Prospective evaluation of nanopore-based metagenomic sequencing for rapid detection of bacterial pathogens in patients with lower respiratory tract infections

Abstract

Background: The diagnosis of bacterial pathogens in lower respiratory tract infections (LRIs) using conventional culture methods remains challenging and time-consuming. Objectives: To evaluate the nanopore-based metagenomic sequencing for rapid detection of bacterial pathogens in patients with lower respiratory tract infections. Methods: We launched a single-center, prospective cohort study that enrolled 292 consecutively hospitalized patients with LRIs from November 2018 to June 2019. The nanopore metagenomic sequencing results were compared with those of routine microbiology tests, and the discordant results were further verified by real-time PCR. And then, the nanopore sequencing data were evaluated by two senior clinicians against patients9 medical records for clinical relevance. Results: This study enrolled patients from the ICU and general wards at a ratio of 1:1, collected 171 bronchoalveolar lavage fluid (BALF) and 121 sputum samples, and studied 6 types of diseases.Compared with culture and qPCR tests, nanopore sequencing achieved overall sensitivity of 96.6% and specificity of 88.0%. Furthermore, nanopore metagenomics identified pathogens in 63 out of 161 culture-negative samples, and 50(79.4%) of such samples were successfully verified. By improving the identification rate of fastidious and anaerobe species, nanopore metagenomics has proven that anaerobe species are significantly enriched in patients with lung abscess. Conclusions: Nanopore metagenomic sequencing can rapidly identify the bacteria pathogens and medical review proved that valuable adjustment could be made if the results were reported to clinicians in time.