The microbiological diagnostic performance of metagenomic next-generation sequencing in patients with sepsis

Di Ren,Dan Zhou,Yanhong Chen,Xiaohong Li,Shuiqing Gui,Yu Ye,Kai Lai,Renqi Yao,Jia Liu,Haoli Li,Chao Ren,Xiaomin Liang,Jiaze Wang,Guiyun Li,Sha Wen,Ying Li,Xisi He,Lin Zhang,Xinke Meng

doi:10.1186/s12879-021-06934-7

Abstract

BackgroundIn this study, we aimed to perform a comprehensive analysis on the metagenomic next-generation sequencing for the etiological diagnosis of septic patients, and further to establish optimal read values for detecting common pathogens.Methods In this single-center retrospective study, septic patients who underwent pathogen detection by both microbial culture and metagenomic next-generation sequencing in the intensive care unit of the Second People’s Hospital of Shenzhen from June 24, 2015, to October 20, 2019, were included.ResultsA total of 193 patients with 305 detected specimens were included in the final analysis. The results of metagenomic next-generation sequencing showed significantly higher positive rates in samples from disparate loci, including blood, bronchoalveolar lavage fluid, and cerebrospinal fluid, as well as in the determination of various pathogens. The optimal diagnostic reads were 2893, 1825.5, and 892.5 for Acinetobacter baumannii, Pseudomonas aeruginosa, and Klebsiella pneumoniae, respectively.ConclusionsThe metagenomic next-generation sequencing is capable of identifying multiple pathogens in specimens from septic patients, and shows significantly higher positive rates than culture-based diagnostics. The optimal diagnostic reads for frequently detected microbes might be useful for the clinical application of metagenomic next-generation sequencing in terms of timely and accurately determining etiological pathogens for suspected and confirmed cases of sepsis due to well-performed data interpretation.

Highlights

In this study, we aimed to perform a comprehensive analysis on the metagenomic next-generation sequencing for the etiological diagnosis of septic patients, and further to establish optimal read values for detecting common pathogens
A study by Long et al [9] showed that the diagnostic sensitivity of pathogens in septic patients was significantly increased by next-generation sequencing when compared to blood culture
We performed a comprehensive analysis on the application of Metagenomic next-generation sequencing (mNGS) for the etiological diagnosis of septic patients admitted to the Intensive care unit (ICU), and further established optimal read values for determining common pathogens by making comparisons with the results of routine microbial culture

Summary

Introduction

We aimed to perform a comprehensive analysis on the metagenomic next-generation sequencing for the etiological diagnosis of septic patients, and further to establish optimal read values for detecting common pathogens. Culture-based diagnostic procedures are deemed the golden standard for detecting bacteremia but present limited information due to low positive rates, false results due to contamination and over administration of antibiotics, hindering their usefulness, especially for critically ill patients [6]. We performed a comprehensive analysis on the application of mNGS for the etiological diagnosis of septic patients admitted to the ICU, and further established optimal read values for determining common pathogens by making comparisons with the results of routine microbial culture. We present the following article in accordance with the STARD reporting checklist

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