ArticleBMC infectious diseases2025
Evaluation of hybrid capture-based targeted and metagenomic next-generation sequencing for pathogenic microorganism detection in infectious keratitis.
Article in BMC infectious diseases, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
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Who cites it
2 citing papers in PubMed.
- Validation of a long-read 16S rRNA-gene sequencing approach for analysis of clinical samples and bacterial identification in a routine clinical laboratory.Frontiers in microbiology · 2026Article
- Application of Probe-Capture metagenomics in rabies diagnosis.Virology journal · 2025Article
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Authors and funding
12 authors.
Funding
Abstract
objectiveThis 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.
methodsA 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.
resultshc-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).
conclusionhc-tNGS demonstrates superior performance and cost-effectiveness in detecting potential pathogens of infectious keratitis, especially low-abundance pathogens, whereas mNGS remains valuable for detecting novel pathogens. Owing to its enhanced performance, faster TAT, and reduced costs, hc-tNGS is a promising clinical tool for pathogen detection.
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