Public Health Microbiology reference laboratories fulfil a critical role in providing overarching testing and surveillance for notifiable, emerging and foodborne pathogens. These duties require the laboratory to possess an extensive repertoire of validated assays and the ability to rapidly respond to novel threats and outbreaks. For these, among other reasons, the “one stop shop” approach of whole genome sequencing (WGS) has been embraced by public health microbiology laboratories. Public health genomics played a critical role in Australia’s response to the COVID-19 pandemic and public health laboratories leveraged off existing networks and collaborations to create harmonised national sequence surveillance. This talk will discuss how public health genomics is moving beyond the pandemic and playing an integral real time role in how disease clusters and outbreaks are not only discovered but in informing on transmission and public health responses and control measures. Some case studies will be discussed focusing on how genomics is being utilised for a number of emerging pathogens causing concerning disease clusters in Australia including Burkholderia pseudomallei, toxigenic Corynebacterium diphtheriae and incursions of multi-drug resistant bacteria of public health importance.