Foodborne diseases are a global issue due to the morbidity and mortality they cause, along with the disruption to the food industry. Microbiology is in the midst of a paradigm shift due to the use of bacterial genomics as a frontline tool in the prevention and control of communicable diseases transmitted by food. We present data on the implementation and ongoing use of whole-genome sequencing (WGS) in the characterisation of foodborne and environmental infectious diseases caused by Shiga toxin-producing Escherichia coli (STEC) and Campylobacter jejuni. Both bacteria are important causes of infection in Australia. To date, there is scant genomic data on C. jejuni from Australia despite it being one of the most common causes of diarrhoeal disease, with traditional microbiological diagnostic tests often being unable to provide any significant insights into C. jejuni infections. Although uncommon relative to campylobacteriosis, the impact of STEC infection is also profound, with significant clinical and economic impacts. We are developing a genomic framework for future investigations and potential surveillance of STEC. The framework explores the population structure of Australian STEC collected over the past ten years and characterises the accessory genomes of the STEC isolates and compares the utility and feasibility of in silico typing and virulence gene detection with ‘conventional’ typing approaches. The integration of WGS in the tracking and identification of disease offers the promise of rapid and high-resolution analytical tools to better understand their causes, particularly those that may be foodborne, zoonotic or have environmental reservoirs.