Evaluation of hybrid capture-based targeted and metagenomic next-generation sequencing for pathogenic microorganism detection in infectious keratitis

作者：Qianqian Lan, Zhenfeng Deng, Chunhong Li, Hui Huang, Zhou Zhou, Jiang Li, Fengmei Li, Dan Wu, Min Zheng, Mi Zhou, Qi Chen, Fan Xu · 发表于：BMC Infectious Diseases · 年份：2025 · DOI：10.1186/s12879-025-11608-9 · 被引用次数：3 · 研究领域：Ocular Infections and Treatments、Bacterial Identification and Susceptibility Testing、Microbial infections and disease research

OBJECTIVE: This study aimed to compare the performance of hybrid capture-based targeted next-generation sequencing (hc-tNGS) and metagenomic next-generation sequencing (mNGS) in detecting the causative pathogens of infectious keratitis. METHODS: A total of 60 patients with clinically diagnosed infectious keratitis were enrolled between January and December 2024. Corneal scraping samples were analyzed using hc-tNGS and mNGS. Detection rates, pathogen spectra, normalized reads, turnaround time (TAT), and costs were compared between the two techniques. RESULTS: hc-tNGS exhibited a significantly higher overall detection rate than mNGS (86.7% versus 73.3%, P < 0.001). In particular, hc-tNGS detected 29 pathogens (13 bacteria, 9 viruses, and 7 fungi), whereas mNGS detected 22 pathogens (9 bacteria, 7 viruses, and 6 fungi). Furthermore, hc-tNGS detected additional low-abundance pathogens in 17 mNGS-positive patients (28.3%, 17/60) and 8 mNGS-negative patients (11.3%, 8/60). The normalized reads for viruses, bacteria, and fungi in hc-tNGS were 57.2-, 2.7-, and 3.3-fold higher than those in mNGS, respectively (P < 0.001, P = 0.003, and P = 0.028). Moreover, hc-tNGS reduced TAT by 11.3% (18.0 versus 20.3 h) and costs by 22.4–48.8%. The median of sequencing data size of mNGS was 29.8 million (29.8 M) reads, which was significantly higher than that of tNGS (1.5 M, P < 0.001). CONCLUSION: hc-tNGS demonstrates superior performance and cost-effectiveness in detecting potential pathogens of ...