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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; 9:e0092923. [PMID: 38934598 PMCID: PMC11264604 DOI: 10.1128/msystems.00929-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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Bényei ÉB, Nazeer RR, Askenasy I, Mancini L, Ho PM, Sivarajan GAC, Swain JEV, Welch M. The past, present and future of polymicrobial infection research: Modelling, eavesdropping, terraforming and other stories. Adv Microb Physiol 2024; 85:259-323. [PMID: 39059822 DOI: 10.1016/bs.ampbs.2024.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2024]
Abstract
Over the last two centuries, great advances have been made in microbiology as a discipline. Much of this progress has come about as a consequence of studying the growth and physiology of individual microbial species in well-defined laboratory media; so-called "axenic growth". However, in the real world, microbes rarely live in such "splendid isolation" (to paraphrase Foster) and more often-than-not, share the niche with a plethora of co-habitants. The resulting interactions between species (and even between kingdoms) are only very poorly understood, both on a theoretical and experimental level. Nevertheless, the last few years have seen significant progress, and in this review, we assess the importance of polymicrobial infections, and show how improved experimental traction is advancing our understanding of these. A particular focus is on developments that are allowing us to capture the key features of polymicrobial infection scenarios, especially as those associated with the human airways (both healthy and diseased).
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Affiliation(s)
| | | | - Isabel Askenasy
- Department of Biochemistry, Tennis Court Road, Cambridge, United Kingdom
| | - Leonardo Mancini
- Department of Biochemistry, Tennis Court Road, Cambridge, United Kingdom
| | - Pok-Man Ho
- Department of Biochemistry, Tennis Court Road, Cambridge, United Kingdom
| | | | - Jemima E V Swain
- Department of Biochemistry, Tennis Court Road, Cambridge, United Kingdom
| | - Martin Welch
- Department of Biochemistry, Tennis Court Road, Cambridge, United Kingdom.
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3
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Lussac-Sorton F, Charpentier É, Imbert S, Lefranc M, Bui S, Fayon M, Berger P, Enaud R, Delhaes L. The gut-lung axis in the CFTR modulator era. Front Cell Infect Microbiol 2023; 13:1271117. [PMID: 37780857 PMCID: PMC10540301 DOI: 10.3389/fcimb.2023.1271117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 08/30/2023] [Indexed: 10/03/2023] Open
Abstract
The advent of CFTR modulators represents a turning point in the history of cystic fibrosis (CF) management, changing profoundly the disease's clinical course by improving mucosal hydration. Assessing changes in airway and digestive tract microbiomes is of great interest to better understand the mechanisms and to predict disease evolution. Bacterial and fungal dysbiosis have been well documented in patients with CF; yet the impact of CFTR modulators on microbial communities has only been partially deciphered to date. In this review, we aim to summarize the current state of knowledge regarding the impact of CFTR modulators on both pulmonary and digestive microbiomes. Our analysis also covers the inter-organ connections between lung and gut communities, in order to highlight the gut-lung axis involvement in CF pathophysiology and its evolution in the era of novel modulators therapies.
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Affiliation(s)
- Florian Lussac-Sorton
- Univ. Bordeaux, Centre de Recherche Cardio-Thoracique de Bordeaux, INSERM U1045, Pessac, France
- INSERM, Centre de Recherche Cardio-thoracique de Bordeaux, Pessac, France
| | - Éléna Charpentier
- Univ. Bordeaux, Centre de Recherche Cardio-Thoracique de Bordeaux, INSERM U1045, Pessac, France
- INSERM, Centre de Recherche Cardio-thoracique de Bordeaux, Pessac, France
| | - Sébastien Imbert
- Univ. Bordeaux, Centre de Recherche Cardio-Thoracique de Bordeaux, INSERM U1045, Pessac, France
- INSERM, Centre de Recherche Cardio-thoracique de Bordeaux, Pessac, France
- CHU Bordeaux, Service de Parasitologie et Mycologie, Centre de Ressources et de Compétences de la Mucoviscidose (CRCM), Service de Pédiatrie, Service d’Exploration Fonctionnelle Respiratoire, CIC, Bordeaux, France
| | - Maxime Lefranc
- CHU Bordeaux, Service de Parasitologie et Mycologie, Centre de Ressources et de Compétences de la Mucoviscidose (CRCM), Service de Pédiatrie, Service d’Exploration Fonctionnelle Respiratoire, CIC, Bordeaux, France
| | - Stéphanie Bui
- Univ. Bordeaux, Centre de Recherche Cardio-Thoracique de Bordeaux, INSERM U1045, Pessac, France
- INSERM, Centre de Recherche Cardio-thoracique de Bordeaux, Pessac, France
- CHU Bordeaux, Service de Parasitologie et Mycologie, Centre de Ressources et de Compétences de la Mucoviscidose (CRCM), Service de Pédiatrie, Service d’Exploration Fonctionnelle Respiratoire, CIC, Bordeaux, France
| | - Michael Fayon
- Univ. Bordeaux, Centre de Recherche Cardio-Thoracique de Bordeaux, INSERM U1045, Pessac, France
- INSERM, Centre de Recherche Cardio-thoracique de Bordeaux, Pessac, France
- CHU Bordeaux, Service de Parasitologie et Mycologie, Centre de Ressources et de Compétences de la Mucoviscidose (CRCM), Service de Pédiatrie, Service d’Exploration Fonctionnelle Respiratoire, CIC, Bordeaux, France
| | - Patrick Berger
- Univ. Bordeaux, Centre de Recherche Cardio-Thoracique de Bordeaux, INSERM U1045, Pessac, France
- INSERM, Centre de Recherche Cardio-thoracique de Bordeaux, Pessac, France
- CHU Bordeaux, Service de Parasitologie et Mycologie, Centre de Ressources et de Compétences de la Mucoviscidose (CRCM), Service de Pédiatrie, Service d’Exploration Fonctionnelle Respiratoire, CIC, Bordeaux, France
| | - Raphaël Enaud
- Univ. Bordeaux, Centre de Recherche Cardio-Thoracique de Bordeaux, INSERM U1045, Pessac, France
- INSERM, Centre de Recherche Cardio-thoracique de Bordeaux, Pessac, France
- CHU Bordeaux, Service de Parasitologie et Mycologie, Centre de Ressources et de Compétences de la Mucoviscidose (CRCM), Service de Pédiatrie, Service d’Exploration Fonctionnelle Respiratoire, CIC, Bordeaux, France
| | - Laurence Delhaes
- Univ. Bordeaux, Centre de Recherche Cardio-Thoracique de Bordeaux, INSERM U1045, Pessac, France
- INSERM, Centre de Recherche Cardio-thoracique de Bordeaux, Pessac, France
- CHU Bordeaux, Service de Parasitologie et Mycologie, Centre de Ressources et de Compétences de la Mucoviscidose (CRCM), Service de Pédiatrie, Service d’Exploration Fonctionnelle Respiratoire, CIC, Bordeaux, France
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Miller A, Fantone KM, Tucker SL, Gokanapudi N, Goldberg JB, Rada B. Short chain fatty acids reduce the respiratory burst of human neutrophils in response to cystic fibrosis isolates of Staphylococcus aureus. J Cyst Fibros 2023; 22:756-762. [PMID: 37211502 PMCID: PMC10524534 DOI: 10.1016/j.jcf.2023.04.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 04/21/2023] [Accepted: 04/27/2023] [Indexed: 05/23/2023]
Abstract
Short chain fatty acids (SCFA) are produced by anaerobic bacteria. The most common SCFAs are acetate, propionate and butyrate. SCFAs have been implicated in several inflammatory diseases including cystic fibrosis (CF) where they are present in the airways at millimolar concentrations. Staphylococcus aureus is one of the main respiratory pathogens in CF. Polymorphonuclear neutrophil granulocytes (PMN) represent the most important immune defense the host uses against S. aureus. However, the reason why PMNs are unable to clear S. aureus in CF remains largely unclear. We hypothesized that SCFAs impair effector functions of PMNs in response to S. aureus. To test this, human PMNs were exposed to CF clinical isolates of S. aureus in vitro in the presence or absence of SCFAs and effector functions of PMNs were assessed. Our data show that SCFAs do not affect the viability of PMNs and do not stimulate the release of neutrophil extracellular traps (NET) from human PMNs. Production of reactive oxygen species (ROS), another important antimicrobial function of PMNs, on the other hand, was significantly inhibited by SCFAs in response to the bacterium. SCFAs did not compromise the ability of PMNs to kill CF isolates of S. aureus in vitro. Overall, our results provide new knowledge into the interactions between SCFAs and the immune system, and indicate that SCFAs produced by anaerobic bacteria in the CF lung could interfere with reactive oxidant production of PMNs in response to S. aureus, one of the prominent respiratory pathogens in this disease.
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Affiliation(s)
- Arthur Miller
- Department of Infectious Diseases, College of Veterinary Medicine, The University of Georgia, Athens, GA, USA
| | - Kayla M Fantone
- Department of Infectious Diseases, College of Veterinary Medicine, The University of Georgia, Athens, GA, USA
| | - Samantha L Tucker
- Department of Infectious Diseases, College of Veterinary Medicine, The University of Georgia, Athens, GA, USA
| | - Naveen Gokanapudi
- Department of Infectious Diseases, College of Veterinary Medicine, The University of Georgia, Athens, GA, USA
| | - Joanna B Goldberg
- Division of Pulmonology, Asthma, Cystic Fibrosis and Sleep, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Balázs Rada
- Department of Infectious Diseases, College of Veterinary Medicine, The University of Georgia, Athens, GA, USA.
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5
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Zhou Y, Liu M, Liu K, Wu G, Tan Y. Lung microbiota and potential treatment of respiratory diseases. Microb Pathog 2023:106197. [PMID: 37321423 DOI: 10.1016/j.micpath.2023.106197] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 05/21/2023] [Accepted: 06/06/2023] [Indexed: 06/17/2023]
Abstract
The unique microbiome found in the lungs has been studied and shown to be associated with both pulmonary homeostasis and lung diseases. The lung microbiome has the potential to produce metabolites that modulate host-microbe interactions. Specifically, short-chain fatty acids (SCFAs) produced by certain strains of the lung microbiota have been shown to regulate immune function and maintain gut mucosal health. In response, this review described the distribution and composition of the microbiota in lung diseases and discussed the impact of the lung microbiota on health and lung disease. In addition, the review further elaborated on the mechanism of microbial metabolites in microbial-host interaction and their application in the treatment of lung diseases. A better understanding of the interaction between the microbiota, metabolites, and host will provide potential strategies for the development of novel methods for the treatment of pulmonary microbial induced lung diseases.
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Affiliation(s)
- Yaxuan Zhou
- Department of Psychiatry, Department of Medicine, Xiangya School of Medical, Central South University, Changsha, 410083, Hunan, China
| | - Mengjun Liu
- Department of Clinical Medicine, Xiangya School of Medicine, Central South University, Changsha, 410083, Hunan, China
| | - Kaixuan Liu
- Department of Excellent Doctor Training, Xiangya School of Medicine, Central South University, Changsha, 410083, Hunan, China
| | - Guojun Wu
- Department of Medical Microbiology, School of Basic Medicine, Central South University, Changsha, 410083, Hunan, China.
| | - Yurong Tan
- Department of Medical Microbiology, School of Basic Medicine, Central South University, Changsha, 410083, Hunan, China.
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6
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Ren Z, Pan X, Li J, Dong X, Tu X, Pan LL, Sun J. G protein coupled receptor 41 regulates fibroblast activation in pulmonary fibrosis via Gαi/o and downstream Smad2/3 and ERK1/2 phosphorylation. Pharmacol Res 2023; 191:106754. [PMID: 37019194 DOI: 10.1016/j.phrs.2023.106754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 03/28/2023] [Accepted: 04/02/2023] [Indexed: 04/05/2023]
Abstract
Pulmonary fibrosis is a progressive and fatal fibrotic lung disease with mysterious pathogenesis and limited effective therapies. G protein-coupled receptors (GPRs) participate in a variety of physiologic functions, and several GPRs have critical fibrosis-promoting or -inhibiting roles in pulmonary fibrosis. Here, we explored the role of GPR41 in the pathobiology of pulmonary fibrosis. We found that GPR41 expression was elevated in lung tissues of mice with bleomycin-induced pulmonary fibrosis and lung fibroblasts treated with transforming growth factor-β1 (TGF-β1). Knockout of GPR41 attenuated pulmonary fibrosis in mice, as evidenced by improved lung morphology, decreased lung weight and collagen secretion, and down-regulated α-SMA, collagen type I alpha and fibronectin expression in lungs. Additionally, GPR41 knockout inhibited the differentiation of fibroblasts to myofibroblasts, and decreased myofibroblast migration. By further mechanistic analysis, we demonstrated that GPR41 regulated TGF-β1-induced fibroblast-to-myofibroblast differentiation and Smad2/3 and ERK1/2 phosphorylation via its Gαi/o subunit but not Gβγ subunit. Together, our data indicate that GPR41 is involved in pulmonary fibroblast activation and fibrosis, and GPR41 represents a potential therapeutic target for pulmonary fibrosis.
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Affiliation(s)
- Zhengnan Ren
- School of Medicine and School of Food Science and Technology, Jiangnan University, Wuxi, China; State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Xiaohua Pan
- School of Medicine and School of Food Science and Technology, Jiangnan University, Wuxi, China; State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Jiahong Li
- School of Medicine and School of Food Science and Technology, Jiangnan University, Wuxi, China; State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Xiaoliang Dong
- School of Medicine and School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Xing Tu
- School of Medicine and School of Food Science and Technology, Jiangnan University, Wuxi, China; State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Li-Long Pan
- School of Medicine and School of Food Science and Technology, Jiangnan University, Wuxi, China.
| | - Jia Sun
- School of Medicine and School of Food Science and Technology, Jiangnan University, Wuxi, China; State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.
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7
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Shumyatsky G, Burrell A, Chaney H, Sami I, Koumbourlis AC, Freishtat RJ, Crandall KA, Zemanick ET, Hahn A. Using metabolic potential within the airway microbiome as predictors of clinical state in persons with cystic fibrosis. Front Med (Lausanne) 2023; 9:1082125. [PMID: 36698799 PMCID: PMC9868313 DOI: 10.3389/fmed.2022.1082125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 12/19/2022] [Indexed: 01/11/2023] Open
Abstract
Introduction Pulmonary exacerbations (PEx) in persons with cystic fibrosis (CF) are primarily related to acute or chronic inflammation associated with bacterial lung infections, which may be caused by several bacteria that activate similar bacterial genes and produce similar by-products. The goal of our study was to perform a stratified functional analysis of bacterial genes at three distinct time points in the treatment of a PEx in order to determine the role that specific airway microbiome community members may play within each clinical state (i.e., PEx, end of antibiotic treatment, and follow-up). Our secondary goal was to compare the change between clinical states with the metabolic activity of specific airway microbiome community members. Methods This was a prospective observational study of persons with CF treated with intravenous antibiotics for PEx between 2016 and 2020 at Children's National Hospital. Demographic and clinical information as well as respiratory samples were collected at hospital admission for PEx, end of antibiotic treatment, and follow-up. Metagenomic sequencing was performed; MetaPhlAn3 and HUMANn3 were used to assign sequences to bacterial species and bacterial metabolic genes, respectively. Results Twenty-two persons with CF, with a mean age of 14.5 (range 7-23) years, experienced 45 PEx during the study period. Two-hundred twenty-one bacterial species were identified in the respiratory samples from the study cohort. Ten bacterial species had differential gene abundance across changes in the clinical state including Staphylococcus aureus, Streptococcus salivarius, and Veillonella atypica (all padj < 0.01 and log2FoldChange > |2|). These corresponded to a differential abundance of bacterial genes, with S. aureus accounting for 81% of the genes more abundant in PEx and S. salivarius accounting for 83% of the genes more abundant in follow-up, all compared to the end of treatment. Lastly, 8,653 metabolic pathways were identified across samples, with again S. aureus and S. salivarius contributing to the differential abundance of pathways (106 in PEx vs. 66 in follow-up, respectively). V. atypica was associated with a single metabolic pathway (UDP-N-acetyl-D-glucosamine biosynthesis) increased in follow-up compared to PEx. Discussion Taken together, these data suggest that the metabolic potential of bacterial species can provide more insight into changes across clinical states than the relative abundance of the bacteria alone.
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Affiliation(s)
- Gabriella Shumyatsky
- Jefferson Biotechnology Program, Thomas Jefferson University, Philadelphia, PA, United States
| | - Aszia Burrell
- Center for Genetic Medicine Research, Children's National Research Institute, Washington, DC, United States
| | - Hollis Chaney
- Department of Pediatrics, George Washington University (GWU), Washington, DC, United States.,Division of Pulmonary Medicine, Children's National Hospital (CNH), Washington, DC, United States
| | - Iman Sami
- Department of Pediatrics, George Washington University (GWU), Washington, DC, United States.,Division of Pulmonary Medicine, Children's National Hospital (CNH), Washington, DC, United States
| | - Anastassios C Koumbourlis
- Department of Pediatrics, George Washington University (GWU), Washington, DC, United States.,Division of Pulmonary Medicine, Children's National Hospital (CNH), Washington, DC, United States
| | - Robert J Freishtat
- Center for Genetic Medicine Research, Children's National Research Institute, Washington, DC, United States.,Department of Pediatrics, George Washington University (GWU), Washington, DC, United States.,Division of Emergency Medicine, CNH, Washington, DC, United States
| | - Keith A Crandall
- Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, GWU, Washington, DC, United States
| | - Edith T Zemanick
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Andrea Hahn
- Center for Genetic Medicine Research, Children's National Research Institute, Washington, DC, United States.,Department of Pediatrics, George Washington University (GWU), Washington, DC, United States.,Division of Infectious Diseases, CNH, Washington, DC, United States
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8
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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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9
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Muggeo A, Perotin JM, Brisebarre A, Dury S, Dormoy V, Launois C, Ancel J, Mulette P, de Champs C, Deslée G, Guillard T. Extended Bacteria Culture-Based Clustering Identifies a Phenotype Associating Increased Cough and Enterobacterales in Stable Chronic Obstructive Pulmonary Disease. Front Microbiol 2022; 12:781797. [PMID: 34970242 PMCID: PMC8712763 DOI: 10.3389/fmicb.2021.781797] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 11/11/2021] [Indexed: 11/13/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is a chronic inflammatory lung disease characterized by airflow limitation. This chronic respiratory disease represents the third leading cause of death worldwide. Alteration of the airway microbiota has been reported to be associated with exacerbation frequency in COPD, but its role on the symptoms in patients at stable state is still incompletely described. This study aimed to determine whether bacteria isolated in sputum can be associated with the clinical features of COPD patients within stable state. Our study highlights, for the first time, that altered microbiota with Enterobacterales is associated with pejorative clinical symptoms in stable COPD patients. The airway microbiota of 38 patients was analyzed using an extended culture approach and mass spectrometry identification. Cluster analysis by principal coordinate analysis of the bacterial communities showed that the patients could be classified into three distinct clusters in our cohort. The clusters showed no differences in proportions of the phylum, but one of them was associated with a high prevalence of Enterobacterales (71.4% in cluster 1 vs. 0% in cluster 3), loss of microbiota diversity, and higher bacterial load (107 vs. 105 CFU/ml, respectively) and characterized by predominant cough and impact on mental health. These novel findings, supported by further studies, could lead to modifying the processing of COPD sputum in the everyday practice of clinical microbiology laboratories.
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Affiliation(s)
- Anaëlle Muggeo
- Inserm UMR-S 1250 Pulmonary pathologies and cellular plasticity (P3Cell), Reims-Champagne-Ardenne University, SFR CAP Santé, Reims, France.,Laboratory of Bacteriology-Virology-Hospital Hygiene-Parasitology-Mycology, Reims University Hospital, Reims, France
| | - Jeanne-Marie Perotin
- Inserm UMR-S 1250 Pulmonary pathologies and cellular plasticity (P3Cell), Reims-Champagne-Ardenne University, SFR CAP Santé, Reims, France.,Department of Respiratory Diseases, Reims University Hospital, Reims, France
| | - Audrey Brisebarre
- Inserm UMR-S 1250 Pulmonary pathologies and cellular plasticity (P3Cell), Reims-Champagne-Ardenne University, SFR CAP Santé, Reims, France
| | - Sandra Dury
- Department of Respiratory Diseases, Reims University Hospital, Reims, France
| | - Valérian Dormoy
- Inserm UMR-S 1250 Pulmonary pathologies and cellular plasticity (P3Cell), Reims-Champagne-Ardenne University, SFR CAP Santé, Reims, France
| | - Claire Launois
- Department of Respiratory Diseases, Reims University Hospital, Reims, France
| | - Julien Ancel
- Inserm UMR-S 1250 Pulmonary pathologies and cellular plasticity (P3Cell), Reims-Champagne-Ardenne University, SFR CAP Santé, Reims, France.,Department of Respiratory Diseases, Reims University Hospital, Reims, France
| | - Pauline Mulette
- Inserm UMR-S 1250 Pulmonary pathologies and cellular plasticity (P3Cell), Reims-Champagne-Ardenne University, SFR CAP Santé, Reims, France.,Department of Respiratory Diseases, Reims University Hospital, Reims, France
| | - Christophe de Champs
- Inserm UMR-S 1250 Pulmonary pathologies and cellular plasticity (P3Cell), Reims-Champagne-Ardenne University, SFR CAP Santé, Reims, France.,Laboratory of Bacteriology-Virology-Hospital Hygiene-Parasitology-Mycology, Reims University Hospital, Reims, France
| | - Gaëtan Deslée
- Inserm UMR-S 1250 Pulmonary pathologies and cellular plasticity (P3Cell), Reims-Champagne-Ardenne University, SFR CAP Santé, Reims, France.,Department of Respiratory Diseases, Reims University Hospital, Reims, France
| | - Thomas Guillard
- Inserm UMR-S 1250 Pulmonary pathologies and cellular plasticity (P3Cell), Reims-Champagne-Ardenne University, SFR CAP Santé, Reims, France.,Laboratory of Bacteriology-Virology-Hospital Hygiene-Parasitology-Mycology, Reims University Hospital, Reims, France
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10
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Sosinski LM, H CM, Neugebauer KA, Ghuneim LAJ, Guzior DV, Castillo-Bahena A, Mielke J, Thomas R, McClelland M, Conrad D, Quinn RA. A restructuring of microbiome niche space is associated with Elexacaftor-Tezacaftor-Ivacaftor therapy in the cystic fibrosis lung. J Cyst Fibros 2021; 21:996-1005. [PMID: 34824018 DOI: 10.1016/j.jcf.2021.11.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 10/21/2021] [Accepted: 11/05/2021] [Indexed: 11/25/2022]
Abstract
BACKGROUND Elexacaftor-Tezacaftor-Ivacaftor (ETI) therapy is showing promising efficacy for treatment of cystic fibrosis (CF) and is becoming more widely available since recent FDA approval. However, little is known about how these drugs will affect lung infections, which are the leading cause of morbidity and mortality among people with CF (pwCF). METHODS We analyzed sputum microbiome and metabolome data from pwCF (n=24) before and after ETI therapy using 16S rRNA gene sequencing and untargeted metabolomics. RESULTS The sputum microbiome diversity, particularly its evenness, was increased (p=0.036) and the microbiome profiles were different between individuals before and after therapy (PERMANOVA F=1.92, p=0.044). Despite these changes, the microbiomes remained more similar within an individual than across the sampled population. No specific microbial taxa differed in relative abundance before and after therapy, but the collective log-ratio of classic CF pathogens to anaerobes significantly decreased (p=0.013). The sputum metabolome also showed changes associated with ETI (PERMANOVA F=4.22, p=0.002) and was characterized by greater variation across subjects while on treatment. Changes in the metabolome were driven by a decrease in peptides, amino acids, and metabolites from the kynurenine pathway, which were associated with a decrease in CF pathogens. Metabolism of the three small molecules that make up ETI was extensive, including previously uncharacterized structural modifications. CONCLUSIONS ETI therapy is associated with a changing microbiome and metabolome in airway mucus. This effect was stronger on sputum biochemistry, which may reflect changing niche space for microbial residency in lung mucus as the drug's effects take hold. FUNDING This project was funded by a National Institute of Allergy and Infectious Disease Grant R01AI145925.
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Affiliation(s)
- Lo M Sosinski
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Christian Martin H
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Kerri A Neugebauer
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Lydia-Ann J Ghuneim
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Douglas V Guzior
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA; Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | | | - Jenna Mielke
- Department of Medicine, University of California San Diego, La Jolla, CA
| | - Ryan Thomas
- Department of Pediatrics and Human Development, Michigan State University, East Lansing, MI, USA
| | | | - Doug Conrad
- Department of Medicine, University of California San Diego, La Jolla, CA
| | - Robert A Quinn
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA.
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11
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Reece E, Bettio PHDA, Renwick J. Polymicrobial Interactions in the Cystic Fibrosis Airway Microbiome Impact the Antimicrobial Susceptibility of Pseudomonas aeruginosa. Antibiotics (Basel) 2021; 10:antibiotics10070827. [PMID: 34356747 PMCID: PMC8300716 DOI: 10.3390/antibiotics10070827] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/01/2021] [Accepted: 07/01/2021] [Indexed: 12/19/2022] Open
Abstract
Pseudomonas aeruginosa is one of the most dominant pathogens in cystic fibrosis (CF) airway disease and contributes to significant inflammation, airway damage, and poorer disease outcomes. The CF airway is now known to be host to a complex community of microorganisms, and polymicrobial interactions have been shown to play an important role in shaping P. aeruginosa pathogenicity and resistance. P. aeruginosa can cause chronic infections that once established are almost impossible to eradicate with antibiotics. CF patients that develop chronic P. aeruginosa infection have poorer lung function, higher morbidity, and a reduced life expectancy. P. aeruginosa adapts to the CF airway and quickly develops resistance to several antibiotics. A perplexing phenomenon is the disparity between in vitro antimicrobial sensitivity testing and clinical response. Considering the CF airway is host to a diverse community of microorganisms or 'microbiome' and that these microorganisms are known to interact, the antimicrobial resistance and progression of P. aeruginosa infection is likely influenced by these microbial relationships. This review combines the literature to date on interactions between P. aeruginosa and other airway microorganisms and the influence of these interactions on P. aeruginosa tolerance to antimicrobials.
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12
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Prevotella melaninogenica, a Sentinel Species of Antibiotic Resistance in Cystic Fibrosis Respiratory Niche? Microorganisms 2021; 9:microorganisms9061275. [PMID: 34208093 PMCID: PMC8230849 DOI: 10.3390/microorganisms9061275] [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: 05/19/2021] [Revised: 06/06/2021] [Accepted: 06/08/2021] [Indexed: 12/31/2022] Open
Abstract
The importance and abundance of strict anaerobic bacteria in the respiratory microbiota of people with cystic fibrosis (PWCF) is now established through studies based on high-throughput sequencing or extended-culture methods. In CF respiratory niche, one of the most prevalent anaerobic genera is Prevotella, and particularly the species Prevotella melaninogenica. The objective of this study was to evaluate the antibiotic susceptibility of this anaerobic species. Fifty isolates of P. melaninogenica cultured from sputum of 50 PWCF have been included. Antibiotic susceptibility testing was performed using the agar diffusion method. All isolates were susceptible to the following antibiotics: amoxicillin/clavulanic acid, piperacillin/tazobactam, imipenem and metronidazole. A total of 96% of the isolates (48/50) were resistant to amoxicillin (indicating beta-lactamase production), 34% to clindamycin (17/50) and 24% to moxifloxacin (12/50). Moreover, 10% (5/50) were multidrug-resistant. A significant and positive correlation was found between clindamycin resistance and chronic azithromycin administration. This preliminary study on a predominant species of the lung “anaerobiome” shows high percentages of resistance, potentially exacerbated by the initiation of long-term antibiotic therapy in PWCF. The anaerobic resistome characterization, focusing on species rather than genera, is needed in the future to better prevent the emergence of resistance within lung microbiota.
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13
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Beauruelle C, Guilloux CA, Lamoureux C, Héry-Arnaud G. The Human Microbiome, an Emerging Key-Player in the Sex Gap in Respiratory Diseases. Front Med (Lausanne) 2021; 8:600879. [PMID: 34026772 PMCID: PMC8137850 DOI: 10.3389/fmed.2021.600879] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 04/12/2021] [Indexed: 12/13/2022] Open
Abstract
The sex gap is well-documented in respiratory diseases such as cystic fibrosis and chronic obstructive pulmonary disease. While the differences between males and females in prevalence, severity and prognosis are well-established, the pathophysiology of the sex difference has been poorly characterized to date. Over the past 10 years, metagenomics-based studies have revealed the presence of a resident microbiome in the respiratory tract and its central role in respiratory disease. The lung microbiome is associated with host immune response and health outcomes in both animal models and patient cohorts. The study of the lung microbiome is therefore an interesting new avenue to explore in order to understand the sex gap observed in respiratory diseases. Another important parameter to consider is the gut-lung axis, since the gut microbiome plays a crucial role in distant immune modulation in respiratory diseases, and an intestinal “microgenderome” has been reported: i.e., sexual dimorphism in the gut microbiome. The microgenderome provides new pathophysiological clues, as it defines the interactions between microbiome, sex hormones, immunity and disease susceptibility. As research on the microbiome is increasing in volume and scope, the objective of this review was to describe the state-of-the-art on the sex gap in respiratory medicine (acute pulmonary infection and chronic lung disease) in the light of the microbiome, including evidence of local (lung) or distant (gut) contributions to the pathophysiology of these diseases.
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Affiliation(s)
- Clémence Beauruelle
- Univ Brest, Inserm, EFS, UMR 1078, GGB, Brest, France.,Unité de Bactériologie, Pôle de Biologie-Pathologie, Centre Hospitalier Régional et Universitaire de Brest, Hôpital de la Cavale Blanche, Brest, France
| | | | - Claudie Lamoureux
- Univ Brest, Inserm, EFS, UMR 1078, GGB, Brest, France.,Unité de Bactériologie, Pôle de Biologie-Pathologie, Centre Hospitalier Régional et Universitaire de Brest, Hôpital de la Cavale Blanche, Brest, France
| | - Geneviève Héry-Arnaud
- Univ Brest, Inserm, EFS, UMR 1078, GGB, Brest, France.,Unité de Bactériologie, Pôle de Biologie-Pathologie, Centre Hospitalier Régional et Universitaire de Brest, Hôpital de la Cavale Blanche, Brest, France
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14
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Lamoureux C, Guilloux CA, Beauruelle C, Gouriou S, Ramel S, Dirou A, Le Bihan J, Revert K, Ropars T, Lagrafeuille R, Vallet S, Le Berre R, Nowak E, Héry-Arnaud G. An observational study of anaerobic bacteria in cystic fibrosis lung using culture dependant and independent approaches. Sci Rep 2021; 11:6845. [PMID: 33767218 PMCID: PMC7994387 DOI: 10.1038/s41598-021-85592-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 03/01/2021] [Indexed: 12/11/2022] Open
Abstract
Strict anaerobes are undeniably important residents of the cystic fibrosis (CF) lung but are still unknowns. The main objectives of this study were to describe anaerobic bacteria diversity in CF airway microbiota and to evaluate the association with lung function. An observational study was conducted during eight months. A hundred and one patients were enrolled in the study, and 150 sputum samples were collected using a sterile sample kit designed to preserve anaerobic conditions. An extended-culture approach on 112 sputa and a molecular approach (quantitative PCR targeting three of the main anaerobic genera in CF lung: Prevotella, Veillonella, and Fusobacterium) on 141 sputa were developed. On culture, 91.1% of sputa were positive for at least one anaerobic bacterial species, with an average of six anaerobic species detected per sputum. Thirty-one anaerobic genera and 69 species were found, which is the largest anaerobe diversity ever reported in CF lungs. Better lung function (defined as Forced Expiratory Volume in one second > 70%) was significantly associated with higher quantification of Veillonella. These results raise the question of the potential impact of anaerobes on lung function.
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Affiliation(s)
- Claudie Lamoureux
- INSERM, EFS, Univ Brest, UMR 1078, GGB, 29200, Brest, France.,Department of Bacteriology, Virology, Hospital Hygiene, and Parasitology-Mycology, Brest University Hospital, Boulevard Tanguy Prigent, 29200, Brest, France
| | | | - Clémence Beauruelle
- INSERM, EFS, Univ Brest, UMR 1078, GGB, 29200, Brest, France.,Department of Bacteriology, Virology, Hospital Hygiene, and Parasitology-Mycology, Brest University Hospital, Boulevard Tanguy Prigent, 29200, Brest, France
| | | | - Sophie Ramel
- Cystic Fibrosis Center of Roscoff, Fondation Ildys, Roscoff, France
| | - Anne Dirou
- Cystic Fibrosis Center of Roscoff, Fondation Ildys, Roscoff, France
| | - Jean Le Bihan
- Cystic Fibrosis Center of Roscoff, Fondation Ildys, Roscoff, France
| | - Krista Revert
- Cystic Fibrosis Center of Roscoff, Fondation Ildys, Roscoff, France
| | - Thomas Ropars
- Cystic Fibrosis Center of Roscoff, Fondation Ildys, Roscoff, France
| | | | - Sophie Vallet
- INSERM, EFS, Univ Brest, UMR 1078, GGB, 29200, Brest, France.,Department of Bacteriology, Virology, Hospital Hygiene, and Parasitology-Mycology, Brest University Hospital, Boulevard Tanguy Prigent, 29200, Brest, France
| | - Rozenn Le Berre
- INSERM, EFS, Univ Brest, UMR 1078, GGB, 29200, Brest, France.,Department of Pulmonary and Internal Medicine, Brest University Hospital, Brest, France
| | - Emmanuel Nowak
- INSERM CIC 1412, Brest University Hospital, Brest, France
| | - Geneviève Héry-Arnaud
- INSERM, EFS, Univ Brest, UMR 1078, GGB, 29200, Brest, France. .,Department of Bacteriology, Virology, Hospital Hygiene, and Parasitology-Mycology, Brest University Hospital, Boulevard Tanguy Prigent, 29200, Brest, France.
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15
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Mostafa HH, Fissel JA, Fanelli B, Bergman Y, Gniazdowski V, Dadlani M, Carroll KC, Colwell RR, Simner PJ. Metagenomic Next-Generation Sequencing of Nasopharyngeal Specimens Collected from Confirmed and Suspect COVID-19 Patients. mBio 2020; 11:e01969-20. [PMID: 33219095 PMCID: PMC7686804 DOI: 10.1128/mbio.01969-20] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 10/28/2020] [Indexed: 12/11/2022] Open
Abstract
Metagenomic next-generation sequencing (mNGS) offers an agnostic approach for emerging pathogen detection directly from clinical specimens. In contrast to targeted methods, mNGS also provides valuable information on the composition of the microbiome and might uncover coinfections that may associate with disease progression and impact prognosis. To evaluate the use of mNGS for detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and/or other infecting pathogens, we applied direct Oxford Nanopore long-read third-generation metatranscriptomic and metagenomic sequencing. Nasopharyngeal (NP) swab specimens from 50 patients under investigation for CoV disease 2019 (COVID-19) were sequenced, and the data were analyzed by the CosmosID bioinformatics platform. Further, we characterized coinfections and the microbiome associated with a four-point severity index. SARS-CoV-2 was identified in 77.5% (31/40) of samples positive by RT-PCR, correlating with lower cycle threshold (Ct) values and fewer days from symptom onset. At the time of sampling, possible bacterial or viral coinfections were detected in 12.5% of SARS-CoV-2-positive specimens. A decrease in microbial diversity was observed among COVID-19-confirmed patients (Shannon diversity index, P = 0.0082; Chao richness estimate, P = 0.0097; Simpson diversity index, P = 0.018), and differences in microbial communities were linked to disease severity (P = 0.022). Furthermore, statistically significant shifts in the microbiome were identified among SARS-CoV-2-positive and -negative patients, in the latter of whom a higher abundance of Propionibacteriaceae (P = 0.028) and a reduction in the abundance of Corynebacterium accolens (P = 0.025) were observed. Our study corroborates the growing evidence that increased SARS-CoV-2 RNA detection from NP swabs is associated with the early stages rather than the severity of COVID-19. Further, we demonstrate that SARS-CoV-2 causes a significant change in the respiratory microbiome. This work illustrates the utility of mNGS for the detection of SARS-CoV-2, for diagnosing coinfections without viral target enrichment or amplification, and for the analysis of the respiratory microbiome.IMPORTANCE SARS-CoV-2 has presented a rapidly accelerating global public health crisis. The ability to detect and analyze viral RNA from minimally invasive patient specimens is critical to the public health response. Metagenomic next-generation sequencing (mNGS) offers an opportunity to detect SARS-CoV-2 from nasopharyngeal (NP) swabs. This approach also provides information on the composition of the respiratory microbiome and its relationship to coinfections or the presence of other organisms that may impact SARS-CoV-2 disease progression and prognosis. Here, using direct Oxford Nanopore long-read third-generation metatranscriptomic and metagenomic sequencing of NP swab specimens from 50 patients under investigation for COVID-19, we detected SARS-CoV-2 sequences by applying the CosmosID bioinformatics platform. Further, we characterized coinfections and detected a decrease in the diversity of the microbiomes in these patients. Statistically significant shifts in the microbiome were identified among COVID-19-positive and -negative patients, in the latter of whom a higher abundance of Propionibacteriaceae and a reduction in the abundance of Corynebacterium accolens were observed. Our study also corroborates the growing evidence that increased SARS-CoV-2 RNA detection from NP swabs is associated with the early stages of disease rather than with severity of disease. This work illustrates the utility of mNGS for the detection and analysis of SARS-CoV-2 from NP swabs without viral target enrichment or amplification and for the analysis of the respiratory microbiome.
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Affiliation(s)
- Heba H Mostafa
- Division of Medical Microbiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - John A Fissel
- Division of Medical Microbiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Yehudit Bergman
- Division of Medical Microbiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Victoria Gniazdowski
- Division of Medical Microbiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Karen C Carroll
- Division of Medical Microbiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Rita R Colwell
- CosmosID, Inc., Rockville, Maryland, USA
- University of Maryland College Park, Institute for Advanced Computer Studies, College Park, Maryland, USA
| | - Patricia J Simner
- Division of Medical Microbiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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16
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Beswick E, Amich J, Gago S. Factoring in the Complexity of the Cystic Fibrosis Lung to Understand Aspergillus fumigatus and Pseudomonas aeruginosa Interactions. Pathogens 2020; 9:pathogens9080639. [PMID: 32781694 PMCID: PMC7460534 DOI: 10.3390/pathogens9080639] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/25/2020] [Accepted: 08/04/2020] [Indexed: 02/07/2023] Open
Abstract
Pseudomonas aeruginosa has long been established as the most prevalent respiratory pathogen in Cystic Fibrosis (CF) patients, with opportunistic infection causing profound morbidity and mortality. Recently, Aspergillus fumigatus has also been recognised as a key contributor to CF lung deterioration, being consistently associated with decreased lung function and worsened prognosis in these patients. As clinical evidence for the common occurrence of combined infection with these two pathogens increases, research into the mechanism and consequences of their interaction is becoming more relevant. Clinical evidence suggests a synergistic effect of combined infection, which translates into a poorer prognosis for the patients. In vitro results from the laboratory have identified a variety of possible synergistic and antagonistic interactions between A. fumigatus and P. aeruginosa. Here, we present a comprehensive overview of the complex environment of the CF lung and discuss how it needs to be considered to determine the exact molecular interactions that A. fumigatus and P. aeruginosa undergo during combined infection and their effects on the host.
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Affiliation(s)
- Emily Beswick
- Manchester Fungal Infection Group, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Core Technology Facility, Grafton Street, Manchester M13 9NT, UK
- Academic Unit of Medical Education, Medical School, University of Sheffield, Beech Hill Road, Broomhall, Sheffield S10 2TG, UK;
| | - Jorge Amich
- Manchester Fungal Infection Group, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Core Technology Facility, Grafton Street, Manchester M13 9NT, UK
- Correspondence: (J.A.); (S.G.)
| | - Sara Gago
- Manchester Fungal Infection Group, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Core Technology Facility, Grafton Street, Manchester M13 9NT, UK
- Correspondence: (J.A.); (S.G.)
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17
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Guilloux CA, Lamoureux C, Beauruelle C, Héry-Arnaud G. Porphyromonas: A neglected potential key genus in human microbiomes. Anaerobe 2020; 68:102230. [PMID: 32615270 DOI: 10.1016/j.anaerobe.2020.102230] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 06/11/2020] [Accepted: 06/14/2020] [Indexed: 01/16/2023]
Abstract
Anaerobes form a large part of microbial communities, and have begun to be specifically studied in both healthy and pathologic contexts. Porphyromonas is one of the top ten anaerobic taxa in the microbiome (anaerobiome) in healthy subjects. However, to date, most studies focused on the deleterious role of P. gingivalis, the most widely described species. Interestingly, targeted metagenomics reveals Porphyromonas other than gingivalis (POTG), highlighting other species such as P. catoniae or P. pasteri as potential biomarkers in disease progression or pathogen colonization susceptibility. From the sparse data, it appears that the Porphyromonas genus may also be a relevant target of investigation in several pulmonary diseases. Moreover, deciphering cutaneous, gastric and oral microbiomes hint that Porphyromonas may be a genus of interest in non-pulmonary diseases. This review aims to summarize the major data on POTG and to report their impact on the various human microbiomes in different clinical states.
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Affiliation(s)
| | - Claudie Lamoureux
- Unité de Bactériologie, Pôle de Biologie-Pathologie, Centre Hospitalier Régional et Universitaire de Brest, Hôpital de la Cavale Blanche, Boulevard Tanguy Prigent, Brest, France.
| | - Clémence Beauruelle
- Univ Brest, Inserm, EFS, UMR, 1078, GGB, 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, Brest, France.
| | - Geneviève Héry-Arnaud
- Univ Brest, Inserm, EFS, UMR, 1078, GGB, 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, Brest, France.
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18
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Vandeplassche E, Sass A, Ostyn L, Burmølle M, Kragh KN, Bjarnsholt T, Coenye T, Crabbé A. Antibiotic susceptibility of cystic fibrosis lung microbiome members in a multispecies biofilm. Biofilm 2020; 2:100031. [PMID: 33447816 PMCID: PMC7798459 DOI: 10.1016/j.bioflm.2020.100031] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 06/09/2020] [Accepted: 06/10/2020] [Indexed: 12/13/2022] Open
Abstract
The lungs of cystic fibrosis (CF) patients are often chronically colonized by multiple microbial species that can form biofilms, including the major CF pathogen Pseudomonas aeruginosa. Herewith, lower microbial diversity in CF airways is typically associated with worse health outcomes. In an attempt to treat CF lung infections patients are frequently exposed to antibiotics, which may affect microbial diversity. This study aimed at understanding if common antibiotics that target P. aeruginosa influence microbial diversity. To this end, a microaerophilic multispecies biofilm model of frequently co-isolated members of the CF lung microbiome (Pseudomonas aeruginosa, Staphylococcus aureus, Streptococcus anginosus, Achromobacter xylosoxidans, Rothia mucilaginosa, and Gemella haemolysans) was exposed to antipseudomonal antibiotics. We found that antibiotics that affected several dominant species (i.e. ceftazidime, tobramycin) resulted in higher species evenness compared to colistin, which is only active against P. aeruginosa. Furthermore, susceptibility of individual species in the multispecies biofilm following antibiotic treatment was compared to that of the respective single-species biofilms, showing no differences. Adding three anaerobic species (Prevotella melaninogenica, Veillonella parvula, and Fusobacterium nucleatum) to the multispecies biofilm did not influence antibiotic susceptibility. In conclusion, our study demonstrates antibiotic-dependent effects on microbial community diversity of multispecies biofilms comprised of CF microbiome members.
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Affiliation(s)
- Eva Vandeplassche
- Laboratory of Pharmaceutical Microbiology, Ghent University, Belgium
| | - Andrea Sass
- Laboratory of Pharmaceutical Microbiology, Ghent University, Belgium
| | - Lisa Ostyn
- Laboratory of Pharmaceutical Microbiology, Ghent University, Belgium
| | - Mette Burmølle
- Department of Microbiology, University of Copenhagen, Denmark
| | - Kasper Nørskov Kragh
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Denmark
| | - Thomas Bjarnsholt
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Denmark.,Department of Clinical Microbiology, Copenhagen University Hospital, Denmark
| | - Tom Coenye
- Laboratory of Pharmaceutical Microbiology, Ghent University, Belgium
| | - Aurélie Crabbé
- Laboratory of Pharmaceutical Microbiology, Ghent University, Belgium
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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: 52] [Impact Index Per Article: 13.0] [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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Soret P, Vandenborght LE, Francis F, Coron N, Enaud R, Avalos M, Schaeverbeke T, Berger P, Fayon M, Thiebaut R, Delhaes L. Respiratory mycobiome and suggestion of inter-kingdom network during acute pulmonary exacerbation in cystic fibrosis. Sci Rep 2020; 10:3589. [PMID: 32108159 PMCID: PMC7046743 DOI: 10.1038/s41598-020-60015-4] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 10/14/2019] [Indexed: 12/12/2022] Open
Abstract
Lung infections play a critical role in cystic fibrosis (CF) pathogenesis. CF respiratory tract is now considered to be a polymicrobial niche and advances in high-throughput sequencing allowed to analyze its microbiota and mycobiota. However, no NGS studies until now have characterized both communities during CF pulmonary exacerbation (CFPE). Thirty-three sputa isolated from patients with and without CFPE were used for metagenomic high-throughput sequencing targeting 16S and ITS2 regions of bacterial and fungal rRNA. We built inter-kingdom network and adapted Phy-Lasso method to highlight correlations in compositional data. The decline in respiratory function was associated with a decrease in bacterial diversity. The inter-kingdom network revealed three main clusters organized around Aspergillus, Candida, and Scedosporium genera. Using Phy-Lasso method, we identified Aspergillus and Malassezia as relevantly associated with CFPE, and Scedosporium plus Pseudomonas with a decline in lung function. We corroborated in vitro the cross-domain interactions between Aspergillus and Streptococcus predicted by the correlation network. For the first time, we included documented mycobiome data into a version of the ecological Climax/Attack model that opens new lines of thoughts about the physiopathology of CF lung disease and future perspectives to improve its therapeutic management.
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Affiliation(s)
- Perrine Soret
- Univ. Bordeaux, Inserm, Bordeaux Population Health Research Center, UMR 1219, F-33000, Bordeaux, France
- INRIA SISTM Team, F-33405, Talence, France
| | - Louise-Eva Vandenborght
- Univ. Bordeaux, Centre de Recherche Cardio-Thoracique de Bordeaux, U1045, F-33000, Bordeaux, France
- Genoscreen Society, 59000, Lille, France
| | - Florence Francis
- CHU Bordeaux, Department of Public Health, F-33000, Bordeaux, France
| | - Noémie Coron
- Univ. Bordeaux, Centre de Recherche Cardio-Thoracique de Bordeaux, U1045, F-33000, Bordeaux, France
- CHU de Bordeaux, Univ. Bordeaux, FHU ACRONIM, F-33000, Bordeaux, France
- CHU de Bordeaux: Laboratoire de Parasitologie-Mycologie, Univ. Bordeaux, F-33000, Bordeaux, France
| | - Raphael Enaud
- Univ. Bordeaux, Centre de Recherche Cardio-Thoracique de Bordeaux, U1045, F-33000, Bordeaux, France
- CHU de Bordeaux, Univ. Bordeaux, FHU ACRONIM, F-33000, Bordeaux, France
- CHU de Bordeaux, CRCM Pédiatrique, CIC, 1401, Bordeaux, France
| | - Marta Avalos
- Univ. Bordeaux, Inserm, Bordeaux Population Health Research Center, UMR 1219, F-33000, Bordeaux, France
- INRIA SISTM Team, F-33405, Talence, France
| | | | - Patrick Berger
- Univ. Bordeaux, Centre de Recherche Cardio-Thoracique de Bordeaux, U1045, F-33000, Bordeaux, France
- CHU de Bordeaux, Univ. Bordeaux, FHU ACRONIM, F-33000, Bordeaux, France
| | - Michael Fayon
- Univ. Bordeaux, Centre de Recherche Cardio-Thoracique de Bordeaux, U1045, F-33000, Bordeaux, France
- CHU de Bordeaux, Univ. Bordeaux, FHU ACRONIM, F-33000, Bordeaux, France
- CHU de Bordeaux, CRCM Pédiatrique, CIC, 1401, Bordeaux, France
| | - Rodolphe Thiebaut
- Univ. Bordeaux, Inserm, Bordeaux Population Health Research Center, UMR 1219, F-33000, Bordeaux, France
- INRIA SISTM Team, F-33405, Talence, France
- CHU Bordeaux, Department of Public Health, F-33000, Bordeaux, France
| | - Laurence Delhaes
- Univ. Bordeaux, Centre de Recherche Cardio-Thoracique de Bordeaux, U1045, F-33000, Bordeaux, France.
- CHU de Bordeaux, Univ. Bordeaux, FHU ACRONIM, F-33000, Bordeaux, France.
- CHU de Bordeaux: Laboratoire de Parasitologie-Mycologie, Univ. Bordeaux, F-33000, Bordeaux, France.
- CHU de Bordeaux, CRCM Pédiatrique, CIC, 1401, Bordeaux, France.
- University and CHU of Lille, F-59000, Lille, France.
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