Dataset Information

Deep Metagenomic Sequencing for Endophthalmitis Pathogen Detection Using a Nanopore Platform.

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.

SUBMITTER: Low L

PROVIDER: S-EPMC9850836 | biostudies-literature | 2022 Oct

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Deep Metagenomic Sequencing for Endophthalmitis Pathogen Detection Using a Nanopore Platform.

Low Liying L Nakamichi Kenji K Akileswaran Lakshmi L Lee Cecilia S CS Lee Aaron Y AY Moussa George G Murray Philip I PI Wallace Graham R GR Van Gelder Russell N RN Rauz Saaeha S

American journal of ophthalmology 20220531

<h4>Purpose</h4>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).<h4>Design</h4>Cross-sectional diagnostic comparison.<h4>Methods</h4>Patients with clinically suspected endophthalmitis underwent intraocular vitreous biopsy as per standard care. Clinical samples were c ...[more]

PMID: 35660421

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Dataset Information

Deep Metagenomic Sequencing for Endophthalmitis Pathogen Detection Using a Nanopore Platform.

Purpose

Design

Methods

Results

Conclusions

Publications

Deep Metagenomic Sequencing for Endophthalmitis Pathogen Detection Using a Nanopore Platform.

Similar Datasets

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