Pulmonary Metagenomic Sequencing Suggests Missed Infections in Immunocompromised Children.

Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America
M S ZinterJoseph L. DeRisi

Abstract

Despite improved diagnostics, pulmonary pathogens in immunocompromised children frequently evade detection, leading to significant mortality. Therefore, we aimed 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, parallel RNA/DNA extraction, and metagenomic sequencing. Sequencing reads were aligned to the National Center for Biotechnology Information 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 that contained 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 depress...Continue Reading

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Methods Mentioned

BETA
bronchoalveolar lavages
nucleic acid extraction
RNAseq
BAL
bronchoalveolar lavage
pharmacotherapy
PCR
nucleic acid tests

Software Mentioned

STAR
Bowtie2
HIT
CD
mNGS
PriceSeqFilter
GSNAPL
DUP

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