Ocular Microbiology and Immunology Group
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2024 OMIG Abstract

Adaptive Nanopore Sequencing for Rapid Diagnosis of Infectious Keratitis

Marcus Toral, Kenji Nakamichi, Behrouz Rahimi, Miel Sundararajan, Russell Van Gelder

Department of Ophthalmology, Roger and Karalis Johnson Retina Center, University of Washington,
Seattle, WA

Purpose: To compare adaptive nanopore metagenomic DNA sequencing to microbiological culture for cases of infectious keratitis.

Methods: This work was approved by the University of Washington IRB. Corneal scrapings from subjects with infectious keratitis underwent parallel culturing and adaptive nanopore sequencing. For each sample, pathogenic organisms were identified via culturing and nanopore sequencing and compared in terms of agreement and time-to-result.

Results: Corneal scrapings (n = 20) were collected from 19 subjects with infectious keratitis. Mitigating historical risk factors included topical antibiotic use (74%), recent contact lens wear (53%), recent topical steroid use (37%), and recent eye surgery (21%). Of the 20 samples, sequencing and culture were in agreement on 13 (9 negative by both culture and sequencing and four positive by both). Four samples yielded organisms on culture but not on sequence, and two yielded organisms on sequence but not culture. One sample was discordant for organism between culture and sequence. The median time to result for culture and nanopore sequencing were 47 and 28 hours respectively (p = 0.0012). Three samples with particularly robust nanopore sequencing coverage identified a causative pathogen in several hours, each of which matched culture results.

Conclusions: Preliminary data showed that nanopore sequencing was accurate and significantly faster than culture. While further study in a larger cohort is needed, this work is a promising early proof-of-concept study showing the clinical utility of adaptive nanopore sequencing for diagnosis of infectious keratitis.


Disclosure:

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