Public Health Microbiology reference laboratories fulfil a critical role in providing overarching testing and surveillance for notifiable, emerging and important 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 microbiology reference laboratories. The ability to replace multiple labour intensive assays, with a single technique of superior typeability and discrimination, though not without its challenges, has already begun to change the workflow of reference laboratories.  Some examples of implementation of real time WGS for disease surveillance in Queensland for Salmonella, Shigella and Group A Streptococus will be discussed, highlighting not only the improvements made to outbreak investigations and changes to testing regimes but also where there is still further development required to complete integration of genomics into public health microbiology.

Metagenomic or deep sequencing directly on clinical specimens has more recently emerged as a valuable technique in public health microbiology. This approach may fill the gap in epidemiological data caused by the increase in culture independent diagnostic testing (CIDT) in pathology laboratories. Molecular diagnosis has many advantages for patient care, however the absence of isolates subsequently available for public health surveillance is concerning. Deep sequencing on clinical samples containing N. gonorrhoeae, S. pneumoniae and N. meningitidis demonstrate the utility of this technique for generating molecular epidemiological data including molecular resistance targets.

While individual public health laboratories are making in-roads with genomics, it is important that methods and reporting are not developed independently but rather with national and international standardisation in mind. Only then can WGS fully revolutionise testing strategies employed in public health microbiology.