Detection of respiratory pathogens in clinical samples using metagenomic shotgun sequencing

Chao Qi*, Peter Hountras, Chiagozie Ononye Pickens, James McCauley Walter, Jacqueline M. Kruser, Benjamin Singer, Patrick Casey Seed, Stefan J. Green, Richard G Wunderink

*Corresponding author for this work

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Pages (from-to)996-1002
Number of pages7
JournalJournal of Medical Microbiology
Volume68
Issue number7
DOIs
StatePublished - Jul 1 2019

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Metagenome
Metagenomics
Firearms
Bronchoalveolar Lavage
Pneumonia
Ventilator-Associated Pneumonia

Keywords

  • Respiratory pathogens
  • Shotgun metagenomic sequencing
  • Ventilate-associate pneumonia

ASJC Scopus subject areas

  • Microbiology
  • Microbiology (medical)

Cite this

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title = "Detection of respiratory pathogens in clinical samples using metagenomic shotgun sequencing",
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.",
keywords = "Respiratory pathogens, Shotgun metagenomic sequencing, Ventilate-associate pneumonia",
author = "Chao Qi and Peter Hountras and Pickens, {Chiagozie Ononye} and Walter, {James McCauley} and Kruser, {Jacqueline M.} and Benjamin Singer and Seed, {Patrick Casey} and Green, {Stefan J.} and Wunderink, {Richard G}",
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Detection of respiratory pathogens in clinical samples using metagenomic shotgun sequencing. / Qi, Chao; Hountras, Peter; Pickens, Chiagozie Ononye; Walter, James McCauley; Kruser, Jacqueline M.; Singer, Benjamin; Seed, Patrick Casey; Green, Stefan J.; Wunderink, Richard G.

In: Journal of Medical Microbiology, Vol. 68, No. 7, 01.07.2019, p. 996-1002.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Detection of respiratory pathogens in clinical samples using metagenomic shotgun sequencing

AU - Qi, Chao

AU - Hountras, Peter

AU - Pickens, Chiagozie Ononye

AU - Walter, James McCauley

AU - Kruser, Jacqueline M.

AU - Singer, Benjamin

AU - Seed, Patrick Casey

AU - Green, Stefan J.

AU - Wunderink, Richard G

PY - 2019/7/1

Y1 - 2019/7/1

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AB - 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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KW - Ventilate-associate pneumonia

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