A Study of Infections of the Front of the Eye (Cornea)

Microbial keratitis (MK) is an ophthalmological emergency that can lead to sight threatening complications such as corneal scarring, perforation, endophthalmitis and ultimately blindness. The patient requires aggressive topical antimicrobial therapy and close treatment response monitoring, often including hospitalisation followed by frequent outpatient visits.

Improving outcomes depends on rapidly identifying the causative microorganism. Currently the likely causative microorganism is only isolated in around 30 to 40% of cases using traditional scraping methods and standard conventional diagnostic culture (CDC), with results typically taking up to 4 days to become available to the clinician. More sensitive methods such as microorganism targeted polymerase chain reaction (MTPCR) and metagenomic analysis increase the potential to detect microorganisms but may increase the likelihood of picking up commensal microorganisms, making it difficult for the treating clinician to interpret which of the isolated organisms is likely to be causative in MK.

One of the barriers to identifying the organisms has been the difficulty in collecting samples from the cornea. In 2015, a group led by Professor Kaye at the University of Liverpool developed a non- invasive corneal sampling methodology using a corneal impression membrane (CIM) made from polytetrafluoroethylene. This was shown to have a significantly higher overall isolation rate compared to conventional scraping methods. As it is minimally invasive, the CIM sampling method offers a unique opportunity to sample both the affected cornea and unaffected cornea of patients presenting with MK as well as the eyes of patients unaffected by MK. This will enable a much better understanding of the clinical significance of isolated organisms in MK.

Metagenomic next-generation sequencing (NGS) techniques enable the genomic analysis of all the microbes in a sample, giving a wealth of information regarding the presence and interaction of microorganisms as well as the presence or absence of antimicrobial resistance (AMR) genes. Previous studies attempting to characterise the ocular surface microbiome in health using metagenomics have demonstrated a diverse resident homeostatic microbiome, however, have been limited to swabs taken from the lid, conjunctiva and tears rather than the cornea. Variations in the microbiome have been associated with conditions such as dry eye syndrome, contact lens wear and infectious pathologies, including a pathological microbiome dominated by pseudomonas spp. in a small number of patients with bacterial keratitis. Despite the cornea being the surface affected by MK, there is no data regarding the healthy corneal microbiome because traditional sampling methods have been invasive.

Despite NGS generating personalised results in a matter of hours, its sensitivity to detect all organisms present without an understanding of their clinical significance is a barrier to its introduction into clinical practice. In this project, the CIM sampling method and NGS processing will be used to improve understanding of the causative organisms in MK. Furthermore, through sampling both the affected and unaffected eyes of MK patients and from those without MK, a diagnostic rule will be developed to identify and discount commensal organisms. The inclusion of different control groups will also provide information on the influence of contact lenses and eye drops on the microbiome, which have a role both on the development and treatment of MK. This will greatly facilitate current interpretation of corneal sample results and facilitate potential future use of NGS in routine ophthalmic clinical practice.