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

Reference33 articles.

1. Bronchoalveolar lavage as a diagnostic procedure: a review of known cellular and molecular findings in various lung diseases

2. Understanding the Promises and Hurdles of Metagenomic Next-Generation Sequencing as a Diagnostic Tool for Infectious Diseases

3. Navigating Clinical Utilization of Direct-from-Specimen Metagenomic Pathogen Detection: Clinical Applications, Limitations, and Testing Recommendations

4. Microbiological Diagnostic Performance of Metagenomic Next-generation Sequencing When Applied to Clinical Practice

5. Clinical Impact of Metagenomic Next-Generation Sequencing of Bronchoalveolar Lavage in the Diagnosis and Management of Pneumonia

Cited by 66 articles. 订阅此论文施引文献订阅此论文施引文献，注册后可以免费订阅5篇论文的施引文献，订阅后可以查看论文全部施引文献

1. Comparison of targeted next-generation sequencing and traditional microbial culture in the diagnosis of pulmonary infections;Diagnostic Microbiology and Infectious Disease;2024-12

2. Comparative performance of three next-generation sequencing techniques in real clinical lower respiratory tract infections;2024-09-04

3. Diagnostic limitations and challenges in current clinical guidelines and potential application of metagenomic sequencing to manage pulmonary invasive fungal infections in patients with haematological malignancies;Clinical Microbiology and Infection;2024-09

4. Enhancing lower respiratory tract infection diagnosis: implementation and clinical assessment of multiplex PCR-based and hybrid capture-based targeted next-generation sequencing;eBioMedicine;2024-09

5. Clinical utility of metagenomic next-generation sequencing on bronchoalveolar lavage fluid in diagnosis of lower respiratory tract infections;BMC Pulmonary Medicine;2024-08-29