Evaluation of Metagenomic and Targeted Next-Generation Sequencing Workflows for Detection of Respiratory Pathogens from Bronchoalveolar Lavage Fluid Specimens-Reference-Cited by-同舟云学术

Evaluation of Metagenomic and Targeted Next-Generation Sequencing Workflows for Detection of Respiratory Pathogens from Bronchoalveolar Lavage Fluid Specimens

Published:2022-07-20 Issue:7 Volume:60 Page:
ISSN:0095-1137
Container-title:Journal of Clinical Microbiology
language:en
Short-container-title:J Clin Microbiol

Author:

Gaston David C.¹^ORCID,Miller Heather B.¹,Fissel John A.¹^ORCID,Jacobs Emily¹,Gough Ethan²,Wu Jiajun³,Klein Eili Y.⁴,Carroll Karen C.¹^ORCID,Simner Patricia J.¹^ORCID

Affiliation:

1. Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA

2. Department of International Health, Human Nutrition Program, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA

3. Department of Pediatrics, Biostatistics, Epidemiology and Data Management (BEAD) Core, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA

4. Department of Emergency Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA

Abstract

Next-generation sequencing (NGS) workflows applied to bronchoalveolar lavage (BAL) fluid specimens could enhance the detection of respiratory pathogens, although optimal approaches are not defined. This study evaluated the performance of the Respiratory Pathogen ID/AMR (RPIP) kit (Illumina, Inc.) with automated Explify bioinformatic analysis (IDbyDNA, Inc.), a targeted NGS workflow enriching specific pathogen sequences and antimicrobial resistance (AMR) markers, and a complementary untargeted metagenomic workflow with in-house bioinformatic analysis.

Publisher

American Society for Microbiology

Subject

Microbiology (medical)

Link

https://journals.asm.org/doi/pdf/10.1128/jcm.00526-22

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