Deep Metagenomic Sequencing for Endophthalmitis Pathogen Detection Using a Nanopore Platform.
Nakamichi, Kenji Akileswaran, Lakshmi Lee, Cecilia S Lee, Aaron Y Wallace, Graham R Van Gelder, Russell N
Nakamichi, Kenji
Akileswaran, Lakshmi
Lee, Cecilia S
Lee, Aaron Y
Wallace, Graham R
Van Gelder, Russell N
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Affiliation
Birmingham and Midland Eye Centre, Sandwell and West Birmingham Hospitals NHS Trust; University of Washington School of Medicine; Academic Unit of Ophthalmology, Institute of Inflammation and Ageing, University of Birmingham;
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Publication date
2022-05-31
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Abstract
Purpose: To evaluate the utility of nanopore sequencing for identifying potential causative pathogens in endophthalmitis, comparing culture results against full-length 16S rRNA nanopore sequencing (16S Nanopore), whole genome nanopore sequencing (Nanopore WGS), and Illumina (Illumina WGS).
Design: Cross-sectional diagnostic comparison.
Methods: Patients with clinically suspected endophthalmitis underwent intraocular vitreous biopsy as per standard care. Clinical samples were cultured by conventional methods, together with full-length 16S rRNA and WGS using nanopore and Illumina sequencing platforms.
Results: Of 23 patients (median age 68.5 years [range 47-88]; 14 males [61%]), 18 cases were culture-positive. Nanopore sequencing identified the same cultured organism in all of the culture-positive cases and identified potential pathogens in two culture-negative cases (40%). Nanopore WGS was able to additionally detect the presence of bacteriophages in three samples. The agreements at genus level between culture and 16S Nanopore, Nanopore WGS, and Illumina WGS were 75%, 100%, and 78%, respectively.
Conclusions: Whole genome sequencing has higher sensitivity and provides a viable alternative to culture and 16S sequencing for detecting potential pathogens in endophthalmitis. Moreover, WGS has the ability to detect other potential pathogens in culture-negative cases. Whilst Nanopore and Illumina WGS provide comparable data, nanopore sequencing provides potential for cost-effective point-of-care diagnostics.
Citation
Low, L., Nakamichi, K., Akileswaran, L., Lee, C. S., Lee, A. Y., Moussa, G., Murray, P. I., Wallace, G. R., Van Gelder, R. N., Rauz, S., & West Midlands Collaborative Ophthalmology Network for Clinical Effectiveness & Research by Trainees (WM CONCERT) (2022). Deep Metagenomic Sequencing for Endophthalmitis Pathogen Detection Using a Nanopore Platform. American journal of ophthalmology, 242, 243–251. https://doi.org/10.1016/j.ajo.2022.05.022
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Article