About: Pulmonary Metagenomic Sequencing Suggests Missed Infections in Immunocompromised Children

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

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Pulmonary Metagenomic Sequencing Suggests Missed Infections in Immunocompromised Children
Source	BioRxiv; MedRxiv
abstract	Despite improved diagnostics, pulmonary pathogens in immunocompromised children frequently evade detection, leading to significant morbidity and mortality. To develop a highly sensitive metagenomic next generation sequencing (mNGS) assay capable of evaluating the pulmonary microbiome and identifying diverse pathogens in the lungs of immunocompromised children. We collected 41 lower respiratory specimens from 34 immunocompromised children undergoing evaluation for pulmonary disease at 3 children’s hospitals from 2014-2016. Samples underwent mechanical homogenization, paired RNA/DNA extraction, and metagenomic sequencing. Sequencing reads were aligned to the NCBI nucleotide reference database to determine taxonomic identities. Statistical outliers were determined based on abundance within each sample and relative to other samples in the cohort. We identified a rich cross-domain pulmonary microbiome containing bacteria, fungi, RNA viruses, and DNA viruses in each patient. Potentially pathogenic bacteria were ubiquitous among samples but could be distinguished as possible causes of disease by parsing for outlier organisms. Samples with bacterial outliers had significantly depressed alpha-diversity (median 0.58, IQR 0.33-0.62 vs. median 0.94, IQR 0.93-0.95, p<0.001). Potential pathogens were detected in half of samples previously negative by clinical diagnostics, demonstrating increased sensitivity for missed pulmonary pathogens (p<0.001). An optimized mNGS assay for pulmonary microbes demonstrates significant inoculation of the lower airways of immunocompromised children with diverse bacteria, fungi, and viruses. Potential pathogens can be identified based on absolute and relative abundance. Ongoing investigation is needed to determine the pathogenic significance of outlier microbes in the lungs of immunocompromised children with pulmonary disease.
has issue date	2018-03-29(xsd:dateTime)
bibo:doi	10.1101/291864
has license	medrxiv
sha1sum (hex)	d481e1491e810a6c03e498fa5bb9040888ab713a
schema:url	https://doi.org/10.1101/291864
resource representing a document's title	Pulmonary Metagenomic Sequencing Suggests Missed Infections in Immunocompromised Children
schema:publication	bioRxiv
resource representing a document's body	covid:d481e1491e810a6c03e498fa5bb9040888ab713a#body_text
is schema:about of	named entity 'Infections' named entity 'Pulmonary' named entity 'Immunocompromised' named entity 'respiratory tree' named entity 'solid organ transplantation' named entity 'RNAseq' named entity 'microbiome' named entity 'clinical diagnostics' named entity 'non-infectious' named entity 'immunocompromised' named entity 'RNA sequencing' named entity 'linear regression' named entity 'PCR' named entity 'pulmonary complications' named entity 'Human bocavirus' named entity 'microbiome' named entity 'fungi' named entity 'viral pathogens' named entity 'antigen-based' named entity 'nucleic acid' named entity 'clinical significance' named entity 'organism' named entity 'Aspergillus' named entity 'idiopathic' named entity 'CFU' named entity 'Aspergillus' named entity 'viruses' named entity 'microbiome' named entity 'DNA sequencing' named entity 'microbes' named entity 'Fusarium' named entity 'neurologic' named entity 'viruses' named entity 'lungs' named entity 'Aspergillus' named entity 'immunocompromised' named entity 'sequencing reads' named entity 'nucleic acid' named entity 'hematopoietic cell' named entity 'fungistatic' named entity 'HHV-6' named entity 'polysaccharide' named entity '15,000' named entity 'amplicon' named entity 'metagenomic' named entity 'Sanger sequencing' named entity 'immune function' named entity 'open-source' named entity 'clinical testing' named entity 'immunocompromised' named entity 'Aspergillus' named entity 'Aspergillus' named entity 'pharmacotherapy' named entity 'nucleic acid' named entity 'sequencing reads' named entity 'RNA' named entity 'Adenovirus' named entity 'microbiome' named entity 'life-threatening diseases' named entity 'microbial' named entity 'nucleic acid' named entity 'lower respiratory tract' named entity 'nonpathogenic' named entity 'RNA' named entity 'nucleotide' named entity 'immunocompromised' named entity 'compression ratio' named entity 'standard deviations' named entity 'immunologists' named entity 'viruses' named entity 'nasopharyngeal' named entity 'clinical outcomes' named entity 'clinical testing' named entity 'CLIA' named entity 'galactomannan' named entity 'infectious disease' named entity 'non-significant' named entity 'Autopsy' named entity 'S.pneumoniae' named entity 'pulmonary infections' named entity 'multiplex PCR' named entity 'Aspergillus' named entity 'antimicrobial' named entity 'RNA' named entity 'Aspergillus'

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