单位：[1]China-Japan Friendship Hospital, National Clinical Research Center for Respiratory Diseases, Clinical Center for Pulmonary Infections, Capital Medical University, Beijing, China,[2]Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China,[3]Department of Pulmonary and Critical Care Medicine, Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China,[4]State Key Laboratory of Translational Medicine and Innovative Drug Development, Simcere Diagnostics Co., Ltd., Nanjing, China,[5]Tsinghua University-Peking University Joint Center for Life Sciences, Tsinghua University, Beijing, China,[6]Norwich Medical School, University of East Anglia, Norwich, United Kingdom,[7]Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom
Background The diagnosis of bacterial pathogens in lower respiratory tract infections (LRI) using conventional culture methods remains challenging and time-consuming.</p> Objectives To evaluate the clinical performance of a rapid nanopore-sequencing based metagenomics test for diagnosis of bacterial pathogens in common LRIs through a large-scale prospective study.</p> Methods We enrolled 292 hospitalized patients suspected to have LRIs between November 2018 and June 2019 in a single-center, prospective cohort study. Rapid clinical metagenomics test was performed on-site, and the results were compared with those of routine microbiology tests.</p> Results 171 bronchoalveolar lavage fluid (BAL) and 121 sputum samples were collected from patients with six kinds of LRIs. The turnaround time (from sample registration to result) for the rapid metagenomics test was 6.4 +/- 1.4 hours, compared to 94.8 +/- 34.9 hours for routine culture. Compared with culture and real-time PCR validation tests, rapid metagenomics achieved 96.6% sensitivity and 88.0% specificity and identified pathogens in 63 out of 161 (39.1%) culture-negative samples. Correlation between enriched anaerobes and lung abscess was observed by Gene Set Enrichment Analysis. Moreover, 38 anaerobic species failed in culture was identified by metagenomics sequencing. The hypothetical impact of metagenomics test proposed antibiotic de-escalation in 34 patients compared to 1 using routine culture.</p> Conclusions Rapid clinical metagenomics test improved pathogen detection yield in the diagnosis of LRI. Empirical antimicrobial therapy could be de-escalated if rapid metagenomics test results were hypothetically applied to clinical management.</p>
基金：
Biotechnology and Biological Sciences Research CouncilUK Research & Innovation (UKRI)Biotechnology and Biological Sciences Research Council (BBSRC) [BB/R012504/1, BBS/E/F/000PR10349, BBS/E/F/000PR10348] Funding Source: Medline
第一作者单位：[1]China-Japan Friendship Hospital, National Clinical Research Center for Respiratory Diseases, Clinical Center for Pulmonary Infections, Capital Medical University, Beijing, China,[2]Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China,[3]Department of Pulmonary and Critical Care Medicine, Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China,
共同第一作者：
通讯作者：
通讯机构：[1]China-Japan Friendship Hospital, National Clinical Research Center for Respiratory Diseases, Clinical Center for Pulmonary Infections, Capital Medical University, Beijing, China,[2]Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China,[3]Department of Pulmonary and Critical Care Medicine, Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China,[5]Tsinghua University-Peking University Joint Center for Life Sciences, Tsinghua University, Beijing, China,
推荐引用方式(GB/T 7714)：
Shengrui Mu,Long Hu,Ye Zhang,et al.Prospective Evaluation of a Rapid Clinical Metagenomics Test for Bacterial Pneumonia[J].FRONTIERS in CELLULAR and INFECTION MICROBIOLOGY.2021,11:doi:10.3389/fcimb.2021.684965.
APA：
Shengrui Mu,Long Hu,Ye Zhang,Yingmei Liu,Xiaojing Cui...&Bin Cao.(2021).Prospective Evaluation of a Rapid Clinical Metagenomics Test for Bacterial Pneumonia.FRONTIERS in CELLULAR and INFECTION MICROBIOLOGY,11,
MLA：
Shengrui Mu,et al."Prospective Evaluation of a Rapid Clinical Metagenomics Test for Bacterial Pneumonia".FRONTIERS in CELLULAR and INFECTION MICROBIOLOGY 11.(2021)
