Yale researchers identify corneal ulcer pathogens by testing tears

Using real-time DNA sequencing, scientists can now detect bacterial pathogens in corneal ulcers without the need for traditional corneal scraping. (Image credit: AdobeStock/Vitalii Vodolazskyi)

Researchers at Yale School of Medicine have identified in a new study a novel, noninvasive method for diagnosing bacterial corneal ulcers, a serious ophthalmologic condition that can lead to vision loss.¹

Corneal ulcers, primarily caused by microbial keratitis, represent a global health challenge, contributing to up to 2 million cases of blindness annually. Current diagnostic methods rely on corneal scraping and culturing, which are invasive, time-consuming, and often yield false-negative results.¹

“This work has the potential to redefine the diagnostic standard of care for corneal ulcers,” said Mathieu Bakhoum, MD, PhD, assistant professor of ophthalmology and visual science and senior author of the study. “Timely and targeted treatment prevents ulcer progression, reduces broad-spectrum antibiotic use, and diminishes the downstream need for surgical interventions.”

In a study published in Translational Vision Science and Technology, the Yale team used samples from 10 patients with bacterial corneal ulcers to compare traditional scrape-based culture diagnostics with nanopore-based DNA sequencing performed on tear samples using Oxford Nanopore Technologies’ portable MinION sequencer.¹

“We were able to show that we can amplify the 16S rRNA bacterial gene directly from tears—bypassing both corneal scraping and nucleic-acid extraction—and obtain real-time, species-level identification using a handheld sequencer,” Backhoum said.

Researchers report the nanopore sequencing matched traditional cultures in all cases where the culture identified bacterial pathogens, and even detected bacteria in 2 cases where cultures were inconclusive. The Yale team said the sequencing of tears provided results in hours, compared with days for traditional culture-based methods.

Further research is needed to validate the technique across diverse pathogens and populations. Researchers said faster turnaround times in corneal ulcer diagnosis could reduce delays in treatment and result in better outcomes and less vision loss worldwide.

The research was supported by a grant from the Connecticut Lions Eye Research Foundation.

Reference

1. Dibbs M, Matesva M, Theotoka D, et al. A tear-based approach for rapid identification of bacterial pathogens in corneal ulcers using nanopore sequencing. Transl Vis Sci Technol. 2025;14(4):19. doi:10.1167/tvst.14.4.19