Rapid Pathogen Detection in Severe Infectious Keratitis: Prospective Evaluation of Combined Multiplex PCR Panels Versus Standard Microbiology

Rapid pathogen identification in severe infectious keratitis is critical for targeted therapy to prevent vision loss, but conventional methods are slow and only moderately sensitive. Our objective was to evaluate the diagnostic accuracy and turnaround time of combined FilmArray® Meningitis-Encephalitis (ME)/Blood Culture Identification (BCID) multiplex polymerase chain reaction (PCR) panels versus standard microbiology (culture + pathogen-specific PCR) in severe infectious keratitis. This was a prospective pilot diagnostic study at a French tertiary center (July 2023–April 2025) including 23 adults with severe microbial keratitis. Corneal samples were analyzed using both conventional microbiological testing (culture and pathogen-specific PCR) and rapid multiplex PCR with the FilmArray® ME and BCID panels. Primary outcomes were diagnostic agreement between the FilmArray® multiplex PCR system and conventional microbiological methods, measured by Cohen’s κ coefficient. Turnaround times were compared using the Wilcoxon signed-rank test. Among 23 adult patients (mean age 61.0 [SD 21.2] years, range 24–99; 13 female patients [56.5%]), conventional microbiology identified pathogens in 16 cases (69.5%) versus 15 (65.2%) with multiplex PCR. Overall diagnostic agreement was moderate (κ = 0.50; 95% CI, 0.25–0.76), with perfect concordance (12/12, 100%) for monomicrobial infections detected by both methods. Multiplex PCR significantly reduced mean time to identification (2 h [no variation]) versus conventional methods (102 [SD 42.5] h; P < .001). Both methods were negative in six patients (26.1%) with comparable clinical severity. Combined FilmArray® ME/BCID panels demonstrated complete concordance with standard microbiology for monomicrobial keratitis and reduced turnaround times by > 100 h. This strategy may accelerate targeted therapy, potentially improving visual outcomes. Infectious keratitis is a painful and potentially serious eye infection that can eventually lead to significant vision loss. The agents responsible for these infections are most often bacteria, but fungi or parasites can cause similar symptoms, particularly in contact lens wearers. In order to identify the causative organism, samples are taken from the infected area for microbiological analysis. The treatment of severe infectious keratitis involves the intensive instillation of high doses of local antibiotics, sometimes during hospitalization, in order to limit the progression of the infection as much as possible. This local treatment will then be adapted to the germ identified by the microbiology laboratory. Severe infectious keratitis is frequently challenging to manage due to the inability to identify the causative pathogen in a substantial proportion of cases. To address this issue, we evaluated a novel microbiological detection approach utilizing multiplex polymerase chain reaction (PCR; FilmArray®, BioMérieux, France) in patients with severe infectious keratitis, aiming to expedite targeted therapy initiation. In this pilot study involving 23 patients, conventional microbiological methods identified the causative pathogens in 16 cases (69.5%), compared with 15 (65.2%) detected using the FilmArray® system, showing acceptable concordance between the two methods. The main advantage of FilmArray® is its shorter turnaround time. It provides results in about 2 hours, compared with 102 hours for traditional techniques. These promising results suggest that rapid molecular diagnostics may facilitate earlier adjustment of topical antibiotic therapy, potentially enhancing visual outcomes after such an infection. Nevertheless, validation in larger cohorts is required, and further research should assess the potential impact on long-term visual function.