Methicillin-resistant Staphylococcus aureus (MRSA) are opportunistic commensal bacteria that are evolving to become increasingly resistant to antimicrobial agents. Resistance is due to acquisition of resistance genes encoded by mobile genetic elements (MGEs) but little is known about the gene transfer and conditions influencing this process in clinically important MRSA isolates. In this thesis I showed that populations of MRSA colonizing isolates vary phenotypically in antimicrobial resistance (AMR) and genotypically in MGE profiles. A potential mechanism of horizontal gene transfer (HGT) in colonized patients is generalized transducing bacteriophage and we detected free bacteriophage in nasal swabs. AMR and genetic variability have implications for diagnostics, epidemiology, antimicrobial stewardship and selective pressures driving evolution of MRSA populations. All clinical strains harbour at least one prophage which are potentially capable of HGT. Bacteriophage are thought to be induced by environmental conditions including exposure to antibiotics, and 30% of hospitalized patients who are carriers are prescribed antibiotics. Exposure of clinical MRSA isolates to sub-inhibitory concentration of range of anti microbials resulted in increased phage induction and resistance gene transfer, however the ratio of virulent particles to transducing particles differed for each antimicrobial using the new technology of droplet digital peR. Exposure of colonizing MRSA strains to specific antimicrobials may lead to enhanced horizontal transfer of antimicrobial resistance potentially leading to fully resistant MRSA. MRSA isolates collected from patient admitted to St Georges NHS Healthcare Trust between 1999-2003 versus 2012-2013 showed that the recent isolates more easily induced phages and transferred resistance genes more effectively, especially upon induction with ciprofloxacin, suggesting that MRSA is evolving over time to transfer AMR genes more effectively. I developed a new in vitro model mimicking in vivo colonization conditions in the human host by co-culturing two distinct isolates from MRSA carriers in human plasma. Transfer of DNA via HGT occurred at high frequency in plasmas from all 8 donors. However, the presence of certain resistance genes had a fitness cost in some plasma but not others. Frequent horizontal transfer of antimicrobial resistance and other genes between isolates during colonization may play an important role in host-pathogen adaptation and evolution.