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

BMJ Open Ophthalmol. 2022 May;7(1):e000910. doi: 10.1136/bmjophth-2021-000910. Epub 2022 May 24.


Objective: We 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 analysis: Four 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.

Results: 16S 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.

Conclusion: Using our workflow, 16S rRNA gene analysis using MinION enabled rapid and accurate identification possible in various kinds of bacterial ocular infections.

Keywords: diagnostic tests/investigation; infection; microbiology.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Abscess
  • DNA, Bacterial / genetics
  • Eye Infections, Bacterial* / diagnosis
  • Feasibility Studies
  • Humans
  • Nanopore Sequencing*
  • Nanopores*
  • RNA, Ribosomal, 16S / genetics


  • DNA, Bacterial
  • RNA, Ribosomal, 16S