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Updated: Sep 21, 2025
Nanopore DNA Sequencing for Metagenomic Soil Analysis
Published on: December 14, 2017
Deep Metagenomic Sequencing for Endophthalmitis Pathogen Detection Using a Nanopore Platform
Liying Low1, Kenji Nakamichi2, Lakshmi Akileswaran2
1From the Academic Unit of Ophthalmology, Institute of Inflammation and Ageing, University of Birmingham, United Kingdom (L.L, P.I.M, G.R.W, S.R); Birmingham and Midland Eye Centre, Sandwell and West Birmingham Hospitals NHS Trust, Birmingham, United Kingdom (L.L, G.M, P.I.M, S.R).
Whole genome sequencing (WGS) offers a sensitive alternative to traditional culture and 16S sequencing for identifying endophthalmitis pathogens. Nanopore sequencing, in particular, shows promise for cost-effective, point-of-care diagnostics.
Area of Science:
- Ophthalmology
- Microbiology
- Genomics
Background:
- Endophthalmitis is a serious intraocular infection requiring prompt diagnosis.
- Conventional culture methods can be slow and may fail to detect all causative pathogens.
- Next-generation sequencing offers potential for rapid and comprehensive pathogen identification.
Purpose of the Study:
- To assess the diagnostic utility of nanopore sequencing for identifying endophthalmitis pathogens.
- To compare nanopore sequencing (16S rRNA and whole genome) with conventional culture and Illumina whole genome sequencing (WGS).
Main Methods:
- A cross-sectional study involving patients with suspected endophthalmitis.
- Intraocular vitreous biopsies were subjected to conventional culture, 16S rRNA nanopore sequencing, whole genome nanopore sequencing (WGS), and Illumina WGS.
Main Results:
- Nanopore sequencing correctly identified all culture-positive organisms and detected pathogens in 40% of culture-negative cases.
- Nanopore WGS identified bacteriophages in three samples, a capability not assessed in culture.
- Genus-level agreement with culture was highest for Nanopore WGS (100%), followed by Illumina WGS (78%) and 16S Nanopore (75%).
Conclusions:
- Whole genome sequencing (WGS) demonstrates superior sensitivity for pathogen detection in endophthalmitis compared to culture and 16S sequencing.
- WGS can identify pathogens in culture-negative samples and detect additional microbial elements like bacteriophages.
- Nanopore sequencing presents a viable, potentially cost-effective option for point-of-care endophthalmitis diagnostics.
