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. 2020 Feb;39(2):369-374.
doi: 10.1007/s10096-019-03734-5. Epub 2019 Dec 7.

Application of metagenomic next-generation sequencing for bronchoalveolar lavage diagnostics in critically ill patients

Ying Li #  1 , Bing Sun #  1 , Xiao Tang  1 , Ya-Lan Liu  1 , Hang-Yong He  1 , Xu-Yan Li  1 , Rui Wang  1 , Fei Guo  1 , Zhao-Hui Tong  2
Affiliations

Application of metagenomic next-generation sequencing for bronchoalveolar lavage diagnostics in critically ill patients

Ying Li et al. Eur J Clin Microbiol Infect Dis. 2020 Feb.

Abstract

The purpose of this study was to assess the value of metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) for the diagnosis of severe respiratory diseases based on interpretation of sequencing results. BALF samples were harvested and used for mNGS as well as microbiological detection. Infectious bacteria or fungi were defined according to relative abundance and number of unique reads. We performed mNGS on 35 BALF samples from 32 patients. The positive rate reached 100% in the mNGS analysis of nine immunocompromised patients. Compared with the culture method, mNGS had a diagnostic sensitivity of 88.89% and a specificity of 74.07% with an agreement rate of 77.78% between these two methods. Compared with the smear method and PCR, mNGS had a diagnostic sensitivity of 77.78% and a specificity of 70.00%. In 13 cases, detection results were positive by mNGS but negative by culture/smear and PCR. The mNGS findings in 11/32 (34.4%) cases led to changes in treatment strategies. Linear regression analysis showed that diversity was significantly correlated with interval between disease onset and sampling. Dynamic changes in reads could indirectly reflect therapeutic effectiveness. BALF mNGS improves sensitivity of pathogen detection and provides guidance in clinical practice. Potential pathogens can be identified based on relative abundance and number of unique reads.

Keywords: Bronchoalveolar lavage fluid (BALF); Clinical diagnosis; Metagenomic next-generation sequencing (mNGS); Respiratory failure.

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Conflict of interest statement

The authors declare that they have no conflict of interest.

Figures

Fig. 1
Fig. 1
Genus and species distribution of bacteria and distribution of fungi by mNGS for the constituents for which the number of unique reads was ≥ 50
Fig. 2
Fig. 2
Number of bacterial and fungal genera identified in the bronchoalveolar lavage sample relative to the number of days for which the disease onset occurred before collection of the sample
See this image and copyright information in PMC

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