scholarly journals Alteration of the respiratory microbiome in COVID-19 patients with different severities

2021 ◽  
Author(s):  
Zhengtu Li ◽  
Yinhu Li ◽  
Linghua Li ◽  
Xiaoneng Mo ◽  
Shaoqiang Li ◽  
...  
Keyword(s):  
Respiratory Microbiome

scholarly journals The Role of the Respiratory Microbiome and Viral Presence in Lower Respiratory Tract Infection Severity in the First Five Years of Life

2021 ◽  
Vol 9 (7) ◽  
pp. 1446
Author(s):  
Ivo Hoefnagels ◽  
Josephine van de Maat ◽  
Jeroen J.A. van Kampen ◽  
Annemarie van Rossum ◽  
Charlie Obihara ◽  
...  
Keyword(s):  
Respiratory Tract ◽  
Disease Severity ◽  
Lower Respiratory Tract ◽  
Influenza A ◽  
Pediatric Population ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Detection Rates ◽  
Tract Infections ◽  
Respiratory Microbiome

Lower respiratory tract infections (LRTIs) in children are common and, although often mild, a major cause of mortality and hospitalization. Recently, the respiratory microbiome has been associated with both susceptibility and severity of LRTI. In this current study, we combined respiratory microbiome, viral, and clinical data to find associations with the severity of LRTI. Nasopharyngeal aspirates of children aged one month to five years included in the STRAP study (Study to Reduce Antibiotic prescription in childhood Pneumonia), who presented at the emergency department (ED) with fever and cough or dyspnea, were sequenced with nanopore 16S-rRNA gene sequencing and subsequently analyzed with hierarchical clustering to identify respiratory microbiome profiles. Samples were also tested using a panel of 15 respiratory viruses and Mycoplasma pneumoniae, which were analyzed in two groups, according to their reported virulence. The primary outcome was hospitalization, as measure of disease severity. Nasopharyngeal samples were isolated from a total of 167 children. After quality filtering, microbiome results were available for 54 children and virology panels for 158 children. Six distinct genus-dominant microbiome profiles were identified, with Haemophilus-, Moraxella-, and Streptococcus-dominant profiles being the most prevalent. However, these profiles were not found to be significantly associated with hospitalization. At least one virus was detected in 139 (88%) children, of whom 32.4% had co-infections with multiple viruses. Viral co-infections were common for adenovirus, bocavirus, and enterovirus, and uncommon for human metapneumovirus (hMPV) and influenza A virus. The detection of enteroviruses was negatively associated with hospitalization. Virulence groups were not significantly associated with hospitalization. Our data underlines high detection rates and co-infection of viruses in children with respiratory symptoms and confirms the predominant presence of Haemophilus-, Streptococcus-, and Moraxella-dominant profiles in a symptomatic pediatric population at the ED. However, we could not assess significant associations between microbiome profiles and disease severity measures.

T4 The respiratory microbiome and metabolome in idiopathic pulmonary fibrosis

2021 ◽  
Author(s):  
R Invernizzi ◽  
N Giallourou ◽  
JR Swann ◽  
RJ Hewitt ◽  
P Ghai ◽  
...  
Keyword(s):  
Idiopathic Pulmonary Fibrosis ◽  
Pulmonary Fibrosis ◽  
Respiratory Microbiome

scholarly journals Self-sensitisation of Staphylococcus aureus to the antimicrobial factors found in human blood.

2021 ◽  
Author(s):  
Edward Douglas ◽  
Tarcisio Brignoli ◽  
Mario Recker ◽  
Eoin O'Brien ◽  
Rachel McLoughlin ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Genetic Basis ◽  
Functional Verification ◽  
Invasive Infection ◽  
Opportunistic Pathogens ◽  
Dead End ◽  
Wall Teichoic Acids ◽  
Respiratory Microbiome ◽  
Gwas Approach

For opportunistic pathogens, the switch from a commensal to an invasive lifestyle is often considered an accidental event. But with plentiful opportunity, what leads one accidental event to result in an invasive infection, and another not to? And how much of this apparent stochasticity is driven by bacterial factors? To answer these questions, here we focussed on the major human pathogen Staphylococcus aureus, which can both reside asymptomatically as a member of our respiratory microbiome, or become invasive and cause infections as severe as bacteraemia. Survival upon exposure to the antibacterial factors found in serum is a critical aspect of their ability to cause bacteraemia, and across a collection of 300 clinical isolates we found there to be significant variability in this capability. Utilising a GWAS approach we have uncovered the genetic basis of much of this variability through the identification and functional verification of a number of new polymorphic loci that affect serum survival: tcaA, tarK, gntR, ilvC, arsB, yfhO, and pdhD. The expression of one of these genes, tcaA, was found to be induced upon exposure to serum, while simultaneously enhancing the sensitivity of S. aureus to serum through a process involving the ligation of wall teichoic acids into the cell wall. As blood-stage infections are a transmission dead-end for the bacteria, that S. aureus actively responds to serum to produce a protein which specifically limits their ability to survive in this environment demonstrates that the switch from the commensal to the invasive lifestyle is complex, and that TcaA may contribute to the long-term success of S. aureus by restricting the bacteria to their more readily transmissible commensal state.

scholarly journals The Effects of Corticosteroids on the Respiratory Microbiome: A Systematic Review

2021 ◽  
Vol 8 ◽  
Author(s):  
Julia E. Hartmann ◽  
Werner C. Albrich ◽  
Marija Dmitrijeva ◽  
Christian R. Kahlert
Keyword(s):  
Systematic Review ◽  
Research Question ◽  
Corticosteroid Treatment ◽  
Pulmonary Diseases ◽  
Chronic Obstructive ◽  
Cochrane Central Register ◽  
Obstructive Pulmonary Disease ◽  
Randomized Controlled Studies ◽  
Culture Independent ◽  
Respiratory Microbiome

Background: Since its discovery, the respiratory microbiome has been implicated in the pathogenesis of multiple pulmonary diseases. Even though corticosteroid treatments are widely prescribed for pulmonary diseases, their effects on the respiratory microbiome are still poorly understood. This systematic review summarizes the current understanding of the effects of corticosteroids on the microbiome of the airways.Research Question: How does treatment with corticosteroids impact the respiratory microbiome?Study Design and Methods: According to the PRISMA guidelines, Embase, Medline, and the Cochrane Central Register of Controlled Trials (CENTRAL) databases were systematically searched for all observational or randomized-controlled studies comparing the microbiome parameters of patients receiving corticosteroids to those of controls. The primary outcomes of interest were changes in the diversity, composition and total burden of the respiratory microbiome as assessed by culture-independent molecular methods.Results: Out of 1,943 identified reports, five studies could be included: two on patients with asthma, two on patients with chronic obstructive pulmonary disease and one on patients with chronic rhinosinusitis. The studies were highly heterogeneous with regards to the methods used and the populations investigated. Microbiome diversity increased with corticosteroids at least transiently in three studies and decreased in one study. The effects of corticosteroids on the composition of the respiratory microbiome were significant but without a clear shared direction. A significant increase in microbial burden after corticosteroids was seen in one study.Interpretation: Data on the effect of corticosteroids on the respiratory microbiome are still limited, with considerable heterogeneity between studies. However, available data suggest that corticosteroid treatment may have significant effects on the composition and possibly the diversity of the respiratory microbiome. Further research is needed to better understand the influence of corticosteroids on the respiratory microbiome and thus better target its widespread therapeutic use.

scholarly journals Individual Patterns of Complexity in Cystic Fibrosis Lung Microbiota, Including Predator Bacteria, over a 1-Year Period

mBio ◽  
2017 ◽  
Vol 8 (5) ◽  
Author(s):  
Juan de Dios Caballero ◽  
Rafael Vida ◽  
Marta Cobo ◽  
Luis Máiz ◽  
Lucrecia Suárez ◽  
...  
Keyword(s):  
Computational Model ◽  
Clinical Status ◽  
Sampling Bias ◽  
Microbiota Composition ◽  
Lung Microbiome ◽  
Sequential Samples ◽  
Colonization Patterns ◽  
First Time ◽  
Respiratory Microbiome

ABSTRACT Cystic fibrosis (CF) lung microbiota composition has recently been redefined by the application of next-generation sequencing (NGS) tools, identifying, among others, previously undescribed anaerobic and uncultivable bacteria. In the present study, we monitored the fluctuations of this ecosystem in 15 CF patients during a 1-year follow-up period, describing for the first time, as far as we know, the presence of predator bacteria in the CF lung microbiome. In addition, a new computational model was developed to ascertain the hypothetical ecological repercussions of a prey-predator interaction in CF lung microbial communities. Fifteen adult CF patients, stratified according to their pulmonary function into mild (n = 5), moderate (n = 9), and severe (n = 1) disease, were recruited at the CF unit of the Ramón y Cajal University Hospital (Madrid, Spain). Each patient contributed three or four induced sputum samples during a 1-year follow-up period. Lung microbiota composition was determined by both cultivation and NGS techniques and was compared with the patients’ clinical variables. Results revealed a particular microbiota composition for each patient that was maintained during the study period, although some fluctuations were detected without any clinical correlation. For the first time, Bdellovibrio and Vampirovibrio predator bacteria were shown in CF lung microbiota and reduced-genome bacterial parasites of the phylum Parcubacteria were also consistently detected. The newly designed computational model allows us to hypothesize that inoculation of predators into the pulmonary microbiome might contribute to the control of chronic colonization by CF pathogens in early colonization stages. IMPORTANCE The application of NGS to sequential samples of CF patients demonstrated the complexity of the organisms present in the lung (156 species) and the constancy of basic individual colonization patterns, although some differences between samples from the same patient were observed, probably related to sampling bias. Bdellovibrio and Vampirovibrio predator bacteria were found for the first time by NGS as part of the CF lung microbiota, although their ecological significance needs to be clarified. The newly designed computational model allows us to hypothesize that inoculation of predators into the lung microbiome can eradicate CF pathogens in early stages of the process. Our data strongly suggest that lower respiratory microbiome fluctuations are not necessarily related to the patient’s clinical status. IMPORTANCE The application of NGS to sequential samples of CF patients demonstrated the complexity of the organisms present in the lung (156 species) and the constancy of basic individual colonization patterns, although some differences between samples from the same patient were observed, probably related to sampling bias. Bdellovibrio and Vampirovibrio predator bacteria were found for the first time by NGS as part of the CF lung microbiota, although their ecological significance needs to be clarified. The newly designed computational model allows us to hypothesize that inoculation of predators into the lung microbiome can eradicate CF pathogens in early stages of the process. Our data strongly suggest that lower respiratory microbiome fluctuations are not necessarily related to the patient’s clinical status.

scholarly journals Respiratory microbiome and epithelial interactions shape immunity in the lungs

Immunology ◽  
2020 ◽  
Vol 160 (2) ◽  
pp. 171-182 ◽  
Author(s):  
Rachele Invernizzi ◽  
Clare M. Lloyd ◽  
Philip L. Molyneaux
Keyword(s):  
Respiratory Microbiome

scholarly journals The Respiratory Microbiome in Cystic Fibrosis: Compartment Patterns and Clinical Relationships in Early Stage Disease

2020 ◽  
Vol 11 ◽  
Author(s):  
Marian Garcia-Nuñez ◽  
Miguel Garcia-Gonzalez ◽  
Xavier Pomares ◽  
Concepción Montón ◽  
Laura Millares ◽  
...  
Keyword(s):  
Cystic Fibrosis ◽  
Early Stage ◽  
Early Stage Disease ◽  
Stage Disease ◽  
Respiratory Microbiome

scholarly journals Endotype-driven prediction of acute exacerbations in chronic obstructive pulmonary disease (EndAECOPD): protocol for a prospective cohort study

BMJ Open ◽  
2019 ◽  
Vol 9 (11) ◽  
pp. e034592 ◽  
Author(s):  
Wei Xiao ◽  
Long-yi Du ◽  
Bing Mao ◽  
Ti-wei Miao ◽  
Juan-juan Fu
Keyword(s):  
Chronic Obstructive Pulmonary Disease ◽  
Cohort Study ◽  
Pulmonary Disease ◽  
Prospective Cohort ◽  
Chronic Obstructive ◽  
Obstructive Pulmonary Disease ◽  
Acute Exacerbations ◽  
Symptom Scores ◽  
Clinical Measurements ◽  
Respiratory Microbiome

IntroductionCurrent strategies for the prevention of acute exacerbations in chronic obstructive pulmonary disease (COPD) are primarily based on clinical measurements but fail to target the pathophysiological mechanisms, namely endotypes, of the disease. Studies identifying endotypes underlying exacerbation susceptibility and discovering specific biomarkers may lead to the development of targeted therapeutics but are lacking. This study aims to assess a broad spectrum of biomarkers at multiple biological levels (genetics, airway inflammation and respiratory microbiome) for their ability in predicting acute exacerbations of COPD, thus enables high-resolution disease endotyping and may lead to precision treatment of the disease.Methods and analysisIn this prospective cohort study, participants with stable COPD (n=600) will be recruited and assessed for demographics, symptom scores, spirometry, medication use and comorbidities at baseline. Blood will be obtained for genotyping variants in a panel of nine genes. Induced sputum will be collected for the profile of microbiota using 16S rRNA gene sequencing, quantification of bacterial load, inflammatory mediators assay and sputum cytometry. Participants will be followed up for their exacerbations till 12 months and reassessed for the clinical measurements as baseline. The primary outcomes are total number of exacerbations, severe exacerbations, moderate exacerbations and time to first exacerbation. The secondary outcomes are changes in lung function and symptom scores. The effect of biomarkers representing genetic variants, airway inflammation and respiratory microbiome on predicting the frequent exacerbator phenotype and exacerbation frequency will be analysed with multivariable modelling, and time to first exacerbation with a Cox regression model.Ethics and disseminationThe study has been approved by the Clinical Trial and Biomedical Ethics Committee of West China Hospital of Sichuan University (No. 2018–298). The results of the study will be published on peer-reviewed journals.Trial registration numberChiCTR1800019063.

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