Prospective evaluation of a rapid clinical metagenomics test for bacterial pneumonia

Shengrui Mu, Long Hu, Ye Zhang, Yingmei Liu, Xiaojing Cui, Xiaohui Zou, Yeming Wang, Binghuai Lu, Shuilian Zhou, Xiaoxue Liang, Chen Liang, Nick Xiao, Justin O’Grady, Shela Lee, Bin Cao

Research output: Contribution to journalArticlepeer-review

Abstract

Background: The diagnosis of bacterial pathogens in lower respiratory tract infections (LRI) using conventional culture methods remains challenging and time-consuming. 

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. 

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. 

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. 

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.

Original languageEnglish
Article number684965
JournalFrontiers in Cellular and Infection Microbiology
Volume11
DOIs
Publication statusPublished - 19 Oct 2021

Keywords

  • bacterial pneumonia
  • lower respiratory infections
  • nanopore sequencing
  • pathogenic diagnosis
  • rapid diagnostics

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