iCam microarray PCR and metagenomics in the diagnosis of microbial keratitis: a case series

Abstract: Purpose: To compare the diagnostic performance of an ophthalmology-specific microarray polymerase chain reaction (iCAM PCR) and metagenomic next-generation sequencing (mNGS) against conventional microbiological investigations in microbial keratitis in a case series of patients with microbial keratitis. Methods: Corneal epithelial scrapes from four patients with microbial keratitis were analysed using iCAM microarray PCR (multiplex PCR) and mNGS as part of the iCAM clinical trial (ISRCTN17422545). Parallel samples underwent standard microbiological testing, including microscopy, culture, and real-time PCR according to local protocol. The turnaround time, microbial detection, concordance between modalities, and the influence of results on clinical decision-making are reported. Results: iCAM microarray PCR identified the causative organism in three of four cases (Candida parapsilosis, Streptococcus pneumoniae and Acanthamoeba castellanii), in agreement with conventional methods. iCAM microarray PCR turnaround time was 6 hours, turnaround time for conventional microbiology ranged between 2 and 14 days. mNGS identified the pathogen in all 4 cases with a turnaround time of 1-2 days. Capnocytophaga was exclusively identified by mNGS in a rapidly progressive keratitis, where both iCAM and routine microbial tests had failed to detect the organism. Conclusion: Microarray PCR and mNGS have the potential to improve microbial detection, reduce diagnostic delays and ultimately enhance clinical outcomes in microbial keratitis. Larger studies are required to define their optimal integration into routine clinical practice.