Shigella species are a significant cause of dysentery globally; the two dominant species are Shigella sonnei and Shigella flexneri. Historically considered a foodborne pathogen, Shigella is increasingly being identified as the etiological agent of sexually transmitted infections (STI). In Australia, cases are usually associated in returned travellers from regions with shigellosis endemicity or in men who have sex with men. Alarmingly, some lineages of Shigella have become increasingly resistant to key oral therapeutics, leaving limited-to-no treatment options. The integration of genomic, epidemiological, and phenotypic susceptibility data has enabled the investigation of the changing infection dynamics of Shigella in Australia. Here, we explore increasingly prevalence of multidrug resistance (MDR) and extensive drug resistance (XDR) in lineages of Shigella over a four-year period. We consider future avenues of research to further integrate valuable genomic, epidemiological, and clinical data into population modelling methods using Shigella as pilot organism. These novel approaches will help to inform public heath surveillance and control strategies for a range of bacterial pathogens that represent serious threats to human health.