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. 2021 Dec 16;21(1):1257.
doi: 10.1186/s12879-021-06934-7.

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

Di Ren #  1 , Chao Ren #  2 , Renqi Yao #  2 , Lin Zhang  1 , Xiaomin Liang  1 , Guiyun Li  1 , Jiaze Wang  1 , Xinke Meng  1 , Jia Liu  3 , Yu Ye  4 , Haoli Li  1 , Sha Wen  1 , Yanhong Chen  1 , Dan Zhou  1 , Xisi He  1 , Xiaohong Li  1 , Kai Lai  1 , Ying Li  5 , Shuiqing Gui  6
Affiliations

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

Di Ren et al. BMC Infect Dis. .

Abstract

Background: 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.

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.

Results: A 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.

Conclusions: The 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.

Keywords: Intensive care units; Metagenomic next-generation sequencing; Microbial culture; Pathogens; Sepsis.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
The positivity of disparate sample types between metagenomic next-generation sequencing (mNGS) and microbial culture. Among all detected samples, the positive rates of mNGS were significantly higher than those of culture. A similar tendency was observed in all types of specimens, including blood, bronchoalveolar lavage fluid (BALF) and cerebrospinal fluid (CSF). A P value of McNemar test or Fisher’s exact test lower than 0.05 was deemed as statistically significant
Fig. 2
Fig. 2
The positivity of disparate pathogenic microorganisms between metagenomic next-generation sequencing (mNGS) and microbial culture. Acinetobacter baumannii, Pseudomonas aeruginosa and Klebsiella pneumoniae were the most commonly isolated bacteria from septic specimens, which were also found to be significantly more detectable with mNGS than with conventional culture. Interestingly, the mNGS method demonstrated obviously lower positive rates than culture-based diagnostics in terms of Candida detection. Viral infection was solely detected with mNGS. A P value of McNemar test or Fisher’s exact test lower than 0.05 was deemed as statistically significant
Fig. 3
Fig. 3
Concordance analysis between metagenomic next-generation sequencing (mNGS) and culture. Culture and mNGS showed double positive results in 90 (29.5%) specimens, in which 49 (54.4%) cases were completely matched, while mismatch was observed in 41 (45.6%) cases
Fig. 4
Fig. 4
The optimal reads for commonly detected pathogens. The receiver operating characteristic (ROC) curve analysis was performed for confirming the optimal reads for frequently detected pathogens. The optimal cut-off values of reads were determined in line with the maximum of Youden index at this point. A Acinetobacter baumannii; B Pseudomonas aeruginosa; C Klebsiella pneumoniae
See this image and copyright information in PMC

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