At the commencement of this PhD, next generation sequencing technologies were increasingly being implemented for public health surveillance of infectious diseases; the COVID-19 pandemic has accelerated this globally. The applications of this technology are protean, from detection of novel pathogens, to tracing the source of cases with no obvious transmission link, to surveillance for emerging strains with increased transmissibility or immune evasion, and to detection of determinants of virulence or antimicrobial resistance. The questions that can be addressed and potential implications depend on the ecology, epidemiology, and public health response for each pathogen. In this thesis, I use genomic sequencing to investigate the epidemiology of three bacterial pathogens that cause community-acquired infection in the NT Top End.