Integrating host response and unbiased microbe detection for lower respiratory tract infection diagnosis in critically ill adults.

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PubMed ID: 30482864

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Langelier C, Kalantar KL, Moazed F, Wilson MR, Crawford ED, Deiss T, Belzer A, Bolourchi S, Caldera S, Fung M, Jauregui A, Malcolm K, Lyden A, Khan L, Vessel K, Quan J, Zinter M, Chiu CY, Chow ED, Wilson J, Miller S, Matthay MA, Pollard KS, Christenson S, Calfee CS, DeRisi JL

Proc Natl Acad Sci U S A. Dec 2018. doi: 10.1073/pnas.1809700115



Lower respiratory tract infections (LRTIs) are the leading cause of infectious disease-related deaths worldwide yet remain challenging to diagnose because of limitations in existing microbiologic tests. In critically ill patients, noninfectious respiratory syndromes that resemble LRTIs further complicate diagnosis and confound targeted treatment. To address this, we developed a metagenomic sequencing-based approach that simultaneously interrogates three core elements of acute airway infections: the pathogen, airway microbiome, and host response


We performed metagenomic next-generation sequencing (mNGS) on tracheal aspirates from 92 adults with acute respiratory failure and simultaneously assessed pathogens, the airway microbiome, and the host transcriptome. We performed both metagenomic shotgun DNA sequencing (DNA-seq) as well as RNA sequencing (RNA-seq). host transcriptional profiling, permitted detection of RNA viruses, and enriched for actively transcribing microbes (versus latent or nonviable taxa). From each TA sample, we generated a mean of 19.6 and 32.6 million paired-end sequencing reads, from DNA-seq and RNA-seq, respectively, of which the median fraction of microbial reads was 0.04% (interquartile range, 0.01–0.16%)


Combining pathogen, microbiome, and host gene expression metrics achieved accurate LRTI diagnosis and identified etiologic pathogens in patients with clinically identified infections but otherwise negative testing. 


Eduardo Pareja