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Detection of respiratory pathogens in clinical samples using metagenomic shotgun sequencing

Authors
  • Qi, Chao1
  • Hountras, Peter2
  • Pickens, Chiagozie Ononye2
  • Walter, James M.2
  • Kruser, Jacqueline M.2
  • Singer, Benjamin D.2
  • Seed, Patrick3, 4, 5
  • Green, Stefan J.6
  • Wunderink, Richard G.2
  • 1 Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA , Northwestern University Feinberg School of Medicine, Chicago, IL
  • 2 Division of Pulmonary and Critical Care, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA , Northwestern University Feinberg School of Medicine, Chicago, IL
  • 3 Northwestern University Feinberg School of Medicine, Chicago, IL, USA , Chicago
  • 4 Ann and Robert H. Lurie Childrens Hospital, Chicago IL, USA , Chicago IL
  • 5 Stanley Manne Children’s Research Institute, Chicago IL, USA , Chicago IL
  • 6 University of Illinois at Chicago, Chicago IL, USA , Chicago IL
Type
Published Article
Journal
Journal of Medical Microbiology
Publisher
Microbiology Society
Publication Date
May 28, 2019
Volume
68
Issue
7
Pages
996–1002
Identifiers
DOI: 10.1099/jmm.0.000968
PMID: 31136295
PMCID: PMC6939159
Source
PubMed Central
Keywords
License
Unknown

Abstract

Purpose. In this pilot study, we used shotgun metagenome sequencing (SMS) strategy on bronchoalveolar lavage (BAL) samples from hospitalized patients with suspected ventilate-associated pneumonia (VAP) in order to explore its potential for improving detection of ventilator-associated-pneumonia (VAP) etiology. Methodology. In total, 67BAL samples from patients with VAP were tested with SMS strategy for detection of respiratory pathogens. Results of SMS and routine respiratory culture were compared. Results. SMS detected all pathogens recovered by cultivation approaches. In addition, putative pathogens other than the organisms recovered by culture were detected by SMS in culture-positive samples. In 40 of 45 (89 %) culture-negative samples, a potential pathogen was detected by SMS. Conclusion. This proof-of-concept study demonstrates that SMS is able to detect bacterial, fungal and viral organisms in BAL, including culture-negative cases.

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