1
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Mac Aogáin M. Unsung Heroes? Decoding the Protective Effects of Airway Microbiota in Chronic Obstructive Pulmonary Disease. Am J Respir Crit Care Med 2024; 210:136-138. [PMID: 38358821 DOI: 10.1164/rccm.202401-0189ed] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 02/15/2024] [Indexed: 02/17/2024] Open
Affiliation(s)
- Micheál Mac Aogáin
- Department of Biochemistry St. James's Hospital Dublin, Ireland
- School of Medicine Trinity College Dublin, Ireland
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2
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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 PMCID: PMC11220623 DOI: 10.1183/16000617.0038-2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [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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3
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Short B, Delaney C, Johnston W, Litherland GJ, Lockhart JC, Williams C, Mackay WG, Ramage G. Informed development of a multi-species biofilm in chronic obstructive pulmonary disease. APMIS 2024; 132:336-347. [PMID: 38379455 DOI: 10.1111/apm.13386] [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: 12/04/2023] [Accepted: 02/02/2024] [Indexed: 02/22/2024]
Abstract
Recent evidence indicates that microbial biofilm aggregates inhabit the lungs of COPD patients and actively contribute towards chronic colonization and repeat infections. However, there are no contextually relevant complex biofilm models for COPD research. In this study, a meta-analysis of the lung microbiome in COPD was used to inform development of an optimized biofilm model composed of genera highly associated with COPD. Bioinformatic analysis showed that although diversity matrices of COPD microbiomes were similar to healthy controls, and internal compositions made it possible to accurately differentiate between these cohorts (AUC = 0.939). Genera that best defined these patients included Haemophilus, Moraxella and Streptococcus. Many studies fail to account for fungi; therefore, Candida albicans was included in the creation of an interkingdom biofilm model. These organisms formed a biofilm capable of tolerating high concentrations of antimicrobial therapies with no significant reductions in viability. However, combined therapies of antibiotics and an antifungal resulted in significant reductions in viable cells throughout the biofilm (p < 0.05). This biofilm model is representative of the COPD lung microbiome and results from in vitro antimicrobial challenge experiments indicate that targeting both bacteria and fungi in these interkingdom communities will be required for more positive clinical outcomes.
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Affiliation(s)
- Bryn Short
- School of Medicine, Dentistry and Nursing, College of Medical, Veterinary and Life Sciences (MVLS), University of Glasgow, Glasgow, UK
| | - Christopher Delaney
- School of Medicine, Dentistry and Nursing, College of Medical, Veterinary and Life Sciences (MVLS), University of Glasgow, Glasgow, UK
| | - William Johnston
- Safeguarding Health through Infection Prevention (SHIP) Research Group, Research Centre for Health, Glasgow Caledonian University, Glasgow, UK
| | - Gary J Litherland
- Institute of Biomedical and Environmental Health Research, School of Health and Life Sciences, University of the West of Scotland, Paisley, UK
- Hamilton International Technology Park, Glasgow, UK
| | - John C Lockhart
- Institute of Biomedical and Environmental Health Research, School of Health and Life Sciences, University of the West of Scotland, Paisley, UK
- Hamilton International Technology Park, Glasgow, UK
| | - Craig Williams
- Microbiology Department, Lancaster Royal Infirmary, University of Lancaster, Lancaster, UK
| | - William G Mackay
- Institute of Biomedical and Environmental Health Research, School of Health and Life Sciences, University of the West of Scotland, Paisley, UK
- Hamilton International Technology Park, Glasgow, UK
| | - Gordon Ramage
- School of Medicine, Dentistry and Nursing, College of Medical, Veterinary and Life Sciences (MVLS), University of Glasgow, Glasgow, UK
- Safeguarding Health through Infection Prevention (SHIP) Research Group, Research Centre for Health, Glasgow Caledonian University, Glasgow, UK
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4
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Willis KA, Silverberg M, Martin I, Abdelgawad A, Karabayir I, Halloran BA, Myers ED, Desai JP, White CT, Lal CV, Ambalavanan N, Peters BM, Jain VG, Akbilgic O, Tipton L, Jilling T, Cormier SA, Pierre JF, Talati AJ. The fungal intestinal microbiota predict the development of bronchopulmonary dysplasia in very low birthweight newborns. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.05.29.23290625. [PMID: 37398134 PMCID: PMC10312873 DOI: 10.1101/2023.05.29.23290625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
RATIONALE Bronchopulmonary dysplasia (BPD) is the most common morbidity affecting very preterm infants. Gut fungal and bacterial microbial communities contribute to multiple lung diseases and may influence BPD pathogenesis. METHODS We performed a prospective, observational cohort study comparing the multikingdom fecal microbiota of 144 preterm infants with or without moderate to severe BPD by sequencing the bacterial 16S and fungal ITS2 ribosomal RNA gene. To address the potential causative relationship between gut dysbiosis and BPD, we used fecal microbiota transplant in an antibiotic-pseudohumanized mouse model. Comparisons were made using RNA sequencing, confocal microscopy, lung morphometry, and oscillometry. RESULTS We analyzed 102 fecal microbiome samples collected during the second week of life. Infants who later developed BPD showed an obvious fungal dysbiosis as compared to infants without BPD (NoBPD, p = 0.0398, permutational multivariate ANOVA). Instead of fungal communities dominated by Candida and Saccharomyces, the microbiota of infants who developed BPD were characterized by a greater diversity of rarer fungi in less interconnected community architectures. On successful colonization, the gut microbiota from infants with BPD augmented lung injury in the offspring of recipient animals. We identified alterations in the murine intestinal microbiome and transcriptome associated with augmented lung injury. CONCLUSIONS The gut fungal microbiome of infants who will develop BPD is dysbiotic and may contribute to disease pathogenesis.
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Dora D, Weiss GJ, Megyesfalvi Z, Gállfy G, Dulka E, Kerpel-Fronius A, Berta J, Moldvay J, Dome B, Lohinai Z. Computed Tomography-Based Quantitative Texture Analysis and Gut Microbial Community Signatures Predict Survival in Non-Small Cell Lung Cancer. Cancers (Basel) 2023; 15:5091. [PMID: 37894458 PMCID: PMC10605408 DOI: 10.3390/cancers15205091] [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: 08/25/2023] [Revised: 10/12/2023] [Accepted: 10/18/2023] [Indexed: 10/29/2023] Open
Abstract
This study aims to combine computed tomography (CT)-based texture analysis (QTA) and a microbiome-based biomarker signature to predict the overall survival (OS) of immune checkpoint inhibitor (ICI)-treated non-small cell lung cancer (NSCLC) patients by analyzing their CT scans (n = 129) and fecal microbiome (n = 58). One hundred and five continuous CT parameters were obtained, where principal component analysis (PCA) identified seven major components that explained 80% of the data variation. Shotgun metagenomics (MG) and ITS analysis were performed to reveal the abundance of bacterial and fungal species. The relative abundance of Bacteroides dorei and Parabacteroides distasonis was associated with long OS (>6 mo), whereas the bacteria Clostridium perfringens and Enterococcus faecium and the fungal taxa Cortinarius davemallochii, Helotiales, Chaetosphaeriales, and Tremellomycetes were associated with short OS (≤6 mo). Hymenoscyphus immutabilis and Clavulinopsis fusiformis were more abundant in patients with high (≥50%) PD-L1-expressing tumors, whereas Thelephoraceae and Lachnospiraceae bacterium were enriched in patients with ICI-related toxicities. An artificial intelligence (AI) approach based on extreme gradient boosting evaluated the associations between the outcomes and various clinicopathological parameters. AI identified MG signatures for patients with a favorable ICI response and high PD-L1 expression, with 84% and 79% accuracy, respectively. The combination of QTA parameters and MG had a positive predictive value of 90% for both therapeutic response and OS. According to our hypothesis, the QTA parameters and gut microbiome signatures can predict OS, the response to therapy, the PD-L1 expression, and toxicity in NSCLC patients treated with ICI, and a machine learning approach can combine these variables to create a reliable predictive model, as we suggest in this research.
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Affiliation(s)
- David Dora
- Department of Anatomy, Histology and Embryology, Semmelweis University, 1094 Budapest, Hungary;
| | - Glen J. Weiss
- Department of Medicine, UMass Chan Medical School, Worcester, MA 01655, USA;
| | - Zsolt Megyesfalvi
- Department of Tumor Biology, National Koranyi Institute of Pulmonology, 1122 Budapest, Hungary; (Z.M.); (J.B.); (J.M.)
- Department of Thoracic Surgery, National Institute of Oncology, Semmelweis University, 1122 Budapest, Hungary
- Department of Thoracic Surgery, Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
| | - Gabriella Gállfy
- Pulmonary Hospital Torokbalint, 2045 Torokbalint, Hungary; (G.G.); (E.D.)
| | - Edit Dulka
- Pulmonary Hospital Torokbalint, 2045 Torokbalint, Hungary; (G.G.); (E.D.)
| | - Anna Kerpel-Fronius
- Department of Radiology, National Koranyi Institute of Pulmonology, 1122 Budapest, Hungary
| | - Judit Berta
- Department of Tumor Biology, National Koranyi Institute of Pulmonology, 1122 Budapest, Hungary; (Z.M.); (J.B.); (J.M.)
| | - Judit Moldvay
- Department of Tumor Biology, National Koranyi Institute of Pulmonology, 1122 Budapest, Hungary; (Z.M.); (J.B.); (J.M.)
| | - Balazs Dome
- Department of Tumor Biology, National Koranyi Institute of Pulmonology, 1122 Budapest, Hungary; (Z.M.); (J.B.); (J.M.)
- Department of Thoracic Surgery, National Institute of Oncology, Semmelweis University, 1122 Budapest, Hungary
- Department of Thoracic Surgery, Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
- Department of Translational Medicine, Lund University, 22184 Lund, Sweden
| | - Zoltan Lohinai
- Pulmonary Hospital Torokbalint, 2045 Torokbalint, Hungary; (G.G.); (E.D.)
- Translational Medicine Institute, Semmelweis University, 1094 Budapest, Hungary
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6
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Debourgogne A, Monpierre L, Sy KA, Valsecchi I, Decousser JW, Botterel F. Interactions between Bacteria and Aspergillus fumigatus in Airways: From the Mycobiome to Molecular Interactions. J Fungi (Basel) 2023; 9:900. [PMID: 37755008 PMCID: PMC10533028 DOI: 10.3390/jof9090900] [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: 07/31/2023] [Revised: 08/26/2023] [Accepted: 08/30/2023] [Indexed: 09/28/2023] Open
Abstract
Interactions between different kingdoms of microorganisms in humans are common but not well described. A recent analysis of the mycobiome has described the presence of different fungi and their positive and/or negative interactions with bacteria and other fungi. In chronic respiratory diseases, these different microorganisms form mixed biofilms to live inside. The interactions between Gram-negative bacteria and filamentous fungi in these biofilms have attracted more attention recently. In this review, we analyse the microbiota of the respiratory tract of healthy individuals and patients with chronic respiratory disease. Additionally, we describe the regulatory mechanisms that rule the mixed biofilms of Aspergillus fumigatus and Gram-negative bacteria and the effects of this biofilm on clinical presentations.
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Affiliation(s)
- Anne Debourgogne
- UR 7300, Stress Immunité Pathogène, Université de Lorraine, 54000 Vandoeuvre les Nancy, France;
| | - Lorra Monpierre
- Unité de Parasitologie-Mycologie, Département de Prévention, Diagnostic et Traitement des Infections, CHU Henri Mondor, Assistance Publique des Hôpitaux de Paris (APHP), 94000 Créteil, France;
- UR DYNAMYC 7380, Faculté de Santé, Univ Paris-Est Créteil (UPEC), Ecole Nationale Vétérinaire d’Alfort (ENVA), USC Anses, 94700 Créteil, France; (K.A.S.); (I.V.); (J.-W.D.)
| | - Khadeeja Adam Sy
- UR DYNAMYC 7380, Faculté de Santé, Univ Paris-Est Créteil (UPEC), Ecole Nationale Vétérinaire d’Alfort (ENVA), USC Anses, 94700 Créteil, France; (K.A.S.); (I.V.); (J.-W.D.)
- Institut National de la Santé et de la Recherche Médicale (Inserm) U955, 94010 Créteil, France
| | - Isabel Valsecchi
- UR DYNAMYC 7380, Faculté de Santé, Univ Paris-Est Créteil (UPEC), Ecole Nationale Vétérinaire d’Alfort (ENVA), USC Anses, 94700 Créteil, France; (K.A.S.); (I.V.); (J.-W.D.)
| | - Jean-Winoc Decousser
- UR DYNAMYC 7380, Faculté de Santé, Univ Paris-Est Créteil (UPEC), Ecole Nationale Vétérinaire d’Alfort (ENVA), USC Anses, 94700 Créteil, France; (K.A.S.); (I.V.); (J.-W.D.)
- Department of Infection Control, University Hospital Henri Mondor, Assistance Publique—Hôpitaux de Paris, 94000 Créteil, France
| | - Françoise Botterel
- Unité de Parasitologie-Mycologie, Département de Prévention, Diagnostic et Traitement des Infections, CHU Henri Mondor, Assistance Publique des Hôpitaux de Paris (APHP), 94000 Créteil, France;
- UR DYNAMYC 7380, Faculté de Santé, Univ Paris-Est Créteil (UPEC), Ecole Nationale Vétérinaire d’Alfort (ENVA), USC Anses, 94700 Créteil, France; (K.A.S.); (I.V.); (J.-W.D.)
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7
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Matsumoto K, Read N, Philip KEJ, Allinson JP. Exacerbations in Chronic Obstructive Pulmonary Disease: Clinical, Genetic, and Mycobiome Risk Factors. Am J Respir Crit Care Med 2023; 208:487-489. [PMID: 37104845 DOI: 10.1164/rccm.202303-0581rr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 04/27/2023] [Indexed: 04/29/2023] Open
Affiliation(s)
- Kenki Matsumoto
- Department of Respiratory Medicine, Royal Brompton Hospital, London, United Kingdom; and
| | - Nicola Read
- Department of Respiratory Medicine, Royal Brompton Hospital, London, United Kingdom; and
| | - Keir E J Philip
- Department of Respiratory Medicine, Royal Brompton Hospital, London, United Kingdom; and
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - James P Allinson
- Department of Respiratory Medicine, Royal Brompton Hospital, London, United Kingdom; and
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
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8
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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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Wang R, Huang C, Yang W, Wang C, Wang P, Guo L, Cao J, Huang L, Song H, Zhang C, Zhang Y, Shi G. Respiratory microbiota and radiomics features in the stable COPD patients. Respir Res 2023; 24:131. [PMID: 37173744 PMCID: PMC10176953 DOI: 10.1186/s12931-023-02434-1] [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: 11/21/2022] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
BACKGROUNDS The respiratory microbiota and radiomics correlate with the disease severity and prognosis of chronic obstructive pulmonary disease (COPD). We aim to characterize the respiratory microbiota and radiomics features of COPD patients and explore the relationship between them. METHODS Sputa from stable COPD patients were collected for bacterial 16 S rRNA gene sequencing and fungal Internal Transcribed Spacer (ITS) sequencing. Chest computed tomography (CT) and 3D-CT analysis were conducted for radiomics information, including the percentages of low attenuation area below - 950 Hounsfield Units (LAA%), wall thickness (WT), and intraluminal area (Ai). WT and Ai were adjusted by body surface area (BSA) to WT/[Formula: see text] and Ai/BSA, respectively. Some key pulmonary function indicators were collected, which included forced expiratory volume in one second (FEV1), forced vital capacity (FVC), diffusion lung carbon monoxide (DLco). Differences and correlations of microbiomics with radiomics and clinical indicators between different patient subgroups were assessed. RESULTS Two bacterial clusters dominated by Streptococcus and Rothia were identified. Chao and Shannon indices were higher in the Streptococcus cluster than that in the Rothia cluster. Principal Co-ordinates Analysis (PCoA) indicated significant differences between their community structures. Higher relative abundance of Actinobacteria was detected in the Rothia cluster. Some genera were more common in the Streptococcus cluster, mainly including Leptotrichia, Oribacterium, Peptostreptococcus. Peptostreptococcus was positively correlated with DLco per unit of alveolar volume as a percentage of predicted value (DLco/VA%pred). The patients with past-year exacerbations were more in the Streptococcus cluster. Fungal analysis revealed two clusters dominated by Aspergillus and Candida. Chao and Shannon indices of the Aspergillus cluster were higher than that in the Candida cluster. PCoA showed distinct community compositions between the two clusters. Greater abundance of Cladosporium and Penicillium was found in the Aspergillus cluster. The patients of the Candida cluster had upper FEV1 and FEV1/FVC levels. In radiomics, the patients of the Rothia cluster had higher LAA% and WT/[Formula: see text] than those of the Streptococcus cluster. Haemophilus, Neisseria and Cutaneotrichosporon positively correlated with Ai/BSA, but Cladosporium negatively correlated with Ai/BSA. CONCLUSIONS Among respiratory microbiota in stable COPD patients, Streptococcus dominance was associated with an increased risk of exacerbation, and Rothia dominance was relevant to worse emphysema and airway lesions. Peptostreptococcus, Haemophilus, Neisseria and Cutaneotrichosporon probably affected COPD progression and potentially could be disease prediction biomarkers.
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Affiliation(s)
- Rong Wang
- Department of Pulmonary and Critical Care Medicine, the Affiliated Hospital of Kunming University of Science and Technology, the First People's Hospital of Yunnan Province, Kunming, 650032, People's Republic of China
- Medical School, Kunming University of Science and Technology, Kunming, 650500, People's Republic of China
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine. Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine. Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, 200025, People's Republic of China
| | - Chunrong Huang
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine. Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine. Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, 200025, People's Republic of China
| | - Wenjie Yang
- Department of Radiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, People's Republic of China
| | - Cui Wang
- Department of Pulmonary and Critical Care Medicine, the Third People's Hospital of Kunshan, Suzhou, 215300, People's Republic of China
| | - Ping Wang
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine. Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine. Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, 200025, People's Republic of China
| | - Leixin Guo
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine. Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine. Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, 200025, People's Republic of China
| | - Jin Cao
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine. Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine. Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, 200025, People's Republic of China
| | - Lin Huang
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine. Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine. Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, 200025, People's Republic of China
| | - Hejie Song
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine. Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine. Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, 200025, People's Republic of China
| | - Chenhong Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China.
| | - Yunhui Zhang
- Department of Pulmonary and Critical Care Medicine, the Affiliated Hospital of Kunming University of Science and Technology, the First People's Hospital of Yunnan Province, Kunming, 650032, People's Republic of China.
| | - Guochao Shi
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine. Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine. Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, 200025, People's Republic of China.
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10
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Chen D, Zeng Q, Liu L, Zhou Z, Qi W, Yu S, Zhao L. Global Research Trends on the Link Between the Microbiome and COPD: A Bibliometric Analysis. Int J Chron Obstruct Pulmon Dis 2023; 18:765-783. [PMID: 37180751 PMCID: PMC10167978 DOI: 10.2147/copd.s405310] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 04/30/2023] [Indexed: 05/16/2023] Open
Abstract
Background The pathogenesis of chronic obstructive pulmonary disease (COPD) has been studied in relation to the microbiome, providing space for more targeted interventions and new treatments. Numerous papers on the COPD microbiome have been reported in the last 10 years, yet few publications have used bibliometric methods to evaluate this area. Methods We searched the Web of Science Core Collection for all original research articles in the field of COPD microbiome from January 2011 to August 2022 and used CiteSpace for visual analysis. Results A total of 505 relevant publications were obtained, and the number of global publications in this field is steadily increasing every year, with China and the USA occupying the first two spots in international publications. Imperial College London and the University of Leicester produced the most publications. Brightling C from the UK was the most prolific writer, while Huang Y and Sze M from the USA were first and second among the authors cited. The American Journal of Respiratory and Critical Care Medicine had the highest frequency of citations. The top 10 institutions, cited authors and journals are mostly from the UK and the US. In the ranking of citations, the first article was a paper published by Sze M on changes in the lung tissue's microbiota in COPD patients. The keywords "exacerbation", "gut microbiota", "lung microbiome", "airway microbiome", "bacterial colonization", and "inflammation" were identified as cutting-edge research projects for 2011-2022. Conclusion Based on the visualization results, in the future, we can use the gut-lung axis as the starting point to explore the immunoinflammatory mechanism of COPD, and study how to predict the effects of different treatments of COPD by identifying the microbiota, and how to achieve the optimal enrichment of beneficial bacteria and the optimal consumption of harmful bacteria to improve COPD.
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Affiliation(s)
- Daohong Chen
- Acupuncture and Tuina School, Chengdu University of Traditional Chinese Medicine, Chengdu, People’s Republic of China
| | - Qian Zeng
- Acupuncture and Tuina School, Chengdu University of Traditional Chinese Medicine, Chengdu, People’s Republic of China
| | - Lu Liu
- Acupuncture and Tuina School, Chengdu University of Traditional Chinese Medicine, Chengdu, People’s Republic of China
| | - Ziyang Zhou
- Acupuncture and Tuina School, Chengdu University of Traditional Chinese Medicine, Chengdu, People’s Republic of China
| | - Wenchuan Qi
- Acupuncture and Tuina School, Chengdu University of Traditional Chinese Medicine, Chengdu, People’s Republic of China
| | - Shuguang Yu
- Acupuncture and Tuina School, Chengdu University of Traditional Chinese Medicine, Chengdu, People’s Republic of China
| | - Ling Zhao
- Acupuncture and Tuina School, Chengdu University of Traditional Chinese Medicine, Chengdu, People’s Republic of China
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11
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Zhang J, Cheng H, Di Narzo A, Zhu Y, Xie S, Shao X, Zhang Z, Chung SK, Hao K. Profiling Microbiota from Multiple Sites in the Respiratory Tract to Identify a Biomarker for PM 2.5 Nitrate Exposure-Induced Pulmonary Damages. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:7346-7357. [PMID: 37133311 DOI: 10.1021/acs.est.2c08807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The microbiota present in the respiratory tract (RT) responds to environmental stimuli and engages in a continuous interaction with the host immune system to maintain homeostasis. A total of 40 C57BL/6 mice were divided into four groups and exposed to varying concentrations of PM2.5 nitrate aerosol and clean air. After 10 weeks of exposure, assessments were conducted on the lung and airway microbiome, lung functions, and pulmonary inflammation. Additionally, we analyzed data from both mouse and human respiratory tract (RT) microbiomes to identify possible biomarkers for PM2.5 exposure-induced pulmonary damages. On average, 1.5 and 13.5% inter-individual microbiome variations in the lung and airway were explained by exposure, respectively. In the airway, among the 60 bacterial OTUs (operational taxonomic units) > 0.05% proportion, 40 OTUs were significantly affected by PM2.5 exposure (FDR ≤ 10%). Further, the airway microbiome was associated with peak expiratory flow (PEF) (p = 0.003), pulmonary neutrophil counts (p = 0.01), and alveolar 8-OHdG oxidative lesions (p = 0.0078). The Clostridiales order bacteria showed the strongest signals. For example, the o_Clostridiales;f_;g_ OTU was elevated by PM2.5 nitrate exposure (p = 4.98 × 10-5) and negatively correlated with PEF (r = -0.585 and p = 2.4 × 10-4). It was also associated with the higher pulmonary neutrophil count (p = 8.47 × 10-5) and oxidative lesion (p = 7.17 × 10-3). In human data, we confirmed the association of airway Clostridiales order bacteria with PM2.5 exposure and lung function. For the first time, this study characterizes the impact of PM2.5 exposure on the microbiome of multiple sites in the respiratory tract (RT) and its relevance to airflow obstructive diseases. By analyzing data from both humans and mice, we have identified bacteria belonging to the Clostridiales order as a promising biomarker for PM2.5 exposure-induced decline in pulmonary function and inflammation.
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Affiliation(s)
- Jushan Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai 200072, China
- Department of Respiratory Medicine, Shanghai Tenth People's Hospital, Tongji University, Shanghai 200072, China
- College of Environmental Science and Engineering, Tongji University, Shanghai 200072, China
| | - Haoxiang Cheng
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029-6574, United States
| | - Antonio Di Narzo
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029-6574, United States
| | - Yujie Zhu
- Department of Respiratory Medicine, Shanghai Tenth People's Hospital, Tongji University, Shanghai 200072, China
| | - Shuanshuan Xie
- Department of Respiratory Medicine, Shanghai Tenth People's Hospital, Tongji University, Shanghai 200072, China
| | - Xiaowen Shao
- Department of Obstetrics and Gynecology, Shanghai Tenth People's Hospital, Tongji University, Shanghai 200072, China
| | - Zhongyang Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029-6574, United States
| | - Sookja Kim Chung
- Medical Faculty, Macau University of Science and Technology, Taipa, Macau SAR 999078, China
| | - Ke Hao
- College of Environmental Science and Engineering, Tongji University, Shanghai 200072, China
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029-6574, United States
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12
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Rozaliyani A, Antariksa B, Nurwidya F, Zaini J, Setianingrum F, Hasan F, Nugrahapraja H, Yusva H, Wibowo H, Bowolaksono A, Kosmidis C. The Fungal and Bacterial Interface in the Respiratory Mycobiome with a Focus on Aspergillus spp. Life (Basel) 2023; 13:life13041017. [PMID: 37109545 PMCID: PMC10142979 DOI: 10.3390/life13041017] [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: 02/27/2023] [Revised: 04/08/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
The heterogeneity of the lung microbiome and its alteration are prevalently seen among chronic lung diseases patients. However, studies to date have primarily focused on the bacterial microbiome in the lung rather than fungal composition, which might play an essential role in the mechanisms of several chronic lung diseases. It is now well established that Aspergillus spp. colonies may induce various unfavorable inflammatory responses. Furthermore, bacterial microbiomes such as Pseudomonas aeruginosa provide several mechanisms that inhibit or stimulate Aspergillus spp. life cycles. In this review, we highlighted fungal and bacterial microbiome interactions in the respiratory tract, with a focus on Aspergillus spp.
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Affiliation(s)
- Anna Rozaliyani
- Department of Parasitology, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia
- Indonesia Pulmonary Mycoses Centre, Jakarta 10430, Indonesia
| | - Budhi Antariksa
- Department of Pulmonoloy and Respiratory Medicine, Faculty of Medicinie, Universitas Indonesia, Persahabatan National Respiratory Referral Hospital, Jakarta 13230, Indonesia
| | - Fariz Nurwidya
- Department of Pulmonoloy and Respiratory Medicine, Faculty of Medicinie, Universitas Indonesia, Persahabatan National Respiratory Referral Hospital, Jakarta 13230, Indonesia
| | - Jamal Zaini
- Department of Pulmonoloy and Respiratory Medicine, Faculty of Medicinie, Universitas Indonesia, Persahabatan National Respiratory Referral Hospital, Jakarta 13230, Indonesia
| | - Findra Setianingrum
- Department of Parasitology, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia
- Indonesia Pulmonary Mycoses Centre, Jakarta 10430, Indonesia
| | - Firman Hasan
- Indonesia Pulmonary Mycoses Centre, Jakarta 10430, Indonesia
| | - Husna Nugrahapraja
- Life Science and Biotechnology, Bandung Institute of Technology, Bandung 40312, Indonesia
| | - Humaira Yusva
- Magister Program of Biomedical Sciences, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia
| | - Heri Wibowo
- Department of Parasitology, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia
| | - Anom Bowolaksono
- Department of Biology, Faculty of Mathematics and Natural Sciences (FMIPA), Universitas Indonesia, Depok 16424, Indonesia
| | - Chris Kosmidis
- Manchester Academic Health Science Centre, Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M23 9LT, UK
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13
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Tiew PY, Meldrum OW, Chotirmall SH. Applying Next-Generation Sequencing and Multi-Omics in Chronic Obstructive Pulmonary Disease. Int J Mol Sci 2023; 24:ijms24032955. [PMID: 36769278 PMCID: PMC9918109 DOI: 10.3390/ijms24032955] [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: 01/09/2023] [Revised: 01/31/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Microbiomics have significantly advanced over the last decade, driven by the widespread availability of next-generation sequencing (NGS) and multi-omic technologies. Integration of NGS and multi-omic datasets allow for a holistic assessment of endophenotypes across a range of chronic respiratory disease states, including chronic obstructive pulmonary disease (COPD). Valuable insight has been attained into the nature, function, and significance of microbial communities in disease onset, progression, prognosis, and response to treatment in COPD. Moving beyond single-biome assessment, there now exists a growing literature on functional assessment and host-microbe interaction and, in particular, their contribution to disease progression, severity, and outcome. Identifying specific microbes and/or metabolic signatures associated with COPD can open novel avenues for therapeutic intervention and prognosis-related biomarkers. Despite the promise and potential of these approaches, the large amount of data generated by such technologies can be challenging to analyze and interpret, and currently, there remains a lack of standardized methods to address this. This review outlines the current use and proposes future avenues for the application of NGS and multi-omic technologies in the endophenotyping, prognostication, and treatment of COPD.
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Affiliation(s)
- Pei Yee Tiew
- Department of Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore 169608, Singapore
- Duke-NUS Graduate Medical School, Singapore 169857, Singapore
| | - Oliver W. Meldrum
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, 11 Mandalay Road, Singapore 308232, Singapore
| | - Sanjay H. Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, 11 Mandalay Road, Singapore 308232, Singapore
- Department of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore 308433, Singapore
- Correspondence:
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14
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Otu A, Kosmidis C, Mathioudakis AG, Ibe C, Denning DW. The clinical spectrum of aspergillosis in chronic obstructive pulmonary disease. Infection 2023:10.1007/s15010-022-01960-2. [PMID: 36662439 PMCID: PMC9857914 DOI: 10.1007/s15010-022-01960-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 11/15/2022] [Indexed: 01/21/2023]
Abstract
Chronic obstructive pulmonary disease (COPD) is the third leading cause of death worldwide. In this review, we present the clinical spectrum and pathogenesis of syndromes caused by Aspergillus in COPD namely invasive aspergillosis (IA), community-acquired Aspergillus pneumonia, chronic pulmonary Aspergillosis and Aspergillus sensitisation. Some of these entities are clearly linked to COPD, while others may coexist, but are less clearly liked directly to COPD. We discuss current uncertainties as these pertain to IA in COPD cohorts and explore areas for future research in this field.
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Affiliation(s)
- Akaninyene Otu
- grid.418161.b0000 0001 0097 2705Department of Microbiology, Leeds General Infirmary, Great George Street, Leeds, LS1 3EX UK
| | - Chris Kosmidis
- grid.5379.80000000121662407Division of Evolution, Infection and Genomics, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, M23 9LT UK
| | - Alexander G. Mathioudakis
- grid.5379.80000000121662407Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, The University of Manchester, Manchester, UK ,grid.498924.a0000 0004 0430 9101North West Lung Centre, Wythenshawe Hospital, Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester, UK
| | - Chibuike Ibe
- grid.442675.60000 0000 9756 5366Department of Microbiology, Faculty of Biological Sciences, Abia State University, Uturu, Nigeria
| | - David W. Denning
- grid.5379.80000000121662407Manchester Fungal Infection Group, University of Manchester, Manchester, UK
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15
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Tiew PY, Narayana JK, Quek MSL, Ang YY, Ko FWS, Poh ME, Jaggi TK, Xu H, Thng KX, Koh MS, Tee A, Hui DSC, Abisheganaden JA, Tsaneva-Atanasova K, Chew FT, Chotirmall SH. Sensitisation to recombinant Aspergillus fumigatus allergens and clinical outcomes in COPD. Eur Respir J 2023; 61:13993003.00507-2022. [PMID: 35926878 PMCID: PMC9816419 DOI: 10.1183/13993003.00507-2022] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 07/24/2022] [Indexed: 01/11/2023]
Abstract
BACKGROUND Variable clinical outcomes are reported with fungal sensitisation in chronic obstructive pulmonary disease (COPD), and it remains unclear which fungi and what allergens associate with the poorest outcomes. The use of recombinant as opposed to crude allergens for such assessment is unknown. METHODS A prospective multicentre assessment of stable COPD (n=614) was undertaken in five hospitals across three countries: Singapore, Malaysia and Hong Kong. Clinical and serological assessment was performed against a panel of 35 fungal allergens including crude and recombinant Aspergillus and non-Aspergillus allergens. Unsupervised clustering and topological data analysis (TDA) approaches were employed using the measured sensitisation responses to elucidate if sensitisation subgroups exist and their related clinical outcomes. RESULTS Aspergillus fumigatus sensitisation was associated with increased exacerbations in COPD. Unsupervised cluster analyses revealed two "fungal sensitisation" groups. The first was characterised by Aspergillus sensitisation and increased exacerbations, poorer lung function and worse prognosis. Polysensitisation in this group conferred even poorer outcome. The second group, characterised by Cladosporium sensitisation, was more symptomatic. Significant numbers of individuals demonstrated sensitisation responses to only recombinant (as opposed to crude) A. fumigatus allergens f 1, 3, 5 and 6, and exhibited increased exacerbations, poorer lung function and an overall worse prognosis. TDA validated these findings and additionally identified a subgroup within Aspergillus-sensitised COPD of patients with frequent exacerbations. CONCLUSION Aspergillus sensitisation is a treatable trait in COPD. Measuring sensitisation responses to recombinant Aspergillus allergens identifies an important patient subgroup with poor COPD outcomes that remains overlooked by assessment of only crude Aspergillus allergens.
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Affiliation(s)
- Pei Yee Tiew
- Dept of Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore
| | | | | | - Yan Ying Ang
- Dept of Biological Sciences, National University of Singapore, Singapore
| | - Fanny Wai San Ko
- Dept of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong
| | - Mau Ern Poh
- Dept of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Tavleen Kaur Jaggi
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Huiying Xu
- Dept of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore
| | - Kai Xian Thng
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Mariko Siyue Koh
- Dept of Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore
| | - Augustine Tee
- Dept of Respiratory and Critical Care Medicine, Changi General Hospital, Singapore
| | - David Shu Cheong Hui
- Dept of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong
| | - John Arputhan Abisheganaden
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
- Dept of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore
| | - Krasimira Tsaneva-Atanasova
- Living Systems Institute and Department of Mathematics, College of Engineering, Mathematics and Physical Sciences, University of Exeter, Exeter, UK
- EPSRC Hub for Quantitative Modelling in Healthcare, University of Exeter, Exeter, UK
| | - Fook Tim Chew
- Dept of Biological Sciences, National University of Singapore, Singapore
| | - Sanjay H Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
- Dept of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore
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16
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Raudoniute J, Bironaite D, Bagdonas E, Kulvinskiene I, Jonaityte B, Danila E, Aldonyte R. Human airway and lung microbiome at the crossroad of health and disease (Review). Exp Ther Med 2023; 25:18. [PMID: 36561630 PMCID: PMC9748710 DOI: 10.3892/etm.2022.11718] [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: 08/31/2022] [Accepted: 11/04/2022] [Indexed: 11/23/2022] Open
Abstract
The evolving field of the microbiome and microbiota has become a popular research topic. The human microbiome is defined as a new organ and is considered a living community of commensal, symbiotic and pathogenic microorganisms within a certain body space. The term 'microbiome' is used to define the entire genome of the microbiota. Bacteria, archaea, fungi, algae and small protists are all members of the microbiota, followed by phages, viruses, plasmids and mobile genetic elements. The composition, heterogeneity and dynamics of microbiomes in time and space, their stability and resistance, essential characteristics and key participants, as well as interactions within the microbiome and with the host, are crucial lines of investigation for the development of successful future diagnostics and therapies. Standardization of microbiome studies and harmonized comparable methodologies are required for the transfer of knowledge from fundamental science into the clinic. Human health is dependent on microbiomes and achieved by nurturing beneficial resident microorganisms and their interplay with the host. The present study reviewed scientific knowledge on the major components of the human respiratory microbiome, i.e. bacteria, viruses and fungi, their symbiotic and parasitic roles, and, also, major diseases of the human respiratory tract and their microbial etiology. Bidirectional relationships regulate microbial ecosystems and host susceptibility. Moreover, environmental insults render host tissues and microbiota disease-prone. The human respiratory microbiome reflects the ambient air microbiome. By understanding the human respiratory microbiome, potential therapeutic strategies may be proposed.
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Affiliation(s)
- Jovile Raudoniute
- Department of Regenerative Medicine, State Research Institute Center for Innovative Medicine, Vilnius LT-0840, Lithuania
| | - Daiva Bironaite
- Department of Regenerative Medicine, State Research Institute Center for Innovative Medicine, Vilnius LT-0840, Lithuania
| | - Edvardas Bagdonas
- Department of Regenerative Medicine, State Research Institute Center for Innovative Medicine, Vilnius LT-0840, Lithuania
| | - Ieva Kulvinskiene
- Department of Regenerative Medicine, State Research Institute Center for Innovative Medicine, Vilnius LT-0840, Lithuania
| | - Brigita Jonaityte
- Center of Pulmonology and Allergology, Vilnius University Hospital Santaros Clinic, Vilnius LT-08661, Lithuania
| | - Edvardas Danila
- Center of Pulmonology and Allergology, Vilnius University Hospital Santaros Clinic, Vilnius LT-08661, Lithuania
| | - Ruta Aldonyte
- Department of Regenerative Medicine, State Research Institute Center for Innovative Medicine, Vilnius LT-0840, Lithuania
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17
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Pollock J, Chalmers JD. Aspergillus sensitisation: an underappreciated treatable trait in airway disease. Eur Respir J 2023; 61:61/1/2202042. [PMID: 36609522 DOI: 10.1183/13993003.02042-2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 11/17/2022] [Indexed: 01/09/2023]
Affiliation(s)
- Jennifer Pollock
- 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
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18
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Zhang P, Ma Y, Chen X, Ma Y, Yang L, Zhang M, Gao Z. The Difference in All-Cause Mortality Between Allergic Bronchopulmonary Aspergillosis with and without Chronic Obstructive Pulmonary Disease. J Asthma Allergy 2022; 15:1861-1875. [PMID: 36601290 PMCID: PMC9807121 DOI: 10.2147/jaa.s389985] [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: 10/27/2022] [Accepted: 12/18/2022] [Indexed: 12/31/2022] Open
Abstract
Background Allergic bronchopulmonary aspergillosis (ABPA) primarily complicates the course of asthma, cystic fibrosis, and chronic obstructive pulmonary disease (COPD). Mortality data of ABPA and the difference in all-cause mortality between ABPA with and without COPD are not available. Objective We investigated the difference in all-cause mortality between ABPA with and without COPD. Methods A retrospective review was performed among patients with the diagnosis of ABPA at Peking University People's Hospital between January 2010 and March 2022. Logrank test was performed to investigate the difference between all-cause mortality for ABPA with and without COPD and Cox regression analysis was performed to investigate the independent risk factors for all-cause mortality in patients with ABPA. Results Sixty-one patients with ABPA were enrolled in this study. The follow-up duration was 50.38 months (3-143 months). In the COPD group, 7 patients died (7/10), while in the non-COPD group, 4 patients died (4/51). The 1-year survival rates of ABPA with and without COPD were 60% and 97.8%, respectively. The 5-year survival rates of ABPA with and without COPD were 40% and 94%, respectively. The Cox regression analysis showed that higher C-reactive protein (CRP) (HR = 1.017, 95% CI 1.004-1.031, P = 0.013) and complicating COPD (HR = 8.525, 95% CI 1.827-39.773, P = 0.006) were independent risk factors associated with mortality in patients with ABPA. Conclusion The all-cause mortality for ABPA with COPD is higher than that for ABPA without COPD. Higher CRP and complicating COPD are independent risk factor for mortality in patients with ABPA.
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Affiliation(s)
- Ping’an Zhang
- Department of Respiratory and Critical Care Medicine, Peking University People’s Hospital, Peking University, Beijing, People’s Republic of China
| | - Yanliang Ma
- Department of Respiratory and Critical Care Medicine, Peking University People’s Hospital, Peking University, Beijing, People’s Republic of China,Correspondence: Yanliang Ma, Department of Respiratory and Critical Care Medicine, Peking University People’s Hospital, No. 11 Xizhimen South Street, Xi Cheng District, Beijing, 100044, People’s Republic of China, Tel +86-10-88324641, Email
| | - Xi Chen
- Department of Respiratory and Critical Care Medicine, Peking University People’s Hospital, Peking University, Beijing, People’s Republic of China
| | - Yifan Ma
- Department of Respiratory and Critical Care Medicine, Peking University People’s Hospital, Peking University, Beijing, People’s Republic of China
| | - Luyang Yang
- Department of Respiratory and Critical Care Medicine, Peking University People’s Hospital, Peking University, Beijing, People’s Republic of China
| | - Moqin Zhang
- Department of Respiratory and Critical Care Medicine, Peking University People’s Hospital, Peking University, Beijing, People’s Republic of China
| | - Zhancheng Gao
- Department of Respiratory and Critical Care Medicine, Peking University People’s Hospital, Peking University, Beijing, People’s Republic of China
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19
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Stolz D, Mkorombindo T, Schumann DM, Agusti A, Ash SY, Bafadhel M, Bai C, Chalmers JD, Criner GJ, Dharmage SC, Franssen FME, Frey U, Han M, Hansel NN, Hawkins NM, Kalhan R, Konigshoff M, Ko FW, Parekh TM, Powell P, Rutten-van Mölken M, Simpson J, Sin DD, Song Y, Suki B, Troosters T, Washko GR, Welte T, Dransfield MT. Towards the elimination of chronic obstructive pulmonary disease: a Lancet Commission. Lancet 2022; 400:921-972. [PMID: 36075255 DOI: 10.1016/s0140-6736(22)01273-9] [Citation(s) in RCA: 182] [Impact Index Per Article: 91.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 05/23/2022] [Accepted: 06/28/2022] [Indexed: 10/14/2022]
Affiliation(s)
- Daiana Stolz
- Clinic of Respiratory Medicine and Pulmonary Cell Research, University Hospital Basel, Basel, Switzerland; Department of Clinical Research, University Hospital Basel, Basel, Switzerland; Clinic of Respiratory Medicine and Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Takudzwa Mkorombindo
- Lung Health Center, Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Desiree M Schumann
- Clinic of Respiratory Medicine and Pulmonary Cell Research, University Hospital Basel, Basel, Switzerland
| | - Alvar Agusti
- Respiratory Institute-Hospital Clinic, University of Barcelona IDIBAPS, CIBERES, Barcelona, Spain
| | - Samuel Y Ash
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Mona Bafadhel
- School of Immunology and Microbial Sciences, Faculty of Life Sciences and Medicine, King's College London, London, UK; Department of Respiratory Medicine, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Chunxue Bai
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - James D Chalmers
- Scottish Centre for Respiratory Research, University of Dundee, Dundee, UK
| | - Gerard J Criner
- Department of Thoracic Medicine and Surgery, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA
| | - Shyamali C Dharmage
- Centre for Epidemiology and Biostatistics, School of Population and Global health, University of Melbourne, Melbourne, VIC, Australia
| | - Frits M E Franssen
- Department of Research and Education, CIRO, Horn, Netherlands; Department of Respiratory Medicine, Maastricht University Medical Centre, Maastricht, Netherlands
| | - Urs Frey
- University Children's Hospital Basel, Basel, Switzerland
| | - MeiLan Han
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Nadia N Hansel
- Pulmonary and Critical Care Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Nathaniel M Hawkins
- Centre for Cardiovascular Innovation, University of British Columbia, Vancouver, BC, Canada
| | - Ravi Kalhan
- Department of Preventive Medicine and Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Melanie Konigshoff
- Division of Pulmonary, Allergy and Critical Care Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Fanny W Ko
- The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Trisha M Parekh
- Lung Health Center, Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Maureen Rutten-van Mölken
- Erasmus School of Health Policy & Management and Institute for Medical Technology Assessment, Erasmus University Rotterdam, Rotterdam, Netherlands
| | - Jodie Simpson
- Priority Research Centre for Healthy Lungs, Faculty of Health and Medicine, University of Newcastle, Newcastle, NSW, Australia
| | - Don D Sin
- Centre for Heart Lung Innovation and Division of Respiratory Medicine, Department of Medicine, University of British Columbia, St Paul's Hospital, Vancouver, BC, Canada
| | - Yuanlin Song
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital and National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, China; Shanghai Respiratory Research Institute, Shanghai, China; Jinshan Hospital of Fudan University, Shanghai, China
| | - Bela Suki
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Thierry Troosters
- Department of Rehabilitation Sciences, Research Group for Rehabilitation in Internal Disorders, KU Leuven, Leuven, Belgium
| | - George R Washko
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Tobias Welte
- Department of Respiratory Medicine, Hannover Medical School, Hannover, Germany; Biomedical Research in Endstage and Obstructive Lung Disease, German Center for Lung Research, Hannover, Germany
| | - Mark T Dransfield
- Lung Health Center, Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA; Birmingham VA Medical Center, Birmingham, AL, USA.
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20
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Russo C, Colaianni V, Ielo G, Valle MS, Spicuzza L, Malaguarnera L. Impact of Lung Microbiota on COPD. Biomedicines 2022; 10:biomedicines10061337. [PMID: 35740358 PMCID: PMC9219765 DOI: 10.3390/biomedicines10061337] [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: 05/08/2022] [Revised: 05/28/2022] [Accepted: 06/02/2022] [Indexed: 11/16/2022] Open
Abstract
There is a fine balance in maintaining healthy microbiota composition, and its alterations due to genetic, lifestyle, and environmental factors can lead to the onset of respiratory dysfunctions such as chronic obstructive pulmonary disease (COPD). The relationship between lung microbiota and COPD is currently under study. Little is known about the role of the microbiota in patients with stable or exacerbated COPD. Inflammation in COPD disorders appears to be characterised by dysbiosis, reduced lung activity, and an imbalance between the innate and adaptive immune systems. Lung microbiota intervention could ameliorate these disorders. The microbiota’s anti-inflammatory action could be decisive in the onset of pathologies. In this review, we highlight the feedback loop between microbiota dysfunction, immune response, inflammation, and lung damage in relation to COPD status in order to encourage the development of innovative therapeutic goals for the prevention and management of this disease.
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Affiliation(s)
- Cristina Russo
- Section of Pathology, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy; (C.R.); (V.C.)
| | - Valeria Colaianni
- Section of Pathology, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy; (C.R.); (V.C.)
| | - Giuseppe Ielo
- Department of Clinical and Experimental Medicine, University of Catania, 95123 Catania, Italy; (G.I.); (L.S.)
| | - Maria Stella Valle
- Laboratory of Neuro-Biomechanics, Section of Physiology, Department of Biomedical and Biotechnological Sciences, School of Medicine, University of Catania, 95123 Catania, Italy
- Correspondence: (M.S.V.); (L.M.)
| | - Lucia Spicuzza
- Department of Clinical and Experimental Medicine, University of Catania, 95123 Catania, Italy; (G.I.); (L.S.)
| | - Lucia Malaguarnera
- Section of Pathology, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy; (C.R.); (V.C.)
- Correspondence: (M.S.V.); (L.M.)
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21
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Ancel J, Guecamburu M, Marques Da Silva V, Schilfarth P, Boyer L, Pilette C, Martin C, Devillier P, Berger P, Zysman M, Le Rouzic O, Gonzalez-Bermejo J, Degano B, Burgel PR, Ahmed E, Roche N, Deslee G. [Take-home messages from the COPD 2021 biennial of the French Society of Respiratory Diseases. Understanding to so as to better innovate]. Rev Mal Respir 2022; 39:427-441. [PMID: 35568574 DOI: 10.1016/j.rmr.2022.03.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 03/23/2022] [Indexed: 02/07/2023]
Abstract
INTRODUCTION The first COPD biennial organized by the French Society of Respiratory Diseases (SPLF) took place on 17 December 2021. STATE OF THE ART The objective of the biennial was to discuss current knowledge regarding COPD pathophysiology, current treatments, research development, and future therapeutic approaches. PERSPECTIVES The different lecturers laid emphasis on the complexity of pathophysiologic mechanisms including bronchial, bronchiolar and parenchymal alterations, and also dwelt on the role of microbiota composition in COPD pathenogenesis. They pointed out that addition to inhaled treatments, ventilatory support and endoscopic approaches have been increasingly optimized. The development of new therapeutic pathways such as biotherapy and cell therapy (stem cells…) call for further exploration. CONCLUSIONS The dynamism of COPD research was repeatedly underlined, and needs to be further reinforced, the objective being to "understand so as to better innovate" so as to develop effective new strategies for treatment and management of COPD.
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Affiliation(s)
- J Ancel
- Inserm UMRS-1250, service de pneumologie, université Reims Champagne Ardenne, hôpital Maison Blanche, Reims, France
| | - M Guecamburu
- Service des maladies respiratoires, hôpital du Haut-Lévêque, CHU de Bordeaux, Bordeaux, France
| | - V Marques Da Silva
- Inserm U955, FHU SENEC, université Paris-Est Créteil, institut Mondor de recherche biomédicale, équipe GEIC2O, Créteil, France
| | - P Schilfarth
- Service des maladies respiratoires, hôpital du Haut-Lévêque, CHU de Bordeaux, Bordeaux, France; Inserm U1045, centre de recherche cardio-thoracique de Bordeaux, Pessac, France
| | - L Boyer
- Département de physiologie-explorations fonctionnelles, université Paris-Est, hôpital Henri-Mondor, AP-HP, UMR S955, FHU SENEC, UPEC, Créteil, France
| | - C Pilette
- Département de pneumologie, université catholique de Louvain, cliniques universitaires Saint-Luc et institut de recherche expérimentale et clinique, Bruxelles, Belgique
| | - C Martin
- Inserm U1016, service de pneumologie, AP-HP Paris, hôpital Cochin et institut Cochin, université de Paris, Paris, France
| | - P Devillier
- Département des maladies respiratoires, unité de recherche en pharmacologie respiratoire, VIM Suresnes (UMR 0892, université Paris-Saclay), hôpital Foch, Suresnes, France
| | - P Berger
- Service d'exploration fonctionnelle respiratoire, département de pharmacologie, centre de recherche cardiothoracique, U1045, CIC 1401, Pessac, France
| | - M Zysman
- Service des maladies respiratoires, hôpital du Haut-Lévêque, CHU de Bordeaux, Bordeaux, France; Inserm U1045, centre de recherche cardio-thoracique de Bordeaux, Pessac, France
| | - O Le Rouzic
- Inserm, CIIL Center for infection and immunity of Lille, université de Lille, CHU de Lille, pneumologie et immuno-allergologie, Institut Pasteur de Lille, U1019 - UMR9017, Lille, France
| | - J Gonzalez-Bermejo
- Inserm, UMRS115 neurophysiologie respiratoire expérimentale et clinique, service de pneumologie, médecine intensive et réanimation (département R3S), Sorbonne université, groupe hospitalier universitaire AP-HP, Sorbonne Université, site Pitié-Salpêtrière, Paris, France
| | - B Degano
- Inserm 1042, service de pneumologie physiologie, CHU de Grenoble, Grenoble, France
| | - P-R Burgel
- Inserm U1016, service de pneumologie, AP-HP Paris, hôpital Cochin et institut Cochin, université de Paris, Paris, France
| | - E Ahmed
- Département des maladies respiratoires, IRMB, université de Montpellier, CHU de Montpellier, Montpellier, France
| | - N Roche
- Inserm U1016, service de pneumologie, AP-HP Paris, hôpital Cochin et institut Cochin, université de Paris, Paris, France
| | - G Deslee
- Inserm UMRS-1250, service de pneumologie, université Reims Champagne Ardenne, hôpital Maison Blanche, Reims, France.
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22
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Tiew PY, Thng KX, Chotirmall SH. Clinical Aspergillus Signatures in COPD and Bronchiectasis. J Fungi (Basel) 2022; 8:jof8050480. [PMID: 35628736 PMCID: PMC9146266 DOI: 10.3390/jof8050480] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 04/30/2022] [Accepted: 05/03/2022] [Indexed: 12/21/2022] Open
Abstract
Pulmonary mycoses remain a global threat, causing significant morbidity and mortality. Patients with airways disease, including COPD and bronchiectasis, are at increased risks of pulmonary mycoses and its associated complications. Frequent use of antibiotics and corticosteroids coupled with impaired host defenses predispose patients to fungal colonization and airway persistence, which are associated with negative clinical consequences. Notably, Aspergillus species remain the best-studied fungal pathogen and induce a broad spectrum of clinical manifestations in COPD and bronchiectasis ranging from colonization and sensitization to more invasive disease. Next-generation sequencing (NGS) has gained prominence in the field of respiratory infection, and in some cases is beginning to act as a viable alternative to traditional culture. NGS has revolutionized our understanding of airway microbiota and in particular fungi. In this context, it permits the identification of the previously unculturable, fungal composition, and dynamic change within microbial communities of the airway, including potential roles in chronic respiratory disease. Furthermore, inter-kingdom microbial interactions, including fungi, in conjunction with host immunity have recently been shown to have important clinical roles in COPD and bronchiectasis. In this review, we provide an overview of clinical Aspergillus signatures in COPD and bronchiectasis and cover the current advances in the understanding of the mycobiome in these disease states. The challenges and limitations of NGS will be addressed.
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Affiliation(s)
- Pei Yee Tiew
- Department of Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore 168753, Singapore;
- Duke-NUS Medical School, Singapore 169857, Singapore
| | - Kai Xian Thng
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore;
| | - Sanjay H. Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore;
- Department of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore 308433, Singapore
- Correspondence:
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23
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de Dios Caballero J, Cantón R, Ponce-Alonso M, García-Clemente MM, Gómez G. de la Pedrosa E, López-Campos JL, Máiz L, del Campo R, Martínez-García MÁ. The Human Mycobiome in Chronic Respiratory Diseases: Current Situation and Future Perspectives. Microorganisms 2022; 10:microorganisms10040810. [PMID: 35456861 PMCID: PMC9029612 DOI: 10.3390/microorganisms10040810] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/04/2022] [Accepted: 04/09/2022] [Indexed: 12/15/2022] Open
Abstract
Microbes play an important role in the pathogenesis of chronic lung diseases, such as chronic obstructive pulmonary disease, cystic fibrosis, non-cystic fibrosis bronchiectasis, and asthma. While the role of bacterial pathogens has been extensively studied, the contribution of fungal species to the pathogenesis of chronic lung diseases is much less understood. The recent introduction of next-generation sequencing techniques has revealed the existence of complex microbial lung communities in healthy individuals and patients with chronic respiratory disorders, with fungi being an important part of these communities’ structure (mycobiome). There is growing evidence that the components of the lung mycobiome influence the clinical course of chronic respiratory diseases, not only by direct pathogenesis but also by interacting with bacterial species and with the host’s physiology. In this article, we review the current knowledge on the role of fungi in chronic respiratory diseases, which was obtained by conventional culture and next-generation sequencing, highlighting the limitations of both techniques and exploring future research areas.
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Affiliation(s)
- Juan de Dios Caballero
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Health Research Institute, 28034 Madrid, Spain; (J.d.D.C.); (M.P.-A.); (E.G.G.d.l.P.); (R.d.C.)
- CIBER of Infectious Diseases (CIBERINFEC), Institute of Health Carlos III, 28029 Madrid, Spain
| | - Rafael Cantón
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Health Research Institute, 28034 Madrid, Spain; (J.d.D.C.); (M.P.-A.); (E.G.G.d.l.P.); (R.d.C.)
- CIBER of Infectious Diseases (CIBERINFEC), Institute of Health Carlos III, 28029 Madrid, Spain
- Correspondence: ; Tel.: +34-91-336-88-32 or +34-336-83-30
| | - Manuel Ponce-Alonso
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Health Research Institute, 28034 Madrid, Spain; (J.d.D.C.); (M.P.-A.); (E.G.G.d.l.P.); (R.d.C.)
- CIBER of Infectious Diseases (CIBERINFEC), Institute of Health Carlos III, 28029 Madrid, Spain
| | - Marta María García-Clemente
- Department of Pneumology, Central Asturias University Hospital, 33011 Oviedo, Spain;
- Principality Asturias Health Research Institute (ISPA), 33011 Oviedo, Spain
| | - Elia Gómez G. de la Pedrosa
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Health Research Institute, 28034 Madrid, Spain; (J.d.D.C.); (M.P.-A.); (E.G.G.d.l.P.); (R.d.C.)
- CIBER of Infectious Diseases (CIBERINFEC), Institute of Health Carlos III, 28029 Madrid, Spain
| | - José Luis López-Campos
- Medical-Surgical Unit for Respiratory Diseases (CIBERES), Institute of Biomedicine of Seville (IBiS), Virgen del Rocío University Hospital, University of Seville, 41013 Sevilla, Spain;
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, 28029 Madrid, Spain; (L.M.); (M.Á.M.-G.)
| | - Luis Máiz
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, 28029 Madrid, Spain; (L.M.); (M.Á.M.-G.)
- Department of Pneumology, Ramón y Cajal University Hospital, 28034 Madrid, Spain
| | - Rosa del Campo
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Health Research Institute, 28034 Madrid, Spain; (J.d.D.C.); (M.P.-A.); (E.G.G.d.l.P.); (R.d.C.)
- CIBER of Infectious Diseases (CIBERINFEC), Institute of Health Carlos III, 28029 Madrid, Spain
| | - Miguel Ángel Martínez-García
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, 28029 Madrid, Spain; (L.M.); (M.Á.M.-G.)
- Department of Pneumology, La Fe University and Polytechnic Hospital, 46026 Valencia, Spain
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24
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Campbell CD, Barnett C, Sulaiman I. A clinicians’ review of the respiratory microbiome. Breathe (Sheff) 2022; 18:210161. [PMID: 36338247 PMCID: PMC9584600 DOI: 10.1183/20734735.0161-2021] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 03/02/2022] [Indexed: 11/25/2022] Open
Abstract
The respiratory microbiome and its impact in health and disease is now well characterised. With the development of next-generation sequencing and the use of other techniques such as metabolomics, the functional impact of microorganisms in different host environments can be elucidated. It is now clear that the respiratory microbiome plays an important role in respiratory disease. In some diseases, such as bronchiectasis, examination of the microbiome can even be used to identify patients at higher risk of poor outcomes. Furthermore, the microbiome can aid in phenotyping. Finally, development of multi-omic analysis has revealed interactions between the host and microbiome in some conditions. This review, although not exhaustive, aims to outline how the microbiome is investigated, the healthy respiratory microbiome and its role in respiratory disease. The respiratory microbiome encompasses bacterial, fungal and viral communities. In health, it is a dynamic structure and dysbiotic in disease. Dysbiosis can be related to disease severity and may be utilised to predict patients at clinical risk.https://bit.ly/3pNSgnA
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25
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Palmieri F, Koutsokera A, Bernasconi E, Junier P, von Garnier C, Ubags N. Recent Advances in Fungal Infections: From Lung Ecology to Therapeutic Strategies With a Focus on Aspergillus spp. Front Med (Lausanne) 2022; 9:832510. [PMID: 35386908 PMCID: PMC8977413 DOI: 10.3389/fmed.2022.832510] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 02/22/2022] [Indexed: 12/15/2022] Open
Abstract
Fungal infections are estimated to be the main cause of death for more than 1.5 million people worldwide annually. However, fungal pathogenicity has been largely neglected. This is notably the case for pulmonary fungal infections, which are difficult to diagnose and to treat. We are currently facing a global emergence of antifungal resistance, which decreases the chances of survival for affected patients. New therapeutic approaches are therefore needed to face these life-threatening fungal infections. In this review, we will provide a general overview on respiratory fungal infections, with a focus on fungi of the genus Aspergillus. Next, the immunological and microbiological mechanisms of fungal pathogenesis will be discussed. The role of the respiratory mycobiota and its interactions with the bacterial microbiota on lung fungal infections will be presented from an ecological perspective. Finally, we will focus on existing and future innovative approaches for the treatment of respiratory fungal infections.
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Affiliation(s)
- Fabio Palmieri
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
- *Correspondence: Fabio Palmieri,
| | - Angela Koutsokera
- Faculty of Biology and Medicine, University of Lausanne, Service de Pneumologie, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland
| | - Eric Bernasconi
- Faculty of Biology and Medicine, University of Lausanne, Service de Pneumologie, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland
| | - Pilar Junier
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Christophe von Garnier
- Faculty of Biology and Medicine, University of Lausanne, Service de Pneumologie, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland
| | - Niki Ubags
- Faculty of Biology and Medicine, University of Lausanne, Service de Pneumologie, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland
- Niki Ubags,
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26
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Tiew PY, Mac Aogáin M, Chotirmall SH. The current understanding and future directions for sputum microbiome profiling in chronic obstructive pulmonary disease. Curr Opin Pulm Med 2022; 28:121-133. [PMID: 34839338 DOI: 10.1097/mcp.0000000000000850] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW Next-generation sequencing (NGS) has deepened our understanding of the respiratory microbiome in health and disease. The number of microbiome studies employing sputum as an airway surrogate has continued to increase over the past decade to include multiple large multicentre and longitudinal studies of the microbiome in chronic obstructive pulmonary disease (COPD). In this review, we summarize the recent advances to our understanding of the bacteriome, virome and mycobiome in COPD. RECENT FINDINGS Diverse microbiome profiles are reported in COPD. The neutrophilic Haemophilus-predominant bacteriome remains a prominent COPD phenotype, relatively stable over time and during exacerbations. Studies of the virome remain limited but reveal a potential involvement of viruses and bacteriophages particularly during COPD exacerbations and advancing disease severity. Mycobiome signatures, even in stable COPD are associated with poorer clinical outcomes including mortality. SUMMARY The sputum microbiome in COPD is being increasingly recognized for its clinical relevance, even in the stable state. Future studies integrating microbial kingdoms holistically (i.e. bacterial, viral and fungal) will provide deeper insight into its functionality including the relevance of microbial interactions and effect of treatment on microbiome-associated clinical outcomes.
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Affiliation(s)
- Pei Yee Tiew
- Department of Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore
| | - Micheál Mac Aogáin
- Biochemical Genetics Laboratory, Department of Biochemistry, St. James's Hospital
- Clinical Biochemistry Unit, School of Medicine, Trinity College Dublin, Ireland
| | - Sanjay H Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
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27
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Wang JM, Han MK, Labaki WW. Chronic obstructive pulmonary disease risk assessment tools: is one better than the others? Curr Opin Pulm Med 2022; 28:99-108. [PMID: 34652295 PMCID: PMC8799486 DOI: 10.1097/mcp.0000000000000833] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW Risk assessment tools are essential in COPD care to help clinicians identify patients at higher risk of accelerated lung function decline, respiratory exacerbations, hospitalizations, and death. RECENT FINDINGS Conventional methods of assessing risk have focused on spirometry, patient-reported symptoms, functional status, and a combination of these tools in composite indices. More recently, qualitatively and quantitatively assessed chest imaging findings, such as emphysema, large and small airways disease, and pulmonary vascular abnormalities have been associated with poor long-term outcomes in COPD patients. Although several blood and sputum biomarkers have been investigated for risk assessment in COPD, most still warrant further validation. Finally, novel remote digital monitoring technologies may be valuable to predict exacerbations but their large-scale performance, ease of implementation, and cost effectiveness remain to be determined. SUMMARY Given the complex heterogeneity of COPD, any single metric is unlikely to fully capture the risk of poor long-term outcomes. Therefore, clinicians should review all available clinical data, including spirometry, symptom severity, functional status, chest imaging, and bloodwork, to guide personalized preventive care of COPD patients. The potential of machine learning tools and remote monitoring technologies to refine COPD risk assessment is promising but remains largely untapped pending further investigation.
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Affiliation(s)
- Jennifer M Wang
- Division of Pulmonary and Critical Care Medicine, University of Michigan, Ann Arbor, Michigan, USA
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28
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Pattaroni C, Macowan M, Chatzis R, Daunt C, Custovic A, Shields MD, Power UF, Grigg J, Roberts G, Ghazal P, Schwarze J, Gore M, Turner S, Bush A, Saglani S, Lloyd CM, Marsland BJ. Early life inter-kingdom interactions shape the immunological environment of the airways. MICROBIOME 2022; 10:34. [PMID: 35189979 PMCID: PMC8862481 DOI: 10.1186/s40168-021-01201-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 11/12/2021] [Indexed: 05/03/2023]
Abstract
BACKGROUND There is increasing evidence that the airway microbiome plays a key role in the establishment of respiratory health by interacting with the developing immune system early in life. While it has become clear that bacteria are involved in this process, there is a knowledge gap concerning the role of fungi. Moreover, the inter-kingdom interactions that influence immune development remain unknown. In this prospective exploratory human study, we aimed to determine early post-natal microbial and immunological features of the upper airways in 121 healthy newborns. RESULTS We found that the oropharynx and nasal cavity represent distinct ecological niches for bacteria and fungi. Breastfeeding correlated with changes in microbiota composition of oropharyngeal samples with the greatest impact upon the relative abundance of Streptococcus species and Candida. Host transcriptome profiling revealed that genes with the highest expression variation were immunological in nature. Multi-omics factor analysis of host and microbial data revealed unique co-variation patterns. CONCLUSION These data provide evidence of a diverse multi-kingdom microbiota linked with local immunological characteristics in the first week of life that could represent distinct trajectories for future respiratory health. TRIAL REGISTRATION NHS Health Research Authority, IRAS ID 199053. Registered 5 Oct 2016. https://www.hra.nhs.uk/planning-and-improving-research/application-summaries/research-summaries/breathing-together/ Video abstract.
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Affiliation(s)
- Céline Pattaroni
- Department of Immunology and Pathology, Monash University, Melbourne, Australia
| | - Matthew Macowan
- Department of Immunology and Pathology, Monash University, Melbourne, Australia
| | - Roxanne Chatzis
- Department of Immunology and Pathology, Monash University, Melbourne, Australia
| | - Carmel Daunt
- Department of Immunology and Pathology, Monash University, Melbourne, Australia
| | - Adnan Custovic
- Imperial Centre for Paediatrics and Child Health, Imperial College London, London, UK
| | - Michael D. Shields
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, Belfast, UK
| | - Ultan F. Power
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, Belfast, UK
| | - Jonathan Grigg
- Centre for Child Health, Blizard Institute, Queen Mary University of London, London, UK
| | - Graham Roberts
- Human Development in Health School, University of Southampton Faculty of Medicine, Southampton, UK
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton, UK
- David Hide Asthma and Allergy Research Centre, St Mary’s Hospital, Newport, Isle of Wight UK
| | - Peter Ghazal
- School of Medicine, Systems Immunity Research Institute, Cardiff University, Cardiff, UK
| | - Jürgen Schwarze
- Centre for Inflammation Research, Child Life and Health, The University of Edinburgh, Edinburgh, UK
| | - Mindy Gore
- Imperial Centre for Paediatrics and Child Health, Imperial College London, London, UK
| | - Steve Turner
- Child Health, University of Aberdeen, Aberdeen, UK
- NHS Grampian, Aberdeen, UK
| | - Andrew Bush
- Imperial Centre for Paediatrics and Child Health, Imperial College London, London, UK
- Royal Brompton Hospital, London, UK
- National Heart & Lung Institute, Imperial College London, London, UK
| | - Sejal Saglani
- Imperial Centre for Paediatrics and Child Health, Imperial College London, London, UK
- Royal Brompton Hospital, London, UK
- National Heart & Lung Institute, Imperial College London, London, UK
| | - Clare M. Lloyd
- National Heart & Lung Institute, Imperial College London, London, UK
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29
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Meldrum OW, Belchamber KBR, Chichirelo-Konstantynovych KD, Horton KL, Konstantynovych TV, Long MB, McDonnell MJ, Perea L, Garcia-Basteiro AL, Loebinger MR, Duarte R, Keir HR. ERS International Congress 2021: highlights from the Respiratory Infections Assembly. ERJ Open Res 2022; 8:00642-2021. [PMID: 35615420 PMCID: PMC9124871 DOI: 10.1183/23120541.00642-2021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 01/12/2022] [Indexed: 12/15/2022] Open
Abstract
The European Respiratory Society Annual Congress 2021 took place virtually for the second year running due to the coronavirus pandemic. The congress programme featured more than 400 sessions and 3000 abstract presentations, covering the entire respiratory science and medicine field. In this article, Early Career Members of the Respiratory Infections Assembly summarise a selection of sessions across a broad range of topics, including presentations on bronchiectasis, non-tuberculosis mycobacteria, tuberculosis, cystic fibrosis and COVID-19.
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Ke L, Chen L, Yaling Y, Can G, Jun L, Chuan Z. Investigation on the Pathological Mechanism of Frequent Exacerbators With Chronic Obstructive Pulmonary Disease Based on the Characteristics of Respiratory Flora. Front Med (Lausanne) 2022; 8:816802. [PMID: 35127772 PMCID: PMC8811034 DOI: 10.3389/fmed.2021.816802] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 12/15/2021] [Indexed: 11/17/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is a common obstructive respiratory disease characterized by persistent respiratory symptoms and limited airflow due to airway obstruction. The present study investigates the distribution characteristics of respiratory tract flora in both frequent and infrequent exacerbators of COPD. The 16S sequencing technique was adopted to differentiate the inherent differences of respiratory tract flora between frequent exacerbators and infrequent exacerbators. Additionally, cell counting kit 8 (CCK8), lactate dehydrogenase (LDH) test, flow cytometry, enzyme-linked immunosorbent assay (ELISA), and western blot were carried out in human bronchial epithelial cells cultured in vitro and the regulatory effects of differential flora were verified. The results revealed that the observed species index, Chao1 index, and the ACE estimator of COPD frequent exacerbators were markedly higher than those of COPD infrequent exacerbators. The top five strains of COPD frequent exacerbators included g_Streptococcus (15.565%), g_Prevotella (10.683%), g_Veillonella (6.980%), g_Haemophilus (5.601%), and g_Neisseria (4.631%). Veillonella parvula generated obvious cytotoxicity and substantially reduced the activity of human bronchial epithelial cells (p < 0.01). Furthermore, the results of flow cytometry indicated that the proportion of human bronchial epithelial cells in both the S phase and G2 phase decreased following Veillonella parvula treatment indicated that Veillonella parvula inhibited cell proliferation. Meanwhile, being treated using Veillonella parvula, the expressions of interleukin-1 (IL-1), IL-6, Tumor Necrosis Factor α (TNF-α), and p-nuclear factor kappa B (NF-κB) of the cells were increased markedly (p < 0.01). Taken together, the current research demonstrated that the relative abundance of Veillonella in COPD frequent exacerbators was higher than that of infrequent exacerbators. Veillonella parvula activated the inflammatory pathway, ultimately destroyed the cell viability, and greatly impaired the activity of human bronchial epithelial cells, thereby inhibiting cell proliferation.
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Affiliation(s)
- Li Ke
- Department of Laboratory Medicine, Chongqing the Seventh People's Hospital, Chongqing, China
- *Correspondence: Li Ke
| | - Luo Chen
- Department of Respiratory and Critical Care, Chongqing the Seventh People's Hospital, Chongqing, China
| | - Yuan Yaling
- Department of Laboratory Medicine, Chongqing the Seventh People's Hospital, Chongqing, China
| | - Gao Can
- Department of Laboratory Medicine, Chongqing the Seventh People's Hospital, Chongqing, China
| | - Lin Jun
- Department of Laboratory Medicine, Chongqing the Seventh People's Hospital, Chongqing, China
| | - Zhang Chuan
- Department of Laboratory Medicine, Chongqing the Seventh People's Hospital, Chongqing, China
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Amati F, Stainer A, Mantero M, Gramegna A, Simonetta E, Suigo G, Voza A, Nambiar AM, Cariboni U, Oldham J, Molyneaux PL, Spagnolo P, Blasi F, Aliberti S. Lung Microbiome in Idiopathic Pulmonary Fibrosis and Other Interstitial Lung Diseases. Int J Mol Sci 2022; 23:ijms23020977. [PMID: 35055163 PMCID: PMC8779068 DOI: 10.3390/ijms23020977] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 01/07/2022] [Accepted: 01/12/2022] [Indexed: 02/01/2023] Open
Abstract
Interstitial lung diseases represent a heterogeneous and wide group of diseases in which factors leading to disease initiation and progression are not fully understood. Recent evidence suggests that the lung microbiome might influence the pathogenesis and progression of interstitial lung diseases. In recent years, the utilization of culture-independent methodologies has allowed the identification of complex and dynamic communities of microbes, in patients with interstitial lung diseases. However, the potential mechanisms by which these changes may drive disease pathogenesis and progression are largely unknown. The aim of this review is to discuss the role of the altered lung microbiome in several interstitial lung diseases. Untangling the host–microbiome interaction in the lung and airway of interstitial lung disease patients is a research priority. Thus, lung dysbiosis is a potentially treatable trait across several interstitial lung diseases, and its proper characterization and treatment might be crucial to change the natural history of these diseases and improve outcomes.
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Affiliation(s)
- Francesco Amati
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (A.S.); (G.S.); (A.V.); (S.A.)
- Respiratory Unit, IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano, Italy
- Correspondence:
| | - Anna Stainer
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (A.S.); (G.S.); (A.V.); (S.A.)
- Respiratory Unit, IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano, Italy
| | - Marco Mantero
- Department of Pathophysiology and Transplantation, University of Milan, 20122 Milan, Italy; (M.M.); (A.G.); (E.S.); (F.B.)
- Internal Medicine Department, Respiratory Unit and Cystic Fibrosis Adult Center, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Andrea Gramegna
- Department of Pathophysiology and Transplantation, University of Milan, 20122 Milan, Italy; (M.M.); (A.G.); (E.S.); (F.B.)
- Internal Medicine Department, Respiratory Unit and Cystic Fibrosis Adult Center, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Edoardo Simonetta
- Department of Pathophysiology and Transplantation, University of Milan, 20122 Milan, Italy; (M.M.); (A.G.); (E.S.); (F.B.)
- Internal Medicine Department, Respiratory Unit and Cystic Fibrosis Adult Center, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Giulia Suigo
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (A.S.); (G.S.); (A.V.); (S.A.)
- Respiratory Unit, IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano, Italy
| | - Antonio Voza
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (A.S.); (G.S.); (A.V.); (S.A.)
- Emergency Medicine Unit, IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano, Italy
| | - Anoop M. Nambiar
- Division of Pulmonary and Critical Care, Department of Medicine, University of Texas Health San Antonio, South Texas Health Care System, San Antonio, TX 78229, USA;
| | - Umberto Cariboni
- Department of General and Thoracic Surgery, Humanitas Research Hospital, 20089 Rozzano, Italy;
| | - Justin Oldham
- Division of Pulmonary, Critical Care and Sleep Medicine, University of California Davis, Sacramento, CA 95616, USA;
| | - Philip L. Molyneaux
- National Heart and Lung Institute, Imperial College London, London SW7 2AZ, UK;
| | - Paolo Spagnolo
- Respiratory Disease Unit, Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, 35128 Padova, Italy;
| | - Francesco Blasi
- Department of Pathophysiology and Transplantation, University of Milan, 20122 Milan, Italy; (M.M.); (A.G.); (E.S.); (F.B.)
- Internal Medicine Department, Respiratory Unit and Cystic Fibrosis Adult Center, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Stefano Aliberti
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Italy; (A.S.); (G.S.); (A.V.); (S.A.)
- Respiratory Unit, IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano, Italy
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The Airway Microbiome: Present and Future Applications. Arch Bronconeumol 2022; 58:8-10. [DOI: 10.1016/j.arbres.2021.08.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 08/03/2021] [Indexed: 01/07/2023]
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Future Directions for Clinical Respiratory Fungal Research. Mycopathologia 2021; 186:685-696. [PMID: 34590208 PMCID: PMC8536595 DOI: 10.1007/s11046-021-00579-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 07/03/2021] [Indexed: 12/12/2022]
Abstract
There has been a growing appreciation of the importance of respiratory fungal diseases in recent years, with better understanding of their prevalence as well as their global distribution. In step with the greater awareness of these complex infections, we are currently poised to make major advances in the characterization and treatment of these fungal diseases, which in itself is largely a consequence of post-genomic technologies which have enabled rational drug development and a path towards personalized medicines. These advances are set against a backdrop of globalization and anthropogenic change, which have impacted the world-wide distribution of fungi and antifungal resistance, as well as our built environment. The current revolution in immunomodulatory therapies has led to a rapidly evolving population at-risk for respiratory fungal disease. Whilst challenges are considerable, perhaps the tools we now have to manage these infections are up to this challenge. There has been a welcome acceleration of the antifungal pipeline in recent years, with a number of new drug classes in clinical or pre-clinical development, as well as new focus on inhaled antifungal drug delivery. The "post-genomic" revolution has opened up metagenomic diagnostic approaches spanning host immunogenetics to the fungal mycobiome that have allowed better characterization of respiratory fungal disease endotypes. When these advances are considered together the key challenge is clear: to develop a personalized medicine framework to enable a rational therapeutic approach.
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Respiratory Mycoses: A Call to Action to Recognize, Educate and Invest. Mycopathologia 2021; 186:569-573. [PMID: 34490550 PMCID: PMC8421193 DOI: 10.1007/s11046-021-00589-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 08/21/2021] [Indexed: 02/08/2023]
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Tiew PY, Hou Lim AY, Keir HR, Dicker AJ, Aogáin MM, Pang SL, Boon LT, Hassan TM, Poh ME, Xu H, Ong TH, Koh MS, Abisheganaden JA, Tee A, Chew FT, Chalmers JD, Chotirmall SH. HIGH FREQUENCY OF ALLERGIC BRONCHOPULMONARY ASPERGILLOSIS IN BRONCHIECTASIS-COPD OVERLAP. Chest 2021; 161:40-53. [PMID: 34364870 DOI: 10.1016/j.chest.2021.07.2165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 07/22/2021] [Accepted: 07/25/2021] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Allergic bronchopulmonary aspergillosis (ABPA) is associated with frequent exacerbations and poor outcomes in chronic respiratory disease but remains underdiagnosed. The role of fungal sensitization in bronchiectasis-COPD overlap (BCO) is unknown. RESEARCH QUESTION What is the occurrence and clinical relevance of Aspergillus sensitization and ABPA in BCO when compared to individuals with COPD or bronchiectasis without overlap? STUDY DESIGN Prospective, observational and cross-sectional. METHODS We prospectively recruited n=280 patients during periods of clinical stability with bronchiectasis (n=183), COPD (n=50) and BCO (n=47) from six hospitals across three countries (Singapore, Malaysia, and Scotland). We assessed sensitization responses (as specific IgE) to a panel of recombinant Aspergillus fumigatus (rAsp f) allergens and the occurrence of ABPA (ABPA) in relation to clinical outcomes. RESULTS Individuals with BCO illustrate an increased frequency and clinical severity of ABPA compared to COPD and bronchiectasis without overlap. BCO-associated ABPA demonstrates more severe disease, higher exacerbation rates and lower lung function when compared to ABPA occurring in the absence of overlap. BCO with a severe bronchiectasis severity index (BSI) (>9) significantly associates with the occurrence of ABPA that is unrelated to underlying COPD severity. CONCLUSIONS BCO demonstrates a high frequency of ABPA that associates with a severe BSI (>9) and poor clinical outcomes. Clinicians should maintain a high index of suspicion for the potential development of ABPA in BCO patients with high BSI.
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Affiliation(s)
- Pei Yee Tiew
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore; Department of Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore
| | - Albert Yick Hou Lim
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore; Department of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore
| | - Holly R Keir
- Ninewells Hospital and Medical School, University of Dundee, UK
| | - Alison J Dicker
- Ninewells Hospital and Medical School, University of Dundee, UK
| | - Micheál Mac Aogáin
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Sze Lei Pang
- Department of Biological Sciences, National University of Singapore
| | - Low Teck Boon
- Department of Respiratory and Critical Care Medicine, Changi General Hospital, Singapore
| | | | - Mau Ern Poh
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Huiying Xu
- Department of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore
| | - Thun How Ong
- Department of Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore
| | - Mariko Siyue Koh
- Department of Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore
| | - John Arputhan Abisheganaden
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore; Department of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore
| | - Augustine Tee
- Department of Respiratory and Critical Care Medicine, Changi General Hospital, Singapore
| | - Fook Tim Chew
- Department of Biological Sciences, National University of Singapore
| | | | - Sanjay H Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore.
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Forscher identifizieren Hochrisiko-Mykobiom. Pneumologie 2021. [DOI: 10.1055/a-1481-4113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Pashley CH, Wardlaw AJ. Allergic fungal airways disease (AFAD): an under-recognised asthma endotype. Mycopathologia 2021; 186:609-622. [PMID: 34043134 PMCID: PMC8536613 DOI: 10.1007/s11046-021-00562-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 05/04/2021] [Indexed: 12/13/2022]
Abstract
The term allergic fungal airways disease has a liberal definition based on IgE sensitisation to thermotolerant fungi and evidence of fungal-related lung damage. It arose from a body of work looking into the role of fungi in asthma. Historically fungi were considered a rare complication of asthma, exemplified by allergic bronchopulmonary aspergillosis; however, there is a significant proportion of individuals with Aspergillus fumigatus sensitisation who do not meet these criteria, who are at high risk for the development of lung damage. The fungi that play a role in asthma can be divided into two groups; those that can grow at body temperature referred to as thermotolerant, which are capable of both infection and allergy, and those that cannot but can still act as allergens in IgE sensitised individuals. Sensitisation to thermotolerant filamentous fungi (Aspergillus and Penicillium), and not non-thermotolerant fungi (Alternaria and Cladosporium) is associated with lower lung function and radiological abnormalities (bronchiectasis, tree-in-bud, fleeting shadows, collapse/consolidation and fibrosis). For antifungals to play a role in treatment, the focus should be on fungi capable of growing in the airways thereby causing a persistent chronic allergenic stimulus and releasing tissue damaging proteases and other enzymes which may disrupt the airway epithelial barrier and cause mucosal damage and airway remodelling. All patients with IgE sensitisation to thermotolerant fungi in the context of asthma and other airway disease are at risk of progressive lung damage, and as such should be monitored closely.
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Affiliation(s)
- Catherine H Pashley
- Department of Respiratory Sciences, Institute for Lung Health, University of Leicester, University Road, Leicester, LE1 7RH, UK.
| | - Andrew J Wardlaw
- Department of Respiratory Sciences, Institute for Lung Health, University of Leicester, University Road, Leicester, LE1 7RH, UK
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Wu YX, Zuo YH, Cheng QJ, Huang Y, Bao ZY, Jin XY, Gao XW, Tu CL, Hu WP, Hang JQ, Wang WQ, Zhang FY, Zhang J. Respiratory Aspergillus Colonization Was Associated With Relapse of Acute Exacerbation in Patients With Chronic Obstructive Pulmonary Disease: Analysis of Data From A Retrospective Cohort Study. Front Med (Lausanne) 2021; 8:640289. [PMID: 34017841 PMCID: PMC8129169 DOI: 10.3389/fmed.2021.640289] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 04/06/2021] [Indexed: 12/31/2022] Open
Abstract
Background: Patients with chronic obstructive pulmonary disease (COPD) are more susceptible to Aspergillus colonization or infection. Several studies have demonstrated that invasive pulmonary Aspergillosis (IPA) and Aspergillus hypersensitivity (AH) have a detrimental effect on COPD. However, it remains to be clarified whether Aspergillus colonization is associated with acute exacerbation of COPD (AECOPD). This study aimed to explore the impact of Aspergillus colonization in the lower respiratory tract on AECOPD. Method: Patients with Aspergillus colonization were identified from a retrospective cohort of hospitalized AECOPD from 2011 to 2016 in eight centers in Shanghai, China. The demographic information, conditions of the stable stage, clinical characteristics during hospitalization, and 1-year follow-up information after discharge were collected and compared to participants without fungi colonization. Result: Twenty-six hospitalized AECOPD patients with Aspergillus colonization and 72 controls were included in the final analysis after excluding patients with other fungi isolation and matching. The rates of recurrence of acute exacerbation within 90 days and 180 days after discharge in the patients with Aspergillus colonization were both significantly higher than that in the fungi negative patients (90 days: 19.2 vs. 4.2%, p = 0.029; 180 days: 23.1 vs. 4.2%, p = 0.010), and the all-cause mortality within 1 year was also higher (11.5 vs. 0.0%, p = 0.017). Multivariate logistic regression analysis showed that Aspergillus colonization was an independent risk factor for the recurrence of acute exacerbation within 90 days and 180 days (90 days: OR = 8.661, 95% CI: 1.496-50.159, p = 0.016; 180 days: OR =10.723, 95% CI: 1.936-59.394, p = 0.007). Conclusion:Aspergillus colonization may predict poor prognosis of AECOPD while leading to an increased risk of recurrent AECOPD in a short period.
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Affiliation(s)
- Yi-Xing Wu
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yi-Hui Zuo
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Qi-Jian Cheng
- Department of Respiratory Medicine, Ruijin North Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yi Huang
- Department of Pulmonary and Critical Care Medicine, Changhai Hospital of Shanghai, Second Military Medical University, Shanghai, China
| | - Zhi-Yao Bao
- Department of Respiratory Medicine, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiao-Yan Jin
- Department of Respiratory Medicine, Tongren Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xi-Wen Gao
- Department of Respiratory Medicine, Central Hospital of Minhang District, Shanghai, Fudan University, Shanghai, China
| | - Chun-Lin Tu
- Department of Respiratory Medicine, Central Hospital of Jiading District, Shanghai, Fudan University, Shanghai, China
| | - Wei-Ping Hu
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jing-Qing Hang
- Department of Respiratory Medicine, Shanghai Putuo District People's Hospital, Shanghai, China
| | - Wei-Qin Wang
- Department of Respiratory Medicine, Tongren Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Feng-Ying Zhang
- Department of Respiratory Medicine, Shanghai Putuo District People's Hospital, Shanghai, China
| | - Jing Zhang
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
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Martinsen EMH, Eagan TML, Leiten EO, Haaland I, Husebø GR, Knudsen KS, Drengenes C, Sanseverino W, Paytuví-Gallart A, Nielsen R. The pulmonary mycobiome-A study of subjects with and without chronic obstructive pulmonary disease. PLoS One 2021; 16:e0248967. [PMID: 33826639 PMCID: PMC8026037 DOI: 10.1371/journal.pone.0248967] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 03/08/2021] [Indexed: 12/12/2022] Open
Abstract
Background The fungal part of the pulmonary microbiome (mycobiome) is understudied. We report the composition of the oral and pulmonary mycobiome in participants with COPD compared to controls in a large-scale single-centre bronchoscopy study (MicroCOPD). Methods Oral wash and bronchoalveolar lavage (BAL) was collected from 93 participants with COPD and 100 controls. Fungal DNA was extracted before sequencing of the internal transcribed spacer 1 (ITS1) region of the fungal ribosomal RNA gene cluster. Taxonomic barplots were generated, and we compared taxonomic composition, Shannon index, and beta diversity between study groups, and by use of inhaled steroids. Results The oral and pulmonary mycobiomes from controls and participants with COPD were dominated by Candida, and there were more Candida in oral samples compared to BAL for both study groups. Malassezia and Sarocladium were also frequently found in pulmonary samples. No consistent differences were found between study groups in terms of differential abundance/distribution. Alpha and beta diversity did not differ between study groups in pulmonary samples, but beta diversity varied with sample type. The mycobiomes did not seem to be affected by use of inhaled steroids. Conclusion Oral and pulmonary samples differed in taxonomic composition and diversity, possibly indicating the existence of a pulmonary mycobiome.
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Affiliation(s)
| | - Tomas M. L. Eagan
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway
| | - Elise O. Leiten
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Ingvild Haaland
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Gunnar R. Husebø
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway
| | - Kristel S. Knudsen
- Department of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway
| | - Christine Drengenes
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway
| | | | | | - Rune Nielsen
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway
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Respiratory Mycoses in COPD and Bronchiectasis. Mycopathologia 2021; 186:623-638. [PMID: 33709335 DOI: 10.1007/s11046-021-00539-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/22/2021] [Indexed: 02/07/2023]
Abstract
Chronic obstructive pulmonary disease (COPD) and bronchiectasis represent chronic airway diseases associated with significant morbidity and mortality. Bacteria and viruses are commonly implicated in acute exacerbations; however the significance of fungi in these airways remains poorly defined. While COPD and bronchiectasis remain recognized risk factors for the occurrence of Aspergillus-associated disease including chronic and invasive aspergillosis, underlying mechanisms that lead to the progression from colonization to invasive disease remain uncertain. Nonetheless, advances in molecular technologies have improved our detection, identification and understanding of resident fungi characterizing these airways. Mycobiome sequencing has revealed the complex varied and myriad profile of airway fungi in COPD and bronchiectasis, including their association with disease presentation, progression, and mortality. In this review, we outline the emerging evidence for the clinical importance of fungi in COPD and bronchiectasis, available diagnostic modalities, mycobiome sequencing approaches and association with clinical outcomes.
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