Deep Metagenomic Sequencing for Endophthalmitis Pathogen Detection Using a Nanopore Platform
Year: 2022
Type: article
Study design: Observational Study
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.
Language: English
Subfield: Ophthalmology
Field: Medicine
Domain: Health Sciences
Open Access status: hybrid
Estimated APC paid: $4,260
Funders: Research to Prevent Blindness, Microsoft, Tufts Medical Center, University of Washington, Ministry of Defence, American Academy of Ophthalmology, Sandwell and West Birmingham Hospitals NHS Trust, Lowy Medical Research Institute, National Institute for Health and Care Research, Fight for Sight UK, University of Oxford, University of Birmingham, Carl Zeiss Meditec AG, Santen, Surgical Reconstruction and Microbiology Research Centre, Royal Centre for Defence Medicine, National Institutes of Health, U.S. Food and Drug Administration, Medical Research Council, National Institute on Aging, National Eye Institute, Alcon Research Institute, Medical Research Foundation
Awards: G1797649271, G273314416, G3425063740, G3518750285, G4905407598, Development of a synthetic flowable dressing that prevents corneal scarring, G5310225311, G5588401280, G5643765635, G5999546765, G7950680578, G8153097362, G8323638718, G9000333565, Adult Changes in Thought (ACT) Research Program, Aging eyes and aging brains in studying alzheimer''s disease: Modern ophthalmic data collection in the adult changes in thought (ACT) study
OpenAlex ID: W4281670023