Genomic Sequecing for identification of pathogens in ulcerative keratitis

This is a look into the future. Diagnosing the causative organism in a infectious ulcerative keratitis case is time consuming and has low sensitivity to organisms requiring specialized culture media. Instead of submitting 3 samples for culture why not test to see what organisms are present by checking the genes present. This study found it more sensitive than culture for both bacteria and fungi. Not in the paper are turn around time and cost but I would guess this is coming to a veterinary lab near you soon.
DrO

Evaluation of a commercial NGS service for detection of bacterial and fungal pathogens in infectious ulcerative keratitis
Vet Ophthalmol. 2023 Nov;26(6):500-513. doi: 10.1111/vop.13069. Epub 2023 Mar 21.
Authors
Ashley Bendlin 1 , Anne J Gemensky-Metzler 1 , Dubraska Diaz-Campos 1 , Georgina M Newbold 1 , Eric J Miller 1 , Heather L Chandler 1 2
Affiliations

1 Department of Veterinary Clinical Sciences, The Ohio State University, Columbus, Ohio, USA.
2 College of Optometry, The Ohio State University, Columbus, Ohio, USA.

PMID: 36943705
DOI: 10.1111/vop.13069

Abstract

Objectives: To compare results from a commercial next-generation sequencing (NGS) service to corneal cytology and culture for identification of causative organisms in veterinary patients presenting for infectious ulcerative keratitis (IUK).

Procedure: Swabs for corneal aerobic and fungal cultures and DNA swabs for NGS were submitted for canine and equine normal controls (n = 11 and n = 4, respectively) and IUK patients (n = 22 and n = 8, respectively) for which microbrush cytology specimens confirmed the presence of infectious organisms. The sensitivity of the NGS results was compared with bacterial and fungal culture results. Concordance between the NGS and culture results was determined.

Results: The NGS results were positive for bacterial and fungal organisms in 5 and 1 normal and 18 and 1 IUK cases, respectively. Bacterial and fungal cultures were positive for 7 and 2 normal and 20 and 5 IUK cases, respectively. Sensitivity of NGS was 82.14% (95% confidence interval (CI), 63.11% to 93.94%) and specificity was 76.47% (95% CI, 50.10% to 93.19%). Concordance (complete and partial) between identified bacterial and fungal organisms was found in 79% and 100% of cases, respectively. NGS identified organisms in 3 culture-negative IUK samples.

Conclusion: A commercial NGS service may be useful in the identification of causative agents in IUK cases with a sensitivity greater than the sensitivity previously reported for aerobic culture. Further testing is needed to determine the clinical significance of additional organisms isolated by NGS from infected cases, as well as organisms isolated from normal corneas.

Keywords: bacterial culture; fungal culture; infectious ulcerative keratitis; next-generation sequencing; sensitivity.

© 2023 American College of Veterinary Ophthalmologists.