Performance of a hybrid capture-based target enrichment next-generation sequencing for the identification of respiratory pathogens and resistance-associated genes in patients with severe pneumonia

• Published in: Microbiology spectrum Vol. 13; no. 1; p. e0213024
• Main Authors: Hsu, Wei-Yu, Kao, Ting-Wei, Cho, Hsin-Ching, Ruan, Sheng-Yuan, Lee, Tai-Fen, Huang, Yu-Tsung, Chien, Jung-Yien
• Format: Journal Article
• Language: English
• Published: United States American Society for Microbiology 07.01.2025
• Subjects: Adult; Aged; Aged, 80 and over; Anti-Bacterial Agents - pharmacology; Bacteria - classification; Bacteria - drug effects; Bacteria - genetics; Bacteria - isolation & purification; Clinical Microbiology; Drug Resistance, Bacterial - genetics; Female; FilmArray-PN; High-Throughput Nucleotide Sequencing - methods; Humans; Male; Middle Aged; Multiplex Polymerase Chain Reaction - methods; pathogen detection; Pneumonia - diagnosis; Pneumonia - microbiology; Pneumonia - virology; Prospective Studies; Research Article; RPIP; severe pneumonia; Sputum - microbiology; Viruses - genetics; Viruses - isolation & purification; severe pneumonia; RPIP; pathogen detection; FilmArray-PN
• ISSN: 2165-0497; 2165-0497
• DOI: 10.1128/spectrum.02130-24

Sensitive pathogen detection is pivotal for timely treatment by tailoring adequate antimicrobial agents. Unlike conventional phenotypic approach, novel measures using molecular interrogation appear promising. This study aimed to elucidate the efficacy of a hybrid capture-based target enrichment next-generation sequencing technique (Respiratory Pathogen ID/AMR Enrichment Panel, RPIP) as exemplified in a cohort with severe pneumonia. Pathogen landscape in the population was illustrated by these three methodologies. As compared with multiplex polymerase chain reaction-based FilmArray Pneumonia Panel and conventional culture, RPIP demonstrated significantly improved sensitivity in identifying bacteria, viruses, and fungi. The RPIP also exhibited better performance in identifying different pathogens in patients co-infected with multiple microorganisms. Additionally, the genotypes contributing to antimicrobial resistance were determined by RPIP. The study facilitated the implementation of molecular diagnosis by presenting real-world data, whereas future studies are mandated to generalize such an approach toward different clinical settings.