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

• Published in: Journal of advanced research Vol. 38; pp. 201 - 212
• Main Authors: Diao, Zhenli, Han, Dongsheng, Zhang, Rui, Li, Jinming
• Format: Journal Article
• Language: English
• Published: Egypt Elsevier B.V 01.05.2022; Elsevier
• Subjects: High-Throughput Nucleotide Sequencing; Humans; Medicine; Metagenome; Metagenomics; Microbiota - genetics; mNGS; Next generation sequencing; Pneumonia; Respiratory; Respiratory Tract Infections - diagnosis; Metagenomics; Pneumonia; WGS; PT; RoC; DNase; DASH; RVP; RT-PCR; CSF; NCBI; IQC; DNBs; mNGS; ARGs; PMA; RMB; Fil; QIA; Respiratory; NEB; IQR; Mol; TATs; Next generation sequencing; CAP; LRIs; LDTs; MTB; SMRT; NPA; RT-PCR, Reverse-transcription PCR; mNGS, Metagenomic next-generation sequencing; IQC, Internal quality control; NPA, nasopharyngeal aspirate; RVP, respiratory virus panel; NEB, NEBNext® Microbiome DNA Enrichment Kit; PT, Proficiency testing; RoC, Receiver-operating curve; NCBI, National Center for Biotechnology Information; IQR, Interquartile range; Mol, MolYsis™ Basic; MTB, M. tuberculosis; PMA, Propidium monoazide; WGS, Whole-genome sequencing; LRIs, Lower respiratory tract infections; CSF, Cerebrospinal fluid; TATs, Typical turnaround times; DNase, Deoxyribonuclease; CAP, Community-acquired pneumonia; DNBs, DNA nanoballs; ARGs, antibiotic resistance genes; RMB, renminbi; SMRT, single-molecule real-time sequencing; Fil, 5-μM filtration; LDTs, Laboratory-developed tests; DASH, Depletion of Abundant Sequences by Hybridization; QIA, QIAamp DNA Microbiome Kit
• DOI: 10.1016/j.jare.2021.09.012
• ISSN: 2090-1232; 2090-1224

The typical workflow of mNGS in clinical laboratory. [Display omitted] •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.•The workflow of mNGS used in clinical practice involves the wet-lab pipeline and dry-lab pipeline, the complex workflow poses challenges for its extensive use.•mNGS will become an important tool in the field of infectious disease diagnosis in the next decade. 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.