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Missa KF, Diallo K, Bla KB, Tuo KJ, Gboko KDT, Tiémélé LS, Ouattara AF, Gragnon BG, Ngoi JM, Wilkinson RJ, Awandare GA, Bonfoh B. Association of symptomatic upper respiratory tract infections with the alteration of the oropharyngeal microbiome in a cohort of school children in Côte d'Ivoire. Front Microbiol 2024; 15:1412923. [PMID: 38993497 PMCID: PMC11238735 DOI: 10.3389/fmicb.2024.1412923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 05/29/2024] [Indexed: 07/13/2024] Open
Abstract
Introduction The oropharyngeal microbiome plays an important role in protection against infectious agents when in balance. Despite use of vaccines and antibiotic therapy to prevent respiratory tract infections, they remain one of the major causes of mortality and morbidity in Low- and middle-income countries. Hence the need to explore other approaches to prevention by identifying microbial biomarkers that could be leveraged to modify the microbiota in order to enhance protection against pathogenic bacteria. The aim of this study was to analyze the oropharyngeal microbiome (OPM) of schoolchildren in Côte d'Ivoire presenting symptoms of upper respiratory tract infections (URTI) for better prevention strategy. Methods Primary schools' children in Korhogo (n = 37) and Abidjan (n = 39) were followed for six months with monthly oropharyngeal sampling. Clinical diagnostic of URT infection was performed and nucleic acid extracted from oropharyngeal swabs were used for 16S rRNA metagenomic analysis and RT-PCR. Results The clinical examination of children's throat in Abidjan and Korhogo identified respectively 17 (43.59%) and 15 (40.54%) participants with visible symptoms of URTIs, with 26 episodes of infection in Abidjan and 24 in Korhogo. Carriage of Haemophilus influenzae (12%), Streptococcus pneumoniae (6%) and SARS-CoV-2 (6%) was confirmed by PCR. A significant difference in alpha diversity was found between children colonized by S. pneumoniae and those that were not (p = 0.022). There was also a significant difference in alpha diversity between children colonised with H. influenzae and those who were not (p = 0.017). No significant difference was found for SARS-CoV-2. Sphingomonas, Ralstonia and Rothia were significantly enriched in non-carriers of S. pneumoniae; Actinobacillus was significantly enriched in non-carriers of H. influenzae; Actinobacillus and Porphyromonas were significantly enriched in non-carriers of SARS-CoV-2 (p < 0.001). Discussion Nearly 40% of children showed clinical symptoms of infection not related to geographical location. The OPM showed an imbalance during H. influenzae and S. pneumoniae carriage. This study provides a baseline understanding of microbiome markers in URTIs in children for future research, to develop targeted interventions aimed at restoring the microbial balance and reducing the symptoms associated with RTIs.
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Affiliation(s)
- Kouassi Firmin Missa
- Direction de la Recherche et du Développement, Centre Suisse de Recherches Scientifiques en Côte d'Ivoire, Abidjan, Côte d'Ivoire
- Laboratoire de Biologie et Santé, UFR Biosciences, Université Félix Houphouët Boigny de Cocody, Abidjan, Côte d'Ivoire
| | - Kanny Diallo
- Direction de la Recherche et du Développement, Centre Suisse de Recherches Scientifiques en Côte d'Ivoire, Abidjan, Côte d'Ivoire
- West African Centre for Cell Biology of Infectious Pathogens, Accra, Ghana
| | - Kouakou Brice Bla
- Laboratoire de Biologie et Santé, UFR Biosciences, Université Félix Houphouët Boigny de Cocody, Abidjan, Côte d'Ivoire
| | - Kolotioloman Jérémie Tuo
- Direction de la Recherche et du Développement, Centre Suisse de Recherches Scientifiques en Côte d'Ivoire, Abidjan, Côte d'Ivoire
- Laboratoire de Microbiologie, Biotechnologies et Bio-informatique, Institut National Polytechnique Félix Houphouët-Boigny, Yamoussoukro, Côte d'Ivoire
| | - Kossia Debia Thérèse Gboko
- Direction de la Recherche et du Développement, Centre Suisse de Recherches Scientifiques en Côte d'Ivoire, Abidjan, Côte d'Ivoire
| | - Laurent-Simon Tiémélé
- Direction de la Recherche et du Développement, Centre Suisse de Recherches Scientifiques en Côte d'Ivoire, Abidjan, Côte d'Ivoire
| | - Allassane Foungoye Ouattara
- Direction de la Recherche et du Développement, Centre Suisse de Recherches Scientifiques en Côte d'Ivoire, Abidjan, Côte d'Ivoire
- Laboratoire de Cytologie et Biologie Animale, Université Nangui Abrogoua, Abidjan, Côte d'Ivoire
| | - Biego Guillaume Gragnon
- Laboratoire de Cytologie et Biologie Animale, Université Nangui Abrogoua, Abidjan, Côte d'Ivoire
| | | | - Robert J Wilkinson
- Laboratoire National d'Appui au Développement Agricole, Laboratoire Régional de Korhogo, Korhogo, Côte d'Ivoire
- The Francis Crick Institute, London, United Kingdom
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Gordon A Awandare
- West African Centre for Cell Biology of Infectious Pathogens, Accra, Ghana
| | - Bassirou Bonfoh
- Direction de la Recherche et du Développement, Centre Suisse de Recherches Scientifiques en Côte d'Ivoire, Abidjan, Côte d'Ivoire
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Kruk ME, Mehta S, Murray K, Higgins L, Do K, Johnson JE, Wagner R, Wendt CH, O'Connor JB, Harris JK, Laguna TA, Jagtap PD, Griffin TJ. An integrated metaproteomics workflow for studying host-microbe dynamics in bronchoalveolar lavage samples applied to cystic fibrosis disease. mSystems 2024:e0092923. [PMID: 38934598 DOI: 10.1128/msystems.00929-23] [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: 09/01/2023] [Accepted: 05/13/2024] [Indexed: 06/28/2024] Open
Abstract
Airway microbiota are known to contribute to lung diseases, such as cystic fibrosis (CF), but their contributions to pathogenesis are still unclear. To improve our understanding of host-microbe interactions, we have developed an integrated analytical and bioinformatic mass spectrometry (MS)-based metaproteomics workflow to analyze clinical bronchoalveolar lavage (BAL) samples from people with airway disease. Proteins from BAL cellular pellets were processed and pooled together in groups categorized by disease status (CF vs. non-CF) and bacterial diversity, based on previously performed small subunit rRNA sequencing data. Proteins from each pooled sample group were digested and subjected to liquid chromatography tandem mass spectrometry (MS/MS). MS/MS spectra were matched to human and bacterial peptide sequences leveraging a bioinformatic workflow using a metagenomics-guided protein sequence database and rigorous evaluation. Label-free quantification revealed differentially abundant human peptides from proteins with known roles in CF, like neutrophil elastase and collagenase, and proteins with lesser-known roles in CF, including apolipoproteins. Differentially abundant bacterial peptides were identified from known CF pathogens (e.g., Pseudomonas), as well as other taxa with potentially novel roles in CF. We used this host-microbe peptide panel for targeted parallel-reaction monitoring validation, demonstrating for the first time an MS-based assay effective for quantifying host-microbe protein dynamics within BAL cells from individual CF patients. Our integrated bioinformatic and analytical workflow combining discovery, verification, and validation should prove useful for diverse studies to characterize microbial contributors in airway diseases. Furthermore, we describe a promising preliminary panel of differentially abundant microbe and host peptide sequences for further study as potential markers of host-microbe relationships in CF disease pathogenesis.IMPORTANCEIdentifying microbial pathogenic contributors and dysregulated human responses in airway disease, such as CF, is critical to understanding disease progression and developing more effective treatments. To this end, characterizing the proteins expressed from bacterial microbes and human host cells during disease progression can provide valuable new insights. We describe here a new method to confidently detect and monitor abundance changes of both microbe and host proteins from challenging BAL samples commonly collected from CF patients. Our method uses both state-of-the art mass spectrometry-based instrumentation to detect proteins present in these samples and customized bioinformatic software tools to analyze the data and characterize detected proteins and their association with CF. We demonstrate the use of this method to characterize microbe and host proteins from individual BAL samples, paving the way for a new approach to understand molecular contributors to CF and other diseases of the airway.
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Affiliation(s)
- Monica E Kruk
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minneapolis, Minnesota, USA
| | - Subina Mehta
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minneapolis, Minnesota, USA
| | - Kevin Murray
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minneapolis, Minnesota, USA
- Center for Metabolomics and Proteomics, University of Minnesota, Minneapolis, Minnesota, USA
| | - LeeAnn Higgins
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minneapolis, Minnesota, USA
- Center for Metabolomics and Proteomics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Katherine Do
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minneapolis, Minnesota, USA
| | - James E Johnson
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota, USA
| | - Reid Wagner
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota, USA
| | - Chris H Wendt
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Medical School, University of Minnesota, Minneapolis, Minnesota, USA
- Minneapolis VA Health Care System, Minneapolis, Minnesota, USA
| | - John B O'Connor
- Department of Pediatrics, Division of Pulmonary and Sleep Medicine, Seattle Children's Hospital, Seattle, Washington, USA
| | - J Kirk Harris
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Theresa A Laguna
- Department of Pediatrics, Division of Pulmonary and Sleep Medicine, Seattle Children's Hospital, Seattle, Washington, USA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA
| | - Pratik D Jagtap
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minneapolis, Minnesota, USA
| | - Timothy J Griffin
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minneapolis, Minnesota, USA
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3
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Schwarz C, Bend J, Hebestreit H, Hogardt M, Hügel C, Illing S, Mainz JG, Rietschel E, Schmidt S, Schulte-Hubbert B, Sitter H, Wielpütz MO, Hammermann J, Baumann I, Brunsmann F, Dieninghoff D, Eber E, Ellemunter H, Eschenhagen P, Evers C, Gruber S, Koitschev A, Ley-Zaporozhan J, Düesberg U, Mentzel HJ, Nüßlein T, Ringshausen FC, Sedlacek L, Smaczny C, Sommerburg O, Sutharsan S, Vonberg RP, Weber AK, Zerlik J. [CF Lung Disease - a German S3 Guideline: Pseudomonas aeruginosa]. Pneumologie 2024; 78:367-399. [PMID: 38350639 DOI: 10.1055/a-2182-1907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2024]
Abstract
Cystic Fibrosis (CF) is the most common autosomal recessive genetic multisystemic disease. In Germany, it affects at least 8000 people. The disease is caused by mutations in the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) gene leading to dysfunction of CFTR, a transmembrane chloride channel. This defect causes insufficient hydration of the airway epithelial lining fluid which leads to reduction of the mucociliary clearance.Even if highly effective, CFTR modulator therapy has been available for some years and people with CF are getting much older than before, recurrent and chronic infections of the airways as well as pulmonary exacerbations still occur. In adult CF life, Pseudomonas aeruginosa (PA) is the most relevant pathogen in colonisation and chronic infection of the lung, leading to further loss of lung function. There are many possibilities to treat PA-infection.This is a S3-clinical guideline which implements a definition for chronic PA-infection and demonstrates evidence-based diagnostic methods and medical treatment in order to give guidance for individual treatment options.
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Affiliation(s)
- Carsten Schwarz
- Klinikum Westbrandenburg GmbH, Standort Potsdam, Deutschland
| | - Jutta Bend
- Mukoviszidose Institut gGmbH, Bonn, Deutschland
| | | | - Michael Hogardt
- Klinikum der Johann Wolfgang Goethe-Universität Frankfurt am Main, Institut für Medizinische Mikrobiologie und Krankenhaushygiene, Frankfurt, Deutschland
| | - Christian Hügel
- Klinikum der Johann Wolfgang Goethe-Universität Frankfurt am Main, Deutschland
| | | | - Jochen G Mainz
- Klinikum Westbrandenburg, Standort Brandenburg an der Havel, Universitätsklinikum der Medizinischen Hochschule Brandenburg (MHB), Brandenburg an der Havel, Deutschland
| | - Ernst Rietschel
- Medizinische Fakultät der Universität zu Köln, Mukoviszidose-Zentrum, Klinik und Poliklinik für Kinder- und Jugendmedizin, Köln, Deutschland
| | - Sebastian Schmidt
- Ernst-Moritz-Arndt Universität Greifswald, Kinderpoliklinik, Allgemeine Pädiatrie, Greifswald, Deutschland
| | | | - Helmut Sitter
- Philipps-Universität Marburg, Institut für theoretische Medizin, Marburg, Deutschland
| | - Marc Oliver Wielpütz
- Universitätsklinikum Heidelberg, Klinik für Diagnostische und Interventionelle Radiologie, Heidelberg, Deutschland
| | - Jutta Hammermann
- Universitäts-Mukoviszidose-Zentrum "Christiane Herzog", Dresden, Deutschland
| | - Ingo Baumann
- Universität Heidelberg, Hals-Nasen-Ohrenklinik, Heidelberg, Deutschland
| | - Frank Brunsmann
- Allianz Chronischer Seltener Erkrankungen (ACHSE) e. V., Deutschland (Patient*innenvertreter)
| | | | - Ernst Eber
- Medizinische Universität Graz, Univ. Klinik für Kinder- und Jugendheilkunde, Klinische Abteilung für Pädiatrische Pulmonologie und Allergologie, Graz, Österreich
| | - Helmut Ellemunter
- Tirolkliniken GmbH, Department für Kinderheilkunde, Pädiatrie III, Innsbruck, Österreich
| | | | | | - Saskia Gruber
- Medizinische Universität Wien, Universitätsklinik für Kinder- und Jugendheilkunde, Wien, Österreich
| | - Assen Koitschev
- Klinikum Stuttgart - Standort Olgahospital, Klinik für Hals-Nasen-Ohrenkrankheiten, Stuttgart, Deutschland
| | - Julia Ley-Zaporozhan
- Klinik und Poliklinik für Radiologie, Kinderradiologie, LMU München, Deutschland
| | | | - Hans-Joachim Mentzel
- Universitätsklinikum Jena, Sektion Kinderradiologie, Institut für Diagnostische und Interventionelle Radiologie, Jena, Deutschland
| | - Thomas Nüßlein
- Gemeinschaftsklinikum Mittelrhein, Klinik für Kinder- und Jugendmedizin Koblenz und Mayen, Koblenz, Deutschland
| | - Felix C Ringshausen
- Medizinische Hochschule Hannover, Klinik für Pneumologie und Infektiologie und Deutsches Zentrum für Lungenforschung (DZL), Hannover, Deutschland
| | - Ludwig Sedlacek
- Medizinische Hochschule Hannover, Institut für Medizinische Mikrobiologie und Krankenhaushygiene, Hannover, Deutschland
| | - Christina Smaczny
- Klinikum der Johann Wolfgang Goethe-Universität Frankfurt am Main, Deutschland
| | - Olaf Sommerburg
- Universitätsklinikum Heidelberg, Sektion Pädiatrische Pneumologie, Allergologie und Mukoviszidose-Zentrum, Heidelberg, Deutschland
| | | | - Ralf-Peter Vonberg
- Medizinische Hochschule Hannover, Institut für Medizinische Mikrobiologie und Krankenhaushygiene, Hannover, Deutschland
| | | | - Jovita Zerlik
- Altonaer Kinderkrankenhaus gGmbH, Abteilung Physiotherapie, Hamburg, Deutschland
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Xepapadaki P, Megremis S, Rovina N, Wardzyńska A, Pasioti M, Kritikou M, Papadopoulos NG. Exploring the Impact of Airway Microbiome on Asthma Morbidity: A Focus on the "Constructing a 'Eubiosis Reinstatement Therapy' for Asthma-CURE" Project. Pulm Ther 2024:10.1007/s41030-024-00261-3. [PMID: 38814533 DOI: 10.1007/s41030-024-00261-3] [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: 02/26/2024] [Accepted: 05/02/2024] [Indexed: 05/31/2024] Open
Abstract
The asthma pandemic imposes a huge burden on patients and health systems in both developed and developing countries. Despite available treatments, symptom control is generally suboptimal, and hospitalizations and deaths remain at unacceptably high levels. A pivotal aspect of asthma that warrants further exploration is the influence of the respiratory microbiome and virome in modulating disease activity. A plethora of studies report that the respiratory microbiome is characteristically dysbiotic in asthma. In addition, our data suggest that dysbiosis is also observed on the respiratory virome, partly characterized by the reduced abundance of bacteriophages (phages). Even though phages can naturally infect and control their bacterial prey, phage therapy has been grossly neglected in the Western world, although more recently it is more widely used as a novel tool against bacterial infections. However, it has never been used for tackling microbiome dysbiosis in human non-communicable diseases. This review provides an up-to-date understanding of the microbiome and virome's role within the airways in relation to asthma morbidity. It also advances the rationale and hypothesis for the CURE project. Specifically, the CURE project suggests that managing the respiratory microbiome through phage therapy is viable and may result in restoring eubiosis within the asthmatic airway. This entails controlling immune dysregulation and the clinical manifestation of the disease. To accomplish this goal, it is crucial to predict the effects of introducing specific phage mixtures into the intricate ecology of the airways and devise suitable interventions.
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Affiliation(s)
- Paraskevi Xepapadaki
- Allergy Department, 2nd Paediatric Clinic, National and Kapodistrian University of Athens, 41, Fidippidou, 11527, Athens, Greece.
| | - Spyridon Megremis
- Department of Genetics and Genome Biology, Centre for Phage Research, University of Leicester, Leicester, UK
| | - Nikoletta Rovina
- 1st Department of Respiratory Medicine, Sotiria Hospital, School of Medicine, National and Kapodistrian University of Athens, 11527, Athens, Greece
| | | | - Maria Pasioti
- Allergy Department, 2nd Paediatric Clinic, National and Kapodistrian University of Athens, 41, Fidippidou, 11527, Athens, Greece
| | - Maria Kritikou
- Allergy Department, 2nd Paediatric Clinic, National and Kapodistrian University of Athens, 41, Fidippidou, 11527, Athens, Greece
| | - Nikolaos G Papadopoulos
- Allergy Department, 2nd Paediatric Clinic, National and Kapodistrian University of Athens, 41, Fidippidou, 11527, Athens, Greece
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5
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Chung J, Boutin S, Frey DL, Joachim C, Mall MA, Sommerburg O. Nasal lavage microbiome, but not nasal swab microbiome, correlates with sinonasal inflammation in children with cystic fibrosis. J Cyst Fibros 2024; 23:226-233. [PMID: 38199892 DOI: 10.1016/j.jcf.2023.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 12/08/2023] [Accepted: 12/25/2023] [Indexed: 01/12/2024]
Abstract
BACKGROUND Cystic fibrosis (CF) is characterized by highly viscous mucus obstructing the lower and upper airways, chronic neutrophil inflammation and infection resulting not only in lung destruction but also in paranasal sinus involvement. The pathogenesis of CF-associated chronic rhinosinusitis (CRS) is still not well understood, and it remains unclear how the microbiome in the upper airways (UAW) influences paranasal sinus inflammation. METHODS In a cross-sectional study in pediatric patients with CF under stable disease conditions, we examined the microbiome in relation to inflammation by comparing nasal swabs (NS) and nasal lavage (NL) as two UAW sampling methods. The microbiota structure of both NS and NL was determined by 16S rRNA gene amplicon sequencing. In addition, pro-inflammatory cytokines (IL-1β, IL-6, IL-8, TNF-α) and proteases (SLPI, TIMP-1, NE/A1-AT complex) as well as neutrophil elastase activity were measured in NL. RESULTS Simultaneous NS and NL samples were collected from 36 patients with CF (age range: 7 - 19 years). The microbiome of NS samples was shown to be significantly lower in α-diversity and evenness compared to NL samples. NS samples were particularly found to be colonized with Staphylococcus species. NL microbiome was shown to correlate much better with the sinonasal inflammation status than NS microbiome. Especially the detection of Moraxella in NL was associated with increased inflammatory response. CONCLUSION Our results show that the NL microbiome reflects sinonasal inflammation better than NS and support NL as a promising tool for simultaneous assessment of the UAW microbiome and inflammation in children with CF.
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Affiliation(s)
- Jaehi Chung
- Division of Pediatric Pulmonology & Allergy and Cystic Fibrosis Center, Department of Pediatrics III, University of Heidelberg, Im Neuenheimer Feld 430, Heidelberg 69120, Germany; Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), Im Neuenheimer Feld 156, Heidelberg 69120, Germany.
| | - Sébastien Boutin
- Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), Im Neuenheimer Feld 156, Heidelberg 69120, Germany; Department of Infectiology and Microbiology, University Hospital Schleswig Holstein, Lübeck 23538, Germany
| | - Dario L Frey
- Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), Im Neuenheimer Feld 156, Heidelberg 69120, Germany; Division Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Cornelia Joachim
- Division of Pediatric Pulmonology & Allergy and Cystic Fibrosis Center, Department of Pediatrics III, University of Heidelberg, Im Neuenheimer Feld 430, Heidelberg 69120, Germany
| | - Marcus A Mall
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine and Cystic Fibrosis Center, Charité-Universitätsmedizin Berlin, Berlin 13353, Germany; Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin 10178, Germany; German Center for Lung Research (DZL), Associated Partner Site, Berlin 13353, Germany
| | - Olaf Sommerburg
- Division of Pediatric Pulmonology & Allergy and Cystic Fibrosis Center, Department of Pediatrics III, University of Heidelberg, Im Neuenheimer Feld 430, Heidelberg 69120, Germany; Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), Im Neuenheimer Feld 156, Heidelberg 69120, Germany
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6
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Reuter S, Raspe J, Taube C. Microbes little helpers and suppliers for therapeutic asthma approaches. Respir Res 2024; 25:29. [PMID: 38218816 PMCID: PMC10787474 DOI: 10.1186/s12931-023-02660-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 12/28/2023] [Indexed: 01/15/2024] Open
Abstract
Bronchial asthma is a prevalent and increasingly chronic inflammatory lung disease affecting over 300 million people globally. Initially considered an allergic disorder driven by mast cells and eosinophils, asthma is now recognized as a complex syndrome with various clinical phenotypes and immunological endotypes. These encompass type 2 inflammatory endotypes characterized by interleukin (IL)-4, IL-5, and IL-13 dominance, alongside others featuring mixed or non-eosinophilic inflammation. Therapeutic success varies significantly based on asthma phenotypes, with inhaled corticosteroids and beta-2 agonists effective for milder forms, but limited in severe cases. Novel antibody-based therapies have shown promise, primarily for severe allergic and type 2-high asthma. To address this gap, novel treatment strategies are essential for better control of asthma pathology, prevention, and exacerbation reduction. One promising approach involves stimulating endogenous anti-inflammatory responses through regulatory T cells (Tregs). Tregs play a vital role in maintaining immune homeostasis, preventing autoimmunity, and mitigating excessive inflammation after pathogenic encounters. Tregs have demonstrated their ability to control both type 2-high and type 2-low inflammation in murine models and dampen human cell-dependent allergic airway inflammation. Furthermore, microbes, typically associated with disease development, have shown immune-dampening properties that could be harnessed for therapeutic benefits. Both commensal microbiota and pathogenic microbes have demonstrated potential in bacterial-host interactions for therapeutic purposes. This review explores microbe-associated approaches as potential treatments for inflammatory diseases, shedding light on current and future therapeutics.
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Affiliation(s)
- Sebastian Reuter
- Department of Pulmonary Medicine, University Hospital Essen-Ruhrlandklinik, Tüschener Weg 40, 45239, Essen, Germany.
| | - Jonas Raspe
- Department of Pulmonary Medicine, University Hospital Essen-Ruhrlandklinik, Tüschener Weg 40, 45239, Essen, Germany
| | - Christian Taube
- Department of Pulmonary Medicine, University Hospital Essen-Ruhrlandklinik, Tüschener Weg 40, 45239, Essen, Germany
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7
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Jezkova J, Sonka K, Kreisinger J, Prochazkova P, Tlaskalova-Hogenova H, Nevsimalova S, Buskova J, Merkova R, Dvorakova T, Prihodova I, Dostalova S, Roubalova R. Guardians of Rest? Investigating the gut microbiota in central hypersomnolence disorders. Sleep Med 2024; 113:95-102. [PMID: 37995475 DOI: 10.1016/j.sleep.2023.11.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/03/2023] [Accepted: 11/15/2023] [Indexed: 11/25/2023]
Abstract
In recent years, there has been an increased interest in elucidating the influence of the gut microbiota on sleep physiology. The gut microbiota affects the central nervous system by modulating neuronal pathways through the neuroendocrine and immune system, the hypothalamus-pituitary-adrenal axis, and various metabolic pathways. The gut microbiota can also influence circadian rhythms. In this study, we observed the gut microbiota composition of patients suffering from narcolepsy type 1, narcolepsy type 2, and idiopathic hypersomnia. We did not observe any changes in the alpha diversity of the gut microbiota among patient groups and healthy controls. We observed changes in beta diversity in accordance with Jaccard dissimilarities between the control group and groups of patients suffering from narcolepsy type 1 and idiopathic hypersomnia. Our results indicate that both these patient groups differ from controls relative to the presence of rare bacterial taxa. However, after adjustment for various confounding factors such as BMI, age, and gender, there were no statistical differences among the groups. This indicates that the divergence in beta diversity in the narcolepsy type 1 and idiopathic hypersomnia groups did not arise due to sleep disturbances. This study implies that using metabolomics and proteomics approaches to study the role of microbiota in sleep disorders might prove beneficial.
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Affiliation(s)
- Janet Jezkova
- Laboratory of Cellular and Molecular Immunology, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic; First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Karel Sonka
- Department of Neurology and Center of Clinical Neuroscience, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Jakub Kreisinger
- Faculty of Science, Department of Zoology, Charles University, Prague, Czech Republic
| | - Petra Prochazkova
- Laboratory of Cellular and Molecular Immunology, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Helena Tlaskalova-Hogenova
- Laboratory of Cellular and Molecular Immunology, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Sona Nevsimalova
- Department of Neurology and Center of Clinical Neuroscience, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Jitka Buskova
- National Institute of Mental Health, Klecany, Czech Republic; Third Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Radana Merkova
- National Institute of Mental Health, Klecany, Czech Republic; Third Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Tereza Dvorakova
- National Institute of Mental Health, Klecany, Czech Republic; Third Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Iva Prihodova
- Department of Neurology and Center of Clinical Neuroscience, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Simona Dostalova
- Department of Neurology and Center of Clinical Neuroscience, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Radka Roubalova
- Laboratory of Cellular and Molecular Immunology, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic.
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Harris JK, Wagner BD, Robertson CE, Stevens MJ, Lingard C, Borowitz D, Leung DH, Heltshe SL, Ramsey BW, Zemanick ET. Upper airway microbiota development in infants with cystic fibrosis diagnosed by newborn screen. J Cyst Fibros 2023; 22:644-651. [PMID: 37137746 PMCID: PMC10524365 DOI: 10.1016/j.jcf.2023.04.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 04/03/2023] [Accepted: 04/21/2023] [Indexed: 05/05/2023]
Abstract
BACKGROUND Changes in upper airway microbiota may impact early disease manifestations in infants with cystic fibrosis (CF). To investigate early airway microbiota, the microbiota present in the oropharynx of CF infants over the first year of life was assessed along with the relationships between microbiota and growth, antibiotic use and other clinical variables. METHODS Oropharyngeal (OP) swabs were collected longitudinally between 1 and 12 months of age from infants diagnosed with CF by newborn screen and enrolled in the Baby Observational and Nutrition Study (BONUS). DNA extraction was performed after enzymatic digestion of OP swabs. Total bacterial load was determined by qPCR and community composition assessed using 16S rRNA gene analysis (V1/V2 region). Changes in diversity with age were evaluated using mixed models with cubic B-splines. Associations between clinical variables and bacterial taxa were determined using a canonical correlation analysis. RESULTS 1,052 OP swabs collected from 205 infants with CF were analyzed. Most infants (77%) received at least one course of antibiotics during the study and 131 OP swabs were collected while the infant was prescribed an antibiotic. Alpha diversity increased with age and was only marginally impacted by antibiotic use. Community composition was most highly correlated with age and was only moderately correlated with antibiotic exposure, feeding method and weight z-scores. Relative abundance of Streptococcus decreased while Neisseria and other taxa increased over the first year. CONCLUSIONS Age was more influential on the oropharyngeal microbiota of infants with CF than clinical variables including antibiotics in the first year of life.
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Affiliation(s)
- J Kirk Harris
- Department of Pediatrics, University of Colorado Anschutz Medical Campus and Children's Hospital Colorado, 13123 E. 16th Ave, B-395, Aurora, CO 80045, USA.
| | - Brandie D Wagner
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Charles E Robertson
- Department of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Mark J Stevens
- Department of Pediatrics, University of Colorado Anschutz Medical Campus and Children's Hospital Colorado, 13123 E. 16th Ave, B-395, Aurora, CO 80045, USA
| | - Conor Lingard
- Spartanburg Regional Healthcare Systems, Spartanburg, SC, USA
| | - Drucy Borowitz
- Department of Pediatrics, Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY, USA
| | - Daniel H Leung
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Sonya L Heltshe
- Cystic Fibrosis Foundation Therapeutic Development Network Coordinating Center, Seattle Children's Research Institute, Seattle, WA, USA; Division of Pulmonary and Sleep Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Bonnie W Ramsey
- Cystic Fibrosis Foundation Therapeutic Development Network Coordinating Center, Seattle Children's Research Institute, Seattle, WA, USA; Division of Pulmonary and Sleep Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Edith T Zemanick
- Department of Pediatrics, University of Colorado Anschutz Medical Campus and Children's Hospital Colorado, 13123 E. 16th Ave, B-395, Aurora, CO 80045, USA
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9
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Tosco A, Poli P, Casale A, De Gregorio F, Sepe A, Buonpensiero P, Di Pasqua A, Castaldo A, Cimbalo C, Buzzetti R, Raia V, Berlucchi M, Timpano S, Badolato R, Padoan R, Orlando C. The Role of Bronchoscopy in the Management of Children With Cystic Fibrosis. J Bronchology Interv Pulmonol 2023; 30:258-267. [PMID: 35698279 DOI: 10.1097/lbr.0000000000000874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 04/25/2022] [Indexed: 11/25/2022]
Abstract
BACKGROUND Currently, no consensus guidelines recommend routine bronchoscopy procedure in cystic fibrosis (CF), as no evidence is available concerning its use as either a diagnostic or therapeutic tool. Its efficacy is controversial, and no randomized controlled prospective trials are available to check its effectiveness. The aims of the present study were to evaluate the effectiveness of bronchoscopy as a diagnostic/therapeutic tool in CF children and adolescents; and to verify the effect of serial bronchoscopy on lung disease progression in subjects with CF not responding to a single procedure. METHODS Data of patients who received bronchoscopy at 2 Italian CF centers were collected. Bronchoalveolar lavage was performed during the procedure including airway clearance with mucolytics, inhaled antibiotics, and/or surfactant instillation. RESULTS A total of 16 patients in center 1 and 17 in center 2 underwent, respectively, 28 and 23 bronchoscopic procedure in the study period. Five patients in each center underwent >1 procedure. All procedures were generally well tolerated. No patient required admission to the pediatric intensive therapy unit. In 19.6% of bronchoalveolar lavages, growth of Aspergillus fumigatus was evident, although not detected by sputum analyses. After the procedure, an increase in mean percent predicted forced expiratory volume in the 1 second >10% was observed, and a significant decrease in pulmonary exacerbations yearly was evident. CONCLUSION Based on the results, we suggest bronchoscopy is not to be considered an obsolete tool, and it remains useful in CF management, although in selected cases. We encourage to support longitudinal observational studies to standardize the procedure, focusing on the choice of drugs to be instilled, modalities and timing of serial bronchoscopy and subsequent follow-up in selected severe clinical conditions.
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Affiliation(s)
- Antonella Tosco
- Pediatric Unit, Department of Translational Medical Sciences, Regional Cystic Fibrosis Center, Federico II University
| | - Piercarlo Poli
- Paediatric Department, Cystic Fibrosis Support Centre, University of Brescia, ASST Spedali Civili Brescia
| | - Alida Casale
- Pediatric Unit, Department of Translational Medical Sciences, Regional Cystic Fibrosis Center, Federico II University
| | - Fabiola De Gregorio
- Pediatric Unit, Department of Translational Medical Sciences, Regional Cystic Fibrosis Center, Federico II University
| | - Angela Sepe
- Pediatric Unit, Department of Translational Medical Sciences, Regional Cystic Fibrosis Center, Federico II University
| | - Paolo Buonpensiero
- Pediatric Unit, Department of Translational Medical Sciences, Regional Cystic Fibrosis Center, Federico II University
| | - Antonio Di Pasqua
- Pediatric Unit, Department of Translational Medical Sciences, Regional Cystic Fibrosis Center, Federico II University
| | - Alice Castaldo
- Pediatric Unit, Department of Translational Medical Sciences, Regional Cystic Fibrosis Center, Federico II University
| | - Chiara Cimbalo
- Pediatric Unit, Department of Translational Medical Sciences, Regional Cystic Fibrosis Center, Federico II University
| | - Roberto Buzzetti
- Pediatric Unit, Department of Translational Medical Sciences, Regional Cystic Fibrosis Center, Federico II University
- Freelance Epidemiologist, Bergamo, Italy
| | - Valeria Raia
- Pediatric Unit, Department of Translational Medical Sciences, Regional Cystic Fibrosis Center, Federico II University
| | - Marco Berlucchi
- Unit of Pediatric Otorhinolaryngology, ASST Spedali Civili Brescia
| | - Silviana Timpano
- Paediatric Department, Cystic Fibrosis Support Centre, University of Brescia, ASST Spedali Civili Brescia
| | - Raffaele Badolato
- Paediatric Department, Cystic Fibrosis Support Centre, University of Brescia, ASST Spedali Civili Brescia
- Department of Molecular and Translational Medicine, Angelo Nocivelli Institute for Molecular Medicine, University of Brescia, Brescia
| | - Rita Padoan
- Paediatric Department, Cystic Fibrosis Support Centre, University of Brescia, ASST Spedali Civili Brescia
- Department of Molecular and Translational Medicine, Angelo Nocivelli Institute for Molecular Medicine, University of Brescia, Brescia
| | - Claudio Orlando
- Department of Pediatric Respiratory Endoscopy and Difficult Airways Management, Naples
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10
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Kaufmann B, Seyfried N, Hartmann D, Hartmann P. Probiotics, prebiotics, and synbiotics in nonalcoholic fatty liver disease and alcohol-associated liver disease. Am J Physiol Gastrointest Liver Physiol 2023; 325:G42-G61. [PMID: 37129252 PMCID: PMC10312326 DOI: 10.1152/ajpgi.00017.2023] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 04/26/2023] [Accepted: 04/26/2023] [Indexed: 05/03/2023]
Abstract
The use of probiotics, prebiotics, and synbiotics has become an important therapy in numerous gastrointestinal diseases in recent years. Modifying the gut microbiota, this therapeutic approach helps to restore a healthy microbiome. Nonalcoholic fatty liver disease and alcohol-associated liver disease are among the leading causes of chronic liver disease worldwide. A disrupted intestinal barrier, microbial translocation, and an altered gut microbiome metabolism, or metabolome, are crucial in the pathogenesis of these chronic liver diseases. As pro-, pre-, and synbiotics modulate these targets, they were identified as possible new treatment options for liver disease. In this review, we highlight the current findings on clinical and mechanistic effects of this therapeutic approach in nonalcoholic fatty liver disease and alcohol-associated liver disease.
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Affiliation(s)
- Benedikt Kaufmann
- Department of Surgery, Klinikum rechts der Isar, Technical University Munich, Munich, Germany
| | - Nick Seyfried
- Department of Surgery, Klinikum rechts der Isar, Technical University Munich, Munich, Germany
| | - Daniel Hartmann
- Department of Surgery, Klinikum rechts der Isar, Technical University Munich, Munich, Germany
| | - Phillipp Hartmann
- Department of Surgery, Klinikum rechts der Isar, Technical University Munich, Munich, Germany
- Department of Pediatrics, University of California San Diego, La Jolla, California, United States
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11
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Sarkar S, Routhray S, Ramadass B, Parida PK. A Review on the Nasal Microbiome and Various Disease Conditions for Newer Approaches to Treatments. Indian J Otolaryngol Head Neck Surg 2023; 75:755-763. [PMID: 37206729 PMCID: PMC10188862 DOI: 10.1007/s12070-022-03205-y] [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: 06/10/2022] [Accepted: 09/23/2022] [Indexed: 12/14/2022] Open
Abstract
Introduction: Commensal bacteria have always played a significant role in the maintenance of health and disease but are being unravelled only recently. Studies suggest that the nasal microbiome has a significant role in the development of various disease conditions. Search engines were used for searching articles having a nasal microbiome and disease correlation. In olfactory dysfunction, dysbiosis of the microbiome may have a significant role to play in the pathogenesis. The nasal microbiome influences the phenotype of CRS and is also capable of modulating the immune response and plays a role in polyp formation. Microbiome dysbiosis has a pivotal role in the development of Allergic Rhinitis; but, yet known how is this role played. The nasal microbiome has a close association with the severity and phenotype of asthma. They contribute significantly to the onset, severity, and development of asthma. The nasal microbiome has a significant impact on the immunity and protection of its host. The nasal microbiome has been a stimulus in the development of Otitis Media and its manifestations. Studies suggest that the resident nasal microbiome is responsible for the initiation of neurodegenerative diseases like Parkinson's Disease.Materials and Methods: Literature search from PubMed, Medline, and Google with the Mesh terms: nasal microbiome AND diseases. Conclusion: With increasing evidence on the role of the nasal microbiome on various diseases, it would be interesting to see how this microbiome can be modulated by pro/pre/post biotics to prevent a disease or the severity of illness.
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Affiliation(s)
- Saurav Sarkar
- Department of Otorhinolaryngology and Head Neck Surgery, All India Institute of Medical Sciences, Bhubaneswar, India
| | - Samapika Routhray
- Department of Dentistry, All India Institute of Medical Sciences, Bhubaneswar, India
| | - Balamurugan Ramadass
- Department of Biochemistry, All India Institute of Medical Sciences, Bhubaneswar, India
| | - Pradipta Kumar Parida
- Department of Otorhinolaryngology and Head Neck Surgery, All India Institute of Medical Sciences, Bhubaneswar, India
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12
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Wucherpfennig L, Wuennemann F, Eichinger M, Seitz A, Baumann I, Stahl M, Graeber SY, Zhao S, Chung J, Schenk JP, Alrajab A, Kauczor HU, Mall MA, Sommerburg O, Wielpütz MO. Long-term effects of lumacaftor/ivacaftor on paranasal sinus abnormalities in children with cystic fibrosis detected with magnetic resonance imaging. Front Pharmacol 2023; 14:1161891. [PMID: 37101549 PMCID: PMC10123276 DOI: 10.3389/fphar.2023.1161891] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 03/29/2023] [Indexed: 04/28/2023] Open
Abstract
Introduction: Chronic rhinosinusitis (CRS) usually presents with nasal congestion, rhinorrhea and anosmia impacts quality of life in cystic fibrosis (CF). Especially mucopyoceles pathognomonic for CRS in CF may cause complications such as spread of infection. Previous studies using magnetic resonance imaging (MRI) demonstrated early onset and progression of CRS from infancy to school age in patients with CF, and mid-term improvements of CRS in preschool and school-age children with CF treated with lumacaftor/ivacaftor for at least 2 months. However, long-term data on treatment effects on paranasal sinus abnomalities in preschool and school-age children with CF are lacking. Methods: 39 children with CF homozygous for F508del (mean age at baseline MRI 5.9 ± 3.0 years, range 1-12 years) underwent MRI before (MRI1) and about 7 months after starting lumacaftor/ivacaftor and then annually (median 3 follow-up MRI, range 1-4) (MRI2-4). MRI were evaluated using the previously evaluated CRS-MRI score with excellent inter-reader agreement. For intraindividual analysis ANOVA mixed-effects analysis including Geisser-Greenhouse correction and Fisher's exact test, and for interindividual group analysis Mann-Whitney test were used. Results: The CRS-MRI sum score at baseline was similar in children starting lumacaftor/ivacaftor in school age and children starting therapy at preschool age (34.6 ± 5.2 vs.32.9 ± 7.8, p = 0.847). Mucopyoceles were the dominant abnormality in both, especially in maxillary sinus (65% and 55%, respectively). In children starting therapy in school age the CRS-MRI sum score decreased longitudinally from MRI1 to MRI2 (-2.1 ± 3.5, p < 0.05), MRI3 (-3.0 ± 3.7, p < 0.01) and MRI4 (-3.6 ± 4.7, p < 0.01), mainly due to a decrease in the mucopyoceles subscore (-1.0 ± 1.5, p = 0.059; -1.2 ± 2.0, p < 0.05; -1.6 ± 1.8, p < 0.01; and -2.6 ± 2.8, p = 0.417, respectively). In children starting lumacaftor/ivacaftor in preschool age, the CRS-MRI sum score remained stable under therapy over all three follow-up MRI (0.6 ± 3.3, p = 0.520; 2.4 ± 7.6, p = 0.994; 2.1 ± 10.5, p > 0.999 and -0.5 ± 0.5, p = 0.740; respectively). Conclusion: Longitudinal paranasal sinus MRI shows improvements in paranasal sinus abnormalities in children with CF starting lumacaftor/ivacaftor therapy at school age. Further, MRI detects a prevention of an increase in paranasal sinus abnormalities in children with CF starting lumacaftor/ivacaftor therapy at preschool age. Our data support the role of MRI for comprehensive non-invasive therapy and disease monitoring of paranasal sinus abnormalities in children with CF.
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Affiliation(s)
- Lena Wucherpfennig
- Department of Diagnostic and Interventional Radiology, University Hospital Heidelberg, Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany
- Department of Diagnostic and Interventional Radiology with Nuclear Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Felix Wuennemann
- Department of Diagnostic and Interventional Radiology, University Hospital Heidelberg, Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany
- Department of Diagnostic and Interventional Radiology with Nuclear Medicine, University Hospital Heidelberg, Heidelberg, Germany
- Department of Diagnostic and Interventional Radiology and Neuroradiology, Helios Dr. Horst-Schmidt-Kliniken Wiesbaden, Wiesbaden, Germany
| | - Monika Eichinger
- Department of Diagnostic and Interventional Radiology, University Hospital Heidelberg, Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany
- Department of Diagnostic and Interventional Radiology with Nuclear Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Angelika Seitz
- Department of Neuroradiology, University Hospital Heidelberg, Heidelberg, Germany
| | - Ingo Baumann
- Department of Otorhinolaryngology, Head and Neck Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Mirjam Stahl
- Department of Pediatric Respiratory Medicine, Immunology and Intensive Care Medicine, Charité-Universitätsmedizin Berlin, Berlin, Germany
- German Center for Lung Research (DZL), Berlin, Germany
- Berlin Institute of Health (BIH) at Charité—Universitätsmedizin Berlin, Berlin, Germany
| | - Simon Y. Graeber
- Department of Pediatric Respiratory Medicine, Immunology and Intensive Care Medicine, Charité-Universitätsmedizin Berlin, Berlin, Germany
- German Center for Lung Research (DZL), Berlin, Germany
- Berlin Institute of Health (BIH) at Charité—Universitätsmedizin Berlin, Berlin, Germany
| | - Shengkai Zhao
- Department of Diagnostic and Interventional Radiology, University Hospital Heidelberg, Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany
| | - Jaehi Chung
- Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany
- Division of Pediatric Pulmonology, Allergy, and Cystic Fibrosis Center, Department of Pediatrics III, University Hospital Heidelberg, Heidelberg, Germany
| | - Jens-Peter Schenk
- Department of Diagnostic and Interventional Radiology, University Hospital Heidelberg, Heidelberg, Germany
| | - Abdulsattar Alrajab
- Department of Diagnostic and Interventional Radiology, University Hospital Heidelberg, Heidelberg, Germany
| | - Hans-Ulrich Kauczor
- Department of Diagnostic and Interventional Radiology, University Hospital Heidelberg, Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany
- Department of Diagnostic and Interventional Radiology with Nuclear Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Marcus A. Mall
- Department of Pediatric Respiratory Medicine, Immunology and Intensive Care Medicine, Charité-Universitätsmedizin Berlin, Berlin, Germany
- German Center for Lung Research (DZL), Berlin, Germany
- Berlin Institute of Health (BIH) at Charité—Universitätsmedizin Berlin, Berlin, Germany
| | - Olaf Sommerburg
- Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany
- Division of Pediatric Pulmonology, Allergy, and Cystic Fibrosis Center, Department of Pediatrics III, University Hospital Heidelberg, Heidelberg, Germany
| | - Mark O. Wielpütz
- Department of Diagnostic and Interventional Radiology, University Hospital Heidelberg, Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany
- Department of Diagnostic and Interventional Radiology with Nuclear Medicine, University Hospital Heidelberg, Heidelberg, Germany
- *Correspondence: Mark O. Wielpütz,
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13
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Zhang Y, He B, Wu L, Mi X, Zhang L, Li S, Wang J, Yu X. Exposure to particulate matter 2.5 leading to lung microbiome disorder and the alleviation effect of Auricularia auricular-judae polysaccharide. Int J Occup Med Environ Health 2022; 35:651-664. [PMID: 35913271 PMCID: PMC10464723 DOI: 10.13075/ijomeh.1896.01742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 08/20/2021] [Indexed: 10/16/2022] Open
Abstract
OBJECTIVES The aim of the paper is to explore the role of lung microbiome disorder in lung tissue injury induced by exposure to particulate matter with a maximum diameter of 2.5 μm (PM2.5) and the alleviation effect of Auricularia auricular-judae polysaccharide (AAP). MATERIAL AND METHODS Sprague Dawley rats were given PM2.5 suspension at a dose of 20 mg/l twice a week for 8 weeks. Then, 100 mg/kg or 200 mg/kg of AAP was administered to the rats after PM2.5 exposure. The bronchoalveolar lavage fluid (BALF) and lung tissue samples were collected at the end of the experiment. The BALF was meant to detect changes in lung microbiome by 16S sequences and cluster analysis, with the application of the principal component analysis and the partial least squares discriminant analysis. The levels of interferon-γ (IFN-γ), and interleukin (IL)-4, IL-8, and IL-10 in lung tissue were detected by the enzyme-linked immunosorbent assay method. The pathological changes in lung tissue were observed by hematoxylin and eosin staining. RESULTS After PM2.5 exposure, the alveolar septum was widened, and the structures of alveolar walls were destroyed. There was inflammatory cells infiltration in the alveolar space and the interstitial space. Alpha diversity in BALF showed that the Chao1, ACE, Simpson, and Shannon values were increased, and the lung microbiome analysis revealed that the relative abundance of Firmicutes and Clostridium increased, while the relative abundance of Bacteroidetes and Akkermansia decreased. The contents of IFN-γ and IL-8 in lung tissue increased while the content of IL-10 decreased. After the administration of AAP, the alveolar structure damage was alleviated, and the interstitial hemorrhage, edema, and inflammatory cells infiltration were reduced. The Chao1 and ACE values decreased, and the taxonomic abundance values of Akkermansia were much higher. Simultaneously, the contents of IFN-γ, IL-4, and IL-8 decreased, and the content of IL-10 increased. CONCLUSIONS It was found that PM2.5 resulted in lung microbiome disorder, which might lead to the inflammation of lung tissue. It was also revealed that AAP could alleviate the inflammatory damage of lung tissue induced by PM2.5. Int J Occup Med Environ Health. 2022;35(6):651-64.
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Affiliation(s)
- Yanshu Zhang
- School of Public Health, North China University of Science and Technology, Tangshan, People's Republic of China
- Experiment Animal Center, North China University of Science and Technology, Tangshan, People's Republic of China
| | - Bin He
- School of Public Health, North China University of Science and Technology, Tangshan, People's Republic of China
- Experiment Animal Center, North China University of Science and Technology, Tangshan, People's Republic of China
| | - Lei Wu
- School of Public Health, North China University of Science and Technology, Tangshan, People's Republic of China
| | - Xiaoyi Mi
- School of Public Health, North China University of Science and Technology, Tangshan, People's Republic of China
| | - Lijin Zhang
- School of Public Health, North China University of Science and Technology, Tangshan, People's Republic of China
| | - Shuang Li
- Experiment Animal Center, North China University of Science and Technology, Tangshan, People's Republic of China
| | - Jian Wang
- Experiment Animal Center, North China University of Science and Technology, Tangshan, People's Republic of China
| | - Xiaoyu Yu
- School of Psychology and Mental Health, North China University of Science and Technology, Tangshan, People's Republic of China
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14
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Kahl BC, Moreau K. Editorial: Co-Infection and Consequences in Cystic Fibrosis. Front Cell Infect Microbiol 2022; 12:924527. [PMID: 35719342 PMCID: PMC9199434 DOI: 10.3389/fcimb.2022.924527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 05/05/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Barbara C. Kahl
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany
| | - Karen Moreau
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Lyon, France
- *Correspondence: Karen Moreau,
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15
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Pathogen detection and characterization from throat swabs using unbiased metatranscriptomic analyses. Int J Infect Dis 2022; 122:260-265. [PMID: 35662643 DOI: 10.1016/j.ijid.2022.05.062] [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: 01/06/2022] [Revised: 04/05/2022] [Accepted: 05/27/2022] [Indexed: 11/22/2022] Open
Abstract
OBJECTIVES Infectious diseases are common but are not easily or readily diagnosed with current methodologies. This problem is further exacerbated by the constant presence of mutated, emerging, and novel pathogens. One of the most common sites of infection by many pathogens is the human throat. However, there is no universal diagnostic test that can distinguish these pathogens. Metatranscriptomic (MT) analysis of the throat represents an important and novel development in infectious disease detection and characterization, because it is able to identify all pathogens using a fully unbiased approach. METHODS To test the utility of an MT approach to pathogen detection, throat samples were collected from participants before, during, and after an acute sickness. RESULTS Clear sickness-associated shifts in pathogenic microorganisms were detected in the patients. Important insights into microbial functions and antimicrobial resistance genes were obtained. CONCLUSION MT analysis of the throat represents an effective method for the unbiased identification and characterization of pathogens. Because MT data include all microorganisms in the sample, this approach should not only allow the identification of pathogens, but provide an understanding of the effects of the resident throat microbiome in the context of human health and disease.
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16
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Frey DL, Bridson C, Dittrich S, Graeber SY, Stahl M, Wege S, Herth F, Sommerburg O, Schultz C, Dalpke A, Mall MA, Boutin S. Changes in Microbiome Dominance Are Associated With Declining Lung Function and Fluctuating Inflammation in People With Cystic Fibrosis. Front Microbiol 2022; 13:885822. [PMID: 35633718 PMCID: PMC9136159 DOI: 10.3389/fmicb.2022.885822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/26/2022] [Indexed: 11/30/2022] Open
Abstract
Airway inflammation and microbiome dysbiosis are hallmarks of cystic fibrosis (CF) lung disease. However, longitudinal studies are needed to decipher which factors contribute to the long-term evolution of these key features of CF. We therefore evaluated the relationship between fluctuation in microbiome and inflammatory parameters in a longitudinal study including a short- (1-year) and a long-term (3+ years) period. We collected 118 sputum samples from 26 CF adult patients and analyzed them by 16S rRNA gene sequencing. We measured the levels of inflammatory cytokines, neutrophil elastase, and anti-proteinases; lung function (FEV1% predicted); and BMI. The longitudinal evolution was analyzed based on (i) the rates of changes; (ii) the intra-patient stability of the variables; and (iii) the dependency of the rates of changes on the baseline values. We observed that the diversity of the microbiome was highly variable over a 1-year period, while the inflammatory markers showed a slower evolution, with significant changes only observed in the 3+ year cohort. Further, the degree of fluctuation of the biomass and the dominance of the microbiome were associated with changes in inflammatory markers, especially IL-1β and IL-8. This longitudinal study demonstrates for the first time that the long-term establishment and periodical variation of the abundance of a dominant pathogen is associated with a more severe increase in inflammation. This result indicates that a single time point or 1-year study might fail to reveal the correlation between microbial evolution and clinical degradation in cystic fibrosis.
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Affiliation(s)
- Dario L. Frey
- Translational Lung Research Center (TLRC), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
- Department of Translational Pulmonology, University of Heidelberg, Heidelberg, Germany
| | - Calum Bridson
- Translational Lung Research Center (TLRC), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
- Department of Infectious Diseases, Medical Microbiology and Hygiene, University of Heidelberg, Heidelberg, Germany
| | - Susanne Dittrich
- Translational Lung Research Center (TLRC), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
- Department of Translational Pulmonology, University of Heidelberg, Heidelberg, Germany
- Department of Pneumology and Critical Care Medicine, Thoraxklinik at the University Hospital Heidelberg, Heidelberg, Germany
| | - Simon Y. Graeber
- Translational Lung Research Center (TLRC), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
- Department of Translational Pulmonology, University of Heidelberg, Heidelberg, Germany
- Division of Pediatric Pulmonology and Allergology and Cystic Fibrosis Center, Department of Pediatrics, University of Heidelberg, Heidelberg, Germany
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine and Cystic Fibrosis Center, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
- German Center for Lung Research (DZL), Associated Partner Site, Berlin, Germany
| | - Mirjam Stahl
- Translational Lung Research Center (TLRC), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
- Department of Translational Pulmonology, University of Heidelberg, Heidelberg, Germany
- Division of Pediatric Pulmonology and Allergology and Cystic Fibrosis Center, Department of Pediatrics, University of Heidelberg, Heidelberg, Germany
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine and Cystic Fibrosis Center, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
- German Center for Lung Research (DZL), Associated Partner Site, Berlin, Germany
| | - Sabine Wege
- Department of Pneumology and Critical Care Medicine, Thoraxklinik at the University Hospital Heidelberg, Heidelberg, Germany
| | - Felix Herth
- Translational Lung Research Center (TLRC), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
- Department of Pneumology and Critical Care Medicine, Thoraxklinik at the University Hospital Heidelberg, Heidelberg, Germany
| | - Olaf Sommerburg
- Translational Lung Research Center (TLRC), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
- Division of Pediatric Pulmonology and Allergology and Cystic Fibrosis Center, Department of Pediatrics, University of Heidelberg, Heidelberg, Germany
| | - Carsten Schultz
- Translational Lung Research Center (TLRC), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, OR, United States
| | - Alexander Dalpke
- Translational Lung Research Center (TLRC), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
- Department of Infectious Diseases, Medical Microbiology and Hygiene, University of Heidelberg, Heidelberg, Germany
- Institute of Medical Microbiology and Virology, Technische Universität Dresden, Dresden, Germany
| | - Marcus A. Mall
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine and Cystic Fibrosis Center, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
- German Center for Lung Research (DZL), Associated Partner Site, Berlin, Germany
| | - Sébastien Boutin
- Translational Lung Research Center (TLRC), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
- Department of Infectious Diseases, Medical Microbiology and Hygiene, University of Heidelberg, Heidelberg, Germany
- *Correspondence: Sébastien Boutin,
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17
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Rafiq R, Aleva FE, Schrumpf JA, Daniels JM, Bet PM, Boersma WG, Bresser P, Spanbroek M, Lips P, van den Broek TJ, Keijser BJF, van der Ven AJAM, Hiemstra PS, den Heijer M, de Jongh RT. Vitamin D supplementation in chronic obstructive pulmonary disease patients with low serum vitamin D: a randomized controlled trial. Am J Clin Nutr 2022; 116:491-499. [PMID: 35383823 PMCID: PMC9348978 DOI: 10.1093/ajcn/nqac083] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 03/30/2022] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Vitamin D deficiency is frequently found in patients with chronic obstructive pulmonary disease (COPD). Vitamin D has antimicrobial, anti-inflammatory, and immunomodulatory effects. Therefore, supplementation may prevent COPD exacerbations, particularly in deficient patients. OBJECTIVES We aimed to assess the effect of vitamin D supplementation on exacerbation rate in vitamin D-deficient patients with COPD. METHODS We performed a multicenter, double-blind, randomized controlled trial. COPD patients with ≥1 exacerbations in the preceding year and a vitamin D deficiency (15-50 nmol/L) were randomly allocated in a 1:1 ratio to receive either 16,800 International Units (IU) vitamin D3 or placebo once a week during 1 y. Primary outcome of the study was exacerbation rate. Secondary outcomes included time to first and second exacerbations, time to first and second hospitalizations, use of antibiotics and corticosteroids, pulmonary function, maximal respiratory mouth pressure, physical performance, skeletal muscle strength, systemic inflammatory markers, nasal microbiota composition, and quality of life. RESULTS The intention-to-treat population consisted of 155 participants. Mean ± SD serum 25-hydroxyvitamin D [25(OH)D] concentration after 1 y was 112 ± 34 nmol/L in the vitamin D group, compared with 42 ± 17 nmol/L in the placebo group. Vitamin D supplementation did not affect exacerbation rate [incidence rate ratio (IRR): 0.90; 95% CI: 0.67, 1.21]. In a prespecified subgroup analysis in participants with 25(OH)D concentrations of 15-25 nmol/L (n = 31), no effect of vitamin D supplementation was found (IRR: 0.91; 95% CI: 0.43, 1.93). No relevant differences were found between the intervention and placebo groups in terms of secondary outcomes. CONCLUSIONS Vitamin D supplementation did not reduce exacerbation rate in COPD patients with a vitamin D deficiency.This trial was registered at clinicaltrials.gov as NCT02122627.
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Affiliation(s)
| | - Floor E Aleva
- Department of Pulmonology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Jasmijn A Schrumpf
- Department of Pulmonology, Leiden University Medical Center, Leiden, Netherlands
| | - Johannes M Daniels
- Department of Pulmonology, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Pierre M Bet
- Department of Clinical Pharmacology and Pharmacy, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Wim G Boersma
- Department of Pulmonology, NorthWest Clinics, Alkmaar, Netherlands
| | - Paul Bresser
- Department of Pulmonology, Onze Lieve Vrouwe Gasthuis, Amsterdam, Netherlands
| | - Michiel Spanbroek
- Department of Pulmonology, Canisius Wilhelmina Hospital, Nijmegen, Netherlands
| | - Paul Lips
- Department of Internal Medicine and Endocrinology, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | | | | | | | - Pieter S Hiemstra
- Department of Pulmonology, Leiden University Medical Center, Leiden, Netherlands
| | - Martin den Heijer
- Department of Internal Medicine and Endocrinology, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Renate T de Jongh
- Department of Internal Medicine and Endocrinology, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - PRECOVID-study group
den HeijerMartinDepartment of Internal Medicine and Endocrinology, Amsterdam UMC Vrije Universiteit Amsterdam, Amsterdam, NetherlandsT de JonghRenateDepartment of Internal Medicine and Endocrinology, Amsterdam UMC Vrije Universiteit Amsterdam, Amsterdam, NetherlandsLipsPaulDepartment of Internal Medicine and Endocrinology, Amsterdam UMC Vrije Universiteit Amsterdam, Amsterdam, NetherlandsRafiqRachidaDepartment of Internal Medicine and Endocrinology, Amsterdam UMC Vrije Universiteit Amsterdam, Amsterdam, NetherlandsAlevaFloor EDepartment of Pulmonology, Radboud University Medical Center, Nijmegen, Netherlandsvan der VenAndréDepartment of Internal Medicine, Radboud University Medical Center, Nijmegen, NetherlandsHiemstraPieter SDepartment of Pulmonology, Leiden University Medical Center, Leiden, NetherlandsSchrumpfJasmijn ADepartment of Pulmonology, Leiden University Medical Center, Leiden, NetherlandsSlatsAnnelies MDepartment of Pulmonology, Leiden University Medical Center, Leiden, NetherlandsDaniëlsJohannes M ADepartment of Pulmonology, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, NetherlandsBetPierre MDepartment of Clinical Pharmacology and Pharmacy, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, NetherlandsBoersmaWim GDepartment of Pulmonology, NorthWest Clinics, Alkmaar, NetherlandsBresserPaulDepartment of Pulmonology, Onze Lieve Vrouwe Gasthuis, Amsterdam, NetherlandsSpanbroekMichielDepartment of Pulmonology, Canisius Wilhelmina Hospital, Nijmegen, NetherlandsHuismanPetraDepartment of Pulmonology, Amstelland Hospital, Amstelveen, Netherlandsvan WolferenSerge ADepartment of Pulmonology, Zaans Medical Center, Zaandam, NetherlandsBroedersMarielle E A CDepartment of Pulmonology, Jeroen Bosch Hospital, Den Bosch, Netherlandsvan HengelPeterDepartment of Pulmonology, Flevoziekenhuis, Almere, NetherlandsBraunstahlGert-JanDepartment of Pulmonology, Sint Franciscus Gasthuis, Rotterdam, Netherlands
- Department of Internal Medicine and Endocrinology, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
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18
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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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19
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Einarsson GG, Vanaudenaerde BM, Spence CD, Lee AJ, Boon M, Verleden GM, Elborn JS, Dupont LJ, Van Raemdonck D, Gilpin DF, Vos R, Verleden SE, Tunney MM. Microbial Community Composition in Explanted Cystic Fibrosis and Control Donor Lungs. Front Cell Infect Microbiol 2022; 11:764585. [PMID: 35368453 PMCID: PMC8966769 DOI: 10.3389/fcimb.2021.764585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 12/13/2021] [Indexed: 11/13/2022] Open
Abstract
To date, investigations of the microbiota in the lungs of people with Cystic Fibrosis (PWCF) have primarily focused on microbial community composition in luminal mucus, with fewer studies observing the microbiota in tissue samples from explanted lung tissue. Here, we analysed both tissue and airway luminal mucus samples extracted from whole explanted lungs of PWCF and unused donor lungs. We determined if the lung microbiota in end-stage CF varied within and between patients, was spatially heterogeneous and related to localized structural damage. Microbial community composition was determined by Illumina MiSeq sequencing and related to the CF-Computed Tomography (CT) score and features of end-stage lung disease on micro-CT. Ninety-eight CF tissue (n=11 patients), 20 CF luminal mucus (n=8 patients) and 33 donor tissue (n=4 patients) samples were analysed. Additionally, we compared 20 paired CF tissue and luminal mucus samples that enabled a direct “geographical” comparison of the microbiota in these two niches. Significant differences in microbial communities were apparent between the 3 groups. However, overlap between the three groups, particularly between CF and donor tissue and CF tissue and CF luminal mucus was also observed. Microbial diversity was lower in CF luminal mucus compared to CF tissue, with dominance higher in luminal mucus. For both CF and donor tissue, intra- and inter-patient variability in ecological parameters was observed. No relationships were observed between ecological parameters and CF-CT score, or features of end-stage lung disease. The end-stage CF lung is characterised by a low diversity microbiota, differing within and between individuals. No clear relationship was observed between regional microbiota variation and structural lung damage.
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Affiliation(s)
- Gisli G. Einarsson
- Halo Research Group, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, Belfast, United Kingdom
- *Correspondence: Gisli G. Einarsson,
| | - Bart M. Vanaudenaerde
- Leuven Lung Transplant Unit, Department of Chronic Diseases, Metabolism and Ageing, KU Leuven, Leuven, Belgium
| | - Christopher D. Spence
- Halo Research Group, School of Pharmacy, Queen’s University Belfast, Belfast, United Kingdom
| | - Andrew J. Lee
- Halo Research Group, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, Belfast, United Kingdom
| | - Mieke Boon
- Department of Pediatics, Cystic Fibrosis Center, UZ Leuven, Leuven, Belgium
| | - Geert M. Verleden
- Leuven Lung Transplant Unit, Department of Chronic Diseases, Metabolism and Ageing, KU Leuven, Leuven, Belgium
| | - J. Stuart Elborn
- Halo Research Group, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, Belfast, United Kingdom
| | - Lieven J. Dupont
- Leuven Lung Transplant Unit, Department of Chronic Diseases, Metabolism and Ageing, KU Leuven, Leuven, Belgium
| | - Dirk Van Raemdonck
- Leuven Lung Transplant Unit, Department of Chronic Diseases, Metabolism and Ageing, KU Leuven, Leuven, Belgium
| | - Deirdre F. Gilpin
- Halo Research Group, School of Pharmacy, Queen’s University Belfast, Belfast, United Kingdom
| | - Robin Vos
- Leuven Lung Transplant Unit, Department of Chronic Diseases, Metabolism and Ageing, KU Leuven, Leuven, Belgium
| | - Stijn E. Verleden
- Leuven Lung Transplant Unit, Department of Chronic Diseases, Metabolism and Ageing, KU Leuven, Leuven, Belgium
- Antwerp Surgical Training, Anatomy and Research Centre (ASTARC), University of Antwerp (UA), Wilrijk, Belgium
- Department of Thoracic & Vascular Surgery, University Hospital Antwerp (UZA), Edegem, Belgium
- Department of Pneumology, University Hospital Antwerp (UZA), Edegem, Belgium
| | - Michael M. Tunney
- Halo Research Group, School of Pharmacy, Queen’s University Belfast, Belfast, United Kingdom
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20
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Tony-Odigie A, Wilke L, Boutin S, Dalpke AH, Yi B. Commensal Bacteria in the Cystic Fibrosis Airway Microbiome Reduce P. aeruginosa Induced Inflammation. Front Cell Infect Microbiol 2022; 12:824101. [PMID: 35174108 PMCID: PMC8842722 DOI: 10.3389/fcimb.2022.824101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 01/12/2022] [Indexed: 12/13/2022] Open
Abstract
Chronic Pseudomonas aeruginosa infections play an important role in the progress of lung disease in patients suffering from cystic fibrosis (CF). Recent studies indicate that polymicrobial microbiome profiles in the airway are associated with less inflammation. Thus, the hypothesis was raised that certain commensal bacteria might protect the host from inflammation. We therefore performed a screening study with commensals isolated from CF airway microbiome samples to identify potential beneficial commensals. We isolated more than 80 aerobic or facultative anaerobic commensal strains, including strains from genera Streptococcus, Neisseria, Actinomyces, Corynebacterium, Dermabacter, Micrococcus and Rothia. Through a screening experiment of co-infection in human epithelial cell lines, we identified multiple commensal strains, especially strains belonging to Streptococcus mitis, that reduced P. aeruginosa triggered inflammatory responses. The results were confirmed by co-infection experiments in ex-vivo precision cut lung slices (PCLS) from mice. The underlying mechanisms of the complex host-pathogen-commensal crosstalk were investigated from both the host and the bacterial sides with a focus on S. mitis. Transcriptome changes in the host in response to co-infection and mono-infection were evaluated, and the results indicated that several signalling pathways mediating inflammatory responses were downregulated by co-infection with S. mitis and P. aeruginosa compared to P. aeruginosa mono-infection, such as neutrophil extracellular trap formation. The genomic differences among S. mitis strains with and without protective effects were investigated by whole genome sequencing, revealing genes only present in the S. mitis strains showing protective effects. In summary, through both in vitro and ex vivo studies, we could identify a variety of commensal strains that may reduce host inflammatory responses induced by P. aeruginosa infection. These findings support the hypothesis that CF airway commensals may protect the host from inflammation.
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Affiliation(s)
- Andrew Tony-Odigie
- Institute of Medical Microbiology and Virology, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Leonie Wilke
- Institute of Medical Microbiology and Virology, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Sébastien Boutin
- Translational Lung Research Center (TLRC), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
- Department of Infectious Diseases, Medical Microbiology and Hygiene, University of Heidelberg, Heidelberg, Germany
| | - Alexander H. Dalpke
- Institute of Medical Microbiology and Virology, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Buqing Yi
- Institute of Medical Microbiology and Virology, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- *Correspondence: Buqing Yi,
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21
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Ahmed B, Cox MJ, Cuthbertson L, James P, Gardner L, Cookson W, Davies J, Moffatt M, Bush A. Comparison of the airway microbiota in children with chronic suppurative lung disease. BMJ Open Respir Res 2021; 8:8/1/e001106. [PMID: 34949574 PMCID: PMC8705203 DOI: 10.1136/bmjresp-2021-001106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 11/19/2021] [Indexed: 12/31/2022] Open
Abstract
RATIONALE The airway microbiota is important in chronic suppurative lung diseases, such as primary ciliary dyskinesia (PCD) and cystic fibrosis (CF). This comparison has not previously been described but is important because difference between the two diseases may relate to the differing prognoses and lead to pathological insights and potentially, new treatments. OBJECTIVES To compare the longitudinal development of the airway microbiota in children with PCD to that of CF and relate this to age and clinical status. METHODS Sixty-two age-matched children (age range 0.5-17 years) with PCD or CF (n=31 in each group) were recruited prospectively and followed for 1.1 years. Throat swabs or sputum as well as clinical information were collected at routine clinical appointments. 16S rRNA gene sequencing was performed. MEASUREMENTS AND MAIN RESULTS The microbiota was highly individual and more diverse in PCD and differed in community composition when compared with CF. While Streptococcus was the most abundant genus in both conditions, Pseudomonas was more abundant in CF with Haemophilus more abundant in PCD (Padj=0.0005). In PCD only, an inverse relationship was seen in the relative abundance of Streptococcus and Haemophilus with age. CONCLUSIONS Bacterial community composition differs between children with PCD and those with CF. Pseudomonas is more prevalent in CF and Haemophilus in PCD, at least until infection with Pseudomonas supervenes. Interactions between organisms, particularly members of Haemophilus, Streptococcus and Pseudomonas genera appear important. Study of the interactions between these organisms may lead to new therapies or risk stratification.
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Affiliation(s)
- Bushra Ahmed
- National Heart and Lung Institute, Imperial College London, London, UK .,Department of Respiratory Paediatrics, Royal Brompton Hospital, London, UK
| | - Michael J Cox
- National Heart and Lung Institute, Imperial College London, London, UK
| | | | - Phillip James
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Laura Gardner
- National Heart and Lung Institute, Imperial College London, London, UK.,Department of Respiratory Paediatrics, Royal Brompton Hospital, London, UK
| | | | - Jane Davies
- Department of Respiratory Paediatrics, Royal Brompton Hospital, London, UK.,Gene Therapy, Imperial College London, London, UK
| | | | - Andrew Bush
- Department of Respiratory Paediatrics, Royal Brompton Hospital, London, UK
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22
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Metzger MI, Graeber SY, Stahl M, Sommerburg O, Mall MA, Dalpke AH, Boutin S. A Volatile and Dynamic Longitudinal Microbiome Is Associated With Less Reduction in Lung Function in Adolescents With Cystic Fibrosis. Front Cell Infect Microbiol 2021; 11:763121. [PMID: 34938669 PMCID: PMC8687143 DOI: 10.3389/fcimb.2021.763121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 11/10/2021] [Indexed: 11/13/2022] Open
Abstract
Progressive impairment in lung function caused by chronic polymicrobial airway infection remains the major cause of death in patients with cystic fibrosis (CF). Cross-sectional studies suggest an association between lung function decline and specific lung microbiome ecotypes. However, longitudinal studies on the stability of the airway microbiome are missing for adolescents with CF constituting the age group showing the highest rate of decline in lung function. In this study, we analyzed longitudinal lung function data and sputum samples collected over a period of 3 to 5 years from 12 adolescents with CF. The sputum microbiome was analyzed using 16S rRNA gene sequencing. Our results indicate that the individual course of the lung microbiome is associated with longitudinal lung function. In our cohort, patients with a dynamic, diverse microbiome showed a slower decline of lung function measured by FEV1% predicted, whereas a more stable and less diverse lung microbiome was related to worse outcomes. Specifically, a higher abundance of the phyla Bacteroidetes and Firmicutes was linked to a better clinical outcome, while Proteobacteria were correlated with a decline in FEV1% predicted. Our study indicates that the stability and diversity of the lung microbiome and the abundance of Bacteroidetes and Firmicutes are associated with the lung function decline and are one of the contributing factors to the disease severity.
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Affiliation(s)
- Marisa I Metzger
- Department of Infectious Diseases, Medical Microbiology and Hygiene, University of Heidelberg, Heidelberg, Germany.,Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), University of Heidelberg, Heidelberg, Germany
| | - Simon Y Graeber
- German Centre for Lung Research (DZL), Associated Partner Site, Berlin, Germany.,Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine and Cystic Fibrosis Center, Charité - Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute of Health (BIH), Berlin, Germany
| | - Mirjam Stahl
- German Centre for Lung Research (DZL), Associated Partner Site, Berlin, Germany.,Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine and Cystic Fibrosis Center, Charité - Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute of Health (BIH), Berlin, Germany
| | - Olaf Sommerburg
- Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), University of Heidelberg, Heidelberg, Germany.,Division of Pediatric Pulmonology & Allergy and Cystic Fibrosis Center, Department of Pediatrics, University of Heidelberg, Heidelberg, Germany.,Department of Translational Pulmonology, University of Heidelberg, Heidelberg, Germany
| | - Marcus A Mall
- German Centre for Lung Research (DZL), Associated Partner Site, Berlin, Germany.,Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine and Cystic Fibrosis Center, Charité - Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute of Health (BIH), Berlin, Germany
| | - Alexander H Dalpke
- Institute of Medical Microbiology and Virology, Technische Universität Dresden, Dresden, Germany
| | - Sébastien Boutin
- Department of Infectious Diseases, Medical Microbiology and Hygiene, University of Heidelberg, Heidelberg, Germany.,Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), University of Heidelberg, Heidelberg, Germany
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23
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Chronic Rhinosinusitis and Alzheimer's Disease-A Possible Role for the Nasal Microbiome in Causing Neurodegeneration in the Elderly. Int J Mol Sci 2021; 22:ijms222011207. [PMID: 34681867 PMCID: PMC8541405 DOI: 10.3390/ijms222011207] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/08/2021] [Accepted: 10/14/2021] [Indexed: 12/25/2022] Open
Abstract
Among millions of sufferers of chronic rhinosinusitis (CRS), the challenge is not only constantly coping with CRS-related symptoms, such as congested nose, sinus pain, and headaches, but also various complications, such as attention difficulties and possible depression. These complications suggest that neural activity in the central nervous system may be altered in those patients, leading to unexpected conditions, such as neurodegeneration in elderly patients. Recently, some studies linked the presence of CRS and cognitive impairments that could further develop into Alzheimer’s disease (AD). AD is the leading cause of dementia in the elderly and is characterised by progressive memory loss, cognitive behavioural deficits, and significant personality changes. The microbiome, especially those in the gut, has been recognised as a human organ and plays an important role in the development of various conditions, including AD. However, less attention has been paid to the microbiome in the nasal cavity. Increased nasal inflammatory responses due to CRS may be an initial event that changes local microbiome homeostasis, which may further affect neuronal integrity in the central nervous system resulting in AD. Evidence suggests a potential of β-amyloid deposition starting in olfactory neurons, which is then expanded from the nasal cavity to the central nervous system. In this paper, we reviewed currently available evidence that suggests this potential mechanism to advise the need to investigate the link between these two conditions.
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24
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Fenn D, Abdel-Aziz MI, Brinkman P, Kos R, Neerincx AH, Altenburg J, Weersink E, Haarman EG, Terheggen-Lagro SWJ, Maitland-van der Zee AH, Bos LDJ. Comparison of microbial composition of cough swabs and sputum for pathogen detection in patients with cystic fibrosis. J Cyst Fibros 2021; 21:52-60. [PMID: 34548223 DOI: 10.1016/j.jcf.2021.08.031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 08/18/2021] [Accepted: 08/23/2021] [Indexed: 01/04/2023]
Abstract
BACKGROUND With the continued advancement of CFTR modulator therapies there is likely to be a burgeoning population of adult cystic fibrosis (CF) patients unable to expectorate sputum. Consequently, the detection and surveillance of pulmonary colonisation, previously reliant on sputum culture, needs re-examining. We hypothesised that cough swabs analysed with culture-independent analysis of the 16S gene could serve as a surrogate for colonisation of the lower airways. METHODS Cough swabs and sputum samples were prospectively collected from consecutive adults and children with CF across two sites at regular outpatient appointments. Conventional culture analysis and next generation sequencing were used to compare paired same day samples. RESULTS Twenty-two adults and 8 paediatric patients provided 75 paired cough swabs and sputum samples. Alpha diversity measures showed increased bacterial richness in sputum, while evenness and Simpson's diveristy index were higher in cough swabs. Within each sampling technique, microbial composition showed greater similarity when considering intra-patient variation. Poor concordance was observed between culture independent cough swabs and culture dependent/independent sputum analysis for specific pathogens, with cough swabs unable to accurately identify commonly associated CF pathogens (AUROCC range: 0.51 to 0.64). CONCLUSION Culture independent analysis of cough swabs provides an inaccurate diagnosis of lower respiratory tract colonisation and should not be used as a diagnostic test in patients with CF.
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Affiliation(s)
- Dominic Fenn
- Department of respiratory medicine, Amsterdam UMC location AMC, Amsterdam, the Netherlands; Laboratory of Experimental Intensive Care and Anaesthesiology, Amsterdam UMC location AMC, Amsterdam, the Netherlands.
| | - Mahmoud I Abdel-Aziz
- Department of respiratory medicine, Amsterdam UMC location AMC, Amsterdam, the Netherlands
| | - Paul Brinkman
- Department of respiratory medicine, Amsterdam UMC location AMC, Amsterdam, the Netherlands
| | - Renate Kos
- Department of respiratory medicine, Amsterdam UMC location AMC, Amsterdam, the Netherlands
| | - Anne H Neerincx
- Department of respiratory medicine, Amsterdam UMC location AMC, Amsterdam, the Netherlands
| | - Josje Altenburg
- Department of respiratory medicine, Amsterdam UMC location AMC, Amsterdam, the Netherlands
| | - E Weersink
- Department of respiratory medicine, Amsterdam UMC location AMC, Amsterdam, the Netherlands
| | - Eric G Haarman
- Emma Children's Hospital, Department of Paediatric Pulmonology, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Suzanne W J Terheggen-Lagro
- Emma Children's Hospital, Department of Paediatric Pulmonology, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | | | - Lieuwe D J Bos
- Department of respiratory medicine, Amsterdam UMC location AMC, Amsterdam, the Netherlands; Laboratory of Experimental Intensive Care and Anaesthesiology, Amsterdam UMC location AMC, Amsterdam, the Netherlands; Intensive Care, Amsterdam UMC location AMC, Amsterdam, the Netherlands
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- Department of respiratory medicine, Amsterdam UMC location AMC, Amsterdam, the Netherlands
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25
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Effects of Lumacaftor-Ivacaftor on Lung Clearance Index, Magnetic Resonance Imaging, and Airway Microbiome in Phe508del Homozygous Patients with Cystic Fibrosis. Ann Am Thorac Soc 2021; 18:971-980. [PMID: 33600745 DOI: 10.1513/annalsats.202008-1054oc] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rationale: Previous studies showed that lumacaftor-ivacaftor therapy results in partial rescue of CFTR (cystic fibrosis [CF] transmembrane conductance regulator) activity and a moderate improvement of spirometry in Phe508del homozygous patients with CF. However, the effects of lumacaftor-ivacaftor on lung clearance index (LCI), lung morphology and perfusion detected by chest magnetic resonance imaging (MRI), and effects on the airway microbiome and inflammation remain unknown. Objectives: To investigate the effects of lumacaftor-ivacaftor on LCI, lung MRI scores, and airway microbiome and inflammation. Methods: In this prospective observational study we assessed clinical outcomes including spirometry and body mass index, LCI, lung MRI scores, sputum microbiome, and proinflammatory cytokines in 30 Phe508del homozygous patients with CF 12 years and older before and 8-16 weeks after initiation of lumacaftor-ivacaftor therapy. Results: Lumacaftor-ivacaftor had no effects on forced expiratory volume in 1 second (FEV1% predicted) (1.7%; 95% confidence interval [CI], -1.0% to 4.3%; P = 0.211) but improved LCI (-1.6; 95% CI, -2.6 to -0.5; P < 0.01) and MRI morphology (-1.3; 95% CI, -2.3 to -0.3; P < 0.05) and perfusion score (-1.2; 95% CI, -2.3 to -0.2; P < 0.05) in our study cohort. Furthermore, lumacaftor-ivacaftor decreased the total bacterial load (-1.8; 95% CI, -3.3 to -0.34; P < 0.05) and increased the Shannon diversity of the airway microbiome (0.4; 95% CI, 0.1 to 0.8; P < 0.05), and reduced IL-1β (interleukin-1β) concentration (median change, -324.2 pg/ml; 95% CI, -938.7 to 290.4 pg/ml; P < 0.05) in sputum of Phe508del homozygous patients. Conclusions: This study shows that lumacaftor-ivacaftor has beneficial effects on lung ventilation, morphology, and perfusion, as well as on the airway microbiome and inflammation in Phe508del homozygous patients. Our results suggest that LCI and MRI may be more sensitive than FEV1% predicted to detect response to CFTR modulator therapy in patients with chronic CF lung disease. Clinical trial registered with ClinicalTrials.gov (NCT02807415).
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26
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O'Brien TJ, Hassan MM, Harrison F, Welch M. An in vitro model for the cultivation of polymicrobial biofilms under continuous-flow conditions. F1000Res 2021; 10:801. [PMID: 34557293 PMCID: PMC8442117 DOI: 10.12688/f1000research.55140.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/04/2021] [Indexed: 02/04/2023] Open
Abstract
The airways of people with cystic fibrosis (CF) are often chronically colonised with a diverse array of bacterial and fungal species. However, little is known about the relative partitioning of species between the planktonic and biofilm modes of growth in the airways. Existing in vivo and in vitro models of CF airway infection are ill-suited for the long-term recapitulation of mixed microbial communities. Here we describe a simple, in vitro continuous-flow model for the cultivation of polymicrobial biofilms and planktonic cultures on different substrata. Our data provide evidence for inter-species antagonism and synergism in biofilm ecology. We further show that the type of substratum on which the biofilms grow has a profound influence on their species composition. This happens without any major alteration in the composition of the surrounding steady-state planktonic community. Our experimentally-tractable model enables the systematic study of planktonic and biofilm communities under conditions that are nutritionally reminiscent of the CF airway microenvironment, something not possible using any existing in vivo models of CF airway infection.
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Affiliation(s)
| | | | - Freya Harrison
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Martin Welch
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QR, UK
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27
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Cho HJ, Ha JG, Lee SN, Kim CH, Wang DY, Yoon JH. Differences and similarities between the upper and lower airway: focusing on innate immunity. Rhinology 2021; 59:441-450. [PMID: 34339483 DOI: 10.4193/rhin21.046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The nose is the first respiratory barrier to external pathogens, allergens, pollutants, or cigarette smoke, and vigorous immune responses are triggered when external pathogens come in contact with the nasal epithelium. The mucosal epithelial cells of the nose are essential to the innate immune response against external pathogens and transmit signals that modulate the adaptive immune response. The upper and lower airways share many physiological and immunological features, but there are also numerous differences. It is crucial to understand these differences and their contribution to pathophysiology in order to optimize treatments for inflammatory diseases of the respiratory tract. This review summarizes important differences in the embryological development, histological features, microbiota, immune responses, and cellular subtypes of mucosal epithelial cells of the nose and lungs.
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Affiliation(s)
- H-J Cho
- Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul, Korea.,Global Research Laboratory for Allergic Airway Disease, Yonsei University College of Medicine, Seoul, Korea.,The Airway Mucus Institute, Yonsei University College of Medicine, Seoul, Korea
| | - J G Ha
- Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul, Korea
| | - S N Lee
- Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul, Korea 2 Global Research Laboratory for Allergic Airway Disease, Yonsei University College of Medicine, Seoul, Korea
| | - C-H Kim
- Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul, Korea.,The Airway Mucus Institute, Yonsei University College of Medicine, Seoul, Korea
| | - D-Y Wang
- Department of Otolaryngology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - J-H Yoon
- Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul, Korea.,Global Research Laboratory for Allergic Airway Disease, Yonsei University College of Medicine, Seoul, Korea.,The Airway Mucus Institute, Yonsei University College of Medicine, Seoul, Korea
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28
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Ngunjiri JM, Taylor KJM, Ji H, Abundo MC, Ghorbani A, Kc M, Lee CW. Influenza A virus infection in turkeys induces respiratory and enteric bacterial dysbiosis correlating with cytokine gene expression. PeerJ 2021; 9:e11806. [PMID: 34327060 PMCID: PMC8310620 DOI: 10.7717/peerj.11806] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 06/27/2021] [Indexed: 12/24/2022] Open
Abstract
Turkey respiratory and gut microbiota play important roles in promoting health and production performance. Loss of microbiota homeostasis due to pathogen infection can worsen the disease or predispose the bird to infection by other pathogens. While turkeys are highly susceptible to influenza viruses of different origins, the impact of influenza virus infection on turkey gut and respiratory microbiota has not been demonstrated. In this study, we investigated the relationships between low pathogenicity avian influenza (LPAI) virus replication, cytokine gene expression, and respiratory and gut microbiota disruption in specific-pathogen-free turkeys. Differential replication of two LPAI H5N2 viruses paralleled the levels of clinical signs and cytokine gene expression. During active virus shedding, there was significant increase of ileal and nasal bacterial contents, which inversely corresponded with bacterial species diversity. Spearman’s correlation tests between bacterial abundance and local viral titers revealed that LPAI virus-induced dysbiosis was strongest in the nasal cavity followed by trachea, and weakest in the gut. Significant correlations were also observed between cytokine gene expression levels and relative abundances of several bacteria in tracheas of infected turkeys. For example, interferon γ/λ and interleukin-6 gene expression levels were correlated positively with Staphylococcus and Pseudomonas abundances, and negatively with Lactobacillus abundance. Overall, our data suggest a potential relationship where bacterial community diversity and enrichment or depletion of several bacterial genera in the gut and respiratory tract are dependent on the level of LPAI virus replication. Further work is needed to establish whether respiratory and enteric dysbiosis in LPAI virus-infected turkeys is a result of host immunological responses or other causes such as changes in nutritional uptake.
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Affiliation(s)
- John M Ngunjiri
- Center for Food Animal Health, Ohio Agricultural Research and Development Center, Ohio State University, Wooster, OH, United States of America
| | - Kara J M Taylor
- Center for Food Animal Health, Ohio Agricultural Research and Development Center, Ohio State University, Wooster, OH, United States of America.,Department of Biology, University of Florida, Gainesville, FL, United States of America
| | - Hana Ji
- Center for Food Animal Health, Ohio Agricultural Research and Development Center, Ohio State University, Wooster, OH, United States of America.,Department of Veterinary Preventive Medicine, College of Veterinary Medicine, Ohio State University, Columbus, OH, United States of America
| | - Michael C Abundo
- Center for Food Animal Health, Ohio Agricultural Research and Development Center, Ohio State University, Wooster, OH, United States of America
| | - Amir Ghorbani
- Center for Food Animal Health, Ohio Agricultural Research and Development Center, Ohio State University, Wooster, OH, United States of America.,Department of Veterinary Preventive Medicine, College of Veterinary Medicine, Ohio State University, Columbus, OH, United States of America
| | - Mahesh Kc
- Center for Food Animal Health, Ohio Agricultural Research and Development Center, Ohio State University, Wooster, OH, United States of America.,Department of Veterinary Preventive Medicine, College of Veterinary Medicine, Ohio State University, Columbus, OH, United States of America.,Center for Vaccines and Immunity, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, United States of America
| | - Chang-Won Lee
- Center for Food Animal Health, Ohio Agricultural Research and Development Center, Ohio State University, Wooster, OH, United States of America.,Department of Veterinary Preventive Medicine, College of Veterinary Medicine, Ohio State University, Columbus, OH, United States of America
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29
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Systems Biology and Bile Acid Signalling in Microbiome-Host Interactions in the Cystic Fibrosis Lung. Antibiotics (Basel) 2021; 10:antibiotics10070766. [PMID: 34202495 PMCID: PMC8300688 DOI: 10.3390/antibiotics10070766] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/14/2021] [Accepted: 06/21/2021] [Indexed: 12/16/2022] Open
Abstract
The study of the respiratory microbiota has revealed that the lungs of healthy and diseased individuals harbour distinct microbial communities. Imbalances in these communities can contribute to the pathogenesis of lung disease. How these imbalances occur and establish is largely unknown. This review is focused on the genetically inherited condition of Cystic Fibrosis (CF). Understanding the microbial and host-related factors that govern the establishment of chronic CF lung inflammation and pathogen colonisation is essential. Specifically, dissecting the interplay in the inflammation–pathogen–host axis. Bile acids are important host derived and microbially modified signal molecules that have been detected in CF lungs. These bile acids are associated with inflammation and restructuring of the lung microbiota linked to chronicity. This community remodelling involves a switch in the lung microbiota from a high biodiversity/low pathogen state to a low biodiversity/pathogen-dominated state. Bile acids are particularly associated with the dominance of Proteobacterial pathogens. The ability of bile acids to impact directly on both the lung microbiota and the host response offers a unifying principle underpinning the pathogenesis of CF. The modulating role of bile acids in lung microbiota dysbiosis and inflammation could offer new potential targets for designing innovative therapeutic approaches for respiratory disease.
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30
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Iorio A, Biazzo M, Gardini S, Muda AO, Perno CF, Dallapiccola B, Putignani L. Cross-correlation of virome-bacteriome-host-metabolome to study respiratory health. Trends Microbiol 2021; 30:34-46. [PMID: 34052095 DOI: 10.1016/j.tim.2021.04.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 04/29/2021] [Accepted: 04/30/2021] [Indexed: 12/13/2022]
Abstract
A comprehensive understanding of the microbiome-host relationship in respiratory diseases can be elucidated by exploring the landscape of virome-bacteriome-host metabolome data through unsupervised 'multi-omics' approaches. Here, we describe how the composition and function of airway and gut virome and bacteriome may contribute to pathogen establishment and propagation in airway districts and how the virome-bacteriome communities may react to respiratory diseases. A new systems medicine approach, including the characterization of respiratory and gut microbiome, may be crucial to demonstrate the likelihood and odds of respiratory disease pathophysiology, opening new avenues to the discovery of a chain of causation for key bacteria and viruses in disease severity.
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Affiliation(s)
- Andrea Iorio
- Department of Diagnostic and Laboratory Medicine, Unit of Parasitology and Multimodal Laboratory Medicine Research Area, Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Manuele Biazzo
- The BioArte Ltd, The Victoria Centre, Mosta, Malta; SienaBioActive, University of Siena, Siena, Italy
| | | | - Andrea Onetti Muda
- Department of Diagnostic and Laboratory Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Carlo Federico Perno
- Unit of Microbiology and Immunology, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Bruno Dallapiccola
- Scientific Directorate, Children's Hospital and Research Institute 'Bambino Gesù', IRCCS, Rome
| | - Lorenza Putignani
- Department of Diagnostic and Laboratory Medicine, Unit of Parasitology and Multimodal Laboratory Medicine Research Area, Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.
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31
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Quantification of Phenotypic Variability of Lung Disease in Children with Cystic Fibrosis. Genes (Basel) 2021; 12:genes12060803. [PMID: 34070354 PMCID: PMC8229033 DOI: 10.3390/genes12060803] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/15/2021] [Accepted: 05/19/2021] [Indexed: 12/28/2022] Open
Abstract
Cystic fibrosis (CF) lung disease has the greatest impact on the morbidity and mortality of patients suffering from this autosomal-recessive multiorgan disorder. Although CF is a monogenic disorder, considerable phenotypic variability of lung disease is observed in patients with CF, even in those carrying the same mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene or CFTR mutations with comparable functional consequences. In most patients with CF, lung disease progresses from childhood to adulthood, but is already present in infants soon after birth. In addition to the CFTR genotype, the variability of early CF lung disease can be influenced by several factors, including modifier genes, age at diagnosis (following newborn screening vs. clinical symptoms) and environmental factors. The early onset of CF lung disease requires sensitive, noninvasive measures to detect and monitor changes in lung structure and function. In this context, we review recent progress with using multiple-breath washout (MBW) and lung magnetic resonance imaging (MRI) to detect and quantify CF lung disease from infancy to adulthood. Further, we discuss emerging data on the impact of variability of lung disease severity in the first years of life on long-term outcomes and the potential use of this information to improve personalized medicine for patients with CF.
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32
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Willis JR, Saus E, Iraola-Guzmán S, Cabello-Yeves E, Ksiezopolska E, Cozzuto L, Bejarano LA, Andreu-Somavilla N, Alloza-Trabado M, Blanco A, Puig-Sola A, Broglio E, Carolis C, Ponomarenko J, Hecht J, Gabaldón T. Citizen-science based study of the oral microbiome in Cystic fibrosis and matched controls reveals major differences in diversity and abundance of bacterial and fungal species. J Oral Microbiol 2021; 13:1897328. [PMID: 34104346 PMCID: PMC8143623 DOI: 10.1080/20002297.2021.1897328] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Introduction: Cystic fibrosis (CF) is an autosomal genetic disease, associated with the production of excessively thick mucosa and with life-threatening chronic lung infections. The microbiota of the oral cavity can act as a reservoir or as a barrier for infectious microorganisms that can colonize the lungs. However, the specific composition of the oral microbiome in CF is poorly understood.Methods: In collaboration with CF associations in Spain, we collected oral rinse samples from 31 CF persons (age range 7-47) and matched controls, and then performed 16S rRNA metabarcoding and high-throughput sequencing, combined with culture and proteomics-based identification of fungi to survey the bacterial and fungal oral microbiome.Results: We found that CF is associated with less diverse oral microbiomes, which were characterized by higher prevalence of Candida albicans and differential abundances of a number of bacterial taxa that have implications in both the connection to lung infections in CF, as well as potential oral health concerns, particularly periodontitis and dental caries.Conclusion: Overall, our study provides a first global snapshot of the oral microbiome in CF. Future studies are required to establish the relationships between the composition of the oral and lung microbiomes in CF.
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Affiliation(s)
- Jesse R Willis
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona, Spain.,Life Sciences Programme, Barcelona Supercomputing Centre (BSC-CNS) Jordi Girona, Barcelona, Spain.,Mechanisms of Disease Programme, Institute for Research in Biomedicine (IRB), the Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Ester Saus
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona, Spain.,Life Sciences Programme, Barcelona Supercomputing Centre (BSC-CNS) Jordi Girona, Barcelona, Spain.,Mechanisms of Disease Programme, Institute for Research in Biomedicine (IRB), the Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Susana Iraola-Guzmán
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona, Spain.,Life Sciences Programme, Barcelona Supercomputing Centre (BSC-CNS) Jordi Girona, Barcelona, Spain.,Mechanisms of Disease Programme, Institute for Research in Biomedicine (IRB), the Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Elena Cabello-Yeves
- Life Sciences Programme, Barcelona Supercomputing Centre (BSC-CNS) Jordi Girona, Barcelona, Spain.,Mechanisms of Disease Programme, Institute for Research in Biomedicine (IRB), the Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Ewa Ksiezopolska
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona, Spain.,Life Sciences Programme, Barcelona Supercomputing Centre (BSC-CNS) Jordi Girona, Barcelona, Spain.,Mechanisms of Disease Programme, Institute for Research in Biomedicine (IRB), the Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Luca Cozzuto
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona, Spain.,Experimental and Health Sciences Department, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Luis A Bejarano
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Nuria Andreu-Somavilla
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona, Spain.,Experimental and Health Sciences Department, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Miriam Alloza-Trabado
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona, Spain.,Experimental and Health Sciences Department, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Andrea Blanco
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Anna Puig-Sola
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona, Spain.,Experimental and Health Sciences Department, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Elisabetta Broglio
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona, Spain.,Experimental and Health Sciences Department, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Carlo Carolis
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona, Spain.,Experimental and Health Sciences Department, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Julia Ponomarenko
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona, Spain.,Experimental and Health Sciences Department, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Jochen Hecht
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona, Spain.,Experimental and Health Sciences Department, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Toni Gabaldón
- Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona, Spain.,Life Sciences Programme, Barcelona Supercomputing Centre (BSC-CNS) Jordi Girona, Barcelona, Spain.,Mechanisms of Disease Programme, Institute for Research in Biomedicine (IRB), the Barcelona Institute of Science and Technology, Barcelona, Spain.,Experimental and Health Sciences Department, Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
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33
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Yi B, Dalpke AH, Boutin S. Changes in the Cystic Fibrosis Airway Microbiome in Response to CFTR Modulator Therapy. Front Cell Infect Microbiol 2021; 11:548613. [PMID: 33816324 PMCID: PMC8010178 DOI: 10.3389/fcimb.2021.548613] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 02/24/2021] [Indexed: 12/18/2022] Open
Abstract
The development of CFTR modulator therapies significantly changed the treatment scheme of people with cystic fibrosis. However, CFTR modulator therapy is still a life-long treatment, which is not able to correct the genetic defect and cure the disease. Therefore, it becomes crucial to understand the effects of such modulation of CFTR function on the airway physiology, especially on airway infections and inflammation that are currently the major life-limiting factors in people with cystic fibrosis. In this context, understanding the dynamics of airway microbiome changes in response to modulator therapy plays an essential role in developing strategies for managing airway infections. Whether and how the newly available therapies affect the airway microbiome is still at the beginning of being deciphered. We present here a brief review summarizing the latest information about microbiome alterations in light of modern cystic fibrosis modulator therapy.
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Affiliation(s)
- Buqing Yi
- Medical Faculty, Institute of Medical Microbiology and Virology, Technische Universität Dresden, Dresden, Germany
| | - Alexander H Dalpke
- Medical Faculty, Institute of Medical Microbiology and Virology, Technische Universität Dresden, Dresden, Germany
| | - Sébastien Boutin
- Department of Infectious Diseases, Medical Microbiology and Hygiene, University Hospital Heidelberg, Heidelberg, Germany.,Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), University Hospital Heidelberg, Heidelberg, Germany
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34
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Bringhenti L, Pallu M, Silva J, Tomazi T, Tomazi AC, Rodrigues MX, Duarte LM, Bilby TR, Bicalho RC. Effect of metaphylactic administration of tildipirosin on the incidence of pneumonia and otitis and on the upper respiratory tract and fecal microbiome of preweaning Holstein calves. J Dairy Sci 2021; 104:6020-6038. [PMID: 33685693 DOI: 10.3168/jds.2020-19572] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 01/14/2021] [Indexed: 11/19/2022]
Abstract
The objectives of this study were to evaluate the effect of the metaphylactic use of a semi-synthetic long-acting macrolide (tildipirosin) on the prevention of pneumonia and otitis in preweaning Holstein calves, as well as its effects on the microbiome of their upper respiratory tract (URT) and feces. Newborn healthy Holstein heifers, collectively housed, were randomly allocated to 1 of 2 treatment groups: treatment (TRT; n = 932) or control (CTR; n = 927). Calves in the TRT group received a single subcutaneous injection of 4 mg/kg tildipirosin (Zuprevo, Merck Animal Health) at 7 ± 7 d of life. Calves in the CTR group received no drug injection. All enrolled calves were evaluated from 1 to 63 ± 3 d of life (weaning age) and monitored daily for any adverse health events during this period. Daily physical examination was performed to diagnose pneumonia and otitis, and body weight was measured weekly in all animals. From a randomly selected subset of 217 calves, blood samples for biochemical variables analysis and swabs were collected weekly from the URT and rectum for analysis of the nasal and fecal microbiome, respectively, via next-generation sequencing of the 16S rRNA gene. Total bacterial load was evaluated using quantitative PCR. In addition, another subset of 26 calves was randomly selected and fecal swabs were collected in a more intensive sampling to investigate the short-term effect of tildipirosin administration on the fecal microbiome. We performed general mixed linear models and logistic regression to analyze continuous and binary outcomes, respectively. Tildipirosin metaphylaxis reduced the incidence of otitis (CTR = 47.03%; TRT = 37.55%) and tended to reduce the incidence of pneumonia (CTR = 20.71%; TRT = 17.38%) and the overall mortality risk (CTR = 6.69%; TRT = 4.94%). We observed no significant differences between groups for mortality due to pneumonia (CTR = 0.86%; TRT = 0.97%) or mortality due to otitis (CTR = 2.05%; TRT = 1.39%). Calves in the TRT group had a higher average daily gain than calves in the CTR group. Furthermore, metaphylaxis had no significant effects on the total bacterial load, genus, or phylum analysis of the fecal microbiome from the 2 subset groups. However, for the URT microbiota, we observed a significant decrease in total bacterial load for the TRT group compared to the CTR group 1 week after metaphylactic injection. Tildipirosin metaphylaxis decreased the mean relative abundance of the genera Mannheimia, Moraxella, and Pasteurella but significantly increased the mean relative abundance of Mycoplasma. Although tildipirosin had no positive effect on Mycoplasma, it reduced the mean relative abundance of important pathogenic bacteria in the URT and had positive effects for the control of otitis. The metaphylactic use of tildipirosin can be a suitable strategy for the control of otitis on farms with a high prevalence of this disease.
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Affiliation(s)
- Leonardo Bringhenti
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853-6401
| | - Mariana Pallu
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853-6401
| | - Josiane Silva
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853-6401
| | - Tiago Tomazi
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853-6401
| | - Ana C Tomazi
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853-6401
| | - Marjory X Rodrigues
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853-6401
| | - Livia M Duarte
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853-6401
| | | | - Rodrigo C Bicalho
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853-6401.
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35
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Thavamani A, Salem I, Sferra TJ, Sankararaman S. Impact of Altered Gut Microbiota and Its Metabolites in Cystic Fibrosis. Metabolites 2021; 11:metabo11020123. [PMID: 33671639 PMCID: PMC7926988 DOI: 10.3390/metabo11020123] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/15/2021] [Accepted: 02/20/2021] [Indexed: 12/14/2022] Open
Abstract
Cystic fibrosis (CF) is the most common lethal, multisystemic genetic disorder in Caucasians. Mutations in the gene encoding the cystic fibrosis transmembrane regulator (CFTR) protein are responsible for impairment of epithelial anionic transport, leading to impaired fluid regulation and pH imbalance across multiple organs. Gastrointestinal (GI) manifestations in CF may begin in utero and continue throughout the life, resulting in a chronic state of an altered intestinal milieu. Inherent dysfunction of CFTR leads to dysbiosis of the gut. This state of dysbiosis is further perpetuated by acquired factors such as use of antibiotics for recurrent pulmonary exacerbations. Since the gastrointestinal microbiome and their metabolites play a vital role in nutrition, metabolic, inflammatory, and immune functions, the gut dysbiosis will in turn impact various manifestations of CF-both GI and extra-GI. This review focuses on the consequences of gut dysbiosis and its metabolic implications on CF disease and possible ways to restore homeostasis.
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Affiliation(s)
- Aravind Thavamani
- Department of Pediatrics, Division of Pediatric Gastroenterology, UH Rainbow Babies & Children’s Hospital, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; (A.T.); (T.J.S.)
| | - Iman Salem
- Center for Medial Mycology, Case Western Reserve University School of Medicine, UH Cleveland Medical Center, Cleveland, OH 44106, USA;
| | - Thomas J. Sferra
- Department of Pediatrics, Division of Pediatric Gastroenterology, UH Rainbow Babies & Children’s Hospital, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; (A.T.); (T.J.S.)
| | - Senthilkumar Sankararaman
- Department of Pediatrics, Division of Pediatric Gastroenterology, UH Rainbow Babies & Children’s Hospital, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; (A.T.); (T.J.S.)
- Correspondence: ; Tel.: +1-216-844-1765
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Warncke G, Singer G, Windhaber J, Schabl L, Friehs E, Miekisch W, Gierschner P, Klymiuk I, Eber E, Zeder K, Pfleger A, Obermüller B, Till H, Castellani C. Volatile Organic Compounds, Bacterial Airway Microbiome, Spirometry and Exercise Performance of Patients after Surgical Repair of Congenital Diaphragmatic Hernia. Molecules 2021; 26:molecules26030645. [PMID: 33530644 PMCID: PMC7865878 DOI: 10.3390/molecules26030645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 01/22/2021] [Accepted: 01/22/2021] [Indexed: 11/16/2022] Open
Abstract
The aim of this study was to analyze the exhaled volatile organic compounds (VOCs) profile, airway microbiome, lung function and exercise performance in congenital diaphragmatic hernia (CDH) patients compared to healthy age and sex-matched controls. A total of nine patients (median age 9 years, range 6-13 years) treated for CDH were included. Exhaled VOCs were measured by GC-MS. Airway microbiome was determined from deep induced sputum by 16S rRNA gene sequencing. Patients underwent conventional spirometry and exhausting bicycle spiroergometry. The exhaled VOC profile showed significantly higher levels of cyclohexane and significantly lower levels of acetone and 2-methylbutane in CDH patients. Microbiome analysis revealed no significant differences for alpha-diversity, beta-diversity and LefSe analysis. CDH patients had significantly lower relative abundances of Pasteurellales and Pasteurellaceae. CDH patients exhibited a significantly reduced Tiffeneau Index. Spiroergometry showed no significant differences. This is the first study to report the VOCs profile and airway microbiome in patients with CDH. Elevations of cyclohexane observed in the CDH group have also been reported in cases of lung cancer and pneumonia. CDH patients had no signs of impaired physical performance capacity, fueling controversial reports in the literature.
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MESH Headings
- Acetone/analysis
- Adolescent
- Bacteria/classification
- Bacteria/genetics
- Bacteria/isolation & purification
- Child
- DNA, Bacterial/genetics
- DNA, Ribosomal/genetics
- Exercise
- Female
- Hernias, Diaphragmatic, Congenital/metabolism
- Hernias, Diaphragmatic, Congenital/physiopathology
- Hernias, Diaphragmatic, Congenital/surgery
- Herniorrhaphy/methods
- Humans
- Male
- Microbiota
- Pentanes/analysis
- Phylogeny
- RNA, Ribosomal, 16S/genetics
- Spirometry
- Vital Capacity
- Volatile Organic Compounds/analysis
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Affiliation(s)
- Gert Warncke
- Department of Paediatric and Adolescent Surgery, Medical University Graz, 8036 Graz, Austria; (G.W.); (J.W.); (L.S.); (E.F.); (B.O.); (H.T.); (C.C.)
| | - Georg Singer
- Department of Paediatric and Adolescent Surgery, Medical University Graz, 8036 Graz, Austria; (G.W.); (J.W.); (L.S.); (E.F.); (B.O.); (H.T.); (C.C.)
- Correspondence: ; Tel.: +43-316-385-83722
| | - Jana Windhaber
- Department of Paediatric and Adolescent Surgery, Medical University Graz, 8036 Graz, Austria; (G.W.); (J.W.); (L.S.); (E.F.); (B.O.); (H.T.); (C.C.)
| | - Lukas Schabl
- Department of Paediatric and Adolescent Surgery, Medical University Graz, 8036 Graz, Austria; (G.W.); (J.W.); (L.S.); (E.F.); (B.O.); (H.T.); (C.C.)
| | - Elena Friehs
- Department of Paediatric and Adolescent Surgery, Medical University Graz, 8036 Graz, Austria; (G.W.); (J.W.); (L.S.); (E.F.); (B.O.); (H.T.); (C.C.)
| | - Wolfram Miekisch
- Department of Anesthesiology and Intensive Care Medicine, Rostock Medical Breath Research Analytics and Technologies (ROMBAT), Rostock University Medical Centre, 18057 Rostock, Germany; (W.M.); (P.G.)
| | - Peter Gierschner
- Department of Anesthesiology and Intensive Care Medicine, Rostock Medical Breath Research Analytics and Technologies (ROMBAT), Rostock University Medical Centre, 18057 Rostock, Germany; (W.M.); (P.G.)
| | - Ingeborg Klymiuk
- Core Facility Molecular Biology, Center for Medical Research, Medical University of Graz, 8036 Graz, Austria;
| | - Ernst Eber
- Department of Paediatrics and Adolescent Medicine, Division of Paediatric Pulmonology and Allergology, Medical University of Graz, 8036 Graz, Austria; (E.E.); (K.Z.); (A.P.)
| | - Katarina Zeder
- Department of Paediatrics and Adolescent Medicine, Division of Paediatric Pulmonology and Allergology, Medical University of Graz, 8036 Graz, Austria; (E.E.); (K.Z.); (A.P.)
| | - Andreas Pfleger
- Department of Paediatrics and Adolescent Medicine, Division of Paediatric Pulmonology and Allergology, Medical University of Graz, 8036 Graz, Austria; (E.E.); (K.Z.); (A.P.)
| | - Beate Obermüller
- Department of Paediatric and Adolescent Surgery, Medical University Graz, 8036 Graz, Austria; (G.W.); (J.W.); (L.S.); (E.F.); (B.O.); (H.T.); (C.C.)
| | - Holger Till
- Department of Paediatric and Adolescent Surgery, Medical University Graz, 8036 Graz, Austria; (G.W.); (J.W.); (L.S.); (E.F.); (B.O.); (H.T.); (C.C.)
| | - Christoph Castellani
- Department of Paediatric and Adolescent Surgery, Medical University Graz, 8036 Graz, Austria; (G.W.); (J.W.); (L.S.); (E.F.); (B.O.); (H.T.); (C.C.)
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Frey DL, Boutin S, Dittrich SA, Graeber SY, Stahl M, Wege S, Herth FJF, Sommerburg O, Schultz C, Mall MA, Dalpke AH. Relationship between airway dysbiosis, inflammation and lung function in adults with cystic fibrosis. J Cyst Fibros 2021; 20:754-760. [PMID: 33431308 DOI: 10.1016/j.jcf.2020.12.022] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 11/27/2020] [Accepted: 12/24/2020] [Indexed: 01/04/2023]
Abstract
Airway dysbiosis has been associated with lung disease severity in patients with cystic fibrosis (CF). However, the relationship between dysbiosis, airway inflammation and lung function impairement remains poorly understood. The aim of this study was therefore to determine how the structure of the sputum microbiota, airway inflammation markers and spirometry are related in patients with CF. Sputum samples were collected from 106 CF patients between 12 and 72 years. These were analyzed by 16S rRNA gene amplicon sequencing. Moreover, levels of pro-inflammatory cytokines (IL-1β, IL-8, IL-6 and TNF-α) and Neutrophil elastase (NE) were determined. The relationship between the microbiota, inflammation markers and forced expiratory volume in one second percent predicted (FEV1% predicted) was evaluated by multi-parameter analysis. The microbiota α-diversity correlated inverse with inflammation markers IL-1β, IL-8, TNF-α, NE and positively with FEV1% predicted. Patients could be divided into 7 clusters based on their microbiota structure. The most diverse cluster was defined by oropharyngeal-like flora (OF) while the others were characterized by the dominance of a single pathogen. Patients with the diverse OF microbiota cluster had lower sputum inflammatory markers and higher FEV1% predicted compared to patients with a pathogen-dominated microbiota including Pseudomonas aeruginosa. Our results suggest that the diversity of the airway microbiota is an important biomarker of the severity of airway inflammation linking dysbiosis to lung function decline in patients with CF.
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Affiliation(s)
- Dario L Frey
- Translational Lung Research Center (TLRC), Heidelberg, Germany; Department of Translational Pulmonology, University of Heidelberg, Heidelberg, Germany
| | - Sébastien Boutin
- Translational Lung Research Center (TLRC), Heidelberg, Germany; Department of Infectious Diseases, Medical Microbiology and Hygiene, University of Heidelberg, Heidelberg, Germany.
| | - Susanne A Dittrich
- Translational Lung Research Center (TLRC), Heidelberg, Germany; Department of Translational Pulmonology, University of Heidelberg, Heidelberg, Germany; Department of Pneumology and Critical Care Medicine, Thoraxklinik at the University Hospital Heidelberg, Heidelberg, Germany
| | - Simon Y Graeber
- Translational Lung Research Center (TLRC), Heidelberg, Germany; Department of Translational Pulmonology, University of Heidelberg, Heidelberg, Germany; Division of Pediatric Pulmonology & Allergology and Cystic Fibrosis Center, Department of Pediatrics, University of Heidelberg, Heidelberg, Germany; Department of Pediatric Pulmonology, Immunology and Critical Care Medicine and Cystic Fibrosis Center, Charité-Universitätsmedizin Berlin, Berlin, Germany; Berlin Institute of Health (BIH), Berlin, Germany; German Center for Lung Research (DZL), associated partner site, Berlin, Germany
| | - Mirjam Stahl
- Translational Lung Research Center (TLRC), Heidelberg, Germany; Department of Translational Pulmonology, University of Heidelberg, Heidelberg, Germany; Division of Pediatric Pulmonology & Allergology and Cystic Fibrosis Center, Department of Pediatrics, University of Heidelberg, Heidelberg, Germany; Department of Pediatric Pulmonology, Immunology and Critical Care Medicine and Cystic Fibrosis Center, Charité-Universitätsmedizin Berlin, Berlin, Germany; German Center for Lung Research (DZL), associated partner site, Berlin, Germany
| | - Sabine Wege
- Department of Pneumology and Critical Care Medicine, Thoraxklinik at the University Hospital Heidelberg, Heidelberg, Germany
| | - Felix J F Herth
- Translational Lung Research Center (TLRC), Heidelberg, Germany; Department of Pneumology and Critical Care Medicine, Thoraxklinik at the University Hospital Heidelberg, Heidelberg, Germany
| | - Olaf Sommerburg
- Translational Lung Research Center (TLRC), Heidelberg, Germany; Division of Pediatric Pulmonology & Allergology and Cystic Fibrosis Center, Department of Pediatrics, University of Heidelberg, Heidelberg, Germany
| | - Carsten Schultz
- Translational Lung Research Center (TLRC), Heidelberg, Germany; Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, OR, USA
| | - Marcus A Mall
- Translational Lung Research Center (TLRC), Heidelberg, Germany; Department of Translational Pulmonology, University of Heidelberg, Heidelberg, Germany; Division of Pediatric Pulmonology & Allergology and Cystic Fibrosis Center, Department of Pediatrics, University of Heidelberg, Heidelberg, Germany; Department of Pediatric Pulmonology, Immunology and Critical Care Medicine and Cystic Fibrosis Center, Charité-Universitätsmedizin Berlin, Berlin, Germany; Berlin Institute of Health (BIH), Berlin, Germany; German Center for Lung Research (DZL), associated partner site, Berlin, Germany
| | - Alexander H Dalpke
- Translational Lung Research Center (TLRC), Heidelberg, Germany; Department of Infectious Diseases, Medical Microbiology and Hygiene, University of Heidelberg, Heidelberg, Germany; Institute of Medical Microbiology and Hygiene, Technische Universität Dresden, Dresden, Germany
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38
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Tomazi T, Sumnicht M, Tomazi ACCH, Silva JCC, Bringhenti L, Duarte LM, Silva MMM, Rodrigues MX, Bicalho RC. Negatively controlled, randomized clinical trial comparing different antimicrobial interventions for treatment of clinical mastitis caused by gram-positive pathogens. J Dairy Sci 2020; 104:3364-3385. [PMID: 33358798 DOI: 10.3168/jds.2020-18830] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 10/06/2020] [Indexed: 12/11/2022]
Abstract
The general objective of this study was to evaluate the effect of 3 intramammary antibiotic interventions using 2 commercially available antibiotics with narrow- or broad-spectrum activity on cure rates of clinical mastitis (CM) caused by gram-positive bacteria. We also compared the efficacy of treatment protocols, including a negative control, on outcomes at the cow and mammary quarter level. Before the onset of the study, 5,987 animals more than 12 mo old were randomly preassigned to 1 of 4 protocols in the event of gram-positive CM (except for Staphylococcus aureus and Trueperella pyogenes) during lactation: 3 infusions with 62.5 mg of amoxicillin performed 12 h apart (AMOX-L); 5 infusions once a day with 62.5 mg of amoxicillin (AMOX-EL); 5 infusions once a day with 125 mg of ceftiofur hydrochloride (CEFT-L); or negative control, no treatment performed until 5 d after diagnosis (NEG-CTR). Randomization was performed to preassign 90% of cows to one of the antibiotic protocols (30% in each group) and 10% to the negative control. A total of 696 quarter cases of CM met the inclusion criteria and were evaluated in the study. Quarter-level outcomes were assessed based on 5 milk samples collected up to 14 ± 3 d following enrollment (i.e., first day of treatment), whereas variables at the cow level [composite somatic cell count (SCC), milk production, and survival in the herd] were assessed up to 90 d after CM diagnosis. Streptococcus uberis, followed by Streptococcus dysgalactiae, were the main causes of gram-positive CM. Overall, clinical cure was higher for CEFT-L than for AMOX-EL, and no difference was observed between CEFT-L and AMOX-L. Likewise, no significant differences were detected on overall bacteriological cure, although some treatment effects were observed at the species level. Compared with antibiotic-treated groups, quarters assigned to NEG-CTR had higher counts of colony-forming units (cfu), 16S rRNA gene copy numbers, and Streptococcus relative abundance (RA) until d 5 after enrollment. Quarters treated with AMOX-L had higher cfu counts on d 5, 8, and 14 after enrollment compared with the other antibiotic protocols. In addition, the RA of Streptococcus spp. was higher on d 14 after enrollment for AMOX-treated quarters compared with the CEFT-L group. Linear score of SCC was higher for AMOX-treated cows than for CEFT-L in the first test day after CM. However, cows assigned to AMOX-L had higher milk production than those submitted to the AMOX-EL and CEFT-L protocols. In conclusion, the 2-d protocol with 3 intramammary infusions of amoxicillin (narrow-spectrum antimicrobial) had similar overall clinical and bacteriological cures as 5 administrations (once a day) with ceftiofur hydrochloride (wide spectrum). No significant difference was observed on CM recurrence and cow survival. However, quarters treated with 5-d protocols were more effective at reducing milk cfu counts than quarters in the AMOX-L protocol. In addition, lower Streptococcus spp. RA was observed in ceftiofur-treated quarters compared with the amoxicillin protocols at d 14 after CM diagnosis. Based on results of microbiome and bacterial load (quantitative PCR and cfu count) up to 5 d after CM diagnosis, antibiotic use remains an indispensable strategy for treatment of CM caused by gram-positive bacteria.
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Affiliation(s)
- T Tomazi
- Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, NY 14853-6401
| | - M Sumnicht
- Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, NY 14853-6401
| | - A C C H Tomazi
- Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, NY 14853-6401
| | - J C C Silva
- Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, NY 14853-6401
| | - L Bringhenti
- Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, NY 14853-6401
| | - L M Duarte
- Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, NY 14853-6401
| | - M M M Silva
- Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, NY 14853-6401
| | - M X Rodrigues
- Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, NY 14853-6401
| | - R C Bicalho
- Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, NY 14853-6401.
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Maestrali F, Pilan R, Athanazio R, Sparvoli L, Cortez R, Taddei C, Voegels R. Cystic fibrosis microbiome: analysis of nasal middle meatus and sputum in different lung disease stages. RHINOLOGY ONLINE 2020. [DOI: 10.4193/rhinol/20.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND: Culture independent methods of molecular detection of microbiome have shown the polymicrobial nature of respiratory infections in cystic fibrosis, with pathogenic agents undetectable in conventional culture methods. Composition and diversity of the airway microbiome are still poorly understood. METHODOLOGY: This study evaluated the airway microbiome in 31 adult cystic fibrosis patients via the analysis of 16S rRNA se- quences by next generation sequencing. RESULTS: Staphylococcus, Streptococcus and Corynebacterium were the most abundant genera in the middle meatus, and Pseudo- monas, Haemophilus and Prevotella were the most abundant in sputum. In patients with advanced disease (FEV1< 50%), there was an increase in the prevalence of Pseudomonas in both sample types when studied separately. In each patient, in a paired analysis, the sputum and middle meatus showed similar microbiome composition in mild or moderate disease (FEV1≥ 50%). In patients with severe lung disease, the relative abundance of Pseudomonas had a positive correlation in both collection sites. CONCLUSIONS: This is the first Brazilian study to evaluate the airway microbiome in cystic fibrosis patients. Our findings agree with those in the international literature and indicate the role of Pseudomonas in the sputum and middle meatus in patients with advanced disease.
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40
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Keown K, Reid A, Moore JE, Taggart CC, Downey DG. Coinfection with Pseudomonas aeruginosa and Aspergillus fumigatus in cystic fibrosis. Eur Respir Rev 2020; 29:29/158/200011. [PMID: 33208485 DOI: 10.1183/16000617.0011-2020] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 05/16/2020] [Indexed: 02/06/2023] Open
Abstract
OBJECTIVES Cystic fibrosis (CF) lung disease is characterised by mucus stasis, chronic infection and inflammation, causing progressive structural lung disease and eventual respiratory failure. CF airways are inhabited by an ecologically diverse polymicrobial environment with vast potential for interspecies interactions, which may be a contributing factor to disease progression. Pseudomonas aeruginosa and Aspergillus fumigatus are the most common bacterial and fungal species present in CF airways respectively and coinfection results in a worse disease phenotype. METHODS In this review we examine existing expert knowledge of chronic co-infection with P. aeruginosa and A. fumigatus in CF patients. We summarise the mechanisms of interaction and evaluate the clinical and inflammatory impacts of this co-infection. RESULTS P. aeruginosa inhibits A. fumigatus through multiple mechanisms: phenazine secretion, iron competition, quorum sensing and through diffusible small molecules. A. fumigatus reciprocates inhibition through gliotoxin release and phenotypic adaptations enabling evasion of P. aeruginosa inhibition. Volatile organic compounds secreted by P. aeruginosa stimulate A. fumigatus growth, while A. fumigatus stimulates P. aeruginosa production of cytotoxic elastase. CONCLUSION A complex bi-directional relationship exists between P. aeruginosa and A. fumigatus, exhibiting both mutually antagonistic and cooperative facets. Cross-sectional data indicate a worsened disease state in coinfected patients; however, robust longitudinal studies are required to derive causality and to determine whether interspecies interaction contributes to disease progression.
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Affiliation(s)
- Karen Keown
- Royal Belfast Hospital for Sick Children, Belfast Health and Social Care Trust, Belfast, UK.,Wellcome Wolfson Centre for Experimental Medicine, Queen's University Belfast, Belfast, UK
| | - Alastair Reid
- Royal Belfast Hospital for Sick Children, Belfast Health and Social Care Trust, Belfast, UK
| | - John E Moore
- Northern Ireland Public Health Laboratory, Dept of Bacteriology, Belfast City Hospital, Belfast, UK
| | - Clifford C Taggart
- Wellcome Wolfson Centre for Experimental Medicine, Queen's University Belfast, Belfast, UK
| | - Damian G Downey
- Wellcome Wolfson Centre for Experimental Medicine, Queen's University Belfast, Belfast, UK
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41
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The Domestic Environment and the Lung Mycobiome. Microorganisms 2020; 8:microorganisms8111717. [PMID: 33147738 PMCID: PMC7693370 DOI: 10.3390/microorganisms8111717] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 10/16/2020] [Accepted: 10/30/2020] [Indexed: 12/16/2022] Open
Abstract
This study analyzes the relationship between the mycobiome of the Lower Respiratory Tract (LRT) and the fungi in the domestic environment. Samples studied consisted of Broncho-Alveolar Lavage (BAL) from 45 patients who underwent bronchoscopy for different diagnostic purposes, and dust and air from the houses (ENV) of 20 of them (44.4%). Additionally, five bronchoscopes (BS) were also analyzed and negative controls were included for every procedure. All samples were processed for DNA extraction and cultures, which were performed in Sabouraud Dextrose and Potato Dextrose Agar. The fungal Internal Transcribed Spacer (ITS2) was sequenced by the Solexa/Illumina system and sequences were analyzed by QIIME 1.8.0 and compared with the UNITE Database for identification. The similarity between the two fungal communities (BAL and ENV) for a specific patient was assessed via the percentage of coincidence in the detection of specific operational taxonomic units (OTUs), and about 75% of co-occurrence was detected between the mycobiome of the LRT and the houses. Cultures confirmed the presence of the core mycobiome species. However, the low rate of isolation from BAL suggests that most of its mycobiome corresponds to non-culturable cells. This likely depends on the patient’s immune system activity and inflammatory status.
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42
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Heirali A, Thornton C, Acosta N, Somayaji R, Laforest Lapointe I, Storey D, Rabin H, Waddell B, Rossi L, Arrieta MC, Surette M, Parkins MD. Sputum microbiota in adults with CF associates with response to inhaled tobramycin. Thorax 2020; 75:1058-1064. [PMID: 33139451 DOI: 10.1136/thoraxjnl-2019-214191] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 08/03/2020] [Accepted: 08/09/2020] [Indexed: 11/03/2022]
Abstract
BACKGROUND Inhaled tobramycin powder/solution (TIP/S) use has resulted in improved clinical outcomes in patients with cystic fibrosis (CF) with chronic Pseudomonas aeruginosa. However, TIP/S effect on the CF sputum microbiome has not been explored. We hypothesised that TIP/S has additional 'off-target' effects beyond merely P. aeruginosa and that baseline microbiome prior to initiation of therapy is associated with subsequent patient response. METHODS We drew sputum samples from a prospectively collected biobank. Patients were included if they had one sputum sample in the 18 months before and after TIP/S. Bacterial 16S rRNA gene profiling was used to characterise the sputum microbiome. RESULTS Forty-one patients met our inclusion criteria and 151 sputum samples were assessed. At baseline, median age was 30.4 years (IQR 24.2-35.2) and forced expiratory volume in 1 (FEV1) second was 57% predicted (IQR 44-74). Nineteen patients were defined a priori as responders having no net decrease in FEV1 in the year following TIP/S. No significant changes were observed in key microbiome metrics of alpha (within-sample) or beta (between-sample) diversity for samples collected before and after TIP/S. However, significant beta-diversity (Bray-Curtis) differences were noted at baseline between patients based on response status. Notably, responders were observed to have a higher abundance of Staphylococcus in pretherapy baseline samples. CONCLUSIONS Our longitudinal study demonstrates that the sputum microbiome of patients with CF is relatively stable following inhaled tobramycin over many months. Intriguingly, our findings suggest that baseline microbiome may associate with patient response to TIP/S-suggesting the sputum microbiome could be used to personalise therapy.
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Affiliation(s)
- Alya Heirali
- Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | | | - Nicole Acosta
- Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | | | | | - Douglas Storey
- Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Harvey Rabin
- Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Barbara Waddell
- Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Laura Rossi
- Microbiology, McMaster University, Hamilton, Ontario, Canada
| | - Marie Claire Arrieta
- Pediatrics, Calgary, Alberta, Canada.,Physiology & Pharmacology, University of Calgary, Calgary, Alberta, Canada
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Zhang C, Zhang T, Lu W, Duan X, Luo X, Liu S, Chen Y, Li Y, Chen J, Liao J, Zhou D, Chen X, Feng H, Gu G, Wang T, Tang H, Makino A, Zhong N, Yuan JXJ, Yang K, Wang J. Altered Airway Microbiota Composition in Patients With Pulmonary Hypertension. Hypertension 2020; 76:1589-1599. [PMID: 32921193 DOI: 10.1161/hypertensionaha.120.15025] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Alteration in microbiota composition of respiratory tract has been reported in the progression of many chronic lung diseases, yet, the correlation and causal link between respiratory tract microbiota and the disease development of pulmonary hypertension (PH) remain largely unknown. This study aims to define and compare the respiratory microbiota composition in pharyngeal swab samples between patients with PH and reference subjects. A total of 118 patients with PH and 79 reference subjects were recruited, and the pharyngeal swab samples were collected to sequence the 16S ribosomal RNA (16S rRNA) V3-V4 region of respiratory microbiome. The relative abundances in patients with PH were profoundly different from reference subjects. The Ace and Sobs indexes indicated that the microbiota richness of pharynx value is significantly higher; while the community diversity value is markedly lower in patients with PH, comparing to those of the reference subjects. The microbiota on pharynx showed a different profile between the 2 groups by principal component analysis. The linear discriminant analysis effect size also revealed a significantly higher proportion of Streptococcus, Lautropia, and Ralstonia in patients with PH than reference subjects. The linear discriminant analysis effect size output, which represents the microbial gene functions, suggest genes related to bacterial invasion of epithelial cells, bacterial toxins were enhanced, while genes related to energy metabolism, protein digestion and absorption, and cell division pathways were attenuated in patients with PH versus reference subjects. In summary, our study reports the first systematic definition and divergent profile of the upper respiratory tract microbiota between patients with PH and reference subjects.
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Affiliation(s)
- Chenting Zhang
- From the State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, China (C.Z., T.Z., W.L., X.L., S.L., Y.C., Y.L., J.C., J.L., D.Z., X.C., H.F., G.G., T.W., H.T., N.Z., K.Y., J.W.)
| | - Tingting Zhang
- From the State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, China (C.Z., T.Z., W.L., X.L., S.L., Y.C., Y.L., J.C., J.L., D.Z., X.C., H.F., G.G., T.W., H.T., N.Z., K.Y., J.W.)
| | - Wenju Lu
- From the State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, China (C.Z., T.Z., W.L., X.L., S.L., Y.C., Y.L., J.C., J.L., D.Z., X.C., H.F., G.G., T.W., H.T., N.Z., K.Y., J.W.)
| | - Xin Duan
- State Key Laboratory of Cardiovascular Disease, Department of Cardiology, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China (X.D.)
| | - Xiaoyun Luo
- From the State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, China (C.Z., T.Z., W.L., X.L., S.L., Y.C., Y.L., J.C., J.L., D.Z., X.C., H.F., G.G., T.W., H.T., N.Z., K.Y., J.W.)
| | - Shiyun Liu
- From the State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, China (C.Z., T.Z., W.L., X.L., S.L., Y.C., Y.L., J.C., J.L., D.Z., X.C., H.F., G.G., T.W., H.T., N.Z., K.Y., J.W.)
| | - Yuqin Chen
- From the State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, China (C.Z., T.Z., W.L., X.L., S.L., Y.C., Y.L., J.C., J.L., D.Z., X.C., H.F., G.G., T.W., H.T., N.Z., K.Y., J.W.)
| | - Yi Li
- From the State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, China (C.Z., T.Z., W.L., X.L., S.L., Y.C., Y.L., J.C., J.L., D.Z., X.C., H.F., G.G., T.W., H.T., N.Z., K.Y., J.W.)
| | - Jiyuan Chen
- From the State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, China (C.Z., T.Z., W.L., X.L., S.L., Y.C., Y.L., J.C., J.L., D.Z., X.C., H.F., G.G., T.W., H.T., N.Z., K.Y., J.W.)
| | - Jing Liao
- From the State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, China (C.Z., T.Z., W.L., X.L., S.L., Y.C., Y.L., J.C., J.L., D.Z., X.C., H.F., G.G., T.W., H.T., N.Z., K.Y., J.W.)
| | - Dansha Zhou
- From the State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, China (C.Z., T.Z., W.L., X.L., S.L., Y.C., Y.L., J.C., J.L., D.Z., X.C., H.F., G.G., T.W., H.T., N.Z., K.Y., J.W.)
| | - Xu Chen
- From the State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, China (C.Z., T.Z., W.L., X.L., S.L., Y.C., Y.L., J.C., J.L., D.Z., X.C., H.F., G.G., T.W., H.T., N.Z., K.Y., J.W.)
| | - Huazhuo Feng
- From the State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, China (C.Z., T.Z., W.L., X.L., S.L., Y.C., Y.L., J.C., J.L., D.Z., X.C., H.F., G.G., T.W., H.T., N.Z., K.Y., J.W.)
| | - Guoping Gu
- From the State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, China (C.Z., T.Z., W.L., X.L., S.L., Y.C., Y.L., J.C., J.L., D.Z., X.C., H.F., G.G., T.W., H.T., N.Z., K.Y., J.W.)
| | - Tao Wang
- From the State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, China (C.Z., T.Z., W.L., X.L., S.L., Y.C., Y.L., J.C., J.L., D.Z., X.C., H.F., G.G., T.W., H.T., N.Z., K.Y., J.W.)
| | - Haiyang Tang
- Departments of Medicine and Physiology, The University of Arizona College of Medicine, Tucson (H.T.)
| | - Ayako Makino
- Department of Medicine, University of California San Diego, La Jolla (A.M., J.-X.-J.Y., J.W.)
| | - Nanshan Zhong
- From the State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, China (C.Z., T.Z., W.L., X.L., S.L., Y.C., Y.L., J.C., J.L., D.Z., X.C., H.F., G.G., T.W., H.T., N.Z., K.Y., J.W.)
| | - Jason X-J Yuan
- Department of Medicine, University of California San Diego, La Jolla (A.M., J.-X.-J.Y., J.W.)
| | - Kai Yang
- From the State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, China (C.Z., T.Z., W.L., X.L., S.L., Y.C., Y.L., J.C., J.L., D.Z., X.C., H.F., G.G., T.W., H.T., N.Z., K.Y., J.W.)
| | - Jian Wang
- Division of Pulmonary and Critical Care Medicine, The People's Hospital of Inner Mongolia, Huhhot, China (J.W.).,Department of Medicine, University of California San Diego, La Jolla (A.M., J.-X.-J.Y., J.W.)
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44
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Paramasivan S, Bassiouni A, Shiffer A, Dillon MR, Cope EK, Cooksley C, Ramezanpour M, Moraitis S, Ali MJ, Bleier B, Callejas C, Cornet ME, Douglas RG, Dutra D, Georgalas C, Harvey RJ, Hwang PH, Luong AU, Schlosser RJ, Tantilipikorn P, Tewfik MA, Vreugde S, Wormald P, Caporaso JG, Psaltis AJ. The international sinonasal microbiome study: A multicentre, multinational characterization of sinonasal bacterial ecology. Allergy 2020; 75:2037-2049. [PMID: 32167574 DOI: 10.1111/all.14276] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 11/20/2019] [Accepted: 12/18/2019] [Indexed: 02/06/2023]
Abstract
The sinonasal microbiome remains poorly defined, with our current knowledge based on a few cohort studies whose findings are inconsistent. Furthermore, the variability of the sinus microbiome across geographical divides remains unexplored. We characterize the sinonasal microbiome and its geographical variations in both health and disease using 16S rRNA gene sequencing of 410 individuals from across the world. Although the sinus microbial ecology is highly variable between individuals, we identify a core microbiome comprised of Corynebacterium, Staphylococcus, Streptococcus, Haemophilus and Moraxella species in both healthy and chronic rhinosinusitis (CRS) cohorts. Corynebacterium (mean relative abundance = 44.02%) and Staphylococcus (mean relative abundance = 27.34%) appear particularly dominant in the majority of patients sampled. Amongst patients suffering from CRS with nasal polyps, a statistically significant reduction in relative abundance of Corynebacterium (40.29% vs 50.43%; P = .02) was identified. Despite some measured differences in microbiome composition and diversity between some of the participating centres in our cohort, these differences would not alter the general pattern of core organisms described. Nevertheless, atypical or unusual organisms reported in short-read amplicon sequencing studies and that are not part of the core microbiome should be interpreted with caution. The delineation of the sinonasal microbiome and standardized methodology described within our study will enable further characterization and translational application of the sinus microbiota.
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Affiliation(s)
- Sathish Paramasivan
- Department of Otolaryngology, Head and Neck Surgery University of Adelaide Adelaide SA Australia
| | - Ahmed Bassiouni
- Department of Otolaryngology, Head and Neck Surgery University of Adelaide Adelaide SA Australia
| | - Arron Shiffer
- Pathogen and Microbiome Institute Northern Arizona University Flagstaff AZ USA
| | - Matthew R. Dillon
- Pathogen and Microbiome Institute Northern Arizona University Flagstaff AZ USA
| | - Emily K. Cope
- Pathogen and Microbiome Institute Northern Arizona University Flagstaff AZ USA
| | - Clare Cooksley
- Department of Otolaryngology, Head and Neck Surgery University of Adelaide Adelaide SA Australia
| | - Mahnaz Ramezanpour
- Department of Otolaryngology, Head and Neck Surgery University of Adelaide Adelaide SA Australia
| | - Sophia Moraitis
- Department of Otolaryngology, Head and Neck Surgery University of Adelaide Adelaide SA Australia
| | | | - Benjamin Bleier
- Department of Otolaryngology Massachusetts Eye and Ear Infirmary Harvard Medical School Boston MA USA
| | - Claudio Callejas
- Department of Otolaryngology Pontificia Universidad Catolica de Chile Santiago Chile
| | | | | | - Daniel Dutra
- Department of Otorhinolaryngology University of Sao Paulo Sao Paulo Brazil
| | - Christos Georgalas
- Department of Otorhinolaryngology Amsterdam UMC Amsterdam The Netherlands
| | - Richard J. Harvey
- Department of Otolaryngology, Rhinology and Skull base University of New South Wales Sydney NSW Australia
- Faculty of Medicine and Health sciences Macquarie University Sydney NSW Australia
| | - Peter H. Hwang
- Department of Otolaryngology ‐Head and Neck Surgery Stanford University Stanford CA USA
| | - Amber U. Luong
- Department of Otolaryngology ‐Head and Neck Surgery University of Texas Austin TX USA
| | - Rodney J. Schlosser
- Department of Otolaryngology Medical University of South Carolina Charleston SC USA
| | - Pongsakorn Tantilipikorn
- Department of Otorhinolaryngology Faculty of Medicine Siriraj Hospital Mahidol University Bangkok Thailand
| | - Marc A. Tewfik
- Department of Otolaryngology ‐ Head and Neck Surgery McGill University Montreal QC Canada
| | - Sarah Vreugde
- Department of Otolaryngology, Head and Neck Surgery University of Adelaide Adelaide SA Australia
| | - Peter‐John Wormald
- Department of Otolaryngology, Head and Neck Surgery University of Adelaide Adelaide SA Australia
| | - J. Gregory Caporaso
- Pathogen and Microbiome Institute Northern Arizona University Flagstaff AZ USA
| | - Alkis J. Psaltis
- Department of Otolaryngology, Head and Neck Surgery University of Adelaide Adelaide SA Australia
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45
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Garcia-Nuñez M, Garcia-Gonzalez M, Pomares X, Montón C, Millares L, Quero S, Prina E, Asensio O, Bosque M, Capilla S, Cuevas O, Monsó E. The Respiratory Microbiome in Cystic Fibrosis: Compartment Patterns and Clinical Relationships in Early Stage Disease. Front Microbiol 2020; 11:1463. [PMID: 32695090 PMCID: PMC7339930 DOI: 10.3389/fmicb.2020.01463] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 06/04/2020] [Indexed: 11/28/2022] Open
Abstract
We compared the bacterial microbiomes lodged in the bronchial tree, oropharynx and nose of patients with early stage cystic fibrosis (CF) not using chronic antibiotics, determining their relationships with lung function and exacerbation frequency. CF patients were enrolled in a cohort study during stability and were checked regularly over the following 9 months. Upper respiratory samples (sputum [S], oropharyngeal swab [OP] and nasal washing [N]) were collected at the first visit and every 3 months. 16S rRNA gene amplification and sequencing was performed and analyzed with QIIME. Seventeen CF patients were enrolled (16.6 SD 9.6 years). Alpha-diversity of bacterial communities between samples was significantly higher in S than in OP (Shannon index median 4.6 [IQR: 4.1–4.9] vs. 3.7 [IQR: 3-1-4.1], p = 0.003/Chao 1 richness estimator median 97.75 [IQR: 85.1–110.9] vs. 43.9 [IQR: 31.7–59.9], p = 0.003) and beta-diversity analysis also showed significant differences in the microbial composition of both respiratory compartments (Adonis test of Bray Curtis dissimilarity matrix, p = 0.001). Dominant taxa were found at baseline in five patients (29.4%), who showed lower forced expiratory volume in the first second (FEV1%, mean 74.8 [SD 19] vs. 97.2 [SD 17.8], p = 0.035, Student t test). The Staphylococcus genus had low RAs in most samples (median 0.26% [IQR 0.01–0.69%]), but patients with RA > 0.26% of Staphylococcus in bronchial secretions suffered more exacerbations during follow-up (median 2 [IQR 1–2.25] vs. 0 [0–1], p = 0.026. Mann–Whitney U test), due to S. aureus in more than a half of the cases, microorganism that often persists as bronchial colonized in these patients (9/10 [90%] vs. 2/7 [28.6%], p = 0.034, Fisher’s exact test). In conclusion, the bronchial microbiome had significantly higher diversity than the microbial flora lodged in the oropharynx in early stage CF. Although the RA of the Staphylococcus genus was low in bronchial secretions and did not reach a dominance pattern, slight overrepresentations of this genus was associated with higher exacerbation frequencies in these patients.
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Affiliation(s)
- Marian Garcia-Nuñez
- Department of Respiratory Medicine, Institut d'Investigació i Innovació Parc Taulí (I3PT), Hospital Universitari Parc Taulí, Sabadell, Spain.,Centro de Investigación en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Miguel Garcia-Gonzalez
- Cystic Fibrosis Unit, Hospital Universitari Parc Taulí, Sabadell, Spain.,Department of Pediatrics, Institut d'Investigació i Innovació Parc Taulí (I3PT), Hospital Universitari Parc Taulí, Sabadell, Spain.,Universitat Autonoma de Barcelona, Barcelona, Spain
| | - Xavier Pomares
- Department of Respiratory Medicine, Institut d'Investigació i Innovació Parc Taulí (I3PT), Hospital Universitari Parc Taulí, Sabadell, Spain.,Centro de Investigación en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain.,Cystic Fibrosis Unit, Hospital Universitari Parc Taulí, Sabadell, Spain
| | - Concepción Montón
- Department of Respiratory Medicine, Institut d'Investigació i Innovació Parc Taulí (I3PT), Hospital Universitari Parc Taulí, Sabadell, Spain.,Cystic Fibrosis Unit, Hospital Universitari Parc Taulí, Sabadell, Spain
| | - Laura Millares
- Department of Respiratory Medicine, Institut d'Investigació i Innovació Parc Taulí (I3PT), Hospital Universitari Parc Taulí, Sabadell, Spain.,Centro de Investigación en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain.,Infectious and Respiratory Disease Research Group, Fundació Institut d'Investigació Germans Trias i Pujol, Badalona, Spain
| | - Sara Quero
- Department of Respiratory Medicine, Institut d'Investigació i Innovació Parc Taulí (I3PT), Hospital Universitari Parc Taulí, Sabadell, Spain.,Centro de Investigación en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain.,Infectious and Respiratory Disease Research Group, Fundació Institut d'Investigació Germans Trias i Pujol, Badalona, Spain
| | - Elena Prina
- Department of Respiratory Medicine, Institut d'Investigació i Innovació Parc Taulí (I3PT), Hospital Universitari Parc Taulí, Sabadell, Spain
| | - Oscar Asensio
- Cystic Fibrosis Unit, Hospital Universitari Parc Taulí, Sabadell, Spain.,Department of Pediatrics, Institut d'Investigació i Innovació Parc Taulí (I3PT), Hospital Universitari Parc Taulí, Sabadell, Spain
| | - Montserrat Bosque
- Cystic Fibrosis Unit, Hospital Universitari Parc Taulí, Sabadell, Spain.,Department of Pediatrics, Institut d'Investigació i Innovació Parc Taulí (I3PT), Hospital Universitari Parc Taulí, Sabadell, Spain
| | - Silvia Capilla
- Department of Microbiology, Hospital Universitari Parc Taulí, Sabadell, Spain
| | - Oscar Cuevas
- Department of Pediatrics, Institut d'Investigació i Innovació Parc Taulí (I3PT), Hospital Universitari Parc Taulí, Sabadell, Spain
| | - Eduard Monsó
- Department of Respiratory Medicine, Institut d'Investigació i Innovació Parc Taulí (I3PT), Hospital Universitari Parc Taulí, Sabadell, Spain.,Centro de Investigación en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain.,Universitat Autonoma de Barcelona, Barcelona, Spain
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46
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Xia Y. Correlation and association analyses in microbiome study integrating multiomics in health and disease. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 171:309-491. [PMID: 32475527 DOI: 10.1016/bs.pmbts.2020.04.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Correlation and association analyses are one of the most widely used statistical methods in research fields, including microbiome and integrative multiomics studies. Correlation and association have two implications: dependence and co-occurrence. Microbiome data are structured as phylogenetic tree and have several unique characteristics, including high dimensionality, compositionality, sparsity with excess zeros, and heterogeneity. These unique characteristics cause several statistical issues when analyzing microbiome data and integrating multiomics data, such as large p and small n, dependency, overdispersion, and zero-inflation. In microbiome research, on the one hand, classic correlation and association methods are still applied in real studies and used for the development of new methods; on the other hand, new methods have been developed to target statistical issues arising from unique characteristics of microbiome data. Here, we first provide a comprehensive view of classic and newly developed univariate correlation and association-based methods. We discuss the appropriateness and limitations of using classic methods and demonstrate how the newly developed methods mitigate the issues of microbiome data. Second, we emphasize that concepts of correlation and association analyses have been shifted by introducing network analysis, microbe-metabolite interactions, functional analysis, etc. Third, we introduce multivariate correlation and association-based methods, which are organized by the categories of exploratory, interpretive, and discriminatory analyses and classification methods. Fourth, we focus on the hypothesis testing of univariate and multivariate regression-based association methods, including alpha and beta diversities-based, count-based, and relative abundance (or compositional)-based association analyses. We demonstrate the characteristics and limitations of each approaches. Fifth, we introduce two specific microbiome-based methods: phylogenetic tree-based association analysis and testing for survival outcomes. Sixth, we provide an overall view of longitudinal methods in analysis of microbiome and omics data, which cover standard, static, regression-based time series methods, principal trend analysis, and newly developed univariate overdispersed and zero-inflated as well as multivariate distance/kernel-based longitudinal models. Finally, we comment on current association analysis and future direction of association analysis in microbiome and multiomics studies.
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Affiliation(s)
- Yinglin Xia
- Department of Medicine, University of Illinois at Chicago, Chicago, IL, United States.
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47
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Françoise A, Héry-Arnaud G. The Microbiome in Cystic Fibrosis Pulmonary Disease. Genes (Basel) 2020; 11:E536. [PMID: 32403302 PMCID: PMC7288443 DOI: 10.3390/genes11050536] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 04/20/2020] [Accepted: 05/08/2020] [Indexed: 12/19/2022] Open
Abstract
Cystic fibrosis (CF) is a genetic disease with mutational changes leading to profound dysbiosis, both pulmonary and intestinal, from a very young age. This dysbiosis plays an important role in clinical manifestations, particularly in the lungs, affected by chronic infection. The range of microbiological tools has recently been enriched by metagenomics based on next-generation sequencing (NGS). Currently applied essentially in a gene-targeted manner, metagenomics has enabled very exhaustive description of bacterial communities in the CF lung niche and, to a lesser extent, the fungi. Aided by progress in bioinformatics, this now makes it possible to envisage shotgun sequencing and opens the door to other areas of the microbial world, the virome, and the archaeome, for which almost everything remains to be described in cystic fibrosis. Paradoxically, applying NGS in microbiology has seen a rebirth of bacterial culture, but in an extended manner (culturomics), which has proved to be a perfectly complementary approach to NGS. Animal models have also proved indispensable for validating microbiome pathophysiological hypotheses. Description of pathological microbiomes and correlation with clinical status and therapeutics (antibiotic therapy, cystic fibrosis transmembrane conductance regulator (CFTR) modulators) revealed the richness of microbiome data, enabling description of predictive and follow-up biomarkers. Although monogenic, CF is a multifactorial disease, and both genotype and microbiome profiles are crucial interconnected factors in disease progression. Microbiome-genome interactions are thus important to decipher.
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Affiliation(s)
- Alice Françoise
- UMR 1078 GGB, University of Brest, Inserm, EFS, F-29200 Brest, France;
| | - Geneviève Héry-Arnaud
- UMR 1078 GGB, University of Brest, Inserm, EFS, F-29200 Brest, France;
- Unité de Bactériologie, Pôle de Biologie-Pathologie, Centre Hospitalier Régional et Universitaire de Brest, Hôpital de la Cavale Blanche, Boulevard Tanguy Prigent, 29200 Brest, France
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48
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Hahn A, Whiteson K, Davis TJ, Phan J, Sami I, Koumbourlis AC, Freishtat RJ, Crandall KA, Bean HD. Longitudinal Associations of the Cystic Fibrosis Airway Microbiome and Volatile Metabolites: A Case Study. Front Cell Infect Microbiol 2020; 10:174. [PMID: 32411616 PMCID: PMC7198769 DOI: 10.3389/fcimb.2020.00174] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 04/01/2020] [Indexed: 01/15/2023] Open
Abstract
The identification of 16S rDNA biomarkers from respiratory samples to describe the continuum of clinical disease states within persons having cystic fibrosis (CF) has remained elusive. We sought to combine 16S, metagenomics, and metabolomics data to describe multiple transitions between clinical disease states in 14 samples collected over a 12-month period in a single person with CF. We hypothesized that each clinical disease state would have a unique combination of bacterial genera and volatile metabolites as a potential signature that could be utilized as a biomarker of clinical disease state. Taxonomy identified by 16S sequencing corroborated clinical culture results, with the majority of the 109 PCR amplicons belonging to the bacteria grown in clinical cultures (Escherichia coli and Staphylococcus aureus). While alpha diversity measures fluctuated across disease states, no significant trends were present. Principle coordinates analysis showed that treatment samples trended toward a different community composition than baseline and exacerbation samples. This was driven by the phylum Bacteroidetes (less abundant in treatment, log2 fold difference -3.29, p = 0.015) and the genus Stenotrophomonas (more abundant in treatment, log2 fold difference 6.26, p = 0.003). Across all sputum samples, 466 distinct volatile metabolites were identified with total intensity varying across clinical disease state. Baseline and exacerbation samples were rather uniform in chemical composition and similar to one another, while treatment samples were highly variable and differed from the other two disease states. When utilizing a combination of the microbiome and metabolome data, we observed associations between samples dominated Staphylococcus and Escherichia and higher relative abundances of alcohols, while samples dominated by Achromobacter correlated with a metabolomics shift toward more oxidized volatiles. However, the microbiome and metabolome data were not tightly correlated; examining both the metagenomics and metabolomics allows for more context to examine changes across clinical disease states. In our study, combining the sputum microbiome and metabolome data revealed stability in the sputum composition through the first exacerbation and treatment episode, and into the second exacerbation. However, the second treatment ushered in a prolonged period of instability, which after three additional exacerbations and treatments culminated in a new lung microbiome and metabolome.
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Affiliation(s)
- Andrea Hahn
- Division of Infectious Diseases, Children's National Health System, Washington, DC, United States.,Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC, United States.,Center for Genetic Medicine Research, The Children's Research Institute, Washington, DC, United States
| | - Katrine Whiteson
- Department of Molecular Biology and Biochemistry, University of California at Irvine, Irvine, CA, United States
| | - Trenton J Davis
- School of Life Sciences, Arizona State University, Tempe, AZ, United States.,Center for Fundamental and Applied Microbiomics, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | - Joann Phan
- Department of Molecular Biology and Biochemistry, University of California at Irvine, Irvine, CA, United States
| | - Iman Sami
- Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC, United States.,Division of Pulmonary and Sleep Medicine, Children's National Health System, Washington, DC, United States
| | - Anastassios C Koumbourlis
- Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC, United States.,Division of Pulmonary and Sleep Medicine, Children's National Health System, Washington, DC, United States
| | - Robert J Freishtat
- Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC, United States.,Division of Emergency Medicine, Children's National Health System, Washington, DC, United States
| | - Keith A Crandall
- Computational Biology Institute and Department of Biostatistics & Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, DC, United States
| | - Heather D Bean
- School of Life Sciences, Arizona State University, Tempe, AZ, United States.,Center for Fundamental and Applied Microbiomics, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
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49
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Acosta N, Waddell B, Heirali A, Somayaji R, Surette MG, Workentine ML, Rabin HR, Parkins MD. Cystic Fibrosis Patients Infected With Epidemic Pseudomonas aeruginosa Strains Have Unique Microbial Communities. Front Cell Infect Microbiol 2020; 10:173. [PMID: 32426295 PMCID: PMC7212370 DOI: 10.3389/fcimb.2020.00173] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 04/01/2020] [Indexed: 11/13/2022] Open
Abstract
Pseudomonas aeruginosa is the archetypal cystic fibrosis (CF) pathogen. However, the clinical course experienced by infected individuals varies markedly. Understanding these differences is imperative if further improvements in outcomes are to be achieved. Multiple studies have found that patients infected with epidemic P. aeruginosa (ePA) strains may have a worse clinical prognosis than those infected with unique, non-clonal strains. Additionally, the traditionally uncultured CF lung bacterial community (i.e., CF microbiome) may further influence the outcome. We sought to identify if these two important variables, not identified through routine culture, associate and together may contribute to disease pathogenesis. Patients were classified as being infected with Prairie Epidemic ePA (PES) or a non-clonal strain, unique PA strains (uPA), through a retrospective assessment of a comprehensive strain biobank using a combination of PFGE and PES-specific PCR. Patients were matched to age, sex, time-period controls and sputum samples from equivalent time periods were identified from a sputum biobank. Bacterial 16S rRNA gene profiling and Pseudomonas qPCR was used to characterize the respiratory microbiome. We identified 31 patients infected with PES and matched them with uPA controls. Patients infected with PES at baseline have lower microbial diversity (P = 0.02) and higher P. aeruginosa relative abundance (P < 0.005). Microbial community structure was found to cluster by PA strain type, although it was not the main determinant of community structure as additional factors were also found to be drivers of CF community structure. Communities from PES infected individuals were enriched with Pseudomonas, Streptococcus and Prevotella OTUs. The disproportionate disease experienced by ePA infected CF patients may be mediated through a combination of pathogen-pathogen factors as opposed to strictly enhanced virulence of infecting P. aeruginosa strains.
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Affiliation(s)
- Nicole Acosta
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada
| | - Barbara Waddell
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada
| | - Alya Heirali
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada
| | - Ranjani Somayaji
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada.,Department of Medicine, University of Calgary, Calgary, AB, Canada
| | - Michael G Surette
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada.,Departments of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | | | - Harvey R Rabin
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada.,Department of Medicine, University of Calgary, Calgary, AB, Canada
| | - Michael D Parkins
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada.,Department of Medicine, University of Calgary, Calgary, AB, Canada
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Scoffone VC, Barbieri G, Buroni S, Scarselli M, Pizza M, Rappuoli R, Riccardi G. Vaccines to Overcome Antibiotic Resistance: The Challenge of Burkholderia cenocepacia. Trends Microbiol 2020; 28:315-326. [DOI: 10.1016/j.tim.2019.12.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 12/03/2019] [Accepted: 12/09/2019] [Indexed: 12/26/2022]
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