Evaluation of Metagenomic and Targeted Next-Generation Sequencing Workflows for Detection of Respiratory Pathogens from Bronchoalveolar Lavage Fluid Specimens
David C. Gaston, Heather B. Miller, John A. Fissel, Emily Jacobs, Ethan Gough, Jiajun Wu, Eili Klein, Karen C. Carroll, Patricia J. Simner
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.
Topics & Concepts
MetagenomicsBronchoalveolar lavageWorkflowBiologyComputational biologyMicrobiologyMedicineComputer scienceLungInternal medicineGeneGeneticsDatabaseGut microbiota and healthRespiratory viral infections researchPneumonia and Respiratory Infections