Integrating DNA and RNA sequencing for enhanced pathogen detection in respiratory infections

• DOI: 10.1186/s12967-025-06342-4
• Publication Date: 2025-03-14T10:28:55Z
• Authors: Dejian Gu; Jie Liu; Jiaping Wang; Yuting Yi; Yuxing Chu; Rui Gao; Hao Liu; Jun She; Binghuai Lu
• Keywords: Pathogenic organism

The clinical value of shotgun metagenomic next-generation sequencing (mNGS) in improving the detection rates respiratory pathogens is well-established. However, mNGS complex and expensive. This study designed evaluated performance targeted NGS (tNGS) diagnosing infections. We retrospectively included samples from 281 patients with lower tract infections to establish thresholds pathogens. Subsequently, target were selected a probe hybridization system was established. manifestations tNGS for 306 using simulated samples. method took 16 h data sizes 5 M reads. limit-of-detection 100–200 CFU/mL, respectively. Bioinformatics simulation confirmed method's high specificity robustness. In validation cohort, exhibited sensitivity 97.73% 75.41% compared composite reference standard, which notably surpasses those culture-based conventional microbiological methods (CMT). detecting bacterial viral infection, demonstrated superior relative CMT. Notably, 61.40% viruses subtype-resolved initial establishment reliable typing cutoffs, subtyping results being completely consistent PCR results. allowed concurrent identification antimicrobial resistance (AMR) markers subtyping. 80.56% AMR identified by susceptibility testing. research established robust our tailored assay simultaneous DNA RNA pathogens, underscoring its prospective suitability widespread use diagnostics.