Detection of respiratory pathogens in clinical samples using metagenomic shotgun sequencing

被引：28

作者：

Qi, Chao ^{[1
]}

Hountras, Peter ^{[2
]}

Pickens, Chiagozie Ononye ^{[2
]}

Walter, James M. ^{[2
]}

Kruser, Jacqueline M. ^{[2
]}

Singer, Benjamin D. ^{[2
]}

Seed, Patrick ^{[3
,4
,5
]}

Green, Stefan J. ^{[6
]}

Wunderink, Richard G. ^{[2
]}

机构：

[1] Northwestern Univ, Dept Pathol, Feinberg Sch Med, Chicago, IL 60611 USA

[2] Northwestern Univ, Dept Med, Feinberg Sch Med, Div Pulm & Crit Care, Chicago, IL 60611 USA

[3] Northwestern Univ, Dept Pediat, Feinberg Sch Med, Chicago, IL 60611 USA

[4] Ann & Robert H Lurie Childrens Hosp, Chicago, IL USA

[5] Stanley Manne Childrens Res Inst, Chicago, IL USA

[6] Univ Illinois, Res Resources Ctr, Chicago, IL USA

来源：

JOURNAL OF MEDICAL MICROBIOLOGY | 2019年 / 68卷 / 07期

关键词：

shotgun metagenomic sequencing; ventilate-associate pneumonia; respiratory pathogens; MECHANICALLY VENTILATED PATIENTS; TROPHERYMA-WHIPPLEI; COMMUNITY STRUCTURE; PNEUMONIA; DIAGNOSIS; MICROORGANISMS; REPEATABILITY; MICROBIOME;

D O I：

10.1099/jmm.0.000968

中图分类号：

Q93 [微生物学];

学科分类号：

071005 ; 100705 ;

摘要：

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.

引用

页码：996 / 1002

页数：7

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