The Doherty Centre for Applied Microbial Genomics (DCAMG) is an initiative of the Department of Microbiology and Immunology and the Microbiological Diagnostic Unit, within the Doherty Institute at the University of Melbourne. The five different affiliations within this first sentence may seem confusing but the mission for DCAMG is not, which is to facilitate research relevant to implementing microbial genomics as a routine tool in public health and clinical microbiology and to provide leadership and training in this area. Applied microbial genomics is a rapidly emerging field and significant progress is being made in utilising this evolving technology for public health and clinical microbiology. Here, we demonstrate the capacity of the Centre in using genomics to enhance investigations of food borne pathogen-mediated disease, for tracking infections caused by antibiotic resistant pathogens and for the characterisation of a diverse range of pathogenic microorganisms of both humans and animals.