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Comparison the pathogen diagnosis of severe pneumonia by using next generation sequencing and traditional detection methods, China, 2010-2018

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  • Comparison the pathogen diagnosis of severe pneumonia by using next generation sequencing and traditional detection methods, China, 2010-2018

    J Infect. 2018 Sep 17. pii: S0163-4453(18)30277-9. doi: 10.1016/j.jinf.2018.09.004. [Epub ahead of print]
    Comparison the pathogen diagnosis of severe pneumonia by using next generation sequencing and traditional detection methods, China, 2010-2018.

    Xie Y1, Du J1, Jin W1, Teng X1, Cheng R1, Huang P1, Xie H1, Zhou Z1, Feng T2, Tian R3, Wang R1.
    Author information

    Abstract

    Severe pneumonia is one of the most common infectious diseases and can be fatal. The benefits of early pathogen diagnosis in intensive care units are known, but the association between early pathogen diagnosis by next-generation sequencing (NGS) and in-hospital mortality of patients with severe pneumonia has rarely been studied. The study aims to explore the association between early pathogen diagnosis by NGS and the mortality of patients with severe pneumonia admitted to intensive care units, effects of early pathogen diagnosis on ICU and hospital lengths of stay, and other clinical outcome. This is a retrospective study enrolling 178 severe pneumonia patients whose samples were collected between January 2010 and June 2018 in the ICU of Shanghai General Hospital. A total of 130 patients was assigned to conventional detection group (control group) using conventional microbiologic tests to exam sputum, blood, or BAL fluid samples. 48 patients were assigned to early pathogen diagnosis group (NGS group) using NGS to exam samples. Data, including basic information, clinical symptoms, microbiologic test results, laboratory results, APACHE II score, SOFA score, CT and other serum biomarkers, was collected. The mortality, length of stay in hospital, MODS and other complications, time of mechanical ventilation, and etiological diagnosis were compared between two groups.The 28-day and 90-day mortality of NGS group was significantly lower than the control group. The bacterial detection rate of NGS group was significantly higher than the control group, particularly in Streptococcus pneumoniae, Haemophilus influenza and Prevotella melaninogenicus.This study suggests that NGS might lead to more rapid and accurate diagnosis with better clinical prognosis than conventional detection methods in severe pneumonia in ICU.


    KEYWORDS:

    Mortality; Next-generation sequencing; Pathogens diagnosis; Severe pneumonia

    PMID: 30237069 DOI: 10.1016/j.jinf.2018.09.004
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