Total Infectome Characterization of Eye Infections: a Metagenomic Sequencing Based Observational Study

This is an investigator-initiated observational study to describe the total infectome of eye infections using metagenomic sequencing. The eye infections, including acute conjunctivitis, keratitis, uveitis, and endophthalmitis, are diagnosed by experienced ophthalmologists according to routine clinical exams.

For the collection of additional biological samples apart from the diagnosis and treatment process, written informed consent is required from the eligible subjects or their legal guardians at the recruitment time is required. The application for exemption of informed consent has been made for using clinical surplus samples. After completing informed consent, subjects will be sampled, and their clinical information will be collected.

Biospecimens, including conjunctival sac swabs (1 swab for each involving eye), or intraocular fluid (more than 100μl), will be collected for metagenomic sequencing using the Illumina NovaSeq X Plus platform.

The clinical information of participants will be collated from electronic medical record information system, including (1) demographic characteristics: age, sex, comorbidities; (2) laboratory examination: blood routine test, immune inflammatory factors, clinical microbiology examination (PCR, serological examination, culture, etc.); (3) imaging examination: anterior segment photograph, corneal endothelial cell examination, corneal confocal microscopy, fundus photograph.

Meta-transcriptomic analysis of the ocular samples will be conducted to identify viruses, bacteria, fungi and parasites. The abundance of pathogens is indicated as the RPKM (i.e. Reads Per Million divided by the length of the reference genome, measured in kilobases).