Deep metagenomic sequencing for endophthalmitis pathogen detection using a nanopore platform

PURPOSE: To evaluate the utility of nanopore sequencing for identification of 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 twenty-three patients (median age 68.5[range 47–88] years; 14[61%] male), 18 cases were culture-positive. Nanopore sequencing identified the same cultured organism as in all of the culture-positive cases and identified potential pathogens in 2(40%) of culture-negative cases. Nanopore WGS was able to additionally detect the presence of bacteriophages in three samples. The agreement at genus level between culture and 16S Nanopore, Nanopore WGS and Illumina WGS were 75%, 100% and 78% respectively. CONCLUSIONS: WGS has higher sensitivity and provides a viable alternative to culture and 16S sequencing for detection of 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.