For more than a decade, whole genome sequencing (WGS) technologies have been successfully implemented to track the transmission of bacteria throughout global public health systems. Unprecedented advances in the accuracy, speed, and throughput of these sequencing technologies have driven an explosion of bacterial WGS data and catapulted the integration of genomic pipelines directly into healthcare settings.
Despite the many advances in genomic surveillance of pathogens, one of the main challenges remaining is how to track plasmids, which are known to be important drivers of both antimicrobial resistance and virulence. In this talk, I will discuss advances in bioinformatics methods for plasmid epidemiology and transmission in healthcare settings, by utilising publicly available data and the plasmid pangenome.