Antimicrobial resistance surveillance: lessons learnt from large databases of antimicrobial resistance genes

Ocular infections, caused by a variety of microbes, are likely to become more difficult to treat due to the global increase in antimicrobial resistance (AMR). Traditional assays for resistance only analyse a small proportion of the possible resistance capability of microbes. This review discusses the use of genomic datasets for predicting AMR and their current applications in investigating ocular infections. The use of whole genome sequencing coupled with several large databases on antimicrobial resistance genes (ARGs) can predict phenotypic resistance and multidrug resistance in bacteria. Use of this technology for viral and fungal infections is less advanced and would be a useful area for future research. Metagenomic analysis of the ocular surface microbiome for ARGs could be a sensitive and rapid method for tracking resistance in ocular infections, and monitoring commensal reservoirs of transferable ARGs. Applications of these newer technologies to ocular infections also have the potential to assess the long-term impact of topical antibiotics, disinfectants and preservative use on the ocular microbiome, as well as being used in epidemiological studies to study acquisition and transmission of ARGs.