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 M.
AU - Kruser, Jacqueline M.
AU - Singer, Benjamin D.
AU - Seed, Patrick
AU - Green, Stefan J.
AU - Wunderink, Richard G.
N1 - Publisher Copyright:
© 2019 The Authors.
PY - 2019/7
Y1 - 2019/7
N2 - 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.
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.
KW - Respiratory pathogens
KW - Shotgun metagenomic sequencing
KW - Ventilate-associate pneumonia
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U2 - 10.1099/jmm.0.000968
DO - 10.1099/jmm.0.000968
M3 - Article
C2 - 31136295
AN - SCOPUS:85069238262
SN - 0022-2615
VL - 68
SP - 996
EP - 1002
JO - Journal of medical microbiology
JF - Journal of medical microbiology
IS - 7
ER -
