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ORIGINAL RESEARCH article

Front. Bacteriol.
Sec. Pathogenesis, Vaccines, and Immunity of Bacterial Infections
Volume 3 - 2024 | doi: 10.3389/fbrio.2024.1424135
This article is part of the Research Topic Listeria Monocytogenes - Transmission, Mechanisms of Bacterial Virulence and Host-pathogen interaction View all articles

Metagenomic next-generation sequencing: Elucidating the distribution of respiratory pathogens in severe COVID-19 patients

Provisionally accepted
Chong Wang Chong Wang Shuo Yang Shuo Yang Qi Liu Qi Liu Hongchao Liu Hongchao Liu Sisi Ma Sisi Ma Jing Li Jing Li Liyan Cui Liyan Cui *
  • Peking University Third Hospital, Haidian, China

The final, formatted version of the article will be published soon.

    【Abstract】： 【Background】：The COVID-19 pandemic poses a significant challenge to global public health. Infection with the virus can result in alterations to the respiratory microbiome of affected individuals, alterations that are intimately tied to the therapeutic management and ultimate outcome of the disease.Traditional methods are limited to the detection of common pathogenic bacteria, failing to capture broader changes in respiratory tract flora.The advent and expedited advancement of metagenomic next-generation sequencing (mNGS) has offered innovative perspectives for the clinical diagnosis and therapeutic analysis of lower respiratory tract infections (LRTI). 【Methods】：We retrospectively analyzed 43 patients with LRTI from December 2022 to March 2023 (including 14 critically ill patients with COVID-19, 20 patients with non-critically ill COVID-19 and 9 patients with LRTI without COVID-19 infection. COVID-19 diagnostic criteria refer to flow chart). Sputum samples from 43 patients were collected. The sputum samples of patients were detected by Traditional technology(mainly microbial culture and drug sensitivity identification) and mNGS. 【Results】：The positive rate of mNGS exceeded that of conventional culture in detecting sputum samples from COVID-19 patients, reaching 95.35% compared to 81.08% respectively.The mNGS pathogen coverage encompassed 36.36% (12/33) of bacteria isolated through conventional culture methods and 74.07% (20/27) of fungi similarly isolated. In detail, microbial detection and mNGS outcomes aligned in 27 cases (71.05%), including 5 from the control group, 14 from the non-critical group, and 8 from the critical group. The clinical outcomes of COVID-19 patients demonstrated a positive correlation with PCT, N-proBNP, neutrophil percentage, LDH,

    Keywords: COVID - 19, respiratory flora, metagenomic next-generation sequencing, Lower respiratory tract infection, Bacteria

    Received: 27 Apr 2024; Accepted: 25 Jul 2024.

    Copyright: © 2024 Wang, Yang, Liu, Liu, Ma, Li and Cui. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

    * Correspondence: Liyan Cui, Peking University Third Hospital, Haidian, China

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