifa, Israel
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15
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Konovalovas A, Armalytė J, Klimkaitė L, Liveikis T, Jonaitytė B, Danila E, Bironaitė D, Mieliauskaitė D, Bagdonas E, Aldonytė R. Human nasal microbiota shifts in healthy and chronic respiratory disease conditions. BMC Microbiol 2024; 24:150. [PMID: 38678223 PMCID: PMC11055347 DOI: 10.1186/s12866-024-03294-5] [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: 11/30/2023] [Accepted: 04/04/2024] [Indexed: 04/29/2024] Open
Abstract
BACKGROUND An increasing number of studies investigate various human microbiotas and their roles in the development of diseases, maintenance of health states, and balanced signaling towards the brain. Current data demonstrate that the nasal microbiota contains a unique and highly variable array of commensal bacteria and opportunistic pathogens. However, we need to understand how to harness current knowledge, enrich nasal microbiota with beneficial microorganisms, and prevent pathogenic developments. RESULTS In this study, we have obtained nasal, nasopharyngeal, and bronchoalveolar lavage fluid samples from healthy volunteers and patients suffering from chronic respiratory tract diseases for full-length 16 S rRNA sequencing analysis using Oxford Nanopore Technologies. Demographic and clinical data were collected simultaneously. The microbiome analysis of 97 people from Lithuania suffering from chronic inflammatory respiratory tract disease and healthy volunteers revealed that the human nasal microbiome represents the microbiome of the upper airways well. CONCLUSIONS The nasal microbiota of patients was enriched with opportunistic pathogens, which could be used as indicators of respiratory tract conditions. In addition, we observed that a healthy human nasal microbiome contained several plant- and bee-associated species, suggesting the possibility of enriching human nasal microbiota via such exposures when needed. These candidate probiotics should be investigated for their modulating effects on airway and lung epithelia, immunogenic properties, neurotransmitter content, and roles in maintaining respiratory health and nose-brain interrelationships.
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Affiliation(s)
- Aleksandras Konovalovas
- Life Sciences Center, Institute of Biosciences, Vilnius University, Vilnius, Lithuania
- State Research Institute Centre for Innovative Medicine, Vilnius, Lithuania
| | - Julija Armalytė
- Life Sciences Center, Institute of Biosciences, Vilnius University, Vilnius, Lithuania.
| | - Laurita Klimkaitė
- Life Sciences Center, Institute of Biosciences, Vilnius University, Vilnius, Lithuania
| | - Tomas Liveikis
- Life Sciences Center, Institute of Biosciences, Vilnius University, Vilnius, Lithuania
| | - Brigita Jonaitytė
- Clinic of Chest Diseases, Immunology, and Allergology, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Edvardas Danila
- Clinic of Chest Diseases, Immunology, and Allergology, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
- Centre of Pulmonology and Allergology, Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania
| | - Daiva Bironaitė
- State Research Institute Centre for Innovative Medicine, Vilnius, Lithuania
| | | | - Edvardas Bagdonas
- State Research Institute Centre for Innovative Medicine, Vilnius, Lithuania
| | - Rūta Aldonytė
- State Research Institute Centre for Innovative Medicine, Vilnius, Lithuania.
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16
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Lira-Junior R, Aogáin MM, Crncalo E, Ekberg NR, Chotirmall SH, Pettersson S, Gustafsson A, Brismar K, Bostanci N. Effects of intermittent fasting on periodontal inflammation and subgingival microbiota. J Periodontol 2024. [PMID: 38655661 DOI: 10.1002/jper.23-0676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 03/21/2024] [Accepted: 03/29/2024] [Indexed: 04/26/2024]
Abstract
BACKGROUND Studies on the impact of intermittent fasting on periodontal health are still scarce. Thus, this study evaluated the effects of long-term intermittent fasting on periodontal health and the subgingival microbiota. METHODS This pilot study was part of a nonrandomized controlled trial. Overweight/obese participants (n = 14) entered an intermittent fasting program, specifically the 5:2 diet, in which they restricted caloric intake to about a quarter of the normal total daily caloric expenditure for two nonconsecutive days/week. Subjects underwent a thorough clinical and laboratory examination, including an assessment of their periodontal condition, at baseline and 6 months after starting the diet. Additionally, subgingival microbiota was assessed by 16S rRNA gene sequencing. RESULTS After 6 months of intermittent fasting, weight, body mass index, C-reactive protein, hemoglobin A1c (HbA1c), and the cholesterol profile improved significantly (p < 0.05). Moreover, significant reductions were observed in bleeding on probing (p = 0.01) and the presence of shallow periodontal pockets after fasting (p < 0.001), while no significant change was seen in plaque index (p = 0.14). While we did not observe significant changes in α- or β-diversity of the subgingival microbiota related to dietary intervention (p > 0.05), significant differences were seen in the abundances of several taxa among individuals exhibiting ≥60% reduction (good responders) in probing pocket depth of 4-5 mm compared to those with <60% reduction (bad responders). CONCLUSION Intermittent fasting decreased systemic and periodontal inflammation. Although the subgingival microbiota was unaltered by this intervention, apparent taxonomic variability was observed between good and bad responders.
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Affiliation(s)
- Ronaldo Lira-Junior
- Section of Oral Diagnostics and Surgery, Division of Oral Diagnostics and Rehabilitation, Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Micheál Mac Aogáin
- Biochemical Genetics Laboratory, Department of Biochemistry, St. James's Hospital, Dublin, Ireland
- Clinical Biochemistry Unit, School of Medicine, Trinity College Dublin, Dublin, Ireland
| | - Eva Crncalo
- Division of Oral Health and Periodontology, Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Neda Rajamand Ekberg
- Department of Molecular Medicine and Surgery, Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, Stockholm, Sweden
| | - Sanjay H Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Department of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore, Singapore
| | - Sven Pettersson
- Department of Microbiology and Immunology, National University of Singapore, Singapore, Singapore
| | - Anders Gustafsson
- Division of Oral Health and Periodontology, Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Kerstin Brismar
- Department of Molecular Medicine and Surgery, Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, Stockholm, Sweden
| | - Nagihan Bostanci
- Division of Oral Health and Periodontology, Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden
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17
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Xiao W, Chen YL, Du LY, Wu J, Wang Z, Mao B, Wen FQ, Gibson PG, McDonald VM, Yu H, Fu JJ. Bacterial interactome disturbance in chronic obstructive pulmonary disease clinical stability and exacerbations. Respir Res 2024; 25:173. [PMID: 38643126 PMCID: PMC11032604 DOI: 10.1186/s12931-024-02802-5] [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: 11/08/2023] [Accepted: 04/03/2024] [Indexed: 04/22/2024] Open
Abstract
RATIONALE Our understanding of airway dysbiosis in chronic obstructive pulmonary disease (COPD) remains incomplete, which may be improved by unraveling the complexity in microbial interactome. OBJECTIVES To characterize reproducible features of airway bacterial interactome in COPD at clinical stability and during exacerbation, and evaluate their associations with disease phenotypes. METHODS We performed weighted ensemble-based co-occurrence network analysis of 1742 sputum microbiomes from published and new microbiome datasets, comprising two case-control studies of stable COPD versus healthy control, two studies of COPD stability versus exacerbation, and one study with exacerbation-recovery time series data. RESULTS Patients with COPD had reproducibly lower degree of negative bacterial interactions, i.e. total number of negative interactions as a proportion of total interactions, in their airway microbiome compared with healthy controls. Evaluation of the Haemophilus interactome showed that the antagonistic interaction networks of this established pathogen rather than its abundance consistently changed in COPD. Interactome dynamic analysis revealed reproducibly reduced antagonistic interactions but not diversity loss during COPD exacerbation, which recovered after treatment. In phenotypic analysis, unsupervised network clustering showed that loss of antagonistic interactions was associated with worse clinical symptoms (dyspnea), poorer lung function, exaggerated neutrophilic inflammation, and higher exacerbation risk. Furthermore, the frequent exacerbators (≥ 2 exacerbations per year) had significantly reduced antagonistic bacterial interactions while exhibiting subtle compositional changes in their airway microbiota. CONCLUSIONS Bacterial interactome disturbance characterized by reduced antagonistic interactions, rather than change in pathogen abundance or diversity, is a reproducible feature of airway dysbiosis in COPD clinical stability and exacerbations, which suggests that we may target interactome rather than pathogen alone for disease treatment.
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Affiliation(s)
- Wei Xiao
- Division of Pulmonary Medicine, Department of Internal Medicine, Institute of Integrated Traditional Chinese and Western Medicine, West China Hospital of Sichuan University, No. 37, Guoxue Lane, Wuhou District, Chengdu, 610041, China
- Divison of Pulmonary diseases, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, China
| | - Yi-Long Chen
- West China Biomedical Big Data Center, West China Hospital of Sichuan University, Chengdu, China
- Med-X Center for Informatics, Sichuan University, Chengdu, China
| | - Long-Yi Du
- Division of Pulmonary Medicine, Department of Internal Medicine, Institute of Integrated Traditional Chinese and Western Medicine, West China Hospital of Sichuan University, No. 37, Guoxue Lane, Wuhou District, Chengdu, 610041, China
| | - Jiqiu Wu
- West China Biomedical Big Data Center, West China Hospital of Sichuan University, Chengdu, China
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Zhang Wang
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Bing Mao
- Division of Pulmonary Medicine, Department of Internal Medicine, Institute of Integrated Traditional Chinese and Western Medicine, West China Hospital of Sichuan University, No. 37, Guoxue Lane, Wuhou District, Chengdu, 610041, China
| | - Fu-Qiang Wen
- Divison of Pulmonary diseases, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, China
- Department of Respiratory and Critical Care Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Peter Gerard Gibson
- Priority Research Centre for Healthy Lungs, The University of Newcastle, Newcastle, NSW, Australia
| | - Vanessa M McDonald
- Priority Research Centre for Healthy Lungs, The University of Newcastle, Newcastle, NSW, Australia
| | - Haopeng Yu
- West China Biomedical Big Data Center, West China Hospital of Sichuan University, Chengdu, China
- Med-X Center for Informatics, Sichuan University, Chengdu, China
| | - Juan-Juan Fu
- Division of Pulmonary Medicine, Department of Internal Medicine, Institute of Integrated Traditional Chinese and Western Medicine, West China Hospital of Sichuan University, No. 37, Guoxue Lane, Wuhou District, Chengdu, 610041, China.
- Divison of Pulmonary diseases, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, China.
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18
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Rosenboom I, Thavarasa A, Richardson H, Long MB, Wiehlmann L, Davenport CF, Shoemark A, Chalmers JD, Tümmler B. Sputum metagenomics of people with bronchiectasis. ERJ Open Res 2024; 10:01008-2023. [PMID: 38444657 PMCID: PMC10910388 DOI: 10.1183/23120541.01008-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 01/08/2024] [Indexed: 03/07/2024] Open
Abstract
Background The microbiota in the sputum of people with bronchiectasis has repeatedly been investigated in cohorts of different geographic origin, but so far has not been studied to the species level in comparison to control populations including healthy adults and smokers without lung disease. Methods The microbial metagenome from sputa of 101 European Bronchiectasis Registry (EMBARC) study participants was examined by using whole-genome shotgun sequencing. Results Our analysis of the metagenome of people with bronchiectasis revealed four clusters characterised by a predominance of Haemophilus influenzae, Pseudomonas aeruginosa or polymicrobial communities with varying compositions of nonpathogenic commensals and opportunistic pathogens. The metagenomes of the severely affected patients showed individual profiles characterised by low alpha diversity. Importantly, nearly 50% of patients with severe disease were grouped in a cluster characterised by commensals. Comparisons with the sputum metagenomes of healthy smokers and healthy nonsmokers revealed a gradient of depletion of taxa in bronchiectasis, most often Neisseria subflava, Fusobacterium periodonticum and Eubacterium sulci. Conclusion The gradient of depletion of commensal taxa found in healthy airways is a key feature of bronchiectasis associated with disease severity.
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Affiliation(s)
- Ilona Rosenboom
- Department of Paediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Ajith Thavarasa
- Department of Paediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Hollian Richardson
- Division of Molecular and Clinical Medicine, University of Dundee, Dundee, UK
| | - Merete B. Long
- Division of Molecular and Clinical Medicine, University of Dundee, Dundee, UK
| | - Lutz Wiehlmann
- Research Core Unit Genomics, Hannover Medical School, Hannover, Germany
| | | | - Amelia Shoemark
- Division of Molecular and Clinical Medicine, University of Dundee, Dundee, UK
| | - James D. Chalmers
- Division of Molecular and Clinical Medicine, University of Dundee, Dundee, UK
| | - Burkhard Tümmler
- Department of Paediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), German Centre for Lung Research, Hannover, Germany
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19
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Mac Aogáin M, Tiew PY, Jaggi TK, Narayana JK, Singh S, Hansbro PM, Segal LN, Chotirmall SH. Targeting respiratory microbiomes in COPD and bronchiectasis. Expert Rev Respir Med 2024; 18:111-125. [PMID: 38743428 DOI: 10.1080/17476348.2024.2355155] [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: 01/31/2024] [Accepted: 05/10/2024] [Indexed: 05/16/2024]
Abstract
INTRODUCTION This review summarizes our current understanding of the respiratory microbiome in COPD and Bronchiectasis. We explore the interplay between microbial communities, host immune responses, disease pathology, and treatment outcomes. AREAS COVERED We detail the dynamics of the airway microbiome, its influence on chronic respiratory diseases, and analytical challenges. Relevant articles from PubMed and Medline (January 2010-March 2024) were retrieved and summarized. We examine clinical correlations of the microbiome in COPD and bronchiectasis, assessing how current therapies impact upon it. The potential of emerging immunotherapies, antiinflammatories and antimicrobial strategies is discussed, with focus on the pivotal role of commensal taxa in maintaining respiratory health and the promising avenue of microbiome remodeling for disease management. EXPERT OPINION Given the heterogeneity in microbiome composition and its pivotal role in disease development and progression, a shift toward microbiome-directed therapeutics is appealing. This transition, from traditional 'pathogencentric' diagnostic and treatment modalities to those acknowledging the microbiome, can be enabled by evolving crossdisciplinary platforms which have the potential to accelerate microbiome-based interventions into routine clinical practice. Bridging the gap between comprehensive microbiome analysis and clinical application, however, remains challenging, necessitating continued innovation in research, diagnostics, trials, and therapeutic development pipelines.
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Affiliation(s)
- Micheál Mac Aogáin
- Department of Biochemistry, St. James's Hospital, Dublin, Ireland
- School of Medicine, Trinity College Dublin, Dublin, Ireland
| | - Pei Yee Tiew
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
- Department of Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Tavleen Kaur Jaggi
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | | | - Shivani Singh
- Division of Pulmonary Critical Care & Sleep Medicine, Department of Medicine, New York University School of Medicine, New York, NY, USA
| | - Philip M Hansbro
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, Australia
| | - Leopoldo N Segal
- Division of Pulmonary Critical Care & Sleep Medicine, Department of Medicine, New York University School of Medicine, New York, NY, USA
| | - Sanjay H Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
- Department of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore
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20
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Taylor SL, Rogers GB. The evolving focus of cystic fibrosis microbiome research. J Cyst Fibros 2024; 23:185-186. [PMID: 38604888 DOI: 10.1016/j.jcf.2024.03.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 03/29/2024] [Indexed: 04/13/2024]
Affiliation(s)
- Steven L Taylor
- Microbiome and Host Health Program, South Australian Health and Medical Research Institute, Adelaide, SA, Australia; Infection and Immunity, Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia
| | - Geraint B Rogers
- Microbiome and Host Health Program, South Australian Health and Medical Research Institute, Adelaide, SA, Australia; Infection and Immunity, Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia.
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21
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Xu C, Jiang H, Feng LJ, Jiang MZ, Wang YL, Liu SJ. Christensenella minuta interacts with multiple gut bacteria. Front Microbiol 2024; 15:1301073. [PMID: 38440147 PMCID: PMC10910051 DOI: 10.3389/fmicb.2024.1301073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 01/30/2024] [Indexed: 03/06/2024] Open
Abstract
Introduction Gut microbes form complex networks that significantly influence host health and disease treatment. Interventions with the probiotic bacteria on the gut microbiota have been demonstrated to improve host well-being. As a representative of next-generation probiotics, Christensenella minuta (C. minuta) plays a critical role in regulating energy balance and metabolic homeostasis in human bodies, showing potential in treating metabolic disorders and reducing inflammation. However, interactions of C. minuta with the members of the networked gut microbiota have rarely been explored. Methods In this study, we investigated the impact of C. minuta on fecal microbiota via metagenomic sequencing, focusing on retrieving bacterial strains and coculture assays of C. minuta with associated microbial partners. Results Our results showed that C. minuta intervention significantly reduced the diversity of fecal microorganisms, but specifically enhanced some groups of bacteria, such as Lactobacillaceae. C. minuta selectively enriched bacterial pathways that compensated for its metabolic defects on vitamin B1, B12, serine, and glutamate synthesis. Meanwhile, C. minuta cross-feeds Faecalibacterium prausnitzii and other bacteria via the production of arginine, branched-chain amino acids, fumaric acids and short-chain fatty acids (SCFAs), such as acetic. Both metagenomic data analysis and culture experiments revealed that C. minuta negatively correlated with Klebsiella pneumoniae and 14 other bacterial taxa, while positively correlated with F. prausnitzii. Our results advance our comprehension of C. minuta's in modulating the gut microbial network. Conclusions C. minuta disrupts the composition of the fecal microbiota. This disturbance is manifested through cross-feeding, nutritional competition, and supplementation of its own metabolic deficiencies, resulting in the specific enrichment or inhibition of the growth of certain bacteria. This study will shed light on the application of C. minuta as a probiotic for effective interventions on gut microbiomes and improvement of host health.
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Affiliation(s)
- Chang Xu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - He Jiang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Li-Juan Feng
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Min-Zhi Jiang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Yu-Lin Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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22
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Yang X, Zeng Q, Gou S, Wu Y, Ma X, Zou H, Zhao K. Phenotypic heterogeneity unveils a negative correlation between antibiotic resistance and quorum sensing in Pseudomonas aeruginosa clinical isolates. Front Microbiol 2024; 15:1327675. [PMID: 38410387 PMCID: PMC10895058 DOI: 10.3389/fmicb.2024.1327675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 01/29/2024] [Indexed: 02/28/2024] Open
Abstract
Colonization of Pseudomonas aeruginosa in the lung environments frequently leads to the enrichment of strains displaying enhanced antibiotic resistance and reduced production of quorum-sensing (QS) controlled products. However, the relationship between the emergence of QS deficient variants and antibiotic resistance remains less understood. In this study, 67 P. aeruginosa strains were isolated from the lungs of 14 patients with chronic obstructive pulmonary disease, followed by determining their genetic relationship, QS-related phenotypes and resistance to commonly used antibiotics. The integrity of P. aeruginosa QS system was checked by DNA sequencing. The relationship between the QS system and antibiotic resistance was then assessed by correlation analyses. The function of the LasR protein and bacterial virulence were evaluated through homology modeling and nematode-infection assay. The influence of antibiotic on the development of extracellular protease production ability of P. aeruginosa was tested by an evolutionary experiment. The results showed that P. aeruginosa clinical strains displayed abundant diversity in phenotype and genotype. The production of extracellular proteases was significantly negatively correlated with antibiotic resistance. The strains with enhanced antibiotic resistance also showed a notable overlap with the mutation of lasR gene, which is the core regulatory gene of P. aeruginosa QS system. Molecular docking and Caenorhabditis elegans infection assays further suggested that P. aeruginosa with impaired LasR protein could also have varying pathogenicity. Moreover, in vitro evolution experiments demonstrated that antibiotic-mediated selective pressure, particularly from Levofloxacin contributed to the emergence of extracellular protease-negative strains. Therefore, this study provides evidence for the connection of P. aeruginosa QS system and antibiotic resistance, and holds significance for developing targeted strategies to address antibiotic resistance and improving the management of antibiotic-resistant infections in chronic respiratory diseases.
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Affiliation(s)
- Xiting Yang
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu University, Chengdu, Sichuan, China
| | - Qianglin Zeng
- Affiliated Hospital of Chengdu University, Chengdu University, Chengdu, Sichuan, China
| | - Shiyi Gou
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu University, Chengdu, Sichuan, China
| | - Yi Wu
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu University, Chengdu, Sichuan, China
| | - Xiaoling Ma
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu University, Chengdu, Sichuan, China
| | - Hang Zou
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu University, Chengdu, Sichuan, China
| | - Kelei Zhao
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, School of Pharmacy, Chengdu University, Chengdu, Sichuan, China
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23
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Cohen R, Shteinberg M. Unravelling the "frequent exacerbator" phenotype in cystic fibrosis. Eur Respir J 2024; 63:2400068. [PMID: 38388000 DOI: 10.1183/13993003.00068-2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 01/12/2024] [Indexed: 02/24/2024]
Affiliation(s)
- Raya Cohen
- Pulmonology Institute and CF center, Carmel Medical Center, Haifa, Israel
- The B. Rappaport Faculty of Medicine, Technion - Israel Institute of Technology Haifa, Haifa, Israel
| | - Michal Shteinberg
- Pulmonology Institute and CF center, Carmel Medical Center, Haifa, Israel
- The B. Rappaport Faculty of Medicine, Technion - Israel Institute of Technology Haifa, Haifa, Israel
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24
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Wang J, Ren J, Li X, Wang J, Chang C, Sun L, Sun Y. Symptoms and medical resource utilization of patients with bronchiectasis after SARS-CoV-2 infection. Front Med (Lausanne) 2024; 10:1276763. [PMID: 38264053 PMCID: PMC10804846 DOI: 10.3389/fmed.2023.1276763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Accepted: 12/11/2023] [Indexed: 01/25/2024] Open
Abstract
Background The impact of COVID-19 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on patients with bronchiectasis in terms of symptoms, self-management and medical resource utilization was unknown. Objective To describe the impact of infection by SARS-CoV-2 on fluctuation of symptoms, self-management and medical resource utilization of patients with bronchiectasis during the pandemic of COVID-19. Methods This was a single-center cross-sectional questionnaire study performed in Peking University Third Hospital. An online questionnaire investigation addressing the impact of SARS-CoV-2 infection on respiratory symptoms, self-management and medical resource utilization was conducted among patients with bronchiectasis during the COVID-19 surge in December 2022 in Beijing, China. Results Five hundred patients with bronchiectasis, with 285 (57%) females, and a mean (± S D ) age of 57.9 ± 15.1 years, completed the telephone questionnaire. The reported prevalence of COVID-19 was 81.2% (406/500). Of the 406 COVID-19 patients, 89.2% experienced fever lasting mostly for no more than 3 days, 70.6 and 61.8% reported exacerbated cough and sputum production respectively, and 17.7% reported worsened dyspnea. Notable 37.4% of the patients with COVID-19 experienced symptoms consistent with the definition of an acute exacerbation of bronchiectasis. However, 76.6% (311/406) of the infected patients did not seek medical care but managed at home. Of the patients who visited hospitals, 26.3% (25/95) needed hospitalization and 2.1% (2/95) needed ICU admission. Multi-factors logistic regression analysis showed that younger age (p = 0.012) and not using a bronchodilator agent(p = 0.022) were independently associated with SARS-CoV-2 infection, while a history of exacerbation of bronchiectasis in the past year (p = 0.006) and daily use of expectorants (p = 0.002) were associated with emergency visit and/or hospitalization for patients with bronchiectasis after SARS-CoV-2 infection. Conclusion During the COVID-19 surge, the infection rate of SARS-CoV-2 in patients with bronchiectasis was high, and most of the patients experienced new-onset or exacerbated respiratory symptoms, but only a minority needed medical visits. Our survey results further underscore the importance of patients' disease awareness and self-management skills during a pandemic like COVID-19.
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Affiliation(s)
| | | | | | | | | | - Lina Sun
- Department of Respiratory and Critical Care Medicine, Peking University Third Hospital. Research Center for Chronic Airway Diseases, Peking University Health Science Center, Beijing, China
| | - Yongchang Sun
- Department of Respiratory and Critical Care Medicine, Peking University Third Hospital. Research Center for Chronic Airway Diseases, Peking University Health Science Center, Beijing, China
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25
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Gao YH, Lu HW, Zheng HZ, Cao C, Chu DJ, Fan H, Fan XY, Gu HY, Guan WJ, Jie ZJ, Jin Y, Li W, Li YP, Li YY, Liu L, Liu XD, Luo H, Lv XD, Mo WQ, Song YL, Wang DX, Wang LW, Wang CZ, Xie M, Zhang M, Zheng CX, Mao B, Chotirmall SH, Chalmers JD, Qu JM, Xu JF. A phase 4 multicentre, 2×2 factorial randomised, double-blind, placebo-controlled trial to investigate the efficacy and safety of tobramycin inhalation solution for Pseudomonas aeruginosa eradication in bronchiectasis: ERASE. ERJ Open Res 2024; 10:00938-2023. [PMID: 38410702 PMCID: PMC10895435 DOI: 10.1183/23120541.00938-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 01/05/2024] [Indexed: 02/28/2024] Open
Abstract
Chronic Pseudomonas aeruginosa (PA) infection significantly contributes to morbidity and mortality in bronchiectasis patients. Initiating antibiotics early may lead to the eradication of PA. Here we outline the design of a trial (ERASE; NCT06093191) assessing the efficacy and safety of inhaled tobramycin, alone or with oral ciprofloxacin, in bronchiectasis patients with a new isolation of PA. This multicentre, 2×2 factorial randomised, double-blind, placebo-controlled, parallel-group trial includes a 2-week screening period, a 12-week treatment phase (with a combination of ciprofloxacin or a placebo at initial 2 weeks) and a 24-week follow-up. 364 adults with bronchiectasis and a new PA isolation will be randomly assigned to one of four groups: placebo (inhaled saline and ciprofloxacin placebo twice daily), ciprofloxacin alone (750 mg ciprofloxacin and inhaled saline twice daily), inhaled tobramycin alone (inhaled 300 mg tobramycin and ciprofloxacin placebo twice daily) or a combination of both drugs (inhaled 300 mg tobramycin and 750 mg ciprofloxacin twice daily). The primary objective of this study is to assess the proportion of patients successfully eradicating PA in each group by the end of the study. Efficacy will be evaluated based on the eradication rate of PA at other time points (12, 24 and 36 weeks), the occurrence of exacerbations and hospitalisations, time to first pulmonary exacerbations, patient-reported outcomes, symptom measures, pulmonary function tests and the cost of hospitalisations. To date no randomised trial has evaluated the benefit of different PA eradication strategies in bronchiectasis patients. The ERASE trial will therefore generate crucial data to inform future clinical guidelines.
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Affiliation(s)
- Yong-Hua Gao
- Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
- Institute of Respiratory Medicine, School of Medicine, Tongji University, Shanghai, China
- These authors contributed equally as first authors
| | - Hai-Wen Lu
- Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
- Institute of Respiratory Medicine, School of Medicine, Tongji University, Shanghai, China
- These authors contributed equally as first authors
| | - Hui-Zhen Zheng
- Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
- Institute of Respiratory Medicine, School of Medicine, Tongji University, Shanghai, China
- These authors contributed equally as first authors
| | - Chao Cao
- Department of Respiratory Medicine, The Affiliated Hospital of School of Medicine, Ningbo University, Ningbo, China
| | - De-Jie Chu
- Department of Respiratory Medicine, The Eighth People's Hospital of Shanghai, Shanghai, China
| | - Hong Fan
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Xiao-Yun Fan
- Department of Geriatric Respiratory and Critical Care, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Hong-Yan Gu
- Department of Pulmonary and Critical Care Medicine, The Sixth People's Hospital of Nantong, Nantong, China
| | - Wei-Jie Guan
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zhi-Jun Jie
- Department of Respiratory and Critical Care Medicine, Shanghai Fifth People's Hospital, Fudan University, Shanghai, China
| | - Yang Jin
- Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Pulmonary Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wen Li
- Key Laboratory of Respiratory Disease of Zhejiang Province, Department of Respiratory and Critical Care Medicine, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Yu-Ping Li
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yuan-Yuan Li
- Department of Respiratory Medicine, Branch of National Clinical Research Center for Respiratory Disease, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Lin Liu
- Department of Respiratory Medicine, Guizhou Provincial People Hospital, Guiyang City, China
| | | | - Hong Luo
- Department of Pulmonary and Critical Care Medicine, Second Xiangya Hospital, Central South University, Changsha, China
| | - Xiao-Dong Lv
- Department of Respiration, The First Hospital of Jiaxing, Jiaxing, China
| | - Wei-Qiang Mo
- Department of Respiration, The Second Affiliated Hospital of Jiaxing University, Jiaxing, China
| | - Yuan-Lin Song
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Dao-Xin Wang
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Ling-Wei Wang
- Pulmonary and Critical Care Department, Shenzhen People's Hospital, Shenzhen Institute of Respiratory Diseases, Shenzhen, China
| | - Chang-Zheng Wang
- Department of Respiratory Medicine, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Min Xie
- Department of Respiratory and Critical Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Min Zhang
- Department of Respiratory and Critical Care Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Cui-Xia Zheng
- Department of Respiratory Medicine, Shanghai Yangpu District Central Hospital, Tongji University, Shanghai, China
| | - Bei Mao
- Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
- Institute of Respiratory Medicine, School of Medicine, Tongji University, Shanghai, China
| | - Sanjay H Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Department of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore, Singapore
| | - James D Chalmers
- Division of Molecular and Clinical Medicine, University of Dundee, Dundee, UK
- These authors contributed equally as senior authors
| | - Jie-Ming Qu
- Department of Respiratory and Critical Care Medicine, Ruijin Hospital Affiliated Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Institute of Respiratory Diseases, School of Medicine, Shanghai Jiaotong University, Shanghai, China
- These authors contributed equally as senior authors
| | - Jin-Fu Xu
- Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
- Institute of Respiratory Medicine, School of Medicine, Tongji University, Shanghai, China
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26
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Atto B, Anteneh Y, Bialasiewicz S, Binks MJ, Hashemi M, Hill J, Thornton RB, Westaway J, Marsh RL. The Respiratory Microbiome in Paediatric Chronic Wet Cough: What Is Known and Future Directions. J Clin Med 2023; 13:171. [PMID: 38202177 PMCID: PMC10779485 DOI: 10.3390/jcm13010171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 12/13/2023] [Accepted: 12/17/2023] [Indexed: 01/12/2024] Open
Abstract
Chronic wet cough for longer than 4 weeks is a hallmark of chronic suppurative lung diseases (CSLD), including protracted bacterial bronchitis (PBB), and bronchiectasis in children. Severe lower respiratory infection early in life is a major risk factor of PBB and paediatric bronchiectasis. In these conditions, failure to clear an underlying endobronchial infection is hypothesised to drive ongoing inflammation and progressive tissue damage that culminates in irreversible bronchiectasis. Historically, the microbiology of paediatric chronic wet cough has been defined by culture-based studies focused on the detection and eradication of specific bacterial pathogens. Various 'omics technologies now allow for a more nuanced investigation of respiratory pathobiology and are enabling development of endotype-based models of care. Recent years have seen substantial advances in defining respiratory endotypes among adults with CSLD; however, less is understood about diseases affecting children. In this review, we explore the current understanding of the airway microbiome among children with chronic wet cough related to the PBB-bronchiectasis diagnostic continuum. We explore concepts emerging from the gut-lung axis and multi-omic studies that are expected to influence PBB and bronchiectasis endotyping efforts. We also consider how our evolving understanding of the airway microbiome is translating to new approaches in chronic wet cough diagnostics and treatments.
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Affiliation(s)
- Brianna Atto
- School of Health Sciences, University of Tasmania, Launceston, TAS 7248, Australia;
| | - Yitayal Anteneh
- Child and Maternal Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT 0811, Australia; (Y.A.); (M.J.B.); (J.W.)
| | - Seweryn Bialasiewicz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia;
| | - Michael J. Binks
- Child and Maternal Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT 0811, Australia; (Y.A.); (M.J.B.); (J.W.)
- SAHMRI Women and Kids, South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia
| | - Mostafa Hashemi
- Department of Chemical and Biological Engineering, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada; (M.H.); (J.H.)
| | - Jane Hill
- Department of Chemical and Biological Engineering, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada; (M.H.); (J.H.)
- Spire Health Technology, PBC, Seattle, WA 98195, USA
| | - Ruth B. Thornton
- Centre for Child Health Research, University of Western Australia, Perth, WA 6009, Australia;
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, Perth, WA 6009, Australia
| | - Jacob Westaway
- Child and Maternal Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT 0811, Australia; (Y.A.); (M.J.B.); (J.W.)
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Cairns, QLD 4811, Australia
| | - Robyn L. Marsh
- School of Health Sciences, University of Tasmania, Launceston, TAS 7248, Australia;
- Child and Maternal Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT 0811, Australia; (Y.A.); (M.J.B.); (J.W.)
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Lu D, Li C, Zhong Z, Abudouaini M, Amar A, Wu H, Wei X. Changes in the airway microbiome in patients with bronchiectasis. Medicine (Baltimore) 2023; 102:e36519. [PMID: 38115299 PMCID: PMC10727580 DOI: 10.1097/md.0000000000036519] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 11/06/2023] [Accepted: 11/16/2023] [Indexed: 12/21/2023] Open
Abstract
This study used metagenomic next-generation sequencing (mNGS) technology to explore the changes of the microbial characteristics in the lower respiratory tract in patients with acute exacerbations of bronchiectasis (noncystic fibrosis) to guide clinical treatment and improve patients' quality of life and prognosis. This prospective study included 54 patients with acute exacerbation and 46 clinically stable patients admitted to the Respiratory and Critical Care Medicine Center of the People's Hospital of Xinjiang Uygur Autonomous Region from January 2020 to July 2022. Sputum was subjected to routine microbiological tests, and bronchoalveolar lavage fluid (BALF) samples were subjected to microbiological tests and mNGS of BALF before empirical antibiotic therapy. Serum inflammatory markers (white blood cell count, interleukin-6, procalcitonin, and C-reactive protein) were measured. In addition, we evaluated the pathogen of mNGS and compared the airway microbiome composition of patients with acute exacerbation and control patients. The mean age of our cohort was 56 ± 15.2 years. Eighty-nine patients had positive results by mNGS. There was a significant difference in the detection of viruses between the groups (χ2 = 6.954, P < .01). The fungal species Candida albicans, Pneumocystis jirovecii, and Aspergillus fumigatus were significantly more common in patients with acute exacerbations (χ2 = 5.98, P = .014). The bacterial species Acinetobacter baumannii, Mycobacterium tuberculosis, Haemophilus influenzae, Haemophilus parahaemolyticus, Abiotrophia defectiva, and Micromonas micros were significantly more prevalent in patients with acute exacerbations (χ2 = 4.065, P = .044). The most common bacterial species isolated from the sputum and BALF samples of patients with acute exacerbation was A. baumannii. Chlamydia psittaci was found in 4 patients. In addition, of 77 patients with negative sputum culture, 66 had positive results by mNGS, demonstrating the increased sensitivity and accuracy of mNGS. Patients with acute exacerbation of bronchiectasis tend to have mixed infections in the lower respiratory tract. The frequency of viruses, fungi, and Mycoplasma was higher in these patients. Our findings suggest that mNGS could be used to identify pathogenic microorganisms in these patients, increasing the effectiveness of antibiotic therapy.
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Affiliation(s)
- Dongmei Lu
- Division of Respiratory and Critical Care Medicine, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang Uygur Autonomous Region, China
| | - Chenxi Li
- Department of Oral and Maxillofacial Oncology Surgery, the First Affiliated Hospital of Xinjiang Medical University, School/Hospital of Stomatology, Xinjiang Medical University, Stomatological Research Institute of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang Uygur Autonomous Region, China
| | - Zhiwei Zhong
- Division of Respiratory and Critical Care Medicine, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang Uygur Autonomous Region, China
- Graduate School, Xinjiang Medical University, Urumqi, Xinjiang Uygur Autonomous Region, China
| | - Maidina Abudouaini
- Division of Respiratory and Critical Care Medicine, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang Uygur Autonomous Region, China
- Graduate School, Xinjiang Medical University, Urumqi, Xinjiang Uygur Autonomous Region, China
| | - Aynazar Amar
- Division of Respiratory and Critical Care Medicine, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang Uygur Autonomous Region, China
- Graduate School, Xinjiang Medical University, Urumqi, Xinjiang Uygur Autonomous Region, China
| | - Hongtao Wu
- Division of Respiratory and Critical Care Medicine, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang Uygur Autonomous Region, China
| | - Xuemei Wei
- Division of Respiratory and Critical Care Medicine, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang Uygur Autonomous Region, China
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28
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Zhou W, Guo Z, Chen J, Chen Y, He C, Lu A, Qian L. Airway microbiota correlated with pulmonary exacerbation in primary ciliary dyskinesia patients. Microbiol Spectr 2023; 11:e0221323. [PMID: 37796006 PMCID: PMC10715216 DOI: 10.1128/spectrum.02213-23] [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: 05/25/2023] [Accepted: 08/16/2023] [Indexed: 10/06/2023] Open
Abstract
IMPORTANCE PCD is a rare disease characterized by productive cough, rhinitis, and recurrent infections of the upper and lower airways. Because the diagnosis of PCD is often delayed, patients receive more antibiotics, experience a heavier financial burden, and have a worse prognosis; thus, it is very important to identify the pathogeny and use the correct antibiotic. In this large single-center study of PCD microbiota, we identified an outline of the bacterial microbes from the respiratory tract; furthermore, we found that the microbiota diversity in pediatric sputum was richer than that in pediatric BALF through sequencing, indicating a heterogeneous community structure. The microbiota diversity and richness were lower during pulmonary exacerbation than during pulmonary stabilization. A significantly higher abundance of Pseudomonas had a moderate distinguishing effect for lung exacerbation, which attracted more attention for the study of Pseudomonas therapy in pediatric patients with PCD.
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Affiliation(s)
- Weitao Zhou
- Department of Respiratory Medicine, Children’s Hospital of Fudan University, Shanghai, China
| | - Zhuoyao Guo
- Department of Respiratory Medicine, Children’s Hospital of Fudan University, Shanghai, China
| | - Jinglong Chen
- Department of Respiratory Medicine, Children’s Hospital of Fudan University, Shanghai, China
| | - Yao Chen
- Department of Respiratory Medicine, Children’s Hospital of Fudan University, Shanghai, China
| | - Chen He
- Department of Respiratory Medicine, Children’s Hospital of Fudan University, Shanghai, China
| | - Aizhen Lu
- Department of Respiratory Medicine, Children’s Hospital of Fudan University, Shanghai, China
| | - Liling Qian
- Department of Respiratory Medicine, Children’s Hospital of Fudan University, Shanghai, China
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29
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Choi H, Ryu S, Keir HR, Giam YH, Dicker AJ, Perea L, Richardson H, Huang JTJ, Cant E, Blasi F, Pollock J, Shteinberg M, Finch S, Aliberti S, Sibila O, Shoemark A, Chalmers JD. Inflammatory Molecular Endotypes in Bronchiectasis: A European Multicenter Cohort Study. Am J Respir Crit Care Med 2023; 208:1166-1176. [PMID: 37769155 DOI: 10.1164/rccm.202303-0499oc] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 09/27/2023] [Indexed: 09/30/2023] Open
Abstract
Rationale: Although inflammation and infection are key disease drivers in bronchiectasis, few studies have integrated host inflammatory and microbiome data to guide precision medicine. Objectives: To identify clusters among patients with bronchiectasis on the basis of inflammatory markers and to assess the association between inflammatory endotypes, microbiome characteristics, and exacerbation risk. Methods: Patients with stable bronchiectasis were enrolled at three European centers, and cluster analysis was used to stratify the patients according to the levels of 33 sputum and serum inflammatory markers. Clusters were compared in terms of microbiome composition (16S ribosomal RNA sequencing) and exacerbation risk over a 12-month follow-up. Measurements and Main Results: A total of 199 patients were enrolled (109 [54.8%] female; median age, 69 yr). Four clusters of patients were defined according to their inflammatory profiles: cluster 1, milder neutrophilic inflammation; cluster 2, mixed-neutrophilic and type 2; cluster 3, most severe neutrophilic; and cluster 4, mixed-epithelial and type 2. Lower microbiome diversity was associated with more severe inflammatory clusters (P < 0.001), and β-diversity analysis demonstrated distinct microbiome profiles associated with each inflammatory cluster (P = 0.001). Proteobacteria and Pseudomonas at phylum and genus levels, respectively, were more enriched in clusters 2 and 3 than in clusters 1 and 4. Furthermore, patients in cluster 2 (rate ratio [RR], 1.49; 95% confidence interval [CI], 1.16-1.92) and cluster 3 (RR, 1.61; 95% CI, 1.12-2.32) were at higher risk of exacerbation over a 12-month follow-up compared with cluster 1, even after adjustment for prior exacerbation history. Conclusions: Bronchiectasis inflammatory endotypes are associated with distinct microbiome profiles and future exacerbation risk.
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Affiliation(s)
- Hayoung Choi
- Division of Molecular and Clinical Medicine and
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Internal Medicine, Hallym University Kangnam Sacred Heart Hospital, Seoul, Republic of Korea
| | - Soorack Ryu
- Biostatistical Consulting and Research Lab, Medical Research Collaborating Center, Hanyang University, Seoul, Republic of Korea
| | | | | | | | - Lidia Perea
- Division of Molecular and Clinical Medicine and
| | | | - Jeffrey T J Huang
- Division of Systems Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, United Kingdom
| | - Erin Cant
- Division of Molecular and Clinical Medicine and
| | - Francesco Blasi
- Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | | | - Michal Shteinberg
- Pulmonology Institute and CF Center, Carmel Medical Center and the Technion-Israel Institute of Technology, Haifa, Israel
| | - Simon Finch
- Division of Molecular and Clinical Medicine and
| | - Stefano Aliberti
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
- Respiratory Unit, IRCCS Humanitas Research Hospital, Milan, Italy; and
| | - Oriol Sibila
- Respiratory Department, Hospital Clínic, IDIBAPS, CIBERES, Universitat de Barcelona, Barcelona, Spain
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30
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Cheng WY, Liu WX, Ding Y, Wang G, Shi Y, Chu ESH, Wong S, Sung JJY, Yu J. High Sensitivity of Shotgun Metagenomic Sequencing in Colon Tissue Biopsy by Host DNA Depletion. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:1195-1205. [PMID: 36174929 PMCID: PMC11082407 DOI: 10.1016/j.gpb.2022.09.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 08/29/2022] [Accepted: 09/19/2022] [Indexed: 06/16/2023]
Abstract
The high host genetic background of tissue biopsies hinders the application of shotgun metagenomic sequencing in characterizing the tissue microbiota. We proposed an optimized method that removed host DNA from colon biopsies and examined the effect on metagenomic analysis. Human or mouse colon biopsies were divided into two groups, with one group undergoing host DNA depletion and the other serving as the control. Host DNA was removed through differential lysis of mammalian and bacterial cells before sequencing. The impact of host DNA depletion on microbiota was compared based on phylogenetic diversity analyses and regression analyses. Removing host DNA enhanced bacterial sequencing depth and improved species discovery, increasing bacterial reads by 2.46 ± 0.20 folds while reducing host reads by 6.80% ± 1.06%. Moreover, 2.40 times more of bacterial species were detected after host DNA depletion. This was confirmed from mouse colon tissues, increasing bacterial reads by 5.46 ± 0.42 folds while decreasing host reads by 10.2% ± 0.83%. Similarly, significantly more bacterial species were detected in the mouse colon tissue upon host DNA depletion (P < 0.001). Furthermore, an increased microbial richness was evident in the host DNA-depleted samples compared with non-depleted controls in human colon biopsies and mouse colon tissues (P < 0.001). Our optimized method of host DNA depletion improves the sensitivity of shotgun metagenomic sequencing in bacteria detection in the biopsy, which may yield a more accurate taxonomic profile of the tissue microbiota and identify bacteria that are important for disease initiation or progression.
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Affiliation(s)
- Wing Yin Cheng
- State Key Laboratory of Digestive Disease, Institute of Digestive Disease and The Department of Medicine and Therapeutics, Li Ka Shing Institute of Health Sciences, Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong Special Administrative Region 999077, China
| | - Wei-Xin Liu
- State Key Laboratory of Digestive Disease, Institute of Digestive Disease and The Department of Medicine and Therapeutics, Li Ka Shing Institute of Health Sciences, Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong Special Administrative Region 999077, China
| | - Yanqiang Ding
- State Key Laboratory of Digestive Disease, Institute of Digestive Disease and The Department of Medicine and Therapeutics, Li Ka Shing Institute of Health Sciences, Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong Special Administrative Region 999077, China
| | - Guoping Wang
- State Key Laboratory of Digestive Disease, Institute of Digestive Disease and The Department of Medicine and Therapeutics, Li Ka Shing Institute of Health Sciences, Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong Special Administrative Region 999077, China
| | - Yu Shi
- State Key Laboratory of Digestive Disease, Institute of Digestive Disease and The Department of Medicine and Therapeutics, Li Ka Shing Institute of Health Sciences, Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong Special Administrative Region 999077, China
| | - Eagle S H Chu
- State Key Laboratory of Digestive Disease, Institute of Digestive Disease and The Department of Medicine and Therapeutics, Li Ka Shing Institute of Health Sciences, Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong Special Administrative Region 999077, China
| | - Sunny Wong
- State Key Laboratory of Digestive Disease, Institute of Digestive Disease and The Department of Medicine and Therapeutics, Li Ka Shing Institute of Health Sciences, Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong Special Administrative Region 999077, China
| | - Joseph J Y Sung
- State Key Laboratory of Digestive Disease, Institute of Digestive Disease and The Department of Medicine and Therapeutics, Li Ka Shing Institute of Health Sciences, Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong Special Administrative Region 999077, China; Lee Kong Chian School of Medicine, Nanyang Technology University, Singapore 639798, Singapore
| | - Jun Yu
- State Key Laboratory of Digestive Disease, Institute of Digestive Disease and The Department of Medicine and Therapeutics, Li Ka Shing Institute of Health Sciences, Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong Special Administrative Region 999077, China.
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31
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McShane PJ. Investigation and Management of Bronchiectasis in Nontuberculous Mycobacterial Pulmonary Disease. Clin Chest Med 2023; 44:731-742. [PMID: 37890912 DOI: 10.1016/j.ccm.2023.07.005] [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] [Indexed: 10/29/2023]
Abstract
Patients with nontuberculous mycobacterial (NTM) lung infection require life-long attention to their bronchiectasis, whether or not their NTM infection has been cured. The identification of the cause of bronchiectasis and/or coexisting diseases is important because it may affect therapeutic strategies. Airway clearance is the mainstay of bronchiectasis management. It can include multiple breathing techniques, devices, and mucoactive agents. The exact airway clearance regimen should be customized to each individual patient. Chronic pathogenic airway bacteria, such as Pseudomonas aeruginosa, may warrant consideration of eradication therapy and/or chronic use of maintenance inhaled antibiotics.
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Affiliation(s)
- Pamela J McShane
- Department of Medicine, University of Texas Health Science Center at Tyler, 11937 Hwy 271, Tyler, TX 75708, USA.
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32
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Mugunthan S, Wong LL, Winnerdy FR, Summers S, Bin Ismail MH, Foo YH, Jaggi TK, Meldrum OW, Tiew PY, Chotirmall SH, Rice SA, Phan AT, Kjelleberg S, Seviour T. RNA is a key component of extracellular DNA networks in Pseudomonas aeruginosa biofilms. Nat Commun 2023; 14:7772. [PMID: 38012164 PMCID: PMC10682433 DOI: 10.1038/s41467-023-43533-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 11/13/2023] [Indexed: 11/29/2023] Open
Abstract
The extracellular matrix of bacterial biofilms consists of diverse components including polysaccharides, proteins and DNA. Extracellular RNA (eRNA) can also be present, contributing to the structural integrity of biofilms. However, technical difficulties related to the low stability of RNA make it difficult to understand the precise roles of eRNA in biofilms. Here, we show that eRNA associates with extracellular DNA (eDNA) to form matrix fibres in Pseudomonas aeruginosa biofilms, and the eRNA is enriched in certain bacterial RNA transcripts. Degradation of eRNA associated with eDNA led to a loss of eDNA fibres and biofilm viscoelasticity. Compared with planktonic and biofilm cells, the biofilm matrix was enriched in specific mRNA transcripts, including lasB (encoding elastase). The mRNA transcripts colocalised with eDNA fibres in the biofilm matrix, as shown by single molecule inexpensive FISH microscopy (smiFISH). The lasB mRNA was also observed in eDNA fibres in a clinical sputum sample positive for P. aeruginosa. Thus, our results indicate that the interaction of specific mRNAs with eDNA facilitates the formation of viscoelastic networks in the matrix of Pseudomonas aeruginosa biofilms.
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Affiliation(s)
- Sudarsan Mugunthan
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore
| | - Lan Li Wong
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore
| | | | - Stephen Summers
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore
- St John's Island National Marine Laboratory c/o Tropical Marine Science Institute, National University of Singapore, 119227, Singapore
| | | | - Yong Hwee Foo
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore
- Institute for Digital Molecular Analytics and Science (IDMxS), Nanyang Technological University, Singapore, 636921, Singapore
| | - Tavleen Kaur Jaggi
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 636921, Singapore
| | - Oliver W Meldrum
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 636921, Singapore
| | - Pei Yee Tiew
- Department of Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore, Singapore
| | - Sanjay H Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 636921, Singapore
- Department of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore, Singapore
| | - Scott A Rice
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore
- The iThree Institute, University of Technology Sydney, Sydney, 2007, Australia
- CSIRO, Agriculture and Food, Westmead and Microbiomes for One Systems Health, Canberra, Australia
| | - Anh Tuân Phan
- School of Physical & Mathematical Sciences, Nanyang Technological University, Singapore, 637371, Singapore
| | - Staffan Kjelleberg
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore.
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore.
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, 2052, Australia.
| | - Thomas Seviour
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore.
- Centre for Water Technology (WATEC), Department of Biological and Chemical Engineering, Aarhus University, Aarhus, 8000, Denmark.
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33
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Pan S, Jiang X, Zhang K. WSGMB: weight signed graph neural network for microbial biomarker identification. Brief Bioinform 2023; 25:bbad448. [PMID: 38084923 PMCID: PMC10714318 DOI: 10.1093/bib/bbad448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 11/07/2023] [Accepted: 11/14/2023] [Indexed: 12/18/2023] Open
Abstract
The stability of the gut microenvironment is inextricably linked to human health, with the onset of many diseases accompanied by dysbiosis of the gut microbiota. It has been reported that there are differences in the microbial community composition between patients and healthy individuals, and many microbes are considered potential biomarkers. Accurately identifying these biomarkers can lead to more precise and reliable clinical decision-making. To improve the accuracy of microbial biomarker identification, this study introduces WSGMB, a computational framework that uses the relative abundance of microbial taxa and health status as inputs. This method has two main contributions: (1) viewing the microbial co-occurrence network as a weighted signed graph and applying graph convolutional neural network techniques for graph classification; (2) designing a new architecture to compute the role transitions of each microbial taxon between health and disease networks, thereby identifying disease-related microbial biomarkers. The weighted signed graph neural network enhances the quality of graph embeddings; quantifying the importance of microbes in different co-occurrence networks better identifies those microbes critical to health. Microbes are ranked according to their importance change scores, and when this score exceeds a set threshold, the microbe is considered a biomarker. This framework's identification performance is validated by comparing the biomarkers identified by WSGMB with actual microbial biomarkers associated with specific diseases from public literature databases. The study tests the proposed computational framework using actual microbial community data from colorectal cancer and Crohn's disease samples. It compares it with the most advanced microbial biomarker identification methods. The results show that the WSGMB method outperforms similar approaches in the accuracy of microbial biomarker identification.
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Affiliation(s)
- Shuheng Pan
- Institute of Data and Information, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518005, China
| | - Xinyi Jiang
- Institute of Data and Information, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518005, China
| | - Kai Zhang
- Institute of Data and Information, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518005, China
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34
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Yi XZ, Yang JH, Huang Y, Han XR, Li HM, Cen LJ, Lin ZH, Pan CX, Wang Z, Guan WJ. Differential airway resistome and its correlations with clinical characteristics in Haemophilus- or Pseudomonas-predominant microbial subtypes of bronchiectasis. Respir Res 2023; 24:264. [PMID: 37919749 PMCID: PMC10623730 DOI: 10.1186/s12931-023-02562-8] [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: 06/15/2023] [Accepted: 10/11/2023] [Indexed: 11/04/2023] Open
Abstract
The prevalence and clinical correlates of antibiotic resistance genes (ARGs) in bronchiectasis are not entirely clear. We aimed to profile the ARGs in sputum from adults with bronchiectasis, and explore the association with airway microbiome and disease severity and subtypes. In this longitudinal study, we prospectively collected 118 sputum samples from stable and exacerbation visits of 82 bronchiectasis patients and 19 healthy subjects. We profiled ARGs with shotgun metagenomic sequencing, and linked these to sputum microbiome and clinical characteristics, followed by validation in an international cohort. We compared ARG profiles in bronchiectasis according to disease severity, blood and sputum inflammatory subtypes. Unsupervised clustering revealed a Pseudomonas predominant subgroup (n = 16), Haemophilus predominant subgroup (n = 48), and balanced microbiome subgroup (N = 54). ARGs of multi-drug resistance were over-dominant in the Pseudomonas-predominant subgroup, while ARGs of beta-lactam resistance were most abundant in the Haemophilus-predominant subgroup. Pseudomonas-predominant subgroup yielded the highest ARG diversity and total abundance, while Haemophilus-predominant subgroup and balanced microbiota subgroup were lowest in ARG diversity and total abundance. PBP-1A, ksgA and emrB (multidrug) were most significantly enriched in Haemophilus-predominant subtype. ARGs generally correlated positively with Bronchiectasis Severity Index, fluoroquinolone use, and modified Reiff score. 68.6% of the ARG-clinical correlations could be validated in an independent international cohort. In conclusion, ARGs are differentially associated with the dominant microbiome and clinical characteristics in bronchiectasis.
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Affiliation(s)
- Xin-Zhu Yi
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, 55 Zhongshan Boulevard West, Guangzhou, China
| | - Jun-Hao Yang
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, 55 Zhongshan Boulevard West, Guangzhou, China
| | - Yan Huang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, 151 Yanjiang Road, Guangzhou, Guangdong, China
- Department of Geriatrics, National Key Clinical Specialty, Guangzhou First People's Hospital, South China University of Technology, Guangzhou, China
| | - Xiao-Rong Han
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Hui-Min Li
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, 55 Zhongshan Boulevard West, Guangzhou, China
| | - Lai-Jian Cen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, 151 Yanjiang Road, Guangzhou, Guangdong, China
| | - Zhen-Hong Lin
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, 151 Yanjiang Road, Guangzhou, Guangdong, China
| | - Cui-Xia Pan
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, 151 Yanjiang Road, Guangzhou, Guangdong, China
| | - Zhang Wang
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, 55 Zhongshan Boulevard West, Guangzhou, China.
| | - Wei-Jie Guan
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, 151 Yanjiang Road, Guangzhou, Guangdong, China.
- Department of Thoracic Surgery, Guangzhou Institute of Respiratory Disease, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China.
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Petti M, Farina L. Network medicine for patients' stratification: From single-layer to multi-omics. WIREs Mech Dis 2023; 15:e1623. [PMID: 37323106 DOI: 10.1002/wsbm.1623] [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: 10/14/2022] [Revised: 03/08/2023] [Accepted: 05/30/2023] [Indexed: 06/17/2023]
Abstract
Precision medicine research increasingly relies on the integrated analysis of multiple types of omics. In the era of big data, the large availability of different health-related information represents a great, but at the same time untapped, chance with a potentially fundamental role in the prevention, diagnosis and prognosis of diseases. Computational methods are needed to combine this data to create a comprehensive view of a given disease. Network science can model biomedical data in terms of relationships among molecular players of different nature and has been successfully proposed as a new paradigm for studying human diseases. Patient stratification is an open challenge aimed at identifying subtypes with different disease manifestations, severity, and expected survival time. Several stratification approaches based on high-throughput gene expression measurements have been successfully applied. However, few attempts have been proposed to exploit the integration of various genotypic and phenotypic data to discover novel sub-types or improve the detection of known groupings. This article is categorized under: Cancer > Biomedical Engineering Cancer > Computational Models Cancer > Genetics/Genomics/Epigenetics.
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Affiliation(s)
- Manuela Petti
- Department of Computer, Control and Management Engineering, Sapienza University of Rome, Rome, Italy
| | - Lorenzo Farina
- Department of Computer, Control and Management Engineering, Sapienza University of Rome, Rome, Italy
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Martins M, Keir HR, Chalmers JD. Endotypes in bronchiectasis: moving towards precision medicine. A narrative review. Pulmonology 2023; 29:505-517. [PMID: 37030997 DOI: 10.1016/j.pulmoe.2023.03.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 03/10/2023] [Accepted: 03/13/2023] [Indexed: 04/09/2023] Open
Abstract
Bronchiectasis is a highly complex entity that can be very challenging to investigate and manage. Patients are diverse in their aetiology, symptoms, risk of complications and outcomes. "Endotypes"- subtypes of disease with distinct biological mechanisms, has been proposed as a means of better managing bronchiectasis. This review discusses the emerging field of endotyping in bronchiectasis. We searched PubMed and Google Scholar for randomized controlled trials (RCT), observational studies, systematic reviews and meta-analysis published from inception until October 2022, using the terms: "bronchiectasis", "endotypes", "biomarkers", "microbiome" and "inflammation". Exclusion criteria included commentaries and non-English language articles as well as case reports. Duplicate articles between databases were initially identified and appropriately excluded. Studies identified suggest that it is possible to classify bronchiectasis patients into multiple endotypes deriving from their co-morbidities or underlying causes to complex infective or inflammatory endotypes. Specific biomarkers closely related to a particular endotype might be used to determine response to treatment and prognosis. The most clearly defined examples of endotypes in bronchiectasis are the underlying causes such as immunodeficiency or allergic bronchopulmonary aspergillosis where the underlying causes are clearly related to a specific treatment. The heterogeneity of bronchiectasis extends, however, far beyond aetiology and it is now possible to identify subtypes of disease based on inflammatory mechanisms such airway neutrophil extracellular traps and eosinophilia. In future biomarkers of host response and infection, including the microbiome may be useful to guide treatments and to increase the success of randomized trials. Advances in the understanding the inflammatory pathways, microbiome, and genetics in bronchiectasis are key to move towards a personalized medicine in bronchiectasis.
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Affiliation(s)
- M Martins
- Pulmonology Department, Centro Hospitalar Universitário de São João, Porto, Portugal.
| | - H R Keir
- Division of Molecular and Clinical Medicine, Ninewells Hospital and Medical School, Dundee, DD1 9SY, Scotland, United Kinkdom
| | - J D Chalmers
- Division of Molecular and Clinical Medicine, Ninewells Hospital and Medical School, Dundee, DD1 9SY, Scotland, United Kinkdom
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Csader S, Chen X, Leung H, Männistö V, Pentikäinen H, Tauriainen MM, Savonen K, El-Nezami H, Schwab U, Panagiotou G. Gut ecological networks reveal associations between bacteria, exercise, and clinical profile in non-alcoholic fatty liver disease patients. mSystems 2023; 8:e0022423. [PMID: 37606372 PMCID: PMC10654067 DOI: 10.1128/msystems.00224-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 07/15/2023] [Indexed: 08/23/2023] Open
Abstract
IMPORTANCE Our study is applying a community-based approach to examine the influence of exercise on gut microbiota (GM) and discover GM structures linked with NAFLD improvements during exercise. The majority of microbiome research has focused on finding specific species that may contribute to the development of human diseases. However, we believe that complex diseases, such as NAFLD, would be more efficiently treated using consortia of species, given that bacterial functionality is based not only on its own genetic information but also on the interaction with other microorganisms. Our results revealed that exercise significantly changes the GM interaction and that structural alterations can be linked with improvements in intrahepatic lipid content and metabolic functions. We believe that the identification of these characteristics in the GM enhances the development of exercise treatment for NAFLD and will attract general interest in this field.
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Affiliation(s)
- Susanne Csader
- Department of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Xiuqiang Chen
- Microbiome Dynamics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Howell Leung
- Microbiome Dynamics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
| | - Ville Männistö
- Departments of Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | | | - Milla-Maria Tauriainen
- Department of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
- Departments of Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Kai Savonen
- Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
- Department of Clinical Physiology and Nuclear Medicine, Kuopio University Hospital, Kuopio, Finland
| | - Hani El-Nezami
- Department of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
- University of Hong Kong School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Ursula Schwab
- Department of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
- Department of Medicine, Endocrinology and Clinical Nutrition, Kuopio University Hospital, Kuopio, Finland
| | - Gianni Panagiotou
- Microbiome Dynamics, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Jena, Germany
- Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
- Department of Medicine, The University of Hong Kong, Hong Kong SAR, China
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38
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Li P, Liang X, Shi R, Wang Y, Han S, Zhang Y. Unraveling the functional instability of bacterial consortia in crude oil degradation via integrated co-occurrence networks. Front Microbiol 2023; 14:1270916. [PMID: 37901814 PMCID: PMC10602786 DOI: 10.3389/fmicb.2023.1270916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 09/20/2023] [Indexed: 10/31/2023] Open
Abstract
Introduction Soil ecosystems are threatened by crude oil contamination, requiring effective microbial remediation. However, our understanding of the key microbial taxa within the community, their interactions impacting crude oil degradation, and the stability of microbial functionality in oil degradation remain limited. Methods To better understand these key points, we enriched a crude oil-degrading bacterial consortium generation 1 (G1) from contaminated soil and conducted three successive transfer passages (G2, G3, and G4). Integrated Co-occurrence Networks method was used to analyze microbial species correlation with crude oil components across G1-G4. Results and discussion In this study, G1 achieved a total petroleum hydrocarbon (TPH) degradation rate of 32.29% within 10 days. Through three successive transfer passages, G2-G4 consortia were established, resulting in a gradual decrease in TPH degradation to 23.14% at the same time. Specifically, saturated hydrocarbon degradation rates ranged from 18.32% to 14.17% among G1-G4, and only G1 exhibited significant aromatic hydrocarbon degradation (15.59%). Functional annotation based on PICRUSt2 and FAPROTAX showed that functional potential of hydrocarbons degradation diminished across generations. These results demonstrated the functional instability of the bacterial consortium in crude oil degradation. The relative abundance of the Dietzia genus showed the highest positive correlation with the degradation efficiency of TPH and saturated hydrocarbons (19.48, 18.38, p < 0.05, respectively), Bacillus genus demonstrated the highest positive correlation (21.94, p < 0.05) with the efficiency of aromatic hydrocarbon degradation. The key scores of Dietzia genus decreased in successive generations. A significant positive correlation (16.56, p < 0.05) was observed between the Bacillus and Mycetocola genera exclusively in the G1 generation. The decline in crude oil degradation function during transfers was closely related to changes in the relative abundance of key genera such as Dietzia and Bacillus as well as their interactions with other genera including Mycetocola genus. Our study identified key bacterial genera involved in crude oil remediation microbiome construction, providing a theoretical basis for the next step in the construction of the oil pollution remediation microbiome.
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Affiliation(s)
- Ping Li
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaolong Liang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Rongjiu Shi
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Yongfeng Wang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Siqin Han
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Ying Zhang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
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Gao J, Yi X, Wang Z. The application of multi-omics in the respiratory microbiome: Progresses, challenges and promises. Comput Struct Biotechnol J 2023; 21:4933-4943. [PMID: 37867968 PMCID: PMC10585227 DOI: 10.1016/j.csbj.2023.10.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 10/10/2023] [Accepted: 10/10/2023] [Indexed: 10/24/2023] Open
Abstract
The study of the respiratory microbiome has entered a multi-omic era. Through integrating different omic data types such as metagenome, metatranscriptome, metaproteome, metabolome, culturome and radiome surveyed from respiratory specimens, holistic insights can be gained on the lung microbiome and its interaction with host immunity and inflammation in respiratory diseases. The power of multi-omics have moved the field forward from associative assessment of microbiome alterations to causative understanding of the lung microbiome in the pathogenesis of chronic, acute and other types of respiratory diseases. However, the application of multi-omics in respiratory microbiome remains with unique challenges from sample processing, data integration, and downstream validation. In this review, we first introduce the respiratory sample types and omic data types applicable to studying the respiratory microbiome. We next describe approaches for multi-omic integration, focusing on dimensionality reduction, multi-omic association and prediction. We then summarize progresses in the application of multi-omics to studying the microbiome in respiratory diseases. We finally discuss current challenges and share our thoughts on future promises in the field.
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Affiliation(s)
- Jingyuan Gao
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, Guangzhou, Guangdong Province, China
| | - Xinzhu Yi
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, Guangzhou, Guangdong Province, China
| | - Zhang Wang
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, Guangzhou, Guangdong Province, China
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Lee H, Kim SH, Lee SK, Choi H, Chung SJ, Park DW, Park TS, Moon JY, Kim TH, Kim SH, Sohn JW, Yoon HJ. Impact of air pollution on healthcare utilization in patients with bronchiectasis. Front Med (Lausanne) 2023; 10:1233516. [PMID: 37886356 PMCID: PMC10598766 DOI: 10.3389/fmed.2023.1233516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 09/05/2023] [Indexed: 10/28/2023] Open
Abstract
Introduction Air pollutants are increasingly recognized to affect long-term outcomes in patients with bronchiectasis. We aimed to figure out the association between air pollutants and the risk of healthcare utilization in patients with bronchiectasis. Methods Data for 1,029 subjects with bronchiectasis in Seoul were extracted. The air pollutants included particulate matter of 10 μm or less in diameter (PM10), particulate matter of 2.5 μm or less in diameter (PM2.5), sulfur dioxide (SO2), carbon monoxide (CO), ozone (O3), and nitrogen dioxide (NO2). The outcome was all-cause healthcare uses, defined as outpatient visit, emergency department visit, or hospitalization. The concentration-response curves between each air pollutant and relative risks for healthcare utilization were obtained. Results There were significant correlations between air pollutant concentrations and the risk of healthcare utilization, particularly for PM10, NO2, SO2, and CO. This risk was observed even at concentrations below the recommended safe thresholds for the general population. The slopes for the association between PM10 and NO2 and the risk of healthcare use showed a logarithmic growth pattern, with the steepest increase up to 30 μg/m3 and 0.030 parts per million (ppm), respectively. The curves for SO2 and CO showed an inverted U-shaped pattern, with a peak at 0.0045 ppm and a slow upward curve, respectively. No specific trends were observed for PM2.5 and O3 and the risk of healthcare use. Discussion Increased concentrations of PM10, NO2, SO2, and CO were associated with increased healthcare utilization in patients with bronchiectasis. For patients with bronchiectasis, there were no safety thresholds for those air pollutants, and even low levels of air pollutant exposure can negatively impact bronchiectasis outcomes.
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Affiliation(s)
- Hyun Lee
- Division of Pulmonary Medicine and Allergy, Department of Internal Medicine, Hanyang University College of Medicine, Seoul, Republic of Korea
| | - Sang Hyuk Kim
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Internal Medicine, Dongguk University Gyeongju Hospital, Dongguk University College of Medicine, Gyeongju, Republic of Korea
| | - Sun-Kyung Lee
- Division of Pulmonary Medicine and Allergy, Department of Internal Medicine, Hanyang University College of Medicine, Seoul, Republic of Korea
- Department of Mathematics, College of Natural Sciences, Hanyang University, Seoul, Republic of Korea
| | - Hayoung Choi
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Internal Medicine, Hallym University Kangnam Sacred Heart Hospital, Hallym University College of Medicine, Seoul, Republic of Korea
| | - Sung Jun Chung
- Division of Pulmonary Medicine and Allergy, Department of Internal Medicine, Hanyang University College of Medicine, Seoul, Republic of Korea
| | - Dong Won Park
- Division of Pulmonary Medicine and Allergy, Department of Internal Medicine, Hanyang University College of Medicine, Seoul, Republic of Korea
| | - Tai Sun Park
- Division of Pulmonary Medicine and Allergy, Department of Internal Medicine, Hanyang University College of Medicine, Seoul, Republic of Korea
| | - Ji-Yong Moon
- Division of Pulmonary Medicine and Allergy, Department of Internal Medicine, Hanyang University College of Medicine, Seoul, Republic of Korea
| | - Tae-Hyung Kim
- Division of Pulmonary Medicine and Allergy, Department of Internal Medicine, Hanyang University College of Medicine, Seoul, Republic of Korea
| | - Sang-Heon Kim
- Division of Pulmonary Medicine and Allergy, Department of Internal Medicine, Hanyang University College of Medicine, Seoul, Republic of Korea
| | - Jang Won Sohn
- Division of Pulmonary Medicine and Allergy, Department of Internal Medicine, Hanyang University College of Medicine, Seoul, Republic of Korea
| | - Ho Joo Yoon
- Division of Pulmonary Medicine and Allergy, Department of Internal Medicine, Hanyang University College of Medicine, Seoul, Republic of Korea
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Flahaut M, Leprohon P, Pham NP, Gingras H, Bourbeau J, Papadopoulou B, Maltais F, Ouellette M. Distinctive features of the oropharyngeal microbiome in Inuit of Nunavik and correlations of mild to moderate bronchial obstruction with dysbiosis. Sci Rep 2023; 13:16622. [PMID: 37789055 PMCID: PMC10547696 DOI: 10.1038/s41598-023-43821-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 09/28/2023] [Indexed: 10/05/2023] Open
Abstract
Inuit of Nunavik are coping with living conditions that can influence respiratory health. Our objective was to investigate associations between respiratory health in Inuit communities and their airway microbiome. Oropharyngeal samples were collected during the Qanuilirpitaa? 2017 Inuit Health Survey and subjected to metagenomic analyses. Participants were assigned to a bronchial obstruction group or a control group based on their clinical history and their pulmonary function, as monitored by spirometry. The Inuit microbiota composition was found to be distinct from other studied populations. Within the Inuit microbiota, differences in diversity measures tend to distinguish the two groups. Bacterial taxa found to be more abundant in the control group included candidate probiotic strains, while those enriched in the bronchial obstruction group included opportunistic pathogens. Crossing taxa affiliation method and machine learning consolidated our finding of distinct core microbiomes between the two groups. More microbial metabolic pathways were enriched in the control participants and these were often involved in vitamin and anti-inflammatory metabolism, while a link could be established between the enriched pathways in the disease group and inflammation. Overall, our results suggest a link between microbial abundance, interactions and metabolic activities and respiratory health in the Inuit population.
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Affiliation(s)
- Mathilde Flahaut
- Centre de Recherche en Infectiologie and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec City, QC, Canada
| | - Philippe Leprohon
- Centre de Recherche en Infectiologie and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec City, QC, Canada
| | - Nguyen Phuong Pham
- Centre de Recherche en Infectiologie and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec City, QC, Canada
| | - Hélène Gingras
- Centre de Recherche en Infectiologie and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec City, QC, Canada
| | - Jean Bourbeau
- Department of Medicine, Division of Respiratory Medicine, McGill University Health Center, Montréal, QC, Canada
| | - Barbara Papadopoulou
- Centre de Recherche en Infectiologie and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec City, QC, Canada
| | - François Maltais
- Groupe de Recherche en Santé Respiratoire, Centre de Recherche de L'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Faculté de Médecine, Université Laval, Québec City, QC, Canada
| | - Marc Ouellette
- Centre de Recherche en Infectiologie and Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec City, QC, Canada.
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Chotirmall SH, Abisheganaden JA, Chew FT, See KC, Cove ME, Goh AEN, Koh MS, Loh CH, Phua J, Lim AYH. Letter from Singapore: Thirty years of progress in clinical care and research. Respirology 2023; 28:966-968. [PMID: 37648425 DOI: 10.1111/resp.14584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 08/02/2023] [Indexed: 09/01/2023]
Affiliation(s)
- Sanjay H Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Department of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore, Singapore
| | - John A Abisheganaden
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Department of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore, Singapore
| | - Fook Tim Chew
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Kay Choong See
- Division of Respiratory and Critical Care Medicine, Department of Medicine, National University Hospital, Singapore, Singapore
- National University Cancer Institute, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Matthew E Cove
- Division of Respiratory and Critical Care Medicine, Department of Medicine, National University Hospital, Singapore, Singapore
| | - Anne E N Goh
- Department of Paediatrics, KK Women's and Children's Hospital, Singapore, Singapore
| | - Mariko Siyue Koh
- Department of Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Chee Hong Loh
- Department of Respiratory and Critical Care Medicine, Changi General Hospital, Singapore, Singapore
| | - Jason Phua
- Division of Respiratory and Critical Care Medicine, Department of Medicine, National University Hospital, Singapore, Singapore
- FAST and Chronic Programmes, Alexandra Hospital, National University Health System, Singapore, Singapore
| | - Albert Y H Lim
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Department of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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Scialò F, Vitale M, D'Agnano V, Mariniello DF, Perrotta F, Castaldo A, Campbell SFM, Pastore L, Cazzola M, Bianco A. Lung Microbiome as a Treatable Trait in Chronic Respiratory Disorders. Lung 2023; 201:455-466. [PMID: 37752217 DOI: 10.1007/s00408-023-00645-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 08/29/2023] [Indexed: 09/28/2023]
Abstract
Once thought to be a sterile environment, it is now established that lungs are populated by various microorganisms that participate in maintaining lung function and play an important role in shaping lung immune surveillance. Although our comprehension of the molecular and metabolic interactions between microbes and lung cells is still in its infancy, any event causing a persistent qualitative or quantitative variation in the composition of lung microbiome, termed "dysbiosis", has been virtually associated with many respiratory diseases. A deep understanding of the composition and function of the "healthy" lung microbiota and how dysbiosis can cause or participate in disease progression will be pivotal in finding specific therapies aimed at preventing diseases and restoring lung function. Here, we review lung microbiome dysbiosis in different lung pathologies and the mechanisms by which these bacteria can cause or contribute to the severity of the disease. Furthermore, we describe how different respiratory disorders can be caused by the same pathogen, and that the real pathogenetic mechanism is not only dependent by the presence and amount of the main pathogen but can be shaped by the interaction it can build with other bacteria, fungi, and viruses present in the lung. Understanding the nature of this bacteria crosstalk could further our understanding of each respiratory disease leading to the development of new therapeutic strategies.
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Affiliation(s)
- Filippo Scialò
- Department of Translational Medical Science, University of Campania Luigi Vanvitelli, Naples, Italy
- CEINGE-Biotecnologie Avanzate-Franco Salvatore, Naples, Italy
| | - Maria Vitale
- CEINGE-Biotecnologie Avanzate-Franco Salvatore, Naples, Italy
| | - Vito D'Agnano
- Department of Translational Medical Science, University of Campania Luigi Vanvitelli, Naples, Italy
| | | | - Fabio Perrotta
- Department of Translational Medical Science, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Alice Castaldo
- Department of Translational Medical Sciences, University of Naples Federico II, Naples, Italy
| | - Susan F M Campbell
- Department of Translational Medical Science, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Lucio Pastore
- CEINGE-Biotecnologie Avanzate-Franco Salvatore, Naples, Italy
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
| | - Mario Cazzola
- Dipartimento di Medicina Sperimentale, University of Rome "Tor Vergata", Rome, Italy
| | - Andrea Bianco
- Department of Translational Medical Science, University of Campania Luigi Vanvitelli, Naples, Italy.
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Pérez-Cobas AE, Ginevra C, Rusniok C, Jarraud S, Buchrieser C. The respiratory tract microbiome, the pathogen load, and clinical interventions define severity of bacterial pneumonia. Cell Rep Med 2023; 4:101167. [PMID: 37633274 PMCID: PMC10518590 DOI: 10.1016/j.xcrm.2023.101167] [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: 12/05/2022] [Revised: 06/18/2023] [Accepted: 08/02/2023] [Indexed: 08/28/2023]
Abstract
Bacterial pneumonia is a considerable problem worldwide. Here, we follow the inter-kingdom respiratory tract microbiome (RTM) of a unique cohort of 38 hospitalized patients (n = 97 samples) with pneumonia caused by Legionella pneumophila. The RTM composition is characterized by diversity drops early in hospitalization and ecological species replacement. RTMs with the highest bacterial and fungal loads show low diversity and pathogen enrichment, suggesting high biomass as a biomarker for secondary and/or co-infections. The RTM structure is defined by a "commensal" cluster associated with a healthy RTM and a "pathogen" enriched one, suggesting that the cluster equilibrium drives the microbiome to recovery or dysbiosis. Legionella biomass correlates with disease severity and co-morbidities, while clinical interventions influence the RTM dynamics. Fungi, archaea, and protozoa seem to contribute to progress of pneumonia. Thus, the interplay of the RTM equilibrium, the pathogen load dynamics, and clinical interventions play a critical role in patient recovery.
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Affiliation(s)
- Ana Elena Pérez-Cobas
- Institut Pasteur, Université Paris Cité, Biologie des Bactéries Intracellulaires, Paris, France; CNRS UMR 6047, 75724 Paris, France.
| | - Christophe Ginevra
- Hospices Civils de Lyon, Centre National de Référence des Légionelles, Bron, France; Centre International de Recherche en Infectiologie, Université Lyon 1, UMR CNRS 5308, U1111 Inserm, École Normale Supérieure de Lyon, Lyon, France
| | - Christophe Rusniok
- Institut Pasteur, Université Paris Cité, Biologie des Bactéries Intracellulaires, Paris, France; CNRS UMR 6047, 75724 Paris, France
| | - Sophie Jarraud
- Hospices Civils de Lyon, Centre National de Référence des Légionelles, Bron, France; Centre International de Recherche en Infectiologie, Université Lyon 1, UMR CNRS 5308, U1111 Inserm, École Normale Supérieure de Lyon, Lyon, France
| | - Carmen Buchrieser
- Institut Pasteur, Université Paris Cité, Biologie des Bactéries Intracellulaires, Paris, France; CNRS UMR 6047, 75724 Paris, France.
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Zhu R, Hong X, Zhang D, Xiao Y, Xu Q, Wu B, Guo J, Han X, Yang Q, Zhao Y, Wu W. Application of metagenomic sequencing of drainage fluid in rapid and accurate diagnosis of postoperative intra-abdominal infection: a diagnostic study. Int J Surg 2023; 109:2624-2630. [PMID: 37288562 PMCID: PMC10498887 DOI: 10.1097/js9.0000000000000500] [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: 12/06/2022] [Accepted: 05/11/2023] [Indexed: 06/09/2023]
Abstract
BACKGROUND Postoperative intra-abdominal infection (PIAI) is one of the most serious complications of abdominal surgery, increasing the risk of postoperative morbidity and mortality and prolonging hospital stay. Rapid diagnosis of PIAI is of great clinical value. Unfortunately, the current diagnostic methods of PIAI are not fast and accurate enough. METHODS The authors performed an exploratory study to establish a rapid and accurate diagnostic method of PIAI. The authors explored the turnaround time and accuracy of metagenomic next-generation sequencing (mNGS) in diagnosing PIAI. Patients who underwent elective abdominal surgery and routine abdominal drainage with suspected PIAI were enroled in the study. The fresh midstream abdominal drainage fluid was collected for mNGS and culturing. RESULTS The authors found that the median sample-to-answer turnaround time of mNGS was dramatically decreased than that of culture-based methods (<24 h vs. 59.5-111 h). The detection coverage of mNGS was much broader than culture-based methods. The authors found 26 species from 15 genera could only be detected by mNGS. The accuracy of mNGS was not inferior to culture-based methods in the 8 most common pathogens detected from abdominal drainage fluid (sensitivity ranged from 75 to 100%, specificity ranged from 83.3 to 100%, and kappa values were higher than 0.5). Moreover, the composition of the microbial spectrum established by mNGS varied between upper and lower gastrointestinal surgery, enhancing the understanding of PIAI pathogenesis. CONCLUSION This study preliminarily revealed the clinical value of mNGS in the rapid diagnosis of PIAI and provided a rationale for further research.
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Affiliation(s)
- Ruizhe Zhu
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases
| | - Xiafei Hong
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases
| | - Dong Zhang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yi Xiao
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases
| | - Qiang Xu
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases
| | - Bin Wu
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases
| | - Junchao Guo
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases
| | - Xianlin Han
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases
| | - Qiwen Yang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yupei Zhao
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases
| | - Wenming Wu
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases
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Pérez-Cobas AE, Rodríguez-Beltrán J, Baquero F, Coque TM. Ecology of the respiratory tract microbiome. Trends Microbiol 2023; 31:972-984. [PMID: 37173205 DOI: 10.1016/j.tim.2023.04.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 04/05/2023] [Accepted: 04/13/2023] [Indexed: 05/15/2023]
Abstract
A thriving multi-kingdom microbial ecosystem inhabits the respiratory tract: the respiratory tract microbiome (RTM). In recent years, the contribution of the RTM to human health has become a crucial research aspect. However, research into the key ecological processes, such as robustness, resilience, and microbial interaction networks, has only recently started. This review leans on an ecological framework to interpret the human RTM and determine how the ecosystem functions and assembles. Specifically, the review illustrates the ecological RTM models and discusses microbiome establishment, community structure, diversity stability, and critical microbial interactions. Lastly, the review outlines the RTM responses to ecological disturbances, as well as the promising approaches for restoring ecological balance.
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Affiliation(s)
- Ana Elena Pérez-Cobas
- Department of Microbiology, Ramón y Cajal Institute for Health Research (IRYCIS), Ramón y Cajal University Hospital, Madrid, Spain; CIBER in Infectious Diseases (CIBERINFEC), Madrid, Spain.
| | - Jerónimo Rodríguez-Beltrán
- Department of Microbiology, Ramón y Cajal Institute for Health Research (IRYCIS), Ramón y Cajal University Hospital, Madrid, Spain; CIBER in Infectious Diseases (CIBERINFEC), Madrid, Spain
| | - Fernando Baquero
- Department of Microbiology, Ramón y Cajal Institute for Health Research (IRYCIS), Ramón y Cajal University Hospital, Madrid, Spain; CIBER in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Teresa M Coque
- Department of Microbiology, Ramón y Cajal Institute for Health Research (IRYCIS), Ramón y Cajal University Hospital, Madrid, Spain; CIBER in Infectious Diseases (CIBERINFEC), Madrid, Spain
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Hong H, Wang L, Qi Y. Characteristics of the oropharyngeal microbiota among infants with pneumonia and their effects on immune response and subsequent respiratory morbidity. Eur J Pediatr 2023; 182:3649-3658. [PMID: 37261548 DOI: 10.1007/s00431-023-05037-6] [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: 05/15/2022] [Revised: 04/14/2023] [Accepted: 05/23/2023] [Indexed: 06/02/2023]
Abstract
Changes in airway microbiota among infants with pneumonia and their impact on subsequent respiratory health are largely unknown. The present study aimed to analyze the oropharyngeal microbiota of infants with pneumonia and to explore the impact of disturbances of the microbiota on disease severity and long-term respiratory morbidities. The oropharyngeal microbiome was characterized using 16S ribosomal RNA-based sequencing, while serum immune mediators were assessed using cytometric bead array, and invariant natural killer T (iNKT) cells were detected using flow cytometry in infants with pneumonia < 6 months of age. Patients were followed up to 3 years of age, and clinical and respiratory morbidity data were collected. A total of 106 infants with pneumonia were enrolled in this study. Diversity of the respiratory microbiota was inversely correlated with the severity of pneumonia and length of hospitalization. Patients who experienced wheezing during pneumonia exhibited lower percentages of total iNKT cells, CD8-positive ( +), and CD4-CD8- subsets, and higher CD4 + subsets than those without. The relative abundances of Prevotella and Veillonella species were lower in patients with severe pneumonia. The abundance of Veillonella was higher in patients who experienced wheezing during pneumonia and in those with subsequent recurrent wheezing than in those without wheezing. The relative abundance and total counts of Bifidobacterium, Lactobacillus, and Neisseria were higher in patients who did not experience subsequent recurrent wheezing. CONCLUSIONS Diversity of the respiratory microbiota was inversely associated with pneumonia severity, and the percentage of iNKT cells was associated with wheezing during pneumonia. Several species may be associated with subsequent respiratory morbidities and warrant further investigation. WHAT IS KNOWN • Early life airway microbiota symbiosis affects the severity of respiratory infection and the risk for the development of asthma. • Changes in airway microbiota among infants with pneumonia and their impact on subsequent respiratory health are largely unknown. WHAT IS NEW • The diversity of the airway microbiome was inversely associated with the severity of pneumonia and length of hospitalization. • The abundance of Veillonella was higher in patients who experienced wheezing during pneumonia and in those with subsequent recurrent wheezing.
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Affiliation(s)
- Huihui Hong
- Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Libo Wang
- Department of Respiratory Disease, Children's Hospital of Fudan University, National Children's Medical Center, No. 399 Wanyuan Road, Shanghai, 201102, China
| | - Yuanyuan Qi
- Department of Respiratory Disease, Children's Hospital of Fudan University, National Children's Medical Center, No. 399 Wanyuan Road, Shanghai, 201102, China.
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Yuan X, Xie L, Shi Z, Zhou M. Application of mNGS in the study of pulmonary microbiome in pneumoconiosis complicated with pulmonary infection patients and exploration of potential biomarkers. Front Cell Infect Microbiol 2023; 13:1200157. [PMID: 37545858 PMCID: PMC10403237 DOI: 10.3389/fcimb.2023.1200157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 06/26/2023] [Indexed: 08/08/2023] Open
Abstract
Background Pneumoconiosis patients have a high prevalence of pulmonary infections, which can complicate diagnosis and treatment. And there is no comprehensive study of the microbiome of patients with pneumoconiosis. The application of metagenomic next-generation sequencing (mNGS) fills the gap to some extent by analyzing the lung microbiota of pneumoconiosis population while achieving accurate diagnosis. Methods We retrospectively analyzed 44 patients with suspected pneumoconiosis complicated with pulmonary infection between Jan 2020 and Nov 2022. Bronchoalveolar lavage fluid (BALF) specimens from 44 patients were collected and tested using the mNGS technology. Results Among the lung microbiome of pneumoconiosis patients with complicated pulmonary infection (P group), the most frequently detected bacteria and fungi at the genus level were Streptococcus and Aspergillus, at the species level were Streptococcus pneumoniae and Aspergillus flavus, respectively, and the most frequently detected DNA virus was Human gammaherpesvirus 4. There was no significant difference in α diversity between the P group and the non-pneumoconiosis patients complicated with pulmonary infection group (Non-P group) in pulmonary flora, while P< 0.01 for β diversity analysis, and the differential species between the two groups were Mycobacterium colombiense and Fusobacterium nucleatum. In addition, we monitored a high distribution of Malassezia and Pneumocystis in the P group, while herpes virus was detected in the majority of samples. Conclusions Overall, we not only revealed a comprehensive lung microbiome profile of pneumoconiosis patients, but also compared the differences between their microbiome and that of non-pneumoconiosis complicated with pulmonary infection patients. This provides a good basis for a better understanding of the relationship between pneumoconiosis and microorganisms, and for the search of potential biomarkers.
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Affiliation(s)
- Xingya Yuan
- Department of Respiratory Medicine, West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Linshen Xie
- Department of Respiratory Medicine, West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | | | - Min Zhou
- Department of Respiratory Medicine, West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
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Rosenboom I, Pust MM, Pirr S, Bakker A, Willers M, Davenport CF, Wiehlmann L, Viemann D, Tümmler B. Longitudinal development of the airway metagenome of preterm very low birth weight infants during the first two years of life. ISME COMMUNICATIONS 2023; 3:75. [PMID: 37474785 PMCID: PMC10359316 DOI: 10.1038/s43705-023-00285-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 07/06/2023] [Accepted: 07/12/2023] [Indexed: 07/22/2023]
Abstract
Preterm birth is accompanied with many complications and requires severe therapeutic regimens at the neonatal intensive care unit. The influence of the above-mentioned factors on the premature-born infants' respiratory metagenome or more generally its maturation is unknown. We therefore applied shotgun metagenome sequencing of oropharyngeal swabs to analyze the airway metagenome development of 24 preterm infants from one week postpartum to 15 months of age. Beta diversity analysis revealed a distinct clustering of airway microbial communities from hospitalized preterms and samples after hospital discharge. At nine and 15 months of age, the preterm infants lost their hospital-acquired individual metagenome signatures towards a common taxonomic structure. However, ecological network analysis and Random Forest classification of cross-sectional data revealed that by this age the preterm infants did not succeed in establishing the uniform and stable bacterial community structures that are characteristic for healthy full-term infants.
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Affiliation(s)
- Ilona Rosenboom
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Marie-Madlen Pust
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Sabine Pirr
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Alina Bakker
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Maike Willers
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Colin F Davenport
- Research Core Unit Genomics, Hannover Medical School, Hannover, Germany
| | - Lutz Wiehlmann
- Research Core Unit Genomics, Hannover Medical School, Hannover, Germany
| | - Dorothee Viemann
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- Translational Pediatrics, Department of Pediatrics, University Hospital Würzburg, Würzburg, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
- Center for Infection Research, University Würzburg, Würzburg, Germany
| | - Burkhard Tümmler
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany.
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Lin L, Yi X, Liu H, Meng R, Li S, Liu X, Yang J, Xu Y, Li C, Wang Y, Xiao N, Li H, Liu Z, Xiang Z, Shu W, Guan WJ, Zheng XY, Sun J, Wang Z. The airway microbiome mediates the interaction between environmental exposure and respiratory health in humans. Nat Med 2023:10.1038/s41591-023-02424-2. [PMID: 37349537 DOI: 10.1038/s41591-023-02424-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 05/26/2023] [Indexed: 06/24/2023]
Abstract
Exposure to environmental pollution influences respiratory health. The role of the airway microbial ecosystem underlying the interaction of exposure and respiratory health remains unclear. Here, through a province-wide chronic obstructive pulmonary disease surveillance program, we conducted a population-based survey of bacterial (n = 1,651) and fungal (n = 719) taxa and metagenomes (n = 1,128) from induced sputum of 1,651 household members in Guangdong, China. We found that cigarette smoking and higher PM2.5 concentration were associated with lung function impairment through the mediation of bacterial and fungal communities, respectively, and that exposure was associated with an enhanced inter-kingdom microbial interaction resembling the pattern seen in chronic obstructive pulmonary disease. Enrichment of Neisseria was associated with a 2.25-fold increased risk of high respiratory symptom burden, coupled with an elevation in Aspergillus, in association with occupational pollution. We developed an individualized microbiome-based health index, which covaried with exposure, respiratory symptoms and diseases, with potential generalizability to global datasets. Our results may inform environmental risk prevention and guide interventions that harness airway microbiome.
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Affiliation(s)
- Lifeng Lin
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China.
| | - Xinzhu Yi
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Haiyue Liu
- Xiamen Key Laboratory of Genetic Testing, Department of Laboratory Medicine, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Ruilin Meng
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Saiqiang Li
- School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Xiaomin Liu
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Junhao Yang
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Yanjun Xu
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Chuan Li
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Ye Wang
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Ni Xiao
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Huimin Li
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute for Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zuheng Liu
- Xiamen Key Laboratory of Cardiac Electrophysiology, Department of Cardiology, Xiamen Institute of Cardiovascular Diseases, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Zhiming Xiang
- Department of Radiology, Panyu Central Hospital, Guangzhou, China
| | - Wensheng Shu
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Wei-Jie Guan
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute for Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
- Department of Thoracic Surgery, Guangzhou Institute for Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
| | - Xue-Yan Zheng
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China.
| | - Jiufeng Sun
- Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China.
| | - Zhang Wang
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, Guangzhou, China.
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