Whole genome sequencing (WGS) using next generation sequencing technologies has become a vital tool for surveillance of pathogens and outbreak investigations. WGS offers unambiguous high-resolution typing of isolates and unparalleled information on strain identity. However, routine use of WGS data for surveillance is still challenging as approaches have not yet been standardised. In attempt to address these issues, we developed a multilevel genome typing (MGT) system. MGT is based on the well-established multilocus sequence typing (MLST) approach and is consisted of a series of MLST schemes with increasing resolution. We have developed MGT schemes for Salmonella, Bordetella pertussis, Vibrio cholerae and Staphylococcus aureus. The MGT databases (https://mgtdb.unsw.edu.au/) are open to the public, currently hosting over 220,000 genomes with daily updates from NCBI publicly released genome data. The application and advantage of MGT on global epidemiology, local epidemiology and outbreak investigation will be presented using examples from different pathogens. MGT can detect and track existing and emerging strains using stable and standardised nomenclature, to facilitate surveillance and the design of new strategies to reduce the global burden of these pathogens.