StaphSCAN: a genome-based tool for Surveillance through Comprehensive Analysis and staNdardized reporting of Staphylococcus aureus.

StaphSCAN is a genome-based framework for the surveillance of Staphylococcus aureus.

It integrates the following steps:

• Species identification
• Qcheck of genome assembly
• MLST typing
• spa typing
• Capsular polysaccharide typing
• SCCmec typing
• Detection of virulence genes (including biofilm)
• Detection of antimicrobial resistance genes (inclduing relevant mutations)

For more information, see the Modules section.

Acknowledgements

StaphSCAN is inspired by Kleborate.