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2026 OMIG Abstract

Metagenomic RNA Sequencing Reveals Diverse Pathogens in Infectious Keratitis in a German Cohort

Yaser Abu Dail¹, Loay Daas¹, Loic Hamon¹, Elias Flockerzi¹, Tim Berger¹, Alberic Sneyers¹, Zamira Hoxha¹, Julian Kahlert¹, Ori Saban^2,3, Kelly Ngo², Danny Yu², Thomas Abraham², YuHeng Liu², Armin Hinterwirth², Berthold Seitz¹, Thuy Doan^2,3, and Gerami D. Seitzman^2,3 on behalf of the capriCORN Study Group

¹Department of Ophthalmology, Saarland University Medical Center, Homburg, Germany; ²Francis I. Proctor Foundation, University of California, San Francisco, California; ³Department of Ophthalmology, University of California, San Francisco, California

Purpose: To characterize the microbial etiologies of infectious keratitis at a German tertiary ophthalmology center using metagenomic RNA sequencing (RNA-seq) and to identify clinical factors associated with pathogen detection.

Methods: Patients with presumed infectious keratitis presenting to Saarland University Medical Center between July 2023 and April 2025 were prospectively enrolled in the NEI-funded capriCORN study. Corneal swabs obtained at presentation were analyzed by RNA-seq. Clinical factors were compared between RNA-seq-positive and RNA-seq-negative cases using chi-square tests.

Results: Of 121 patients enrolled, a likely pathogen was identified in 57 (47%). Bacteria predominated among positive cases (40/57, 70%), followed by viruses (6/57, 11%), polymicrobial infections (6/57, 11%), fungi (4/57, 7%), and Acanthamoeba spp. (1/57, 2%). Moraxella spp. and Pseudomonas spp. were the most frequently identified bacteria. Several uncommon or unexpected pathogens were also detected, including Rothia spp., Achromobacter xylosoxidans, Alternaria alternata, Abiotrophia defectiva, and human herpesvirus 6A. Patients presenting with hypopyon were more likely to be RNA-seq-positive than those without (17/24, 71% vs. 37/92, 40%; P=0.007), whereas patients reporting corneal trauma were more likely to be RNA-seq-negative (11/13, 85% vs. 53/107, 50%; P=0.015).

Conclusions: Metagenomic RNA sequencing revealed a broad spectrum of infectious keratitis pathogens in this German cohort, including several uncommon organisms that targeted diagnostic methods may miss. Hypopyon was associated with increased pathogen detection. These findings highlight the potential value of metagenomic sequencing for defining regional microbial epidemiology and detecting unexpected pathogens.