16S rRNA nanopore sequencing for the diagnosis of ocular infection: a feasibility study

ObjectiveWe conducted a feasibility study to verify the effectiveness of 16S ribosomal RNA (rRNA) gene analysis using the nanopore sequencer MinION for identifying causative bacteria in several types of ocular infections.Methods and AnalysisFour cases of corneal ulcers, one case of endophthalmitis a...

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Bibliographic Details
Published in:BMJ open ophthalmology 2022-05, Vol.7 (1), p.e000910
Main Authors: Omi, Masatoshi, Matsuo, Yoshiyuki, Araki-Sasaki, Kaoru, Oba, Shimpei, Yamada, Haruhiko, Hirota, Kiichi, Takahashi, Kanji
Format: Article
Language:English
Subjects:
Abscess
Abscesses
Antibiotics
Bacteria
Bacterial infections
Classification
Cornea
Cysts
diagnostic tests/investigation
DNA, Bacterial - genetics
Eye Infections, Bacterial - diagnosis
Feasibility Studies
Genes
Genetics
Humans
Identification
infection
microbiology
Nanopore Sequencing
Nanopores
Organisms
Patients
RNA, Ribosomal, 16S - genetics
Software
Streptococcus infections
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Summary:ObjectiveWe conducted a feasibility study to verify the effectiveness of 16S ribosomal RNA (rRNA) gene analysis using the nanopore sequencer MinION for identifying causative bacteria in several types of ocular infections.Methods and AnalysisFour cases of corneal ulcers, one case of endophthalmitis and one case of a conjunctival abscess were included in this study. DNA was extracted from corneal scraping, vitreous samples and secretions from the conjunctival abscess. We conducted 16S rRNA gene amplicon sequencing using MinION and metagenomic DNA analysis. The efficacy of bacterial identification was verified by comparing the conventional culture method with smear observations.Results16S rRNA gene sequencing analysis with MinION identified the causative organisms promptly with high accuracy in approximately 4 hours, from ophthalmic specimens. The results of the conventional culture method and 16S rRNA gene sequencing were consistent in all cases. In four of the six cases, a greater variety of organisms was found in the 16S rRNA gene analysis than in bacterial culture.ConclusionUsing our workflow, 16S rRNA gene analysis using MinION enabled rapid and accurate identification possible in various kinds of bacterial ocular infections.
ISSN:2397-3269
2397-3269
DOI:10.1136/bmjophth-2021-000910