Scanning the genome of the bacteria behind a common eye infection

Research details

  • Type of funding: Project Grant
  • Grant Holder: Professor Craig Winstanley
  • Institute: University of Liverpool
  • Region: North West
  • Start date: October 2014
  • End Date: September 2017
  • Priority: Causes
  • Eye Category: Corneal & external


The cornea is the clear outer layer that covers the front of the eye. It protects the eye and helps to bend incoming light. Bacterial infections in the cornea cause inflammation (bacterial keratitis) and are a major cause of sight loss with 6000 UK infections every year.

About 1 in 4 cases of severe bacterial keratitis are due to bacteria called P. aeruginosa. But current treatments don’t work well and contribute to antibiotic resistance.

P. aeruginosa can cause a range of other infections in different parts of the body and the team’s previous work has shown that there seems to be a population that is specific to eye infection.

In this project the team is doing a more detailed search for the genes that mark out this strain of the bacteria compared to others. If we understand the genetic difference between strains, particularly the strain of P.aeruginosa that causes infection of the cornea, we can start to develop therapies to specifically target that strain as well as tests to work out who might benefit most from treatment.
  • Scientific summary

    Comparative genomics of UK Pseudomonas aeruginosa keratitis isolates to identify links between genotypic and clinical characteristics

    Bacterial infections of the cornea are a major cause of visual loss world-wide, with approximately 6000 cases of bacterial keratitis per year in the UK. Through the UK Microbiology Ophthalmic Group (MOG), the research team has collected 658 isolates of Pseudomonas aeruginosa associated with keratitis (2003-2012), and have linked clinical metadata.

    Previously, they have shown that P. aeruginosa isolates from keratitis form a distinct cluster amongst the wider P. aeruginosa population. In this study, the team is using a much higher resolution genotyping approach. They are using whole genome sequencing (WGS) of each of the isolates in order to comprehensively characterize the UK P. aeruginosa keratitis-associated population.

    Genomic DNA are being isolated from each of the 658 P. aeruginosa isolates, and barcoded sequencing libraries are being prepared using the Illumina Nextera XT protocol, batched and sequenced on the Illumina MiSeq. In addition, a selection of isolates representative of major lineages identified by the study is being sequenced using the Pacific Biosciences RSII platform to serve as reference sequences.

    By using comparative genomics approaches, and linking with other P. aeruginosa genome projects, the team aims to identify keratitis-specific P. aeruginosa genes. In addition, they will use bioinformatics to identify associations between pathogen gene content and characteristics such as clinical response outcomes, antimicrobial susceptibilities, and risk factors (such as contact lens wear). The team will use these approaches to (i) develop meaningful algorithms for the stratification of patients based on pathogen genotypes, and (ii) identify novel therapeutic targets for further development.