Rapid Pathogen Detection in Infectious Uveitis Using Nanopore Metagenomic Next-Generation Sequencing: A Preliminary Study

ABSTRACT

Purpose

We establish an accurate and rapid diagnostic method for pathogen detection in infectious uveitis using nanopore metagenomic next-generation sequencing (NGS).

Methods

In eight patients with suspected infectious uveitis, we prospectively compared the accuracy and time taken for pathogen identification between conventional diagnostic methods, such as cultures and PCR, and nanopore metagenomic NGS.

Results

All causative pathogens were identified using nanopore sequencing, while only five of the eight patients were confirmed positive for a specific pathogen using conventional methods. The overall sample-to-answer turnaround time of nanopore sequencing was much shorter than that of conventional methods in the bacterial and fungal infection (mean, 17 h vs. 4d, respectively; P = .028). The pathogens could be detected even when the quantity or quality of DNA was not optimal.

Conclusion

Nanopore metagenomic NGS is a promising diagnostic tool that can rapidly and accurately identify the causative pathogen in infectious uveitis.

KEYWORDS:

• Metagenomics
• nanopore sequencing
• next generation sequencing
• pathogen detection
• uveitis

Acknowledgments

Involved in design of the study (J.L., M.K.); conduct of the study (J.L., H.J., H.G.K., and M.K.); data collection (J.L., H.J., E.Y.C., C.S.L., S.H.B., and M.K.); data analysis (J.L., H.J., H.G.K., J.P., and M.K.); data interpretation (J.L., H.J., and M.K.); and preparation, review, and approval of the manuscript (J.L., H.J., H.G.K., and M.K.). The authors thank Medical Illustration & Design, part of the Medical Research Support Services of Yonsei University College of Medicine, for all artistic support related to this work.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Data availability statement

The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.

Supplementary material

Supplemental data for this article can be accessed online at https://doi.org/10.1080/09273948.2023.2173243

Additional information

Funding

This study was supported by the “Hankookilbo Myung-Ho Seung” faculty research grant assistance program of Yonsei University College of Medicine [6-2020-0236] and the National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT) [No. 2019R1A2C2086729] and Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education [No. 2021R1I1A1A01045648]. The funding organization had no role in the design or conduct of this research.