Staphylococcus aureus and Enterococcus faecium are major nosocomial pathogens in the Australian health care setting, and treatment of infections caused by these species is complicated by increasing antimicrobial resistance, especially to the glycopeptide antibiotics. Clinical studies have defined the adverse impact of glycopeptide resistance on infection characteristics and clinical outcome, while a deeper understanding of the molecular determinants of emergence and resistance development has been more difficult to define. Whole bacterial genome sequencing (WGS) has provided a new tool to understand how bacterial species are evolving and spreading within the community or health care setting, and how antimicrobial resistance is emerging. In the case of glycopeptide resistance in S. aureus it has helped demonstrate the multifaceted nature of the glycopeptide resistance mechanisms, while in vanB E. faecium it has led to reconsideration of the dynamics of glycopeptide resistance gene transfer in this species. These studies have also led a greater understanding of the evolution of bacterial species during human infection, uncovering a complex relationship between the evolution of antimicrobial resistance and altered host-pathogen interactions during human bacterial infections.