About: The respiratory virome and exacerbations in patients with chronic obstructive pulmonary disease

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An Entity of Type : schema:ScholarlyArticle, within Data Space : wasabi.inria.fr associated with source document(s)

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type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	The respiratory virome and exacerbations in patients with chronic obstructive pulmonary disease
Creator	Mei, Hailiang Pappas, Nikos Sidorov, Igor Claas, Eric Aanerud, Marianne Feltkamp, Mariet Carbo, Ellen De Vries, Jutte Kroes, Aloys Eagan, Tomas Hiemstra, Pieter Van Boheemen Id, Sander Van Rijn Id, Anneloes
Source	Medline; PMC
abstract	INTRODUCTION: Exacerbations are major contributors to morbidity and mortality in patients with chronic obstructive pulmonary disease (COPD), and respiratory bacterial and viral infections are an important trigger. However, using conventional diagnostic techniques, a causative agent is not always found. Metagenomic next-generation sequencing (mNGS) allows analysis of the complete virome, but has not yet been applied in COPD exacerbations. OBJECTIVES: To study the respiratory virome in nasopharyngeal samples during COPD exacerbations using mNGS. STUDY DESIGN: 88 nasopharyngeal swabs from 63 patients from the Bergen COPD Exacerbation Study (2006–2010) were analysed by mNGS and in-house qPCR for respiratory viruses. Both DNA and RNA were sequenced simultaneously using an Illumina library preparation protocol with in-house adaptations. RESULTS: By mNGS, 24/88 samples tested positive. Sensitivity and specificity, as compared with PCR, were 96% and 98% for diagnostic targets (23/24 and 1093/1120, respectively). Additional viral pathogens detected by mNGS were herpes simplex virus type 1 and coronavirus OC43. A positive correlation was found between Cq value and mNGS viral normalized species reads (log value) (p = 0.002). Patients with viral pathogens had lower percentages of bacteriophages (p<0.001). No correlation was found between viral reads and clinical markers. CONCLUSIONS: The mNGS protocol used was highly sensitive and specific for semi-quantitative detection of respiratory viruses. Excellent negative predictive value implicates the power of mNGS to exclude any pathogenic respiratory viral infectious cause in one test, with consequences for clinical decision making. Reduced abundance of bacteriophages in COPD patients with viral pathogens implicates skewing of the virome during infection, with potential consequences for the bacterial populations, during infection.
has issue date	2019-10-24(xsd:dateTime)
bibo:doi	10.1371/journal.pone.0223952
bibo:pmid	31647831
has license	cc-by
sha1sum (hex)	085d2f0a23b102cb7492350434746878eb834785
schema:url	https://doi.org/10.1371/journal.pone.0223952
resource representing a document's title	The respiratory virome and exacerbations in patients with chronic obstructive pulmonary disease
has PubMed Central identifier	PMC6812800
has PubMed identifier	31647831
schema:publication	PLoS One
resource representing a document's body	covid:085d2f0a23b102cb7492350434746878eb834785#body_text
is schema:about of	named entity 'CHRONIC OBSTRUCTIVE PULMONARY DISEASE' named entity 'TRIGGER' named entity 'CAUSATIVE AGENT' named entity 'CONVENTIONAL' named entity 'DIAGNOSTIC TECHNIQUES' named entity 'CHRONIC OBSTRUCTIVE PULMONARY DISEASE' named entity 'NEXT-GENERATION SEQUENCING' named entity 'COPD' named entity 'MORBIDITY AND MORTALITY' named entity 'VIRAL INFECTIONS' named entity 'RESPIRATORY' named entity 'BUT' named entity 'APPLIED' named entity 'BACTERIAL' named entity 'USING' named entity 'PATIENTS' named entity 'RESPIRATORY' named entity 'MAJOR' named entity 'ANALYSIS' named entity 'PATIENTS' named entity 'FOUND' named entity 'ALLOWS' named entity 'COMPLETE' named entity 'IMPORTANT' covid:arg/085d2f0a23b102cb7492350434746878eb834785 named entity 'next-generation sequencing' named entity 'virome' named entity 'next-generation sequencing' named entity 'causative agent' named entity 'Centrifuge' named entity 'PCR' named entity 'informed consent' named entity 'COPD' named entity 'infection' named entity 'microbial' named entity 'nucleotide sequences' named entity 'nasopharyngeal' named entity 'sensitivity and specificity' named entity 'Nasopharyngeal' named entity 'bacterial overgrowth' named entity 'one-way ANOVA' named entity 'quality assessment' named entity 'PCR' named entity 'PCR' named entity 'gene' named entity 'real-time PCR' named entity 'assay' named entity 'rhinovirus' named entity 'parainfluenza' named entity 'virus' named entity 'viruses' named entity 'bacterial phyla' named entity 'spirometry' named entity 'library preparation' named entity 'FEV' named entity 'bronchoscopy' named entity 'Sensitivity, specificity' named entity 'dysbiosis' named entity 'Centrifuge' named entity 'ROC curve' named entity 'qPCR' named entity 'eukaryotic' named entity 'PCR' named entity 'qPCR' named entity 'PCR' named entity 'coronavirus' named entity 'human bocavirus' named entity 'CDHR3' named entity 'qPCR'

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