Typing and prediction of antibiotic resistance and virulence determinants in S. aureus using shotgun-metagenomics data from prosthetic joint tissue on blood culture bottles

Analyses of Shotgun-metagenomics (SMg) may give valuable clinical information beyond the detection of the potential pathogen(s). Characterization of pathogens including identification of antimicrobial resistance (AMR), virulence profiles, and typing directly from clinical samples has been limited due to challenges arising from incomplete genome coverage, leading to insufficient sequence reads for the detection of AMR genes and virulence determinants. Here, we assess the performance of SMg on positive blood culture bottles (BCBs) (n=19) inoculated with prosthetic joint tissue (PJT) for the identification, typing, and prediction of AMR and virulence profiles in Staphylococcus aureus, the most common cause of prosthetic joint infection (PJI).