Metagenomics next-generation sequencing tests take the stage in the diagnosis of lower respiratory tract infections

Zhenli Diao, Dongsheng Han, Rui Zhang, Jinming Li, Zhenli Diao, Dongsheng Han, Rui Zhang, Jinming Li

Abstract

Metagenomic next-generation sequencing (mNGS) has changed the diagnosis landscape of lower respiratory tract infections (LRIs). With the development of newer sequencing assays, it is now possible to assess all microorganisms in a sample using a single mNGS analysis. The applications of mNGS for LRIs span a wide range of areas including LRI diagnosis, airway microbiome analyses, human host response analyses, and prediction of drug resistance. mNGS is currently in an exciting transitional period; however, before implementation in a clinical setting, there are several barriers to overcome, such as the depletion of human nucleic acid, discrimination between colonization and infection, high costs, and so on. Aim of Review: In this review, we summarize the potential applications and challenges of mNGS in the diagnosis of LRIs to promote the integration of mNGS into the management of patients with respiratory tract infections in a clinical setting. Key Scientific Concepts of Review: Once its analytical validation, clinical validation and clinical utility been demonstrated, mNGS will become an important tool in the field of infectious disease diagnosis.

Keywords: ARGs, antibiotic resistance genes; CAP, Community-acquired pneumonia; CSF, Cerebrospinal fluid; DASH, Depletion of Abundant Sequences by Hybridization; DNBs, DNA nanoballs; DNase, Deoxyribonuclease; Fil, 5-μM filtration; IQC, Internal quality control; IQR, Interquartile range; LDTs, Laboratory-developed tests; LRIs, Lower respiratory tract infections; MTB, M. tuberculosis; Metagenomics; Mol, MolYsis™ Basic; NCBI, National Center for Biotechnology Information; NEB, NEBNext® Microbiome DNA Enrichment Kit; NPA, nasopharyngeal aspirate; Next generation sequencing; PMA, Propidium monoazide; PT, Proficiency testing; Pneumonia; QIA, QIAamp DNA Microbiome Kit; RMB, renminbi; RT-PCR, Reverse-transcription PCR; RVP, respiratory virus panel; Respiratory; RoC, Receiver-operating curve; SMRT, single-molecule real-time sequencing; TATs, Typical turnaround times; WGS, Whole-genome sequencing; mNGS; mNGS, Metagenomic next-generation sequencing.

Conflict of interest statement

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

© 2022 The Authors. Published by Elsevier B.V. on behalf of Cairo University.

Figures

Graphical abstract
Graphical abstract
Fig. 1
Fig. 1
Applications of mNGS in the area of lower respiratory tract infections.
Fig. 2
Fig. 2
The possible contaminations sources of mNGS and the tips for eliminating the contaminations. The sources of contaminations mainly include four components: (1) Laboratory environment and operators’ bodies (2) Consumables and reagents (3) Cross contamination and (4) Reference database contamination. It is necessary to adopt some strategies to minimize the impact of contamination.

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