StaphSCAN

StaphSCAN streamlines Staphylococcus aureus genomic analysis by integrating essential typing methods with detection of antimicrobial resistance, virulence, and biofilm-associated genes to produce normalized tabular reports for epidemiological interpretation.

Key Features:

• Typing Methods Integration: StaphSCAN integrates MLST, spa typing, SCCmec typing, and capsular typing for comprehensive strain characterization.
• Antimicrobial Resistance Detection: The tool detects antimicrobial resistance (AMR) genes relevant to S. aureus.
• Virulence Gene Detection: StaphSCAN identifies virulence-associated genes in S. aureus genomes.
• Biofilm Gene Detection: The tool detects biofilm-associated genes relevant to S. aureus pathogenicity.
• Normalized Tabular Reporting: StaphSCAN produces a comprehensive, normalized tabular report suitable for immediate epidemiological interpretation.
• High Throughput Processing: The tool demonstrated high throughput and reliability when validated on 404 clinical S. aureus genomes.

Scientific Applications:

• Genomic Surveillance: StaphSCAN facilitates rapid genomic surveillance of Staphylococcus aureus in hospital and community settings.
• Population Structure Characterization: The tool successfully characterized S. aureus population structure in validated clinical datasets.
• Epidemiological Data Extraction: StaphSCAN extracts actionable epidemiological data from Whole Genome Sequencing (WGS) without requiring fragmented workflows of disparate software tools.

Methodology:

StaphSCAN is a modular, open-source Python tool that integrates essential typing methods with detection of antimicrobial resistance, virulence, and biofilm-associated genes, producing a comprehensive normalized tabular report. Validation was performed using a public dataset of 404 clinical S. aureus genomes collected in 2019 during a StaphNET-SA network study.