Pulmonary Metagenomic Sequencing Suggests Missed Infections in Immunocompromised Children

Matt S. Zinter, Christopher C. Dvorak, Madeline Y. Mayday, Kensho Iwanaga, Ngoc P. Ly, Meghan E. McGarry, Gwynne D. Church, Lauren E. Faricy, Courtney M. Rowan, Janet R. Hume, Marie E. Steiner, Emily D. Crawford, Charles Langelier, Katrina Kalantar, Eric D. Chow, Steve Miller, Kristen Shimano, Alexis Melton, Gregory A. Yanik, Anil SapruJoseph L. Derisi

Research output: Contribution to journalArticlepeer-review

65 Scopus citations


BACKGROUND: 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.

METHODS: 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.

RESULTS: 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 depressed alpha-diversity (median, 0.61; interquartile range [IQR], 0.33-0.72 vs median, 0.96; IQR, 0.94-0.96; P < .001). Potential pathogens were detected in half of samples previously negative by clinical diagnostics, demonstrating increased sensitivity for missed pulmonary pathogens (P < .001).

CONCLUSIONS: 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.

Original languageEnglish (US)
Pages (from-to)1847-1855
Number of pages9
JournalClinical Infectious Diseases
Issue number11
StatePublished - May 17 2019

Bibliographical note

Funding Information:
Financial support. This work was supported by the Eunice Kennedy Shriver National Institute of Child Health and Human Development of the National Institutes of Health (K12HD000850 to M. S. Z.), the Pediatric Blood and Marrow Transplant Foundation (to M. S. Z.), the National Marrow Donor Program Amy Strelzer Manasevit Grant (to M. S. Z.), and the Chan Zuckerberg Biohub (to J. L. D.).

Publisher Copyright:
© The Author(s) 2018. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved.


  • Intensive care units
  • immunocompromised host
  • metagenomics
  • microbiota
  • pediatric
  • respiratory tract infections


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