BMC genomics · 2026
StaphSCAN: a genomic surveillance framework for Staphylococcus aureus.
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Bollini Riccardo, Cento Valeria
Аннотация
BACKGROUND: Staphylococcus aureus is a leading cause of hospital- and community-acquired infections. While Whole Genome Sequencing (WGS) has become the gold standard for surveillance, extracting actionable epidemiological data typically requires assembling fragmented workflows of disparate software tools. We introduce StaphSCAN, a modular, open-source Python tool designed to streamline S. aureus genomic analysis.
RESULTS: StaphSCAN integrates essential typing methods (MLST, spa typing, SCCmec typing, capsular typing) with the detection of antimicrobial resistance (AMR), virulence, and biofilm-associated genes. It produces a comprehensive, normalized tabular report suitable for immediate interpretation. We validated StaphSCAN using a public dataset of 404 clinical S. aureus genomes collected in 2019 during a study conducted by the StaphNET-SA network. The tool successfully characterized the population structure, replicating the main key findings, demonstrating high throughput and reliability.
CONCLUSIONS: In conclusion, StaphSCAN provides a lightweight framework for S. aureus genomics, facilitating rapid genomic surveillance.
RESULTS: StaphSCAN integrates essential typing methods (MLST, spa typing, SCCmec typing, capsular typing) with the detection of antimicrobial resistance (AMR), virulence, and biofilm-associated genes. It produces a comprehensive, normalized tabular report suitable for immediate interpretation. We validated StaphSCAN using a public dataset of 404 clinical S. aureus genomes collected in 2019 during a study conducted by the StaphNET-SA network. The tool successfully characterized the population structure, replicating the main key findings, demonstrating high throughput and reliability.
CONCLUSIONS: In conclusion, StaphSCAN provides a lightweight framework for S. aureus genomics, facilitating rapid genomic surveillance.