The clinical application of metagenomic next-generation sequencing for detecting pathogens in bronchoalveolar lavage fluid: case reports and literature review

Hin Fung Tsang, Allen Chi Shing Yu, Nana Jin, Aldrin Kay Yuen Yim, Wai Ming Stanley Leung, Ka Wai Lam, William Chi Shing Cho, Jiachi Chiou, Sze Chuen Cesar Wong

Research output: Journal article publicationJournal articleAcademic researchpeer-review

Abstract

Introduction: Clinical metagenomic next-generation sequencing (mNGS) allows a comprehensive genetic analysis of microbial materials. Different from other traditional target-driven molecular diagnostic tests, such as PCR, mNGS is a hypothesis-free diagnostic approach that allows a comprehensive genetic analysis of the clinical specimens that cover nearly any common, rare, and new pathogens ranging broadly from viruses, bacteria, fungi to parasites. Areas covered: In this article, we discussed the clinical application of the mNGS using two clinical cases as examples and described the use of mNGS to assist the diagnosis of parasitic pulmonary infection. The advantages and challenges in implementing mNGS in clinical microbiology are also discussed. Expert opinion: mNGS is a promising technology that allows quick diagnosis of infectious diseases. Currently, a plethora of sequencing and analysis methods exists for mNGS, each with individual merits and pitfalls. While standards and best practices were proposed by various metagenomics working groups, they are yet to be widely adopted in the community. The development of a consensus set of guidelines is necessary to guide the usage of this new technology and the interpretation of NGS results before clinical adoption of mNGS testing.

Original languageEnglish
Pages (from-to)575-582
Number of pages8
JournalExpert Review of Molecular Diagnostics
Volume22
Issue number5
DOIs
Publication statusPublished - 2 May 2022

Keywords

  • Lophomonas infection
  • Metagenomic analysis
  • metagenomic NGS
  • mNGS
  • next-generation sequencing (NGS)
  • pathogen detection
  • shortgun sequencing

ASJC Scopus subject areas

  • Pathology and Forensic Medicine
  • Molecular Medicine
  • Molecular Biology
  • Genetics

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