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Zeineldin M, Barakat R. Host-specific signatures of the respiratory microbiota in domestic animals. Res Vet Sci 2023; 164:105037. [PMID: 37801741 DOI: 10.1016/j.rvsc.2023.105037] [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: 06/26/2023] [Revised: 09/14/2023] [Accepted: 09/23/2023] [Indexed: 10/08/2023]
Abstract
While the importance of respiratory microbiota in maintaining respiratory health is increasingly recognized, we still lack a comprehensive understanding of the unique characteristics of respiratory microbiota specific to individual hosts. This study aimed to address this gap by analyzing publicly available 16S rRNA gene datasets from various domestic animals (cats, dogs, pigs, donkeys, chickens, sheep, and cattle) to identify host-specific signatures of respiratory microbiota. The findings revealed that cattle and pigs exhibited the highest Shannon diversity index and observed features, indicating a greater microbial variety compared to other animals. Discriminant analysis demonstrated distinct composition of respiratory microbiota across different animals, with no overlapping abundant taxa. The linear discriminant analysis effect size highlighted prevalent host-specific microbiota signatures in different animal species. Moreover, the composition and diversity of respiratory microbiota were significantly influenced by various factors such as individual study, health status, and sampling sites within the respiratory tract. While associations between host and respiratory microbiota have been uncovered, the relative contributions of host and environment in the selection of respiratory microbiota and their impact on host fitness remain unclear. Further investigations involving diverse hosts are necessary to fully comprehend the significance of host-microbial coevolution in maintaining respiratory health.
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Affiliation(s)
- Mohamed Zeineldin
- Department of Animal Medicine, College of Veterinary Medicine, Benha University, Benha 13511, Egypt.
| | - Radwa Barakat
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa, USA.
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2
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Shen D, Wang K, Fathi MA, Li Y, Win-Shwe TT, Li C. A succession of pulmonary microbiota in broilers during the growth cycle. Poult Sci 2023; 102:102884. [PMID: 37423015 PMCID: PMC10466298 DOI: 10.1016/j.psj.2023.102884] [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: 04/03/2023] [Revised: 06/14/2023] [Accepted: 06/16/2023] [Indexed: 07/11/2023] Open
Abstract
Respiratory health problems in poultry production are frequent and knotty and thus attract the attention of farmers and researchers. The breakthrough of gene sequencing technology has revealed that healthy lungs harbor rich microbiota, whose succession and homeostasis are closely related to lung health status, suggesting a new idea to explore the mechanism of lung injury in broilers with pulmonary microbiota as the entry point. This study aimed to investigate the succession of pulmonary microbiota in healthy broilers during the growth cycle. Fixed and molecular samples were collected from the lungs of healthy broilers at 1, 3, 14, 21, 28, and 42 d of age. Lung tissue morphology was observed by hematoxylin and eosin staining, and the changes in the composition and diversity of pulmonary microbiota were analyzed using 16S rRNA gene sequencing. The results showed that lung index peaked at 3 d, then decreased with age. No significant change was observed in the α diversity of pulmonary microbiota, while the β diversity changed regularly with age during the broilers' growth cycle. The relative abundance of dominant bacteria of Firmicutes and their subordinate Lactobacillus increased with age, while the abundance of Proteobacteria decreased with age. The correlation analysis between the abundance of differential bacteria and predicted function showed that dominant bacteria of Firmicutes, Proteobacteria and Lactobacillus were significantly correlated with most functional abundance, indicating that they may involve in lung functional development and physiological activities of broilers. Collectively, these findings suggest that the lung has been colonized with abundant microbiota in broilers when they were just hatched, and their composition changed regularly with day age. The dominant bacteria, Firmicutes, Proteobacteria, and Lactobacillus, play crucial roles in lung function development and physiological activities. It paves the way for further research on the mechanism of pulmonary microbiota-mediated lung injury in broilers.
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Affiliation(s)
- Dan Shen
- Research Centre for Livestock Environmental Control and Smart Production, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Kai Wang
- Research Centre for Livestock Environmental Control and Smart Production, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Mohamed Ahmed Fathi
- Research Centre for Livestock Environmental Control and Smart Production, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; Animal Production Research Institute, Agricultural Research Centre, Dokki, Giza 12618, Egypt
| | - Yansen Li
- Research Centre for Livestock Environmental Control and Smart Production, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Tin-Tin Win-Shwe
- Health and Environmental Risk Division, National Institute for Environmental Studies, Tsukuba 305-8506, Japan
| | - Chunmei Li
- Research Centre for Livestock Environmental Control and Smart Production, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.
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3
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Rozaliyani A, Antariksa B, Nurwidya F, Zaini J, Setianingrum F, Hasan F, Nugrahapraja H, Yusva H, Wibowo H, Bowolaksono A, Kosmidis C. The Fungal and Bacterial Interface in the Respiratory Mycobiome with a Focus on Aspergillus spp. Life (Basel) 2023; 13:life13041017. [PMID: 37109545 PMCID: PMC10142979 DOI: 10.3390/life13041017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/08/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
The heterogeneity of the lung microbiome and its alteration are prevalently seen among chronic lung diseases patients. However, studies to date have primarily focused on the bacterial microbiome in the lung rather than fungal composition, which might play an essential role in the mechanisms of several chronic lung diseases. It is now well established that Aspergillus spp. colonies may induce various unfavorable inflammatory responses. Furthermore, bacterial microbiomes such as Pseudomonas aeruginosa provide several mechanisms that inhibit or stimulate Aspergillus spp. life cycles. In this review, we highlighted fungal and bacterial microbiome interactions in the respiratory tract, with a focus on Aspergillus spp.
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Affiliation(s)
- Anna Rozaliyani
- Department of Parasitology, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia
- Indonesia Pulmonary Mycoses Centre, Jakarta 10430, Indonesia
| | - Budhi Antariksa
- Department of Pulmonoloy and Respiratory Medicine, Faculty of Medicinie, Universitas Indonesia, Persahabatan National Respiratory Referral Hospital, Jakarta 13230, Indonesia
| | - Fariz Nurwidya
- Department of Pulmonoloy and Respiratory Medicine, Faculty of Medicinie, Universitas Indonesia, Persahabatan National Respiratory Referral Hospital, Jakarta 13230, Indonesia
| | - Jamal Zaini
- Department of Pulmonoloy and Respiratory Medicine, Faculty of Medicinie, Universitas Indonesia, Persahabatan National Respiratory Referral Hospital, Jakarta 13230, Indonesia
| | - Findra Setianingrum
- Department of Parasitology, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia
- Indonesia Pulmonary Mycoses Centre, Jakarta 10430, Indonesia
| | - Firman Hasan
- Indonesia Pulmonary Mycoses Centre, Jakarta 10430, Indonesia
| | - Husna Nugrahapraja
- Life Science and Biotechnology, Bandung Institute of Technology, Bandung 40312, Indonesia
| | - Humaira Yusva
- Magister Program of Biomedical Sciences, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia
| | - Heri Wibowo
- Department of Parasitology, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia
| | - Anom Bowolaksono
- Department of Biology, Faculty of Mathematics and Natural Sciences (FMIPA), Universitas Indonesia, Depok 16424, Indonesia
| | - Chris Kosmidis
- Manchester Academic Health Science Centre, Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M23 9LT, UK
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4
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Pienkowska K, Pust MM, Gessner M, Gaedcke S, Thavarasa A, Rosenboom I, Morán Losada P, Minso R, Arnold C, Hedtfeld S, Dorda M, Wiehlmann L, Mainz JG, Klockgether J, Tümmler B. The Cystic Fibrosis Upper and Lower Airway Metagenome. Microbiol Spectr 2023; 11:e0363322. [PMID: 36892308 PMCID: PMC10101124 DOI: 10.1128/spectrum.03633-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 02/17/2023] [Indexed: 03/10/2023] Open
Abstract
The microbial metagenome in cystic fibrosis (CF) airways was investigated by whole-genome shotgun sequencing of total DNA isolated from nasal lavage samples, oropharyngeal swabs, and induced sputum samples collected from 65 individuals with CF aged 7 to 50 years. Each patient harbored a personalized microbial metagenome unique in microbial load and composition, the exception being monocultures of the most common CF pathogens Staphylococcus aureus and Pseudomonas aeruginosa from patients with advanced lung disease. The sampling of the upper airways by nasal lavage uncovered the fungus Malassezia restricta and the bacterium Staphylococcus epidermidis as prominent species. Healthy and CF donors harbored qualitatively and quantitatively different spectra of commensal bacteria in their sputa, even in the absence of any typical CF pathogen. If P. aeruginosa, S. aureus, or Stenotrophomonas maltophilia belonged to the trio of the most abundant species in the CF sputum metagenome, common inhabitants of the respiratory tract of healthy subjects, i.e., Eubacterium sulci, Fusobacterium periodonticum, and Neisseria subflava, were present only in low numbers or not detectable. Random forest analysis identified the numerical ecological parameters of the bacterial community, such as Shannon and Simpson diversity, as the key parameters that globally distinguish sputum samples from CF and healthy donors. IMPORTANCE Cystic fibrosis (CF) is the most common life-limiting monogenetic disease in European populations and is caused by mutations in the CFTR gene. Chronic airway infections with opportunistic pathogens are the major morbidity that determines prognosis and quality of life in most people with CF. We examined the composition of the microbial communities of the oral cavity and upper and lower airways in CF patients across all age groups. From early on, the spectrum of commensals is different in health and CF. Later on, when the common CF pathogens take up residence in the lungs, we observed differential modes of depletion of the commensal microbiota in the presence of S. aureus, P. aeruginosa, S. maltophilia, or combinations thereof. It remains to be seen whether the implementation of lifelong CFTR (cystic fibrosis transmembrane conductance regulator) modulation will change the temporal evolution of the CF airway metagenome.
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Affiliation(s)
- Katarzyna Pienkowska
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Marie-Madlen Pust
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease, German Center for Lung Research, Hannover, Germany
| | - Margaux Gessner
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Svenja Gaedcke
- Biomedical Research in Endstage and Obstructive Lung Disease, German Center for Lung Research, Hannover, Germany
| | - Ajith Thavarasa
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Ilona Rosenboom
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Patricia Morán Losada
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Rebecca Minso
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Christin Arnold
- Cystic Fibrosis Center for Children and Adults, Jena University Hospital, Jena, Germany
| | - Silke Hedtfeld
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Marie Dorda
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- Research Core Unit Genomics, Hannover Medical School, Hannover, Germany
| | - Lutz Wiehlmann
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease, German Center for Lung Research, Hannover, Germany
- Research Core Unit Genomics, Hannover Medical School, Hannover, Germany
| | - Jochen G. Mainz
- Cystic Fibrosis Center for Children and Adults, Jena University Hospital, Jena, Germany
- Klinik für Kinder- und Jugendmedizin, Medizinische Hochschule Brandenburg, Brandenburg, Germany
| | - Jens Klockgether
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Burkhard Tümmler
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease, German Center for Lung Research, Hannover, Germany
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Campos M, Cickovski T, Fernandez M, Jaric M, Wanner A, Holt G, Donna E, Mendes E, Silva-Herzog E, Schneper L, Segal J, Amador DM, Riveros JD, Aguiar-Pulido V, Banerjee S, Salathe M, Mathee K, Narasimhan G. Lower respiratory tract microbiome composition and community interactions in smokers. Access Microbiol 2023; 5:000497.v3. [PMID: 37091735 PMCID: PMC10118249 DOI: 10.1099/acmi.0.000497.v3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 12/20/2022] [Indexed: 04/03/2023] Open
Abstract
The lung microbiome impacts on lung function, making any smoking-induced changes in the lung microbiome potentially significant. The complex co-occurrence and co-avoidance patterns between the bacterial taxa in the lower respiratory tract (LRT) microbiome were explored for a cohort of active (AS), former (FS) and never (NS) smokers. Bronchoalveolar lavages (BALs) were collected from 55 volunteer subjects (9 NS, 24 FS and 22 AS). The LRT microbiome composition was assessed using 16S rRNA amplicon sequencing. Identification of differentially abundant taxa and co-occurrence patterns, discriminant analysis and biomarker inferences were performed. The data show that smoking results in a loss in the diversity of the LRT microbiome, change in the co-occurrence patterns and a weakening of the tight community structure present in healthy microbiomes. The increased abundance of the genus
Ralstonia
in the lung microbiomes of both former and active smokers is significant. Partial least square discriminant and DESeq2 analyses suggested a compositional difference between the cohorts in the LRT microbiome. The groups were sufficiently distinct from each other to suggest that cessation of smoking may not be sufficient for the lung microbiota to return to a similar composition to that of NS. The linear discriminant analysis effect size (LEfSe) analyses identified several bacterial taxa as potential biomarkers of smoking status. Network-based clustering analysis highlighted different co-occurring and co-avoiding microbial taxa in the three groups. The analysis found a cluster of bacterial taxa that co-occur in smokers and non-smokers alike. The clusters exhibited tighter and more significant associations in NS compared to FS and AS. Higher degree of rivalry between clusters was observed in the AS. The groups were sufficiently distinct from each other to suggest that cessation of smoking may not be sufficient for the lung microbiota to return to a similar composition to that of NS.
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Affiliation(s)
- Michael Campos
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Miller School of Medicine, University of Miami, Miami, FL, USA
- *Correspondence: Michael Campos,
| | - Trevor Cickovski
- Bioinformatics Research Group (BioRG), School of Computing and Information Sciences, Florida International University, Miami, FL, USA
- *Correspondence: Trevor Cickovski,
| | - Mitch Fernandez
- Bioinformatics Research Group (BioRG), School of Computing and Information Sciences, Florida International University, Miami, FL, USA
| | - Melita Jaric
- Bioinformatics Research Group (BioRG), School of Computing and Information Sciences, Florida International University, Miami, FL, USA
| | - Adam Wanner
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Gregory Holt
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Elio Donna
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Eliana Mendes
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Eugenia Silva-Herzog
- Department of Molecular Microbiology and Infectious Diseases, Department Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Lisa Schneper
- Department of Molecular Microbiology and Infectious Diseases, Department Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Jonathan Segal
- Department of Molecular Microbiology and Infectious Diseases, Department Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - David Moraga Amador
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, USA
| | - Juan Daniel Riveros
- Bioinformatics Research Group (BioRG), School of Computing and Information Sciences, Florida International University, Miami, FL, USA
| | - Vanessa Aguiar-Pulido
- Bioinformatics Research Group (BioRG), School of Computing and Information Sciences, Florida International University, Miami, FL, USA
| | - Santanu Banerjee
- Department of Surgery, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Matthias Salathe
- Department of Internal Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Kalai Mathee
- Department of Molecular Microbiology and Infectious Diseases, Department Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
- Florida International University, Biomolecular Sciences Institute, Miami, FL, USA
- *Correspondence: Kalai Mathee,
| | - Giri Narasimhan
- Bioinformatics Research Group (BioRG), School of Computing and Information Sciences, Florida International University, Miami, FL, USA
- Florida International University, Biomolecular Sciences Institute, Miami, FL, USA
- *Correspondence: Giri Narasimhan,
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6
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Pallenberg ST, Pust MM, Rosenboom I, Hansen G, Wiehlmann L, Dittrich AM, Tümmler B. Impact of Elexacaftor/Tezacaftor/Ivacaftor Therapy on the Cystic Fibrosis Airway Microbial Metagenome. Microbiol Spectr 2022; 10:e0145422. [PMID: 36154176 PMCID: PMC9602284 DOI: 10.1128/spectrum.01454-22] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 09/04/2022] [Indexed: 12/31/2022] Open
Abstract
The introduction of mutation-specific combination therapy with the cystic fibrosis transmembrane conductance regulator (CFTR) modulators elexacaftor/tezacaftor/ivacaftor (ELX/TEZ/IVA) has substantially improved lung function and quality of life of people with cystic fibrosis (CF). Collecting deep cough swabs and induced sputum, this postapproval study examined the effect of 14- and 50-week treatment with ELX/TEZ/IVA on the airway microbial metagenome of pancreatic- insufficient CF patients aged 12 years and older. Compared to pretreatment, the total bacterial load decreased, the individual species were more evenly distributed in the community, and the individual microbial metagenomes became more similar in their composition. However, the microbial network remained vulnerable to fragmentation. The initial shift of the CF metagenome was attributable to the ELX/TEZ/IVA-mediated gain of CFTR activity followed by a diversification driven by a group of commensals at the 1-year time point that are typical for healthy airways. IMPORTANCE Shotgun metagenome sequencing of respiratory secretions with spike-in controls for normalization demonstrated that 1 year of high-efficient CFTR modulation with elexacaftor/tezacaftor/ivacaftor extensively reduced the bacterial load. Longer observation periods will be necessary to resolve whether the partial reversion of the basic defect that is achieved with ELX/TEZ/IVA is sufficient in the long run to render the CF lungs robust against the recolonization with common opportunistic pathogens.
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Affiliation(s)
- Sophia T. Pallenberg
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- German Center for Lung Research, Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Hannover Medical School, Hannover, Germany
| | - Marie-Madlen Pust
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- German Center for Lung Research, Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Hannover Medical School, Hannover, Germany
| | - Ilona Rosenboom
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Gesine Hansen
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- German Center for Lung Research, Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Hannover Medical School, Hannover, Germany
| | - Lutz Wiehlmann
- Research Core Unit Genomics, Hannover Medical School, Hannover, Germany
| | - Anna-Maria Dittrich
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- German Center for Lung Research, Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Hannover Medical School, Hannover, Germany
| | - Burkhard Tümmler
- Department for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- German Center for Lung Research, Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Hannover Medical School, Hannover, Germany
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7
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Shen D, Guo Z, Huang K, Dai P, Jin X, Li Y, Li C. Inflammation-associated pulmonary microbiome and metabolome changes in broilers exposed to particulate matter in broiler houses. JOURNAL OF HAZARDOUS MATERIALS 2022; 421:126710. [PMID: 34332479 DOI: 10.1016/j.jhazmat.2021.126710] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 06/21/2021] [Accepted: 07/18/2021] [Indexed: 06/13/2023]
Abstract
The particulate matter (PM) in livestock houses, one of the primary sources of atmospheric PM, is not only detrimental to the respiratory health of animals and farmworkers but also poses a threat to the public environment and public health and warrants increased attention. In this study, we investigated the variation in the pulmonary microbiome and metabolome in broiler chickens exposed to PM collected from a broiler house. We examined the pulmonary microbiome and metabolome in broilers, observing that PM induced a visible change in α and β diversity. A total of 66 differential genera, including unclassified_f_Ruminococcaceae and Campylobacter, were associated with pulmonary inflammation. Untargeted metabolomics was utilised to identify 63 differential metabolites induced by PM and correlated with differential bacteria. We observed that PM resulted in injury of the broiler lung and disruption of the microbial community, as well as causing changes in the observed metabolites. These results imply that perturbations to the microbiome and metabolome may play pivotal roles in the mechanism underlying PM-induced broiler lung damage.
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Affiliation(s)
- Dan Shen
- Research Centre for Livestock Environmental Control and Smart Production, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhendong Guo
- Military Veterinary Research Institute, Academy of Military Medical Sciences, Changchun 130117, China
| | - Kai Huang
- Research Centre for Livestock Environmental Control and Smart Production, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Pengyuan Dai
- Research Centre for Livestock Environmental Control and Smart Production, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoming Jin
- Research Centre for Livestock Environmental Control and Smart Production, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Yansen Li
- Research Centre for Livestock Environmental Control and Smart Production, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Chunmei Li
- Research Centre for Livestock Environmental Control and Smart Production, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.
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8
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Transcriptomic Characterization of Tuberculous Sputum Reveals a Host Warburg Effect and Microbial Cholesterol Catabolism. mBio 2021; 12:e0176621. [PMID: 34872348 PMCID: PMC8649757 DOI: 10.1128/mbio.01766-21] [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] [Indexed: 11/23/2022] Open
Abstract
The crucial transmission phase of tuberculosis (TB) relies on infectious sputum and yet cannot easily be modeled. We applied one-step RNA sequencing (RNA-Seq) to sputum from infectious TB patients to investigate the host and microbial environments underlying transmission of Mycobacterium tuberculosis. In such TB sputa, compared to non-TB controls, transcriptional upregulation of inflammatory responses, including an interferon-driven proinflammatory response and a metabolic shift toward glycolysis, was observed in the host. Among all bacterial sequences in the sputum, approximately 1.5% originated from M. tuberculosis, and its transcript abundance was lower in HIV-1-coinfected patients. Commensal bacterial abundance was reduced in the presence of M. tuberculosis infection. Direct alignment to the genomes of the predominant microbiota species also reveals differential adaptation, whereby firmicutes (e.g., streptococci) displayed a nonreplicating phenotype with reduced transcription of ribosomal proteins and reduced activities of ATP synthases, while Neisseria and Prevotella spp. were less affected. The transcriptome of sputum M. tuberculosis more closely resembled aerobic replication and shared similarity in carbon metabolism to in vitro and in vivo models with significant upregulation of genes associated with cholesterol metabolism and downstream propionate detoxification pathways. In addition, and counter to previous reports on intracellular M. tuberculosis infection in vitro, M. tuberculosis in sputum was zinc, but not iron, deprived, and the phoP loci were also significantly downregulated, suggesting that the pathogen is likely extracellular in location.
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9
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Comberiati P, Di Cicco M, Paravati F, Pelosi U, Di Gangi A, Arasi S, Barni S, Caimmi D, Mastrorilli C, Licari A, Chiera F. The Role of Gut and Lung Microbiota in Susceptibility to Tuberculosis. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph182212220. [PMID: 34831976 PMCID: PMC8623605 DOI: 10.3390/ijerph182212220] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 11/16/2021] [Accepted: 11/18/2021] [Indexed: 12/12/2022]
Abstract
Tuberculosis is one of the most common infectious diseases and infectious causes of death worldwide. Over the last decades, significant research effort has been directed towards defining the understanding of the pathogenesis of tuberculosis to improve diagnosis and therapeutic options. Emerging scientific evidence indicates a possible role of the human microbiota in the pathophysiology of tuberculosis, response to therapy, clinical outcomes, and post-treatment outcomes. Although human studies on the role of the microbiota in tuberculosis are limited, published data in recent years, both from experimental and clinical studies, suggest that a better understanding of the gut-lung microbiome axis and microbiome-immune crosstalk could shed light on the specific pathogenetic mechanisms of Mycobacterium tuberculosis infection and identify new therapeutic targets. In this review, we address the current knowledge of the host immune responses against Mycobacterium tuberculosis infection, the emerging evidence on how gut and lung microbiota can modulate susceptibility to tuberculosis, the available studies on the possible use of probiotic-antibiotic combination therapy for the treatment of tuberculosis, and the knowledge gaps and future research priorities in this field.
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Affiliation(s)
- Pasquale Comberiati
- Department of Clinical and Experimental Medicine, University of Pisa, 56126 Pisa, Italy; (M.D.C.); (A.D.G.)
- Allergology and Pulmonology Section, Pediatrics Unit, Pisa University Hospital, 56126 Pisa, Italy
- Department of Clinical Immunology and Allergology, I.M. Sechenov First Moscow State Medical University, Moscow 119991, Russia
- Correspondence:
| | - Maria Di Cicco
- Department of Clinical and Experimental Medicine, University of Pisa, 56126 Pisa, Italy; (M.D.C.); (A.D.G.)
- Allergology and Pulmonology Section, Pediatrics Unit, Pisa University Hospital, 56126 Pisa, Italy
| | - Francesco Paravati
- Department of Pediatrics, San Giovanni di Dio Hospital, 88900 Crotone, Italy; (F.P.); (F.C.)
| | - Umberto Pelosi
- Pediatric Unit, Santa Barbara Hospital, 09016 Iglesias, Italy;
| | - Alessandro Di Gangi
- Department of Clinical and Experimental Medicine, University of Pisa, 56126 Pisa, Italy; (M.D.C.); (A.D.G.)
- Allergology and Pulmonology Section, Pediatrics Unit, Pisa University Hospital, 56126 Pisa, Italy
| | - Stefania Arasi
- Area of Translational Research in Pediatric Specialities, Allergy Unit, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy;
| | - Simona Barni
- Allergic Unit, Department of Pediatric, Meyer Children’s Hospital, 50139 Florence, Italy;
| | - Davide Caimmi
- Allergy Unit, CHU de Montpellier, Université de Montpellier, 34295 Montpellier, France;
- IDESP, UMR A11, Université de Montpellier, 34093 Montpellier, France
| | - Carla Mastrorilli
- Department of Pediatrics, University Hospital Consortium Corporation Polyclinic of Bari, Pediatric Hospital Giovanni XXIII, 70124 Bari, Italy;
| | - Amelia Licari
- Pediatric Clinic, Pediatrics Department, Policlinico San Matteo, University of Pavia, 27100 Pavia, Italy;
| | - Fernanda Chiera
- Department of Pediatrics, San Giovanni di Dio Hospital, 88900 Crotone, Italy; (F.P.); (F.C.)
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10
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Baradaran Ghavami S, Pourhamzeh M, Farmani M, Keshavarz H, Shahrokh S, Shpichka A, Asadzadeh Aghdaei H, Hakemi-Vala M, Hossein-khannazer N, Timashev P, Vosough M. Cross-talk between immune system and microbiota in COVID-19. Expert Rev Gastroenterol Hepatol 2021; 15:1281-1294. [PMID: 34654347 PMCID: PMC8567289 DOI: 10.1080/17474124.2021.1991311] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 10/06/2021] [Indexed: 02/08/2023]
Abstract
INTRODUCTION Human gut microbiota plays a crucial role in providing protective responses against pathogens, particularly by regulating immune system homeostasis. There is a reciprocal interaction between the gut and lung microbiota, called the gut-lung axis (GLA). Any alteration in the gut microbiota or their metabolites can cause immune dysregulation, which can impair the antiviral activity of the immune system against respiratory viruses such as severe acute respiratory syndrome coronavirus (SARS-CoV) and SARS-CoV-2. AREAS COVERED This narrative review mainly outlines emerging data on the mechanisms underlying the interactions between the immune system and intestinal microbial dysbiosis, which is caused by an imbalance in the levels of essential metabolites. The authors will also discuss the role of probiotics in restoring the balance of the gut microbiota and modulation of cytokine storm. EXPERT OPINION Microbiota-derived signals regulate the immune system and protect different tissues during severe viral respiratory infections. The GLA's equilibration could help manage the mortality and morbidity rates associated with SARS-CoV-2 infection.
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Affiliation(s)
- Shaghayegh Baradaran Ghavami
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Thran, Iran
| | - Mahsa Pourhamzeh
- Department of Regenerative Medicine, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
- Division of Neuroscience, Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Maryam Farmani
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Thran, Iran
| | - Hediye Keshavarz
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Thran, Iran
| | - Shabnam Shahrokh
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Thran, Iran
| | - Anastasia Shpichka
- Institute for Regenerative Medicine, Sechenov First Moscow State Medical University, Moscow, Russia
- World-Class Research Center “Digital Biodesign and Personalized Healthcare”, Sechenov First Moscow State Medical University, Moscow, Russia
- Chemistry Department, Lomonosov Moscow State University, Moscow, Russia
| | - Hamid Asadzadeh Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Thran, Iran
| | - Mojdeh Hakemi-Vala
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Nikoo Hossein-khannazer
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Thran, Iran
| | - Peter Timashev
- Institute for Regenerative Medicine, Sechenov First Moscow State Medical University, Moscow, Russia
- World-Class Research Center “Digital Biodesign and Personalized Healthcare”, Sechenov First Moscow State Medical University, Moscow, Russia
- Chemistry Department, Lomonosov Moscow State University, Moscow, Russia
| | - Massoud Vosough
- Department of Regenerative Medicine, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
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11
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Elgamal Z, Singh P, Geraghty P. The Upper Airway Microbiota, Environmental Exposures, Inflammation, and Disease. ACTA ACUST UNITED AC 2021; 57:medicina57080823. [PMID: 34441029 PMCID: PMC8402057 DOI: 10.3390/medicina57080823] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/09/2021] [Accepted: 08/10/2021] [Indexed: 02/07/2023]
Abstract
Along with playing vital roles in pathogen exclusion and immune system priming, the upper airways (UAs) and their microbiota are essential for myriad physiological functions such as conditioning and transferring inhaled air. Dysbiosis, a microbial imbalance, is linked with various diseases and significantly impedes the quality of one’s life. Daily inhaled exposures and/or underlying conditions contribute to adverse changes to the UA microbiota. Such variations in the microbial community exacerbate UA and pulmonary disorders via modulating inflammatory and immune pathways. Hence, exploring the UA microbiota’s role in maintaining homeostasis is imperative. The microbial composition and subsequent relationship with airborne exposures, inflammation, and disease are crucial for strategizing innovating UA diagnostics and therapeutics. The development of a healthy UA microbiota early in life contributes to normal respiratory development and function in the succeeding years. Although different UA cavities present a unique microbial profile, geriatrics have similar microbes across their UAs. This lost community segregation may contribute to inflammation and disease, as it stimulates disadvantageous microbial–microbial and microbial–host interactions. Varying inflammatory profiles are associated with specific microbial compositions, while the same is true for many disease conditions and environmental exposures. A shift in the microbial composition is also detected upon the administration of numerous therapeutics, highlighting other beneficial and adverse side effects. This review examines the role of the UA microbiota in achieving homeostasis, and the impact on the UAs of environmental airborne pollutants, inflammation, and disease.
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Affiliation(s)
- Ziyad Elgamal
- Department of Biomedical Science, University of Guelph, Guelph, ON N1G 2W1, Canada;
- Department of Medicine, Division of Pulmonary & Critical Care Medicine, State University of New York Downstate Medical Centre, Brooklyn, NY 11203, USA
| | - Pratyush Singh
- Department of Biology, University of Western Ontario, London, ON N6A 5B7, Canada;
| | - Patrick Geraghty
- Department of Medicine, Division of Pulmonary & Critical Care Medicine, State University of New York Downstate Medical Centre, Brooklyn, NY 11203, USA
- Correspondence: ; Tel.: +1-718-270-3141
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12
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Kasela M, Grzegorczyk A, Korona-Głowniak I, Ossowski M, Nowakowicz-Dębek B, Malm A. Transmission and Long-Term Colonization Patterns of Staphylococcus aureus in a Nursing Home. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17218073. [PMID: 33147811 PMCID: PMC7672560 DOI: 10.3390/ijerph17218073] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/25/2020] [Accepted: 10/28/2020] [Indexed: 01/07/2023]
Abstract
Nursing homes might create an environment favorable for the transmission of Staphylococcus aureus because of the presence of hospitalized elderly, overcrowding and close contacts among people. We aimed at identifying risk factors for S. aureus colonization and determining the genetic relatedness of isolates demonstrating transmission among people. We investigated 736 swab samples from 92 residents and personnel for the presence of S. aureus. Swabs from anterior nares and throat were collected quarterly (2018) in a nursing home located in Poland. Genotyping was conducted using the multi-locus variable number of tandem repeats fingerprinting (MLVF) method. We observed high seasonal variation in the proportion of participants colonized with methicillin-resistant Staphylococcus aureus (MRSA) strains (0% to 13.5%). A multivariate analysis revealed that residents aged more than 85 years old are at risk for becoming intermittent S. aureus carriers (p = 0.013). The MLVF analysis revealed a high genetic diversity among methicillin-sensitive S. aureus (MSSA) strains and close genetic relatedness between MRSA strains. We proved the advanced aged were predisposed to intermittent S. aureus carriage. Genotyping revealed the transmission of S. aureus among the participants living in a closed environment. A high genetic relatedness among isolated MRSA suggests its clonal spread in the nursing home.
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Affiliation(s)
- Martyna Kasela
- Department of Pharmaceutical Microbiology, Medical University of Lublin, 20-093 Lublin, Poland; (A.G.); (I.K.-G.); (A.M.)
- Correspondence:
| | - Agnieszka Grzegorczyk
- Department of Pharmaceutical Microbiology, Medical University of Lublin, 20-093 Lublin, Poland; (A.G.); (I.K.-G.); (A.M.)
| | - Izabela Korona-Głowniak
- Department of Pharmaceutical Microbiology, Medical University of Lublin, 20-093 Lublin, Poland; (A.G.); (I.K.-G.); (A.M.)
| | - Mateusz Ossowski
- Department of Animal Hygiene and Environmental Hazards, University of Life Sciences in Lublin, 20-950 Lublin, Poland; (M.O.); (B.N.-D.)
| | - Bożena Nowakowicz-Dębek
- Department of Animal Hygiene and Environmental Hazards, University of Life Sciences in Lublin, 20-950 Lublin, Poland; (M.O.); (B.N.-D.)
| | - Anna Malm
- Department of Pharmaceutical Microbiology, Medical University of Lublin, 20-093 Lublin, Poland; (A.G.); (I.K.-G.); (A.M.)
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13
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Novak N, Cabanillas B. Viruses and asthma: the role of common respiratory viruses in asthma and its potential meaning for SARS-CoV-2. Immunology 2020; 161:83-93. [PMID: 32687609 PMCID: PMC7405154 DOI: 10.1111/imm.13240] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 07/10/2020] [Accepted: 07/12/2020] [Indexed: 12/20/2022] Open
Abstract
Viral infections and atopic diseases are closely related and contribute to each other. The physiological deficiencies and immune mechanisms that underlie atopic diseases can result in a suboptimal defense against multiple viruses, and promote a suitable environment for their proliferation and dissemination. Viral infections, on the other hand, can induce per se several immunological mechanisms involved in allergic inflammation capable to promote the initiation or exacerbation of atopic diseases such as atopic asthma. In a world that is affected more and more by factors that significantly impact the prevalence of atopic diseases, coronavirus disease 2019 (COVID-19) induced by the novel coronavirus severe acute respiratory syndrome (SARS-CoV-2) is having an unprecedented impact with still unpredictable consequences. Therefore, it is of crucial importance to revise the available scientific literature regarding the association between common respiratory viruses and asthma, as well as the newly emerging data about the molecular mechanisms of SARS-CoV-2 infection and its possible relation with asthma, to better understand the interrelation between common viruses and asthma and its potential meaning on the current global pandemic of COVID-19.
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Affiliation(s)
- Natalija Novak
- Department of Dermatology and Allergy, University Hospital Bonn, Bonn, Germany
| | - Beatriz Cabanillas
- Department of Allergy, Research Institute Hospital 12 de Octubre, Madrid, Spain
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14
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Santacroce L, Charitos IA, Ballini A, Inchingolo F, Luperto P, De Nitto E, Topi S. The Human Respiratory System and its Microbiome at a Glimpse. BIOLOGY 2020; 9:E318. [PMID: 33019595 PMCID: PMC7599718 DOI: 10.3390/biology9100318] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 09/24/2020] [Accepted: 09/25/2020] [Indexed: 02/07/2023]
Abstract
The recent COVID-19 pandemic promoted efforts to better understand the organization of the respiratory microbiome and its evolution from birth to adulthood and how it interacts with external pathogens and the host immune system. This review aims to deepen understanding of the essential physiological functions of the resident microbiome of the respiratory system on human health and diseases. First, the general characteristics of the normal microbiota in the different anatomical sites of the airways have been reported in relation to some factors such as the effect of age, diet and others on its composition and stability. Second, we analyze in detail the functions and composition and the correct functionality of the microbiome in the light of current knowledge. Several studies suggest the importance of preserving the micro-ecosystem of commensal, symbiotic and pathogenic microbes of the respiratory system, and, more recently, its relationship with the intestinal microbiome, and how it also leads to the maintenance of human health, has become better understood.
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Affiliation(s)
- Luigi Santacroce
- Ionian Department, Microbiology and Virology Laboratory, University of Bari “Aldo Moro”, Piazza G. Cesare 11, 70124 Bari, Italy;
- Department of Clinical Disciplines, University of Elbasan, Rruga Ismail Zyma, 3001 Elbasan, Albania;
| | | | - Andrea Ballini
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari “Aldo Moro”, Via Orabona 4, 70125 Bari, Italy
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Vico L. De Crecchio 7, 80138 Naples, Italy
| | - Francesco Inchingolo
- Department of Interdisciplinary Medicine, University of Bari “Aldo Moro”, Piazza G. Cesare 11, 70124 Bari, Italy;
| | - Paolo Luperto
- ENT Service, Brindisi Local Health Agency, Via Dalmazia 3, 72100 Brindisi, Italy;
| | - Emanuele De Nitto
- Department of Basic Medical Sciences, Neurosciences and Sense Organs, University of Bari “Aldo Moro”, Piazza G. Cesare 11, 70124 Bari, Italy;
| | - Skender Topi
- Department of Clinical Disciplines, University of Elbasan, Rruga Ismail Zyma, 3001 Elbasan, Albania;
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15
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Kumpitsch C, Koskinen K, Schöpf V, Moissl-Eichinger C. The microbiome of the upper respiratory tract in health and disease. BMC Biol 2019; 17:87. [PMID: 31699101 PMCID: PMC6836414 DOI: 10.1186/s12915-019-0703-z] [Citation(s) in RCA: 154] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 09/19/2019] [Indexed: 02/08/2023] Open
Abstract
The human upper respiratory tract (URT) offers a variety of niches for microbial colonization. Local microbial communities are shaped by the different characteristics of the specific location within the URT, but also by the interaction with both external and intrinsic factors, such as ageing, diseases, immune responses, olfactory function, and lifestyle habits such as smoking. We summarize here the current knowledge about the URT microbiome in health and disease, discuss methodological issues, and consider the potential of the nasal microbiome to be used for medical diagnostics and as a target for therapy.
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Affiliation(s)
- Christina Kumpitsch
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Neue Stiftingtalstraße 6, 8010 Graz, Austria
| | - Kaisa Koskinen
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Neue Stiftingtalstraße 6, 8010 Graz, Austria
| | - Veronika Schöpf
- Institute of Psychology, University of Graz, Universitaetsplatz 2, 8010 Graz, Austria
- BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria
- Present address: Medical University Vienna, Spitalgasse 23, 1090 Vienna, Austria
| | - Christine Moissl-Eichinger
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Neue Stiftingtalstraße 6, 8010 Graz, Austria
- BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria
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16
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Interactions between microbiome and lungs: Paving new paths for microbiome based bio-engineered drug delivery systems in chronic respiratory diseases. Chem Biol Interact 2019; 310:108732. [DOI: 10.1016/j.cbi.2019.108732] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 06/18/2019] [Accepted: 07/01/2019] [Indexed: 12/18/2022]
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17
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Wootton DG, Cox MJ, Gloor GB, Litt D, Hoschler K, German E, Court J, Eneje O, Keogan L, Macfarlane L, Wilks S, Diggle PJ, Woodhead M, Moffatt MF, Cookson WOC, Gordon SB. A Haemophilus sp. dominates the microbiota of sputum from UK adults with non-severe community acquired pneumonia and chronic lung disease. Sci Rep 2019; 9:2388. [PMID: 30787368 PMCID: PMC6382935 DOI: 10.1038/s41598-018-38090-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 12/18/2018] [Indexed: 11/08/2022] Open
Abstract
The demographics and comorbidities of patients with community acquired pneumonia (CAP) vary enormously but stratified treatment is difficult because aetiological studies have failed to comprehensively identify the pathogens. Our aim was to describe the bacterial microbiota of CAP and relate these to clinical characteristics in order to inform future trials of treatment stratified by co-morbidity. CAP patients were prospectively recruited at two UK hospitals. We used 16S rRNA gene sequencing to identify the dominant bacteria in sputum and compositional data analysis to determine associations with patient characteristics. We analysed sputum samples from 77 patients and found a Streptococcus sp. and a Haemophilus sp. were the most relatively abundant pathogens. The Haemophilus sp. was more likely to be dominant in patients with pre-existing lung disease, and its relative abundance was associated with qPCR levels of Haemophilus influenzae. The most abundant Streptococcus sp. was associated with qPCR levels of Streptococcus pneumoniae but dominance could not be predicted from clinical characteristics. These data suggest chronic lung disease influences the microbiota of sputum in patients with CAP. This finding could inform a trial of stratifying empirical CAP antibiotics to target Haemophilus spp. in addition to Streptococcus spp. in those with chronic lung disease.
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Affiliation(s)
- Daniel G Wootton
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK.
- Department of Respiratory Research, Aintree University Hospital NHS Foundation Trust, Liverpool, UK.
| | - Michael J Cox
- Section of Genomic Medicine, National Heart and Lung Institute, Imperial College London, London, UK
| | - Gregory B Gloor
- Departments of Biochemistry and Applied Mathematics, University of Western Ontario, Ontario, ON, Canada
| | - David Litt
- Respiratory and Vaccine Preventable Bacteria Reference Unit, National Infection Service, Public Health England, London, UK
| | - Katja Hoschler
- Virus Reference Department, National Infection Service, Public Health England, London, UK
| | - Esther German
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Joanne Court
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Odiri Eneje
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Lynne Keogan
- Department of Respiratory Research, Aintree University Hospital NHS Foundation Trust, Liverpool, UK
| | - Laura Macfarlane
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Sarah Wilks
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Peter J Diggle
- CHICAS, Lancaster University Medical School, Lancaster University, Lancaster, UK
| | - Mark Woodhead
- Department of Respiratory Medicine, Central Manchester University Hospitals NHS Foundation Trust, Manchester, UK
- Manchester Academic Health Science Centre and Faculty of Medical and Human Sciences, University of Manchester, Manchester, UK
| | - Miriam F Moffatt
- Section of Genomic Medicine, National Heart and Lung Institute, Imperial College London, London, UK
| | - William O C Cookson
- Section of Genomic Medicine, National Heart and Lung Institute, Imperial College London, London, UK
| | - Stephen B Gordon
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
- The Malawi Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi
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18
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Hanada S, Pirzadeh M, Carver KY, Deng JC. Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia. Front Immunol 2018; 9:2640. [PMID: 30505304 PMCID: PMC6250824 DOI: 10.3389/fimmu.2018.02640] [Citation(s) in RCA: 289] [Impact Index Per Article: 48.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Accepted: 10/26/2018] [Indexed: 12/18/2022] Open
Abstract
Influenza and other respiratory viral infections are the most common type of acute respiratory infection. Viral infections predispose patients to secondary bacterial infections, which often have a more severe clinical course. The mechanisms underlying post-viral bacterial infections are complex, and include multifactorial processes mediated by interactions between viruses, bacteria, and the host immune system. Studies over the past 15 years have demonstrated that unique microbial communities reside on the mucosal surfaces of the gastrointestinal tract and the respiratory tract, which have both direct and indirect effects on host defense against viral infections. In addition, antiviral immune responses induced by acute respiratory infections such as influenza are associated with changes in microbial composition and function (“dysbiosis”) in the respiratory and gastrointestinal tract, which in turn may alter subsequent immune function against secondary bacterial infection or alter the dynamics of inter-microbial interactions, thereby enhancing the proliferation of potentially pathogenic bacterial species. In this review, we summarize the literature on the interactions between host microbial communities and host defense, and how influenza, and other acute respiratory viral infections disrupt these interactions, thereby contributing to the pathogenesis of secondary bacterial infections.
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Affiliation(s)
- Shigeo Hanada
- Division of Pulmonary and Critical Care Medicine, University of Michigan, Ann Arbor, MI, United States.,Toranomon Hospital, Tokyo, Japan
| | - Mina Pirzadeh
- Division of Pulmonary and Critical Care Medicine, University of Michigan, Ann Arbor, MI, United States.,Veterans Affairs Healthcare System, Ann Arbor, MI, United States
| | - Kyle Y Carver
- Division of Pulmonary and Critical Care Medicine, University of Michigan, Ann Arbor, MI, United States.,Veterans Affairs Healthcare System, Ann Arbor, MI, United States
| | - Jane C Deng
- Division of Pulmonary and Critical Care Medicine, University of Michigan, Ann Arbor, MI, United States.,Veterans Affairs Healthcare System, Ann Arbor, MI, United States
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19
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Terranova L, Oriano M, Teri A, Ruggiero L, Tafuro C, Marchisio P, Gramegna A, Contarini M, Franceschi E, Sottotetti S, Cariani L, Bevivino A, Chalmers JD, Aliberti S, Blasi F. How to Process Sputum Samples and Extract Bacterial DNA for Microbiota Analysis. Int J Mol Sci 2018; 19:E3256. [PMID: 30347804 PMCID: PMC6214103 DOI: 10.3390/ijms19103256] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 10/09/2018] [Accepted: 10/13/2018] [Indexed: 02/07/2023] Open
Abstract
Different steps and conditions for DNA extraction for microbiota analysis in sputum have been reported in the literature. We aimed at testing both dithiothreitol (DTT) and enzymatic treatments of sputum samples and identifying the most suitable DNA extraction technique for the microbiota analysis of sputum. Sputum treatments with and without DTT were compared in terms of their median levels and the coefficient of variation between replicates of both DNA extraction yield and real-time PCR for the 16S rRNA gene. Treatments with and without lysozyme and lysostaphin were compared in terms of their median levels of real-time PCR for S. aureus. Two enzyme-based and three beads-based techniques for DNA extraction were compared in terms of their DNA extraction yield, real-time PCR for the 16S rRNA gene and microbiota analysis. DTT treatment decreased the coefficient of variation between replicates of both DNA extraction yield and real-time PCR. Lysostaphin (either 0.18 or 0.36 mg/mL) and lysozyme treatments increased S. aureus detection. One enzyme-based kit offered the highest DNA yield and 16S rRNA gene real-time PCR with no significant differences in terms of alpha-diversity indexes. A condition using both DTT and lysostaphin/lysozyme treatments along with an enzymatic kit seems to be preferred for the microbiota analysis of sputum samples.
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Affiliation(s)
- Leonardo Terranova
- Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Pediatric Highly Intensive Care Unit, 20100 Milan, Italy.
- Department of Clinical Sciences and Community Health, University of Milan, 20100 Milan, Italy.
| | - Martina Oriano
- Department of Pathophysiology and Transplantation, University of Milan, Internal Medicine Department, Respiratory unit and Adult Cystic Fibrosis Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20100 Milan, Italy.
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy.
| | - Antonio Teri
- Cystic Fibrosis Microbiology Laboratory, Fondazione IRCCS Ca' Granda, 20100 Milan, Italy.
| | - Luca Ruggiero
- Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Pediatric Highly Intensive Care Unit, 20100 Milan, Italy.
| | - Camilla Tafuro
- Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Pediatric Highly Intensive Care Unit, 20100 Milan, Italy.
| | - Paola Marchisio
- Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Pediatric Highly Intensive Care Unit, 20100 Milan, Italy.
| | - Andrea Gramegna
- Department of Pathophysiology and Transplantation, University of Milan, Internal Medicine Department, Respiratory unit and Adult Cystic Fibrosis Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20100 Milan, Italy.
| | - Martina Contarini
- Department of Pathophysiology and Transplantation, University of Milan, Internal Medicine Department, Respiratory unit and Adult Cystic Fibrosis Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20100 Milan, Italy.
| | - Elisa Franceschi
- Department of Pathophysiology and Transplantation, University of Milan, Internal Medicine Department, Respiratory unit and Adult Cystic Fibrosis Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20100 Milan, Italy.
| | - Samantha Sottotetti
- Cystic Fibrosis Microbiology Laboratory, Fondazione IRCCS Ca' Granda, 20100 Milan, Italy.
| | - Lisa Cariani
- Cystic Fibrosis Microbiology Laboratory, Fondazione IRCCS Ca' Granda, 20100 Milan, Italy.
| | - Annamaria Bevivino
- Department for Sustainability, Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), 00123 Rome, Italy.
| | - James D Chalmers
- Scottish Centre for Respiratory Research, University of Dundee, Ninewells Hospital and Medical School, DD1 9SY Dundee, UK.
| | - Stefano Aliberti
- Department of Pathophysiology and Transplantation, University of Milan, Internal Medicine Department, Respiratory unit and Adult Cystic Fibrosis Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20100 Milan, Italy.
| | - Francesco Blasi
- Department of Pathophysiology and Transplantation, University of Milan, Internal Medicine Department, Respiratory unit and Adult Cystic Fibrosis Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20100 Milan, Italy.
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20
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Taylor SL, Leong LEX, Mobegi FM, Choo JM, Burr LD, Wesselingh S, Rogers GB. Understanding the impact of antibiotic therapies on the respiratory tract resistome: a novel pooled-template metagenomic sequencing strategy. Multidiscip Respir Med 2018; 13:30. [PMID: 30151191 PMCID: PMC6101085 DOI: 10.1186/s40248-018-0140-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Determining the effects of antimicrobial therapies on airway microbiology at a population-level is essential. Such analysis allows, for example, surveillance of antibiotic-induced changes in pathogen prevalence, the emergence and spread of antibiotic resistance, and the transmission of multi-resistant organisms. However, current analytical strategies for understanding these processes are limited. Culture- and PCR-based assays for specific microbes require the a priori selection of targets, while antibiotic sensitivity testing typically provides no insight into either the molecular basis of resistance, or the carriage of resistance determinants by the wider commensal microbiota. Shotgun metagenomic sequencing provides an alternative approach that allows the microbial composition of clinical samples to be described in detail, including the prevalence of resistance genes and virulence traits. While highly informative, the application of metagenomics to large patient cohorts can be prohibitively expensive. Using sputum samples from a randomised placebo-controlled trial of erythromycin in adults with bronchiectasis, we describe a novel, cost-effective strategy for screening patient cohorts for changes in resistance gene prevalence. By combining metagenomic screening of pooled DNA extracts with validatory quantitative PCR-based analysis of candidate markers in individual samples, we identify population-level changes in the relative abundance of specific macrolide resistance genes. This approach has the potential to provide an important adjunct to current analytical strategies, particularly within the context of antimicrobial clinical trials.
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Affiliation(s)
- Steven L Taylor
- 1Infection and Immunity, South Australian Health and Medical Research Institute, Adelaide, South Australia Australia.,2SAHMRI Microbiome Research Laboratory, College of Medicine and Public Health, Flinders University, Adelaide, South Australia Australia
| | - Lex E X Leong
- 1Infection and Immunity, South Australian Health and Medical Research Institute, Adelaide, South Australia Australia.,2SAHMRI Microbiome Research Laboratory, College of Medicine and Public Health, Flinders University, Adelaide, South Australia Australia
| | - Fredrick M Mobegi
- 1Infection and Immunity, South Australian Health and Medical Research Institute, Adelaide, South Australia Australia.,2SAHMRI Microbiome Research Laboratory, College of Medicine and Public Health, Flinders University, Adelaide, South Australia Australia
| | - Jocelyn M Choo
- 1Infection and Immunity, South Australian Health and Medical Research Institute, Adelaide, South Australia Australia.,2SAHMRI Microbiome Research Laboratory, College of Medicine and Public Health, Flinders University, Adelaide, South Australia Australia
| | - Lucy D Burr
- 3Department of Respiratory Medicine, Mater Health Services, South Brisbane, Queensland, Australia
| | - Steve Wesselingh
- 1Infection and Immunity, South Australian Health and Medical Research Institute, Adelaide, South Australia Australia.,2SAHMRI Microbiome Research Laboratory, College of Medicine and Public Health, Flinders University, Adelaide, South Australia Australia
| | - Geraint B Rogers
- 1Infection and Immunity, South Australian Health and Medical Research Institute, Adelaide, South Australia Australia.,2SAHMRI Microbiome Research Laboratory, College of Medicine and Public Health, Flinders University, Adelaide, South Australia Australia
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21
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Costa AN, Costa FMD, Campos SV, Salles RK, Athanazio RA. The pulmonary microbiome: challenges of a new paradigm. ACTA ACUST UNITED AC 2018; 44:424-432. [PMID: 30066739 PMCID: PMC6467588 DOI: 10.1590/s1806-37562017000000209] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 07/16/2017] [Indexed: 01/06/2023]
Abstract
The study of the human microbiome-and, more recently, that of the respiratory system-by means of sophisticated molecular biology techniques, has revealed the immense diversity of microbial colonization in humans, in human health, and in various diseases. Apparently, contrary to what has been believed, there can be nonpathogenic colonization of the lungs by microorganisms such as bacteria, fungi, and viruses. Although this physiological lung microbiome presents low colony density, it presents high diversity. However, some pathological conditions lead to a loss of that diversity, with increasing concentrations of some bacterial genera, to the detriment of others. Although we possess qualitative knowledge of the bacteria present in the lungs in different states of health or disease, that knowledge has advanced to an understanding of the interaction of this microbiota with the local and systemic immune systems, through which it modulates the immune response. Given this intrinsic relationship between the microbiota and the lungs, studies have put forth new concepts about the pathophysiological mechanisms of homeostasis in the respiratory system and the potential dysbiosis in some diseases, such as cystic fibrosis, COPD, asthma, and interstitial lung disease. This departure from the paradigm regarding knowledge of the lung microbiota has made it imperative to improve understanding of the role of the microbiome, in order to identify possible therapeutic targets and to develop innovative clinical approaches. Through this new leap of knowledge, the results of preliminary studies could translate to benefits for our patients.
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Affiliation(s)
- André Nathan Costa
- . Divisão de Pneumologia, Instituto do Coração - InCor - Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo, São Paulo (SP) Brasil
| | - Felipe Marques da Costa
- . Divisão de Pneumologia, Instituto do Coração - InCor - Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo, São Paulo (SP) Brasil
| | - Silvia Vidal Campos
- . Divisão de Pneumologia, Instituto do Coração - InCor - Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo, São Paulo (SP) Brasil
| | - Roberta Karla Salles
- . Divisão de Pneumologia, Instituto do Coração - InCor - Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo, São Paulo (SP) Brasil
| | - Rodrigo Abensur Athanazio
- . Divisão de Pneumologia, Instituto do Coração - InCor - Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo, São Paulo (SP) Brasil
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22
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Sánchez-Bautista A, Rodríguez-Díaz JC, Garcia-Heredia I, Luna-Paredes C, Alcalá-Minagorre PJ. Airway microbiota in patients with paediatric cystic fibrosis: Relationship with clinical status. Enferm Infecc Microbiol Clin 2018; 37:167-171. [PMID: 30827333 DOI: 10.1016/j.eimc.2018.05.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 04/08/2018] [Accepted: 05/02/2018] [Indexed: 12/21/2022]
Abstract
INTRODUCTION New massive sequencing techniques make it possible to determine the composition of airway microbiota in patients with cystic fibrosis (CF). However, the relationship between the composition of lung microbiome and the clinical status of paediatric patients is still not fully understood. MATERIAL AND METHODS A cross-sectional observational study was conducted on induced sputum samples from children with CF and known mutation in the CFTR gene. The bacterial sequences of the 16SrRNA gene were analyzed and their association with various clinical variables studied. RESULTS Analysis of the 13 samples obtained showed a core microbiome made up of Staphylococcus spp., Streptococcus spp., Rothia spp., Gemella spp. and Granulicatella spp., with a small number of Pseudomonas spp. The cluster of patients with less biodiversity were found to exhibit a greater number of sequences of Staphylococcus spp., mainly Staphylococcus aureus (p 0.009) and a greater degree of lung damage. CONCLUSION An airway microbiome with greater biodiversity may be an indicator of less pronounced disease progression, in which case new therapeutic interventions that prevent reduction in non-pathogenic species of the airway microbiota should be studied.
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Affiliation(s)
- Antonia Sánchez-Bautista
- Department of Microbiology, Hospital General Universitario de Alicante, Instituto de Investigación Sanitaria y Biomédica de Alicante (ISABIAL), Alicante, Spain
| | - Juan Carlos Rodríguez-Díaz
- Department of Microbiology, Hospital General Universitario de Alicante, Instituto de Investigación Sanitaria y Biomédica de Alicante (ISABIAL), Alicante, Spain.
| | - Inmaculada Garcia-Heredia
- Department of Microbiology, Hospital General Universitario de Alicante, Instituto de Investigación Sanitaria y Biomédica de Alicante (ISABIAL), Alicante, Spain
| | - Carmen Luna-Paredes
- Pediatric Cystic Fibrosis Unit, Department of Pediatrics, Hospital Universitario Doce de Octubre, Madrid, Spain
| | - Pedro J Alcalá-Minagorre
- Department of Pediatrics, Hospital General Universitario de Alicante, Instituto de Investigación Sanitaria y Biomédica de Alicante (ISABIAL), Alicante, Spain
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23
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An SQ, Warris A, Turner S. Microbiome characteristics of induced sputum compared to bronchial fluid and upper airway samples. Pediatr Pulmonol 2018; 53:921-928. [PMID: 29727521 DOI: 10.1002/ppul.24037] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 03/30/2018] [Indexed: 12/19/2022]
Abstract
OBJECTIVE The study of the community of microorganisms (the microbiota) in the lower airways in children is restricted to opportunistic sampling in children undergoing elective general anaesthetic. Here we tested the hypothesis that induced sputum is a valid alternative to directly sampling the lower airways to study lower airway microbiota. METHODS Children scheduled for elective operations were recruited. Pre-operatively a sample of induced sputum was obtained. After anaesthesia was induced, a bronchial brushing and swabs of the upper respiratory tract were obtained. Bacterial community analysis was performed by amplification of the V3-V4 16S rRNA gene region. RESULTS Twenty children were recruited, mean age 10.7 years. Induced sputum samples were obtained from 12 children, bronchial brushing from 14 and nasal, mouth, and throat samples in 15, 16, and 17 children. The profile of bacterial communities was similar in the mouth, throat, and sputum samples with the nose and bronchial samples being different. Actinobacteria species dominated the nose and mouth, Fusobacteria were the dominant species in the throat and sputum while Proteobacteria species dominated in bronchial samples. Forty-one percent of detected bacteria in bronchial samples were unclassified. Bacterial communities from the mouth, throat, and induced sputum were tightly clustered and were distinct from nose and those found in bronchial communities. CONCLUSIONS Induced sputum may not be a valid surrogate for microbiome assessment of the lower airways in all individuals. Many bacteria in bronchial samples were not recognized by standard testing, suggesting that our understanding of the lower airway microbiota in children remains rudimentary.
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Affiliation(s)
- Shi-Qi An
- Division of Molecular Microbiology, University of Dundee, Belfast, UK.,Wellcome Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK
| | - Adilia Warris
- Department of Child Health, University of Aberdeen, Aberdeen, UK.,MRC Centre for Medical Mycology, University of Aberdeen, Aberdeen, UK
| | - Steve Turner
- Department of Child Health, University of Aberdeen, Aberdeen, UK
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24
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How can the cystic fibrosis respiratory microbiome influence our clinical decision-making? Curr Opin Pulm Med 2018; 23:536-543. [PMID: 28786882 DOI: 10.1097/mcp.0000000000000419] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
PURPOSE OF REVIEW Almost 15 years have now passed since bacterial community profiling techniques were first used to analyse respiratory samples from people with cystic fibrosis. Since then, many different analytical approaches have been used to try to better understand the contribution of the cystic fibrosis lung microbiota to disease, with varying degrees of success. We examine the extent to which cystic fibrosis respiratory microbiome research has been successful in informing clinical decision-making, and highlight areas that we believe have the potential to yield important insight. RECENT FINDINGS Recent research on the cystic fibrosis lung microbiome can be broadly divided into efforts to better characterize microbiota composition, particularly relative to key clinical events, and attempts to understand the cystic fibrosis lung microbiology as an interactive microbial system. The latter, in particular, has led to the development of a number of models in which microbiome-mediated processes precipitate clinical events. SUMMARY Growing technological sophistication is enabling increasingly detailed microbiological data to be generated from cystic fibrosis respiratory samples. However, translating these data into clinically useful measures that accurately predict outcomes and guide treatments remains a formidable challenge. The development of systems biology approaches that enable the integration of complex microbiome and host-derived data provide an exciting opportunity to address this goal.
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25
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Faverio P, Bini F, Vaghi A, Pesci A. Long-term macrolides in diffuse interstitial lung diseases. Eur Respir Rev 2017; 26:26/146/170082. [DOI: 10.1183/16000617.0082-2017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 09/07/2017] [Indexed: 12/18/2022] Open
Abstract
In the present review we provide currently available evidence for the use of macrolides in the treatment of diffuse interstitial lung diseases (ILDs). Up to now, research on macrolides has mainly focused on three areas. First, macrolides have shown some promising results in cellular models and case reports as antifibrotic agents, by promoting autophagy and clearance of intracellular protein aggregates and acting as regulators of surfactant homeostasis. Secondly, macrolides have an immunomodulatory effect, which has been applied in some organising pneumonia cases. In particular, macrolides have been tested in association with systemic corticosteroids as steroid-sparing agents and alone as either first-line agents in mild cases or second-line agents where steroids were poorly tolerated or had failed. Thirdly, a recent area of research concerns the possible role of macrolides as modulators of lung microbiota and the host–microbiota interaction. This function has been particularly studied in idiopathic pulmonary fibrosis patients, in whom changes in microbiota have been proved to be associated with disease progression. However, the lack of high-quality studies makes the application of macrolide therapy in ILDs a field in which research should be conducted on a large scale.
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26
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The lung microbiome. Emerg Top Life Sci 2017; 1:313-324. [PMID: 33525774 DOI: 10.1042/etls20170043] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Revised: 08/31/2017] [Accepted: 09/29/2017] [Indexed: 12/17/2022]
Abstract
Historically, our understanding of lung microbiology has relied on insight gained through culture-based diagnostic approaches that employ selective culture conditions to isolate specific pathogens. The relatively recent development of culture-independent microbiota-profiling techniques, particularly 16S rRNA (ribosomal ribonucleic acid) gene amplicon sequencing, has enabled more comprehensive characterisation of the microbial content of respiratory samples. The widespread application of such techniques has led to a fundamental shift in our view of respiratory microbiology. Rather than a sterile lung environment that can become colonised by microbes during infection, it appears that a more nuanced balance exists between what we consider respiratory health and disease, mediated by mechanisms that influence the clearance of microbes from the lungs. Where airway defences are compromised, the ongoing transient exposure of the lower airways to microbes can lead to the establishment of complex microbial communities within the lung. Importantly, the characteristics of these communities, and the manner in which they influence lung pathogenesis, can be very different from those of their constituent members when viewed in isolation. The lung microbiome, a construct that incorporates microbes, their genetic material, and the products of microbial genes, is increasingly central to our understanding of the regulation of respiratory physiology and the processes that underlie lung pathogenesis.
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27
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Liu HX, Tao LL, Zhang J, Zhu YG, Zheng Y, Liu D, Zhou M, Ke H, Shi MM, Qu JM. Difference of lower airway microbiome in bilateral protected specimen brush between lung cancer patients with unilateral lobar masses and control subjects. Int J Cancer 2017; 142:769-778. [PMID: 29023689 DOI: 10.1002/ijc.31098] [Citation(s) in RCA: 127] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 09/17/2017] [Accepted: 09/25/2017] [Indexed: 12/20/2022]
Abstract
The functional role of respiratory microbiota has attracted an accumulating attention recently. However, the role of respiratory microbiome in lung carcinogenesis is mostly unknown. Our study aimed to characterize and compare bilateral lower airway microbiome of lung cancer patients with unilateral lobar masses and control subjects. Protected bronchial specimen brushing samples were collected from 24 lung cancer patients with unilateral lobar masses (paired samples from cancerous site and the contralateral noncancerous site) and 18 healthy controls undergoing bronchoscopies and further analyzed by 16S rRNA amplicon sequencing. As results, significant decreases in microbial diversity were observed in patients with lung cancer in comparison to the controls, alpha diversity steadily declined from healthy site to noncancerous to cancerous site. Genus Streptococcus was significantly more abundant in cancer cases than the controls, while Staphylococcus was more abundant in the controls. The area under the curve of genus Streptococcus used to predict lung cancer was 0.693 (sensitivity = 87.5%, specificity = 55.6%). The abundance of genus Streptococcus and Neisseria displayed an increasing trend whereas Staphylococcus and Dialister gradually declined from healthy to noncancerous to cancerous site. Collectively, lung cancer-associated microbiota profile is distinct from that found in healthy controls, and the altered cancer-associated microbiota is not restricted to tumor tissue. The genus Streptococcus was abundant in lung cancer patients and exhibited moderate classification potential. The gradual microbiota profile shift from healthy site to noncancerous to paired cancerous site suggested a change of the microenvironment associated with the development of lung cancer.
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Affiliation(s)
- Hai-Xia Liu
- Huadong Hospital Affiliated to Fudan University, No. 221, West Yan An Road, Shanghai, 200040, China
| | - Li-Li Tao
- UT Southwestern Medical Center, 6000 Harry Hines Blvd, Dallas, TX
| | - Jing Zhang
- Zhongshan Hospital Affiliated to Fudan University, No. 180, Feng Lin Road, Shanghai, 200032, China
| | - Ying-Gang Zhu
- Huadong Hospital Affiliated to Fudan University, No. 221, West Yan An Road, Shanghai, 200040, China
| | - Yu Zheng
- Ren Ji Hospital, School of Medicine, Shanghai Jiaotong University, No. 2000, Jiangyue Road, Shanghai, 200112, China
| | - Dong Liu
- Huadong Hospital Affiliated to Fudan University, No. 221, West Yan An Road, Shanghai, 200040, China
| | - Min Zhou
- Rui Jin Hospital, School of Medicine, Shanghai Jiaotong University, No. 197, Rui Jin Er Road, Shanghai, 200025, China
| | - Hui Ke
- Shanghai Pulmonary Hospital Affiliated to Tongji University, No. 507, Yangpu District, Zheng Min Road, Shanghai, 200433, China
| | - Meng-Meng Shi
- Rui Jin Hospital, School of Medicine, Shanghai Jiaotong University, No. 197, Rui Jin Er Road, Shanghai, 200025, China
| | - Jie-Ming Qu
- Huadong Hospital Affiliated to Fudan University, No. 221, West Yan An Road, Shanghai, 200040, China.,Rui Jin Hospital, School of Medicine, Shanghai Jiaotong University, No. 197, Rui Jin Er Road, Shanghai, 200025, China
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28
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O'Dwyer DN, Dickson RP, Moore BB. The Lung Microbiome, Immunity, and the Pathogenesis of Chronic Lung Disease. THE JOURNAL OF IMMUNOLOGY 2017; 196:4839-47. [PMID: 27260767 DOI: 10.4049/jimmunol.1600279] [Citation(s) in RCA: 227] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 03/24/2016] [Indexed: 12/17/2022]
Abstract
The development of culture-independent techniques for microbiological analysis has uncovered the previously unappreciated complexity of the bacterial microbiome at various anatomic sites. The microbiome of the lung has relatively less bacterial biomass when compared with the lower gastrointestinal tract yet displays considerable diversity. The composition of the lung microbiome is determined by elimination, immigration, and relative growth within its communities. Chronic lung disease alters these factors. Many forms of chronic lung disease demonstrate exacerbations that drive disease progression and are poorly understood. Mounting evidence supports ways in which microbiota dysbiosis can influence host defense and immunity, and in turn may contribute to disease exacerbations. Thus, the key to understanding the pathogenesis of chronic lung disease may reside in deciphering the complex interactions between the host, pathogen, and resident microbiota during stable disease and exacerbations. In this brief review we discuss new insights into these labyrinthine relationships.
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Affiliation(s)
- David N O'Dwyer
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Health System, Ann Arbor, MI 48109; and
| | - Robert P Dickson
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Health System, Ann Arbor, MI 48109; and
| | - Bethany B Moore
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Health System, Ann Arbor, MI 48109; and Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109
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29
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Bacci G, Mengoni A, Fiscarelli E, Segata N, Taccetti G, Dolce D, Paganin P, Morelli P, Tuccio V, De Alessandri A, Lucidi V, Bevivino A. A Different Microbiome Gene Repertoire in the Airways of Cystic Fibrosis Patients with Severe Lung Disease. Int J Mol Sci 2017; 18:E1654. [PMID: 28758937 PMCID: PMC5578044 DOI: 10.3390/ijms18081654] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 07/24/2017] [Accepted: 07/25/2017] [Indexed: 12/12/2022] Open
Abstract
In recent years, next-generation sequencing (NGS) was employed to decipher the structure and composition of the microbiota of the airways in cystic fibrosis (CF) patients. However, little is still known about the overall gene functions harbored by the resident microbial populations and which specific genes are associated with various stages of CF lung disease. In the present study, we aimed to identify the microbial gene repertoire of CF microbiota in twelve patients with severe and normal/mild lung disease by performing sputum shotgun metagenome sequencing. The abundance of metabolic pathways encoded by microbes inhabiting CF airways was reconstructed from the metagenome. We identified a set of metabolic pathways differently distributed in patients with different pulmonary function; namely, pathways related to bacterial chemotaxis and flagellar assembly, as well as genes encoding efflux-mediated antibiotic resistance mechanisms and virulence-related genes. The results indicated that the microbiome of CF patients with low pulmonary function is enriched in virulence-related genes and in genes encoding efflux-mediated antibiotic resistance mechanisms. Overall, the microbiome of severely affected adults with CF seems to encode different mechanisms for the facilitation of microbial colonization and persistence in the lung, consistent with the characteristics of multidrug-resistant microbial communities that are commonly observed in patients with severe lung disease.
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Affiliation(s)
- Giovanni Bacci
- Department of Biology, University of Florence, Florence 50019, Italy.
| | - Alessio Mengoni
- Department of Biology, University of Florence, Florence 50019, Italy.
| | - Ersilia Fiscarelli
- Cystic Fibrosis Microbiology and Cystic Fibrosis Center, "Bambino Gesù" Children's Hospital and Research Institute, Rome 00165, Italy.
| | - Nicola Segata
- Centre for Integrative Biology, University of Trento, Trento 38123, Italy.
| | - Giovanni Taccetti
- Department of Pediatric Medicine, Cystic Fibrosis Center, Anna Meyer Children's University Hospital, Florence 50139, Italy.
| | - Daniela Dolce
- Department of Pediatric Medicine, Cystic Fibrosis Center, Anna Meyer Children's University Hospital, Florence 50139, Italy.
| | - Patrizia Paganin
- Territorial and Production Systems Sustainability Department, ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Casaccia Research Center, Rome 00123, Italy.
| | - Patrizia Morelli
- Cystic Fibrosis Center, IRCCS G. Gaslini Institute, Genoa 16146, Italy.
| | - Vanessa Tuccio
- Cystic Fibrosis Microbiology and Cystic Fibrosis Center, "Bambino Gesù" Children's Hospital and Research Institute, Rome 00165, Italy.
| | | | - Vincenzina Lucidi
- Cystic Fibrosis Microbiology and Cystic Fibrosis Center, "Bambino Gesù" Children's Hospital and Research Institute, Rome 00165, Italy.
| | - Annamaria Bevivino
- Territorial and Production Systems Sustainability Department, ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Casaccia Research Center, Rome 00123, Italy.
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30
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Yadava K, Pattaroni C, Sichelstiel AK, Trompette A, Gollwitzer ES, Salami O, von Garnier C, Nicod LP, Marsland BJ. Microbiota Promotes Chronic Pulmonary Inflammation by Enhancing IL-17A and Autoantibodies. Am J Respir Crit Care Med 2017; 193:975-87. [PMID: 26630356 DOI: 10.1164/rccm.201504-0779oc] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
RATIONALE Changes in the pulmonary microbiota are associated with progressive respiratory diseases including chronic obstructive pulmonary disease (COPD). Whether there is a causal relationship between these changes and disease progression remains unknown. OBJECTIVES To investigate the link between an altered microbiota and disease, we used a murine model of chronic lung inflammation that is characterized by key pathological features found in COPD and compared responses in specific pathogen-free (SPF) mice and mice depleted of microbiota by antibiotic treatment or devoid of a microbiota (axenic). METHODS Mice were challenged with LPS/elastase intranasally over 4 weeks, resulting in a chronically inflamed and damaged lung. The ensuing cellular infiltration, histological damage, and decline in lung function were quantified. MEASUREMENTS AND MAIN RESULTS Similar to human disease, the composition of the pulmonary microbiota was altered in diseased animals. We found that the microbiota richness and diversity were decreased in LPS/elastase-treated mice, with an increased representation of the genera Pseudomonas and Lactobacillus and a reduction in Prevotella. Moreover, the microbiota was implicated in disease development as mice depleted, or devoid, of microbiota exhibited an improvement in lung function, reduced inflammation, and lymphoid neogenesis. The absence of microbial cues markedly decreased the production of IL-17A, whereas intranasal transfer of fluid enriched with the pulmonary microbiota isolated from diseased mice enhanced IL-17A production in the lungs of antibiotic-treated or axenic recipients. Finally, in mice harboring a microbiota, neutralizing IL-17A dampened inflammation and restored lung function. CONCLUSIONS Collectively, our data indicate that host-microbial cross-talk promotes inflammation and could underlie the chronicity of inflammatory lung diseases.
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Affiliation(s)
- Koshika Yadava
- 1 Service de Pneumologie, Faculté de Biologie et de Médecine, Centre Hospitalier Universitaire Vaudoise-Université Lausanne Lausanne, Switzerland.,2 Division of Infectious Diseases, Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Céline Pattaroni
- 1 Service de Pneumologie, Faculté de Biologie et de Médecine, Centre Hospitalier Universitaire Vaudoise-Université Lausanne Lausanne, Switzerland
| | - Anke K Sichelstiel
- 1 Service de Pneumologie, Faculté de Biologie et de Médecine, Centre Hospitalier Universitaire Vaudoise-Université Lausanne Lausanne, Switzerland
| | - Aurélien Trompette
- 1 Service de Pneumologie, Faculté de Biologie et de Médecine, Centre Hospitalier Universitaire Vaudoise-Université Lausanne Lausanne, Switzerland
| | - Eva S Gollwitzer
- 1 Service de Pneumologie, Faculté de Biologie et de Médecine, Centre Hospitalier Universitaire Vaudoise-Université Lausanne Lausanne, Switzerland
| | - Olawale Salami
- 1 Service de Pneumologie, Faculté de Biologie et de Médecine, Centre Hospitalier Universitaire Vaudoise-Université Lausanne Lausanne, Switzerland
| | - Christophe von Garnier
- 3 Department of Respiratory Medicine, Inselspital, Bern University Hospital, Bern, Switzerland; and.,4 Department of Clinical Research, University of Bern, Bern, Switzerland
| | - Laurent P Nicod
- 1 Service de Pneumologie, Faculté de Biologie et de Médecine, Centre Hospitalier Universitaire Vaudoise-Université Lausanne Lausanne, Switzerland
| | - Benjamin J Marsland
- 1 Service de Pneumologie, Faculté de Biologie et de Médecine, Centre Hospitalier Universitaire Vaudoise-Université Lausanne Lausanne, Switzerland
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31
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Prevaes SMPJ, de Steenhuijsen Piters WAA, de Winter-de Groot KM, Janssens HM, Tramper-Stranders GA, Chu MLJN, Tiddens HA, van Westreenen M, van der Ent CK, Sanders EAM, Bogaert D. Concordance between upper and lower airway microbiota in infants with cystic fibrosis. Eur Respir J 2017; 49:49/3/1602235. [PMID: 28356374 DOI: 10.1183/13993003.02235-2016] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 11/23/2016] [Indexed: 12/29/2022]
Abstract
Nasopharyngeal and oropharyngeal samples are commonly used to direct therapy for lower respiratory tract infections in non-expectorating infants with cystic fibrosis (CF).We aimed to investigate the concordance between the bacterial community compositions of 25 sets of nasopharyngeal, oropharyngeal and bronchoalveolar lavage (BAL) samples from 17 infants with CF aged ∼5 months (n=13) and ∼12 months (n=12) using conventional culturing and 16S-rRNA sequencing.Clustering analyses demonstrated that BAL microbiota profiles were in general characterised by a mixture of oral and nasopharyngeal bacteria, including commensals like Streptococcus, Neisseria, Veillonella and Rothia spp. and potential pathogens like Staphylococcus aureus, Haemophilus influenzae and Moraxella spp. Within each individual, however, the degree of concordance differed between microbiota of both upper respiratory tract niches and the corresponding BAL.The inconsistent intra-individual concordance between microbiota of the upper and lower respiratory niches suggests that the lungs of infants with CF may have their own microbiome that seems seeded by, but is not identical to, the upper respiratory tract microbiome.
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Affiliation(s)
- Sabine M P J Prevaes
- Dept of Paediatrics, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Wouter A A de Steenhuijsen Piters
- Dept of Paediatrics, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht, The Netherlands.,Both authors contributed equally
| | - Karin M de Winter-de Groot
- Dept of Paediatrics, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht, The Netherlands.,Both authors contributed equally
| | - Hettie M Janssens
- Dept of Paediatric Pulmonology and Allergology, Sophia Children's Hospital, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Gerdien A Tramper-Stranders
- Dept of Paediatrics, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Mei Ling J N Chu
- Dept of Paediatrics, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Harm A Tiddens
- Dept of Paediatric Pulmonology and Allergology, Sophia Children's Hospital, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Mireille van Westreenen
- Dept of Medical Microbiology and Infectious Diseases, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Cornelis K van der Ent
- Dept of Paediatrics, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Elisabeth A M Sanders
- Dept of Paediatrics, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Debby Bogaert
- Dept of Paediatrics, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht, The Netherlands
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Rubbo B, Behan L, Dehlink E, Goutaki M, Hogg C, Kouis P, Kuehni CE, Latzin P, Nielsen K, Norris D, Nyilas S, Price M, Lucas JS. Proceedings of the COST action BM1407 inaugural conference BEAT-PCD: translational research in primary ciliary dyskinesia - bench, bedside, and population perspectives. BMC Proc 2016; 10:66. [PMID: 28813544 PMCID: PMC5260785 DOI: 10.1186/s12919-016-0067-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Primary ciliary dyskinesia (PCD) is a rare heterogenous condition that causes progressive suppurative lung disease, chronic rhinosinusitis, chronic otitis media, infertility and abnormal situs. 'Better Experimental Approaches to Treat Primary Ciliary Dyskinesia' (BEAT-PCD) is a network of scientists and clinicians coordinating research from basic science through to clinical care with the intention of developing treatments and diagnostics that lead to improved long-term outcomes for patients. BEAT-PCD activities are supported by EU Framework Programme Horizon 2020 funded COST Action (BM1407). The Inaugural Conference of BEAT-PCD was held in December 2015 in Southampton, UK. The conference attracted ninety-six scientists, clinicians, allied health professionals, industrial partners and patient representatives from twenty countries. We aimed to identify the needs for PCD research and clinical care, particularly focussing on basic science, epidemiology, diagnostic testing, clinical management and clinical trials. The multidisciplinary conference provided an interactive platform for exchanging ideas through a program of lectures, poster presentations, breakout sessions and workshops. This allowed us to develop plans for collaborative studies. In this report, we summarize the meeting, highlight developments, and discuss open questions thereby documenting ongoing developments in the field of PCD research.
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Affiliation(s)
- Bruna Rubbo
- Primary Ciliary Dyskinesia Centre, University Hospital Southampton NHS Foundation Trust, Southampton, UK
- University of Southampton Faculty of Medicine, Academic Unit of Clinical and Experimental Medicine, Southampton, UK
| | - Laura Behan
- Primary Ciliary Dyskinesia Centre, University Hospital Southampton NHS Foundation Trust, Southampton, UK
- University of Southampton Faculty of Medicine, Academic Unit of Clinical and Experimental Medicine, Southampton, UK
| | - Eleonora Dehlink
- Primary Ciliary Dyskinesia Centre, Department of Paediatrics, Royal Brompton and Harefield Foundation Trust, London, UK
| | - Myrofora Goutaki
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
- Paediatric Respiratory Medicine, Children’s University Hospital of Bern, University of Bern, Bern, Switzerland
| | - Claire Hogg
- Primary Ciliary Dyskinesia Centre, Department of Paediatrics, Royal Brompton and Harefield Foundation Trust, London, UK
| | - Panayiotis Kouis
- Cyprus International Institute for Environmental & Public Health, Cyprus University of Technology, Limassol, Cyprus
| | - Claudia E. Kuehni
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Philipp Latzin
- Paediatric Respiratory Medicine, Children’s University Hospital of Bern, University of Bern, Bern, Switzerland
| | - Kim Nielsen
- Danish PCD & chILD Centre, CF Centre Copenhagen, Paediatric Pulmonary Service, Department of Paediatrics and Adolescent Medicine, Copenhagen University Hospital, Rigshospitalet, Denmark
| | | | - Sylvia Nyilas
- Paediatric Respiratory Medicine, Children’s University Hospital of Bern, University of Bern, Bern, Switzerland
- Department of Paediatric Pulmonology, University Children’s Hospital Basel (UKBB), Basel, Switzerland
| | - Mareike Price
- Department of Paediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research, Hannover, Germany
| | - Jane S. Lucas
- Primary Ciliary Dyskinesia Centre, University Hospital Southampton NHS Foundation Trust, Southampton, UK
- University of Southampton Faculty of Medicine, Academic Unit of Clinical and Experimental Medicine, Southampton, UK
- Faculty of Medicine Mail Point 803, University Hospital Southampton, Southampton, SO16 6YD UK
| | - on behalf of BEAT-PCD
- Primary Ciliary Dyskinesia Centre, University Hospital Southampton NHS Foundation Trust, Southampton, UK
- University of Southampton Faculty of Medicine, Academic Unit of Clinical and Experimental Medicine, Southampton, UK
- Primary Ciliary Dyskinesia Centre, Department of Paediatrics, Royal Brompton and Harefield Foundation Trust, London, UK
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
- Paediatric Respiratory Medicine, Children’s University Hospital of Bern, University of Bern, Bern, Switzerland
- Cyprus International Institute for Environmental & Public Health, Cyprus University of Technology, Limassol, Cyprus
- Danish PCD & chILD Centre, CF Centre Copenhagen, Paediatric Pulmonary Service, Department of Paediatrics and Adolescent Medicine, Copenhagen University Hospital, Rigshospitalet, Denmark
- MRC Harwell, Harwell Campus, Oxfordshire, UK
- Department of Paediatric Pulmonology, University Children’s Hospital Basel (UKBB), Basel, Switzerland
- Department of Paediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research, Hannover, Germany
- Faculty of Medicine Mail Point 803, University Hospital Southampton, Southampton, SO16 6YD UK
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Kosikowska U, Rybojad P, Stępień-Pyśniak D, Żbikowska A, Malm A. Changes in the prevalence and biofilm formation of Haemophilus influenzae and Haemophilus parainfluenzae from the respiratory microbiota of patients with sarcoidosis. BMC Infect Dis 2016; 16:449. [PMID: 27562460 PMCID: PMC5000413 DOI: 10.1186/s12879-016-1793-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 08/21/2016] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Healthy condition and chronic diseases may be associated with microbiota composition and its properties. The prevalence of respiratory haemophili with respect to their phenotypes including the ability to biofilm formation in patients with sarcoidosis was assayed. METHODS Nasopharynx and sputum specimens were taken in 31 patients with sarcoidosis (average age 42.6 ± 13), and nasopharynx specimens were taken in 37 healthy people (average age 44.6 ± 11.6). Haemophili were identified by API-NH microtest and by the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) system. Biofilm was visualised by crystal violet staining and confocal scanning laser microscopy (CSLM). The statistical analysis was performed with Statgraphics Plus for Windows. RESULTS In total, 30/31 patients with sarcoidosis and 31/37 healthy people were colonized by Haemophilus influenzae (6/30 vs. 1/31) and Haemophilus parainfluenzae (28/30 vs. 31/31) in the nasopharynx. The overall number of nasopharyngeal haemophili isolates was 59 in patients with sarcoidosis and 67 in healthy volunteers (H. influenzae 6/59 vs. 1/67, P = 0.05; H. parainfluenzae 47/59 vs. 65/67, P = 0.0032). Moreover, the decreased number of H. parainfluenzae biofilm-producing isolates was shown in nasopharyngeal samples in patients with sarcoidosis as compared to healthy people (19/31 vs. 57/65, P = 0.006), especially with respect to isolates classified as strong and very strong biofilm-producers (8/31 vs. 39/65, P = 0.002). CONCLUSIONS The obtained data suggest that the qualitative and quantitative changes within the respiratory microbiota concerning the overall prevalence of H. influenzae together with the decreased number of H. parainfluenzae strains and the decreased rate of H. parainfluenzae biofilm-producing isolates as compared to healthy people may be associated with sarcoidosis.
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Affiliation(s)
- Urszula Kosikowska
- Department of Pharmaceutical Microbiology with Laboratory for Microbiological Diagnostics, Medical University of Lublin, Chodzki Str. 1, 20-093, Lublin, Poland.
| | - Paweł Rybojad
- Department of Thoracic Surgery, Medical University of Lublin, Lublin, Poland
| | - Dagmara Stępień-Pyśniak
- Sub-Department of Veterinary Prevention and Avian Diseases, Institute of Biological Bases of Animal Diseases, Faculty of Veterinary Medicine, University of Life Sciences in Lublin, Lublin, Poland
| | - Anna Żbikowska
- Department of Food Technology, Faculty of Food Sciences, Warsaw University of Life Sciences (WULS-SGGW), Warsaw, Poland
| | - Anna Malm
- Department of Pharmaceutical Microbiology with Laboratory for Microbiological Diagnostics, Medical University of Lublin, Chodzki Str. 1, 20-093, Lublin, Poland
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Lal CV, Travers C, Aghai ZH, Eipers P, Jilling T, Halloran B, Carlo WA, Keeley J, Rezonzew G, Kumar R, Morrow C, Bhandari V, Ambalavanan N. The Airway Microbiome at Birth. Sci Rep 2016; 6:31023. [PMID: 27488092 PMCID: PMC4973241 DOI: 10.1038/srep31023] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 07/13/2016] [Indexed: 12/29/2022] Open
Abstract
Alterations of pulmonary microbiome have been recognized in multiple respiratory disorders. It is critically important to ascertain if an airway microbiome exists at birth and if so, whether it is associated with subsequent lung disease. We found an established diverse and similar airway microbiome at birth in both preterm and term infants, which was more diverse and different from that of older preterm infants with established chronic lung disease (bronchopulmonary dysplasia). Consistent temporal dysbiotic changes in the airway microbiome were seen from birth to the development of bronchopulmonary dysplasia in extremely preterm infants. Genus Lactobacillus was decreased at birth in infants with chorioamnionitis and in preterm infants who subsequently went on to develop lung disease. Our results, taken together with previous literature indicating a placental and amniotic fluid microbiome, suggest fetal acquisition of an airway microbiome. We speculate that the early airway microbiome may prime the developing pulmonary immune system, and dysbiosis in its development may set the stage for subsequent lung disease.
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Affiliation(s)
- Charitharth Vivek Lal
- Division of Neonatology, Department of Pediatrics, University of Alabama at Birmingham, AL, USA.,Translational Research in Normal and Disordered Development Program (TReNDD) University of Alabama at Birmingham, AL, USA.,Program in Protease and Matrix Biology, University of Alabama at Birmingham, AL, USA
| | - Colm Travers
- Division of Neonatology, Department of Pediatrics, University of Alabama at Birmingham, AL, USA
| | - Zubair H Aghai
- Department of Pediatrics, Thomas Jefferson University/Nemours, Philadelphia, PA, USA
| | - Peter Eipers
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, AL, USA
| | - Tamas Jilling
- Division of Neonatology, Department of Pediatrics, University of Alabama at Birmingham, AL, USA.,Translational Research in Normal and Disordered Development Program (TReNDD) University of Alabama at Birmingham, AL, USA
| | - Brian Halloran
- Division of Neonatology, Department of Pediatrics, University of Alabama at Birmingham, AL, USA.,Translational Research in Normal and Disordered Development Program (TReNDD) University of Alabama at Birmingham, AL, USA
| | - Waldemar A Carlo
- Division of Neonatology, Department of Pediatrics, University of Alabama at Birmingham, AL, USA
| | - Jordan Keeley
- Division of Neonatology, Department of Pediatrics, University of Alabama at Birmingham, AL, USA
| | - Gabriel Rezonzew
- Division of Neonatology, Department of Pediatrics, University of Alabama at Birmingham, AL, USA
| | - Ranjit Kumar
- Center for Clinical and Translational Sciences, University of Alabama at Birmingham, AL, USA
| | - Casey Morrow
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, AL, USA
| | - Vineet Bhandari
- Department of Pediatrics, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Namasivayam Ambalavanan
- Division of Neonatology, Department of Pediatrics, University of Alabama at Birmingham, AL, USA.,Translational Research in Normal and Disordered Development Program (TReNDD) University of Alabama at Birmingham, AL, USA.,Center for Clinical and Translational Sciences, University of Alabama at Birmingham, AL, USA
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35
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Wilson R, Aksamit T, Aliberti S, De Soyza A, Elborn JS, Goeminne P, Hill AT, Menendez R, Polverino E. Challenges in managing Pseudomonas aeruginosa in non-cystic fibrosis bronchiectasis. Respir Med 2016; 117:179-89. [DOI: 10.1016/j.rmed.2016.06.007] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 05/24/2016] [Accepted: 06/06/2016] [Indexed: 12/19/2022]
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Prevaes SMPJ, de Winter-de Groot KM, Janssens HM, de Steenhuijsen Piters WAA, Tramper-Stranders GA, Wyllie AL, Hasrat R, Tiddens HA, van Westreenen M, van der Ent CK, Sanders EAM, Bogaert D. Development of the Nasopharyngeal Microbiota in Infants with Cystic Fibrosis. Am J Respir Crit Care Med 2016; 193:504-15. [PMID: 26492486 DOI: 10.1164/rccm.201509-1759oc] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
RATIONALE Cystic fibrosis (CF) is characterized by early structural lung disease caused by pulmonary infections. The nasopharynx of infants is a major ecological reservoir of potential respiratory pathogens. OBJECTIVES To investigate the development of nasopharyngeal microbiota profiles in infants with CF compared with those of healthy control subjects during the first 6 months of life. METHODS We conducted a prospective cohort study, from the time of diagnosis onward, in which we collected questionnaires and 324 nasopharynx samples from 20 infants with CF and 45 age-matched healthy control subjects. Microbiota profiles were characterized by 16S ribosomal RNA-based sequencing. MEASUREMENTS AND MAIN RESULTS We observed significant differences in microbial community composition (P < 0.0002 by permutational multivariate analysis of variance) and development between groups. In infants with CF, early Staphylococcus aureus and, to a lesser extent, Corynebacterium spp. and Moraxella spp. dominance were followed by a switch to Streptococcus mitis predominance after 3 months of age. In control subjects, Moraxella spp. enrichment occurred throughout the first 6 months of life. In a multivariate analysis, S. aureus, S. mitis, Corynebacterium accolens, and bacilli were significantly more abundant in infants with CF, whereas Moraxella spp., Corynebacterium pseudodiphtericum and Corynebacterium propinquum and Haemophilus influenzae were significantly more abundant in control subjects, after correction for age, antibiotic use, and respiratory symptoms. Antibiotic use was independently associated with increased colonization of gram-negative bacteria such as Burkholderia spp. and members of the Enterobacteriaceae bacteria family and reduced colonization of potential beneficial commensals. CONCLUSIONS From diagnosis onward, we observed distinct patterns of nasopharyngeal microbiota development in infants with CF under 6 months of age compared with control subjects and a marked effect of antibiotic therapy leading toward a gram-negative microbial composition.
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Affiliation(s)
- Sabine M P J Prevaes
- 1 Department of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Karin M de Winter-de Groot
- 1 Department of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Hettie M Janssens
- 2 Department of Pediatric Pulmonology and Allergology, Sophia Children's Hospital, Erasmus University Medical Center, Rotterdam, the Netherlands; and
| | | | - Gerdien A Tramper-Stranders
- 1 Department of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Anne L Wyllie
- 1 Department of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Raiza Hasrat
- 1 Department of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Harm A Tiddens
- 2 Department of Pediatric Pulmonology and Allergology, Sophia Children's Hospital, Erasmus University Medical Center, Rotterdam, the Netherlands; and
| | - Mireille van Westreenen
- 3 Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Cornelis K van der Ent
- 1 Department of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Elisabeth A M Sanders
- 1 Department of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Debby Bogaert
- 1 Department of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, the Netherlands
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Bacci G, Paganin P, Lopez L, Vanni C, Dalmastri C, Cantale C, Daddiego L, Perrotta G, Dolce D, Morelli P, Tuccio V, De Alessandri A, Fiscarelli EV, Taccetti G, Lucidi V, Bevivino A, Mengoni A. Pyrosequencing Unveils Cystic Fibrosis Lung Microbiome Differences Associated with a Severe Lung Function Decline. PLoS One 2016; 11:e0156807. [PMID: 27355625 PMCID: PMC4927098 DOI: 10.1371/journal.pone.0156807] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 05/19/2016] [Indexed: 02/07/2023] Open
Abstract
Chronic airway infection is a hallmark feature of cystic fibrosis (CF) disease. In the present study, sputum samples from CF patients were collected and characterized by 16S rRNA gene-targeted approach, to assess how lung microbiota composition changes following a severe decline in lung function. In particular, we compared the airway microbiota of two groups of patients with CF, i.e. patients with a substantial decline in their lung function (SD) and patients with a stable lung function (S). The two groups showed a different bacterial composition, with SD patients reporting a more heterogeneous community than the S ones. Pseudomonas was the dominant genus in both S and SD patients followed by Staphylococcus and Prevotella. Other than the classical CF pathogens and the most commonly identified non-classical genera in CF, we found the presence of the unusual anaerobic genus Sneathia. Moreover, the oligotyping analysis revealed the presence of other minor genera described in CF, highlighting the polymicrobial nature of CF infection. Finally, the analysis of correlation and anti-correlation networks showed the presence of antagonism and ecological independence between members of Pseudomonas genus and the rest of CF airways microbiota, with S patients showing a more interconnected community in S patients than in SD ones. This population structure suggests a higher resilience of S microbiota with respect to SD, which in turn may hinder the potential adverse impact of aggressive pathogens (e.g. Pseudomonas). In conclusion, our findings shed a new light on CF airway microbiota ecology, improving current knowledge about its composition and polymicrobial interactions in patients with CF.
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Affiliation(s)
- Giovanni Bacci
- Department of Biology, University of Florence, Florence, Italy
| | - Patrizia Paganin
- Department for Sustainability of Production and Territorial Systems, Biotechnologies and Agro-Industry Division, ENEA Casaccia Research Center, Rome, Italy
| | - Loredana Lopez
- Department of Energy Technologies, Bioenergy, Biorefinery and Green Chemistry Division, ENEA Trisaia Research Center, Rotondella (MT), Italy
| | - Chiara Vanni
- Department of Biology, University of Florence, Florence, Italy
| | - Claudia Dalmastri
- Department for Sustainability of Production and Territorial Systems, Biotechnologies and Agro-Industry Division, ENEA Casaccia Research Center, Rome, Italy
| | - Cristina Cantale
- Department for Sustainability of Production and Territorial Systems, Biotechnologies and Agro-Industry Division, ENEA Casaccia Research Center, Rome, Italy
| | - Loretta Daddiego
- Department of Energy Technologies, Bioenergy, Biorefinery and Green Chemistry Division, ENEA Trisaia Research Center, Rotondella (MT), Italy
| | - Gaetano Perrotta
- Department of Energy Technologies, Bioenergy, Biorefinery and Green Chemistry Division, ENEA Trisaia Research Center, Rotondella (MT), Italy
| | - Daniela Dolce
- Department of Pediatrics, Cystic Fibrosis Center, Meyer Hospital, Florence, Italy
| | - Patrizia Morelli
- Department of Pediatrics, Cystic Fibrosis Center, G. Gaslini Institute, Genoa, Italy
| | - Vanessa Tuccio
- Cystic Fibrosis Microbiology and Cystic Fibrosis Center, Children's Hospital and Research Institute Bambino Gesù, Rome, Italy
| | | | - Ersilia Vita Fiscarelli
- Cystic Fibrosis Microbiology and Cystic Fibrosis Center, Children's Hospital and Research Institute Bambino Gesù, Rome, Italy
| | - Giovanni Taccetti
- Department of Pediatrics, Cystic Fibrosis Center, Meyer Hospital, Florence, Italy
| | - Vincenzina Lucidi
- Cystic Fibrosis Microbiology and Cystic Fibrosis Center, Children's Hospital and Research Institute Bambino Gesù, Rome, Italy
| | | | - Alessio Mengoni
- Department of Biology, University of Florence, Florence, Italy
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38
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Delhaes L, Thumerelle C, Wizla N, Turcq D, Botterel F. Comparaison du microbiote d’un patient atteint de mucoviscidose et de son environnement domestique par NGS. J Mycol Med 2016. [DOI: 10.1016/j.mycmed.2016.04.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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39
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Wong ML, Inserra A, Lewis MD, Mastronardi CA, Leong L, Choo J, Kentish S, Xie P, Morrison M, Wesselingh SL, Rogers GB, Licinio J. Inflammasome signaling affects anxiety- and depressive-like behavior and gut microbiome composition. Mol Psychiatry 2016; 21:797-805. [PMID: 27090302 PMCID: PMC4879188 DOI: 10.1038/mp.2016.46] [Citation(s) in RCA: 360] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 02/19/2016] [Accepted: 02/22/2016] [Indexed: 12/13/2022]
Abstract
The inflammasome is hypothesized to be a key mediator of the response to physiological and psychological stressors, and its dysregulation may be implicated in major depressive disorder. Inflammasome activation causes the maturation of caspase-1 and activation of interleukin (IL)-1β and IL-18, two proinflammatory cytokines involved in neuroimmunomodulation, neuroinflammation and neurodegeneration. In this study, C57BL/6 mice with genetic deficiency or pharmacological inhibition of caspase-1 were screened for anxiety- and depressive-like behaviors, and locomotion at baseline and after chronic stress. We found that genetic deficiency of caspase-1 decreased depressive- and anxiety-like behaviors, and conversely increased locomotor activity and skills. Caspase-1 deficiency also prevented the exacerbation of depressive-like behaviors following chronic stress. Furthermore, pharmacological caspase-1 antagonism with minocycline ameliorated stress-induced depressive-like behavior in wild-type mice. Interestingly, chronic stress or pharmacological inhibition of caspase-1 per se altered the fecal microbiome in a very similar manner. When stressed mice were treated with minocycline, the observed gut microbiota changes included increase in relative abundance of Akkermansia spp. and Blautia spp., which are compatible with beneficial effects of attenuated inflammation and rebalance of gut microbiota, respectively, and the increment in Lachnospiracea abundance was consistent with microbiota changes of caspase-1 deficiency. Our results suggest that the protective effect of caspase-1 inhibition involves the modulation of the relationship between stress and gut microbiota composition, and establishes the basis for a gut microbiota-inflammasome-brain axis, whereby the gut microbiota via inflammasome signaling modulate pathways that will alter brain function, and affect depressive- and anxiety-like behaviors. Our data also suggest that further elucidation of the gut microbiota-inflammasome-brain axis may offer novel therapeutic targets for psychiatric disorders.
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Affiliation(s)
- M-L Wong
- Mind and Brain Theme, South Australian Health and Medical Research Institute, Adelaide, SA, Australia
- Department of Psychiatry, Flinders Medical Centre, Adelaide, SA, Australia
| | - A Inserra
- Mind and Brain Theme, South Australian Health and Medical Research Institute, Adelaide, SA, Australia
- Department of Psychiatry, Flinders Medical Centre, Adelaide, SA, Australia
| | - M D Lewis
- Mind and Brain Theme, South Australian Health and Medical Research Institute, Adelaide, SA, Australia
- Department of Psychiatry, Flinders Medical Centre, Adelaide, SA, Australia
| | - C A Mastronardi
- Genomics and Predictive Medicine, The John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - L Leong
- Infection and Immunity Theme, South Australian Health and Medical Research Institute, Adelaide, SA, Australia
- Department of Microbiology and Infectious Diseases, Flinders University School of Medicine and Flinders Medical Centre, Adelaide, SA, Australia
| | - J Choo
- Infection and Immunity Theme, South Australian Health and Medical Research Institute, Adelaide, SA, Australia
- Department of Microbiology and Infectious Diseases, Flinders University School of Medicine and Flinders Medical Centre, Adelaide, SA, Australia
| | - S Kentish
- Gastrointestinal Vagal Afferent Research Group, The University of Adelaide, Adelaide, SA, Australia
| | - P Xie
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Neurobiology, and Institute of Neuroscience and the Collaborative Innovation Center for Brain Science, Chongqing Medical University, Chongqing, China
| | - M Morrison
- Translational Research Institute, The University of Queensland Diamantine Institute, Wooloongabba, QLD, Australia
| | - S L Wesselingh
- Infection and Immunity Theme, South Australian Health and Medical Research Institute, Adelaide, SA, Australia
- Department of Microbiology and Infectious Diseases, Flinders University School of Medicine and Flinders Medical Centre, Adelaide, SA, Australia
| | - G B Rogers
- Infection and Immunity Theme, South Australian Health and Medical Research Institute, Adelaide, SA, Australia
- Department of Microbiology and Infectious Diseases, Flinders University School of Medicine and Flinders Medical Centre, Adelaide, SA, Australia
| | - J Licinio
- Mind and Brain Theme, South Australian Health and Medical Research Institute, Adelaide, SA, Australia
- Department of Psychiatry, Flinders Medical Centre, Adelaide, SA, Australia
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40
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Moran Losada P, Chouvarine P, Dorda M, Hedtfeld S, Mielke S, Schulz A, Wiehlmann L, Tümmler B. The cystic fibrosis lower airways microbial metagenome. ERJ Open Res 2016; 2:00096-2015. [PMID: 27730195 PMCID: PMC5005179 DOI: 10.1183/23120541.00096-2015] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 03/04/2016] [Indexed: 11/23/2022] Open
Abstract
Chronic airway infections determine most morbidity in people with cystic fibrosis (CF). Herein, we present unbiased quantitative data about the frequency and abundance of DNA viruses, archaea, bacteria, moulds and fungi in CF lower airways. Induced sputa were collected on several occasions from children, adolescents and adults with CF. Deep sputum metagenome sequencing identified, on average, approximately 10 DNA viruses or fungi and several hundred bacterial taxa. The metagenome of a CF patient was typically found to be made up of an individual signature of multiple, lowly abundant species superimposed by few disease-associated pathogens, such as Pseudomonas aeruginosa and Staphylococcus aureus, as major components. The host-associated signatures ranged from inconspicuous polymicrobial communities in healthy subjects to low-complexity microbiomes dominated by the typical CF pathogens in patients with advanced lung disease. The DNA virus community in CF lungs mainly consisted of phages and occasionally of human pathogens, such as adeno- and herpesviruses. The S. aureus and P. aeruginosa populations were composed of one major and numerous minor clone types. The rare clones constitute a low copy genetic resource that could rapidly expand as a response to habitat alterations, such as antimicrobial chemotherapy or invasion of novel microbes. The CF lung metagenome is composed of few viruses and fungi and hundreds of bacterial species, clones and subcloneshttp://ow.ly/ZiqUE
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Affiliation(s)
- Patricia Moran Losada
- Clinic for Paediatric Pneumology, Allergology and Neonatology, OE 6710, Hannover Medical School, Hannover, Germany
| | - Philippe Chouvarine
- Clinic for Paediatric Pneumology, Allergology and Neonatology, OE 6710, Hannover Medical School, Hannover, Germany
| | - Marie Dorda
- Clinic for Paediatric Pneumology, Allergology and Neonatology, OE 6710, Hannover Medical School, Hannover, Germany
| | - Silke Hedtfeld
- Clinic for Paediatric Pneumology, Allergology and Neonatology, OE 6710, Hannover Medical School, Hannover, Germany
| | - Samira Mielke
- Clinic for Paediatric Pneumology, Allergology and Neonatology, OE 6710, Hannover Medical School, Hannover, Germany
| | - Angela Schulz
- Clinic for Paediatric Pneumology, Allergology and Neonatology, OE 6710, Hannover Medical School, Hannover, Germany; Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Member of the German Center for Lung Research, Hannover, Germany
| | - Lutz Wiehlmann
- Clinic for Paediatric Pneumology, Allergology and Neonatology, OE 6710, Hannover Medical School, Hannover, Germany; Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Member of the German Center for Lung Research, Hannover, Germany
| | - Burkhard Tümmler
- Clinic for Paediatric Pneumology, Allergology and Neonatology, OE 6710, Hannover Medical School, Hannover, Germany; Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Member of the German Center for Lung Research, Hannover, Germany
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41
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Edmondson C, Davies JC. Current and future treatment options for cystic fibrosis lung disease: latest evidence and clinical implications. Ther Adv Chronic Dis 2016; 7:170-83. [PMID: 27347364 PMCID: PMC4907071 DOI: 10.1177/2040622316641352] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Treatment for cystic fibrosis (CF) has conventionally targeted downstream consequences of the defect such as mucus plugging and infection. More recently, significant advances have been made in treating the root cause of the disease, namely a defective CF transmembrane conductance regulator (CFTR) gene. This review summarizes current pulmonary treatment options and highlights advances in research and development of new therapies.
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Affiliation(s)
- Claire Edmondson
- Royal Brompton & Harefield NHS Foundation Trust, Paediatric Respiratory Medicine, London, UK
| | - Jane C. Davies
- Imperial College London, Paediatric Respirology and Experimental Medicine, London SW7 2AZ, UK
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42
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Translational aspects of the microbiome-to be exploited. Cell Biol Toxicol 2016; 32:153-6. [PMID: 27098154 DOI: 10.1007/s10565-016-9320-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Accepted: 03/21/2016] [Indexed: 12/19/2022]
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43
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Woloszynek S, Pastor S, Mell JC, Nandi N, Sokhansanj B, Rosen GL. Engineering Human Microbiota: Influencing Cellular and Community Dynamics for Therapeutic Applications. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2016; 324:67-124. [PMID: 27017007 DOI: 10.1016/bs.ircmb.2016.01.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The complex relationship between microbiota, human physiology, and environmental perturbations has become a major research focus, particularly with the arrival of culture-free and high-throughput approaches for studying the microbiome. Early enthusiasm has come from results that are largely correlative, but the correlative phase of microbiome research has assisted in defining the key questions of how these microbiota interact with their host. An emerging repertoire for engineering the microbiome places current research on a more experimentally grounded footing. We present a detailed look at the interplay between microbiota and host and how these interactions can be exploited. A particular emphasis is placed on unstable microbial communities, or dysbiosis, and strategies to reestablish stability in these microbial ecosystems. These include manipulation of intermicrobial communication, development of designer probiotics, fecal microbiota transplantation, and synthetic biology.
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Affiliation(s)
- S Woloszynek
- Department of Electrical and Computer Engineering, Drexel University, Philadelphia, PA, United States of America
| | - S Pastor
- Department of Biomedical Engineering, Drexel University, Philadelphia, PA, United States of America
| | - J C Mell
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States of America
| | - N Nandi
- Division of Gastroenterology, Drexel University College of Medicine, Philadelphia, PA, United States of America
| | - B Sokhansanj
- McKool Smith Hennigan, P. C., Redwood Shores, CA, United States of America
| | - G L Rosen
- Department of Electrical and Computer Engineering, Drexel University, Philadelphia, PA, United States of America.
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44
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Lopez-Campos JL, Calero-Acuña C, Lopez-Ramirez C, Abad-Arranz M, Márquez-Martín E, Ortega-Ruiz F, Arellano E. Implications of the inflammatory response for the identification of biomarkers of chronic obstructive pulmonary disease. Biomark Med 2016; 10:109-22. [PMID: 26808692 DOI: 10.2217/bmm.15.87] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is characterized by both local and systemic inflammation. Because inflammation plays a critical role in the development, course and severity of COPD, inflammatory markers have the potential to improve the current diagnostic and prognostic approaches. Local inflammation in COPD is characterized by an infiltration of inflammatory cells, with an increased expression of cytokines, chemokines, enzymes, growth factors and adhesion molecules. Systemic low-grade inflammation is another common but nonspecific finding in COPD. Exacerbations of COPD are acute clinical events accompanied by an exaggerated inflammatory response. Future investigations in the field of COPD biomarkers should take into account different study designs and biochemical assays, disease course and duration, variations in symptom severity and timing of measurement.
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Affiliation(s)
- Jose Luis Lopez-Campos
- Unidad Médico-Quirúrgica de Enfermedades Respiratorias, Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/Universidad de Sevilla, Seville, Spain.,CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Carmen Calero-Acuña
- Unidad Médico-Quirúrgica de Enfermedades Respiratorias, Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/Universidad de Sevilla, Seville, Spain.,CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Cecilia Lopez-Ramirez
- Unidad Médico-Quirúrgica de Enfermedades Respiratorias, Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/Universidad de Sevilla, Seville, Spain
| | - María Abad-Arranz
- Unidad Médico-Quirúrgica de Enfermedades Respiratorias, Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/Universidad de Sevilla, Seville, Spain
| | - Eduardo Márquez-Martín
- Unidad Médico-Quirúrgica de Enfermedades Respiratorias, Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/Universidad de Sevilla, Seville, Spain
| | - Francisco Ortega-Ruiz
- Unidad Médico-Quirúrgica de Enfermedades Respiratorias, Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/Universidad de Sevilla, Seville, Spain.,CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Elena Arellano
- Unidad Médico-Quirúrgica de Enfermedades Respiratorias, Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/Universidad de Sevilla, Seville, Spain
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45
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Chang AB, Oppenheimer JJ, Weinberger M, Rubin BK, Irwin RS. Children With Chronic Wet or Productive Cough--Treatment and Investigations: A Systematic Review. Chest 2016; 149:120-42. [PMID: 26757284 DOI: 10.1378/chest.15-2065] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 10/14/2015] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Systematic reviews were conducted to examine two related key questions (KQs) in children with chronic (> 4 weeks' duration) wet or productive cough not related to bronchiectasis: KQ1-How effective are antibiotics in improving the resolution of cough? If so, what antibiotic should be used and for how long? KQ2-When should they be referred for further investigations? METHODS The systematic reviews were undertaken based on the protocol established by selected members of the CHEST expert cough panel. Two authors screened searches and selected and extracted data. The study included systematic reviews, randomized controlled trials (RCTs), cohort (prospective and retrospective) studies, and cross-sectional studies published in English. RESULTS Data were presented in Preferred Reporting Items for Systematic Reviews and Meta-Analyses flowcharts, and the summaries were tabulated. Fifteen studies were included in KQ1 (three systematic reviews, three RCTs, five prospective studies, and four retrospective studies) and 17 in KQ2 (one RCT, 11 prospective studies, and five retrospective studies). Combining data from the RCTs (KQ1), the number needed to treat for benefit was 3 (95% CI, 2.0-4.3) in achieving cough resolution. In general, findings from prospective and retrospective studies were consistent, but there were minor variations. CONCLUSIONS There is high-quality evidence that in children aged ≤ 14 years with chronic (> 4 weeks' duration) wet or productive cough, the use of appropriate antibiotics improves cough resolution. There is also high-quality evidence that when specific cough pointers (eg, digital clubbing) are present in children with wet cough, further investigations (eg, flexible bronchoscopy, chest CT scans, immunity tests) should be conducted. When the wet cough does not improve by 4 weeks of antibiotic treatment, there is moderate-quality evidence that children should be referred to a major center for further investigations to determine whether an underlying lung or other disease is present.
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Affiliation(s)
- Anne B Chang
- Child Health Division, Menzies School of Health Research, Darwin, Australia; Department of Respiratory and Sleep Medicine, Lady Cilento Children's Hospital, Queensland Uni of Technology, Children's Health Queensland, Queensland, Australia.
| | - John J Oppenheimer
- New Jersey Medical School, Pulmonary and Allergy Associates, Morristown, NJ
| | - Miles Weinberger
- Pediatric Allergy, Immunology, and Pulmonology Division, University of Iowa Children's Hospital, Iowa City, IA
| | - Bruce K Rubin
- Children's Hospital of Richmond at Virginia Commonwealth University, Richmond, VA
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46
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Abstract
The respiratory tract, once believed to be sterile, harbors diverse bacterial communities. The role of microorganisms within health and disease is slowly being unraveled. Evidence points to the neonatal period as a critical time for establishing stable bacterial communities and influencing immune responses important for long-term respiratory health. This review summarizes the evidence of early airway and lung bacterial colonization and the role the microbiome has on respiratory health in the short and long term. The challenges of neonatal respiratory microbiome studies and future research directions are also discussed.
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Affiliation(s)
- David J Gallacher
- Department of Child Health, School of Medicine, Cardiff University , Cardiff , UK
| | - Sailesh Kotecha
- Department of Child Health, School of Medicine, Cardiff University , Cardiff , UK
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47
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ElMaraachli W, Conrad DJ, Wang ACC. Using Cystic Fibrosis Therapies for Non-Cystic Fibrosis Bronchiectasis. Clin Chest Med 2015; 37:139-46. [PMID: 26857775 DOI: 10.1016/j.ccm.2015.11.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Non-cystic fibrosis bronchiectasis (NCFB) is an increasingly prevalent disease that places a significant burden on patients and health systems globally. Although many of the therapies used to treat NCFB were originally developed as cystic fibrosis (CF) therapies, not all of them have been demonstrated to be efficacious in NCFB and some may even be harmful. This article explores the evidence for which therapeutic strategies used to treat CF have been translated into the care of NCFB. The conclusion is that therapies for adult NCFB cannot be simply extrapolated from CF clinical trials, and in some instances, doing so may actually result in harm.
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Affiliation(s)
- Wael ElMaraachli
- Division of Pulmonary, Critical Care and Sleep Medicine, University of California, San Diego, 200 West Arbor Drive, MC 8372, San Diego, CA 92013, USA
| | - Douglas J Conrad
- Division of Pulmonary, Critical Care and Sleep Medicine, University of California, San Diego, 200 West Arbor Drive, MC 8372, San Diego, CA 92013, USA.
| | - Angela C C Wang
- Division of Chest and Critical Care Medicine, Scripps Clinic, 10666 North Torrey Pines Road, W203, San Diego, CA 92037, USA
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48
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Rogers GB, Wesselingh S. Precision respiratory medicine and the microbiome. THE LANCET RESPIRATORY MEDICINE 2015; 4:73-82. [PMID: 26700443 DOI: 10.1016/s2213-2600(15)00476-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Revised: 11/04/2015] [Accepted: 11/04/2015] [Indexed: 02/06/2023]
Abstract
A decade of rapid technological advances has provided an exciting opportunity to incorporate information relating to a range of potentially important disease determinants in the clinical decision-making process. Access to highly detailed data will enable respiratory medicine to evolve from one-size-fits-all models of care, which are associated with variable clinical effectiveness and high rates of side-effects, to precision approaches, where treatment is tailored to individual patients. The human microbiome has increasingly been recognised as playing an important part in determining disease course and response to treatment. Its inclusion in precision models of respiratory medicine, therefore, is essential. Analysis of the microbiome provides an opportunity to develop novel prognostic markers for airways disease, improve definition of clinical phenotypes, develop additional guidance to aid treatment selection, and increase the accuracy of indicators of treatment effect. In this Review we propose that collaboration between researchers and clinicians is needed if respiratory medicine is to replicate the successes of precision medicine seen in other clinical specialties.
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Affiliation(s)
- Geraint B Rogers
- South Australian Health and Medical Research Institute, Adelaide, SA, Australia; SAHMRI Microbiome Research Laboratory Flinders University School of Medicine, Adelaide, SA, Australia.
| | - Steve Wesselingh
- South Australian Health and Medical Research Institute, Adelaide, SA, Australia; SAHMRI Microbiome Research Laboratory Flinders University School of Medicine, Adelaide, SA, Australia
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49
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Abstract
The pathogenesis of bronchopulmonary dysplasia (BPD) is multifactorial, and the clinical phenotype of BPD is extremely variable. Several clinical and laboratory biomarkers have been proposed for the early identification of infants at higher risk of BPD and for determination of prognosis of infants with a diagnosis of BPD. The authors review available literature on prediction tools and biomarkers of BPD, using clinical variables and biomarkers based on imaging, lung function measures, and measurements of various analytes in different body fluids that have been determined to be associated with BPD either in a targeted manner or by unbiased omic profiling.
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Affiliation(s)
- Charitharth Vivek Lal
- Division of Neonatology, Department of Pediatrics, Women and Infants Center, University of Alabama at Birmingham, 176F Suite 9380, 619 South 19th Street, Birmingham, AL 35249-7335, USA
| | - Namasivayam Ambalavanan
- Division of Neonatology, Department of Pediatrics, Women and Infants Center, University of Alabama at Birmingham, 176F Suite 9380, 619 South 19th Street, Birmingham, AL 35249-7335, USA.
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50
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Thornton CS, Grinwis ME, Sibley CD, Parkins MD, Rabin HR, Surette MG. Antibiotic susceptibility and molecular mechanisms of macrolide resistance in streptococci isolated from adult cystic fibrosis patients. J Med Microbiol 2015; 64:1375-1386. [PMID: 26408040 DOI: 10.1099/jmm.0.000172] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The cystic fibrosis (CF) airways are colonized by polymicrobial communities with high bacterial load and are influenced by frequent antibiotic exposures. This community includes diverse streptococci, some of which have been directly or indirectly associated with pulmonary exacerbations. As many streptococci are naturally competent, horizontal transfer of antibiotic-resistant determinants coupled with frequent and/or chronic antibiotic exposure may contribute to high resistance rates. In this study, we assessed antibiotic resistance in 413 streptococcal isolates from adult CF patients against nine antibiotics relevant in CF treatment. We observed very low rates of cephalosporin resistance [cefepime and ceftriaxone ( < 2%)], and higher rates of resistance to tetracycline (∼34%) and sulfamethoxazole/trimethoprim (∼45%). The highest rate of antibiotic resistance was to the macrolides [azithromycin (56.4%) and erythromycin (51.6%)]. We also investigated the molecular mechanisms of macrolide resistance and found that only half of our macrolide-resistant streptococci isolates contained the mef (efflux pump) or erm (methylation of 23S ribosomal target site) genes. The majority of isolates were, however, found to have point mutations at position 2058 or 2059 of the 23S ribosomal subunit - a molecular mechanism of resistance not commonly reported in the non-pyogenic and non-pneumococcal streptococci, and unique in comparison with previous studies. The high rates of resistance observed here may result in poor outcomes where specific streptococci are contributing to CF airway disease and serve as a reservoir of resistance genes within the CF airway microbiome.
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Affiliation(s)
- Christina S Thornton
- Department of Microbiology and Infectious Diseases, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Margot E Grinwis
- Department of Microbiology and Infectious Diseases, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Christopher D Sibley
- Department of Microbiology and Infectious Diseases, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Michael D Parkins
- Department of Microbiology and Infectious Diseases, University of Calgary, Calgary, Alberta T2N 4N1, Canada.,Department of Medicine, University of Calgary, Calgary, Alberta T2N 4N1, Canada.,Adult Cystic Fibrosis Clinic, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Harvey R Rabin
- Department of Microbiology and Infectious Diseases, University of Calgary, Calgary, Alberta T2N 4N1, Canada.,Department of Medicine, University of Calgary, Calgary, Alberta T2N 4N1, Canada.,Adult Cystic Fibrosis Clinic, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Michael G Surette
- Farncombe Family Digestive Health Research Institute, Department of Medicine, McMaster University, Hamilton, Ontario L8S 4L8, Canada.,Department of Microbiology and Infectious Diseases, University of Calgary, Calgary, Alberta T2N 4N1, Canada
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