ArticleBMC genomics2026
StaphSCAN: a genomic surveillance framework for Staphylococcus aureus.
Article in BMC genomics, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
backgroundStaphylococcus 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.
resultsStaphSCAN 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.
conclusionsIn conclusion, StaphSCAN provides a lightweight framework for S. aureus genomics, facilitating rapid genomic surveillance.
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