Staphylococcus aureus is a commensal colonizing the skin and mucous membranes. it can also act as a pathogen, and is the most common microorganism isolated from prosthetic joint infections (PJIs). The aim of this study was to explore the genomic relatedness between commensal and PJI S. aureus strains as well as microbial traits and host-related risk factors for treatment failure. Whole-genome sequencing (WGS) was performed on S. aureus isolates obtained from PJIs (n = 100) and control isolates from nares (n = 101). Corresponding clinical data for the PJI patients were extracted from medical records. No PJI-specific clusters were found in the WGS phylogeny, and the distribution of the various clonal complexes and prevalence of virulence genes among isolates from PJIs and nares was almost equal. Isolates from patients with treatment success and failure were genetically very similar, while the presence of an antibiotic-resistant phenotype and the use of non-biofilm-active antimicrobial treatment were both associated with failure.In conclusion, commensal and PJI isolates of S. aureus in arthroplasty patients were genetically indistinguishable, suggesting that commensal S. aureus clones are capable of causing PJIs. Furthermore, no association between genetic traits and outcome could be demonstrated, stressing the importance of patient-related factors in the treatment of S. aureus PJIs. Worldwide, millions of patients undergo arthroplasty surgery every year, with an expected increase in the coming years 1. Staphylococcus aureus is a major cause of both community-acquired and nosocomial infections, and is regularly reported to be the most common pathogen in prosthetic joint infections (PJIs) 2,3. Risk factors for developing PJIs are related to deficiencies in host defense due to age, obesity, previous surgery, smoking, and immune deficiencies (e.g. rheumatoid arthritis, diabetes mellitus), as well as exogenous factors such as timing and selection of antibiotic prophylaxis, extended operation time, and blood transfusions 4-8. Implant-sparing curative treatment of acute PJIs, whether occurring early in the postoperative period or later through hematogenous seeding, relies on a regimen of debridement, antibiotics, irrigation, and retention of the prosthesis (DAIR) 9. This is possible, provided that the infection has not persisted for more than approximately three weeks and that the isolate is susceptible to biofilm-active antibiotic treatment (i.e. rifampin for staphylococcal infections) 10. However, there are reports suggesting an even shorter time to intervention is needed for a successful treatment 11,12. The impact of risk factors on outcome of treatment has not been fully explored, but recent reports have proposed new risk scores to better guide the choice of treatment 13-15. S. aureus is a commensal of the human skin, nares, and mucous membranes, but also a human pathogen due to its invasive capacity. S. aureus infections occur among both otherwise-healthy individuals and those with co-morbidities, and nasal carriage...