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Prospective Evaluation of a Rapid Clinical Metagenomics Test for Bacterial Pneumonia
149 Pages Posted: 4 Feb 2021
More...Abstract
Background: The diagnosis of bacterial pathogens in lower respiratory tract infections (LRI) using conventional culture methods remains challenging and time-consuming.
Methods: We enrolled 292 consecutively hospitalized patients suspected to have LRI 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 and evaluated for potential clinical benefit.
Results: 171 bronchoalveolar lavage fluid (BAL) and 121 sputum samples were collected from patients with six kinds of LRI. The turn around-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 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 of anaerobes enrichment with lung abscess was demonstrated as 38 anaerobic species failed in culture but identified by metagenomics sequencing. The hypothetical impact of metagenomics test proposed antibiotic de-escalation in 34 patients compared to 1 using routine culture.
Conclusions: Rapid clinical metagenomics test increased 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.
Funding: The funder of the study had no role in study design, data collection,data analysis, data
interpretation, or writing of the report. The corresponding authors had full access to all the data in the study and had final responsibility for the decision to submit for publication.
Declaration of Interest: None to declare
Ethical Approval: The study was carried out in China-Japan Friendship Hospital, Beijing, China. Ethical approval was obtained from the China-Japan Friendship Hospital Ethics Committee(2018-145-k102). All subjects provided written consents.
Keywords: Nanopore sequencing, lower respiratory infections, rapid diagnostics
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