Next generation sequencing technologies has brought whole genome sequencing (WGS) into reach of many clinical and public health microbiology laboratories. These areas face a number of specific challenges as they implement the use of high throughput genomics in not only outbreak investigations but also for routine molecular surveillance.

The Queensland reference laboratory, Public Health Microbiology (PHM), is uniquely positioned for bacterial outbreak investigations containing specialist public health water, food and clinical microbiology sections. The Molecular Epidemiology team provides molecular support to all areas and is the key contributor to bacterial molecular diagnostics, epidemiological surveillance and outbreak responses.

The integration of WGS into PHM over the last three years has been successful in improving efficiency and capabilities. WGS has been utilised for the real time investigation of number of bacterial outbreaks including a nosocomial Legionella cluster and Salmonella and S. aureus water and food outbreaks. WGS analysis assessed against conventional molecular typing for routine epidemiological surveillance of bacterial diseases such as N. meningitidis and L. monocytogenes has proven to be successful and sustainable. There are many advantages offered by this approach, however the challenges around implementing NGS technology in a public health laboratory are ongoing and will benefit from national coordination.