SCCmecFinder

SCCmecFinder identifies and characterizes staphylococcal cassette chromosome mec (SCCmec) elements from whole-genome sequencing data of Staphylococcus aureus to enable SCCmec typing and surveillance of methicillin resistance.

Key Features:

• Identification of SCCmec Types: Identifies SCCmec types I to XIII and provides subtyping for complex types including SCCmec type IV (2B) and V (5C2).
• Dual Gene Prediction Approaches: Employs a Basic Local Alignment Search Tool (BLAST)-based approach and a k-mer-based approach for gene detection and annotation.
• High Typeability: Demonstrated typeability of 96.7% across 93 clinical isolates, increasing to 98.9% with adjusted default settings.
• Curation and Updates: Maintains a curated reference set and is updated as new SCCmec elements are reported in accordance with the International Working Group on the Classification of Staphylococcal Cassette Chromosome Elements.

Scientific Applications:

• MRSA surveillance and epidemiology: Enables characterization of SCCmec elements to understand the genetic background of methicillin-resistant Staphylococcus aureus for infection control and epidemiological investigations.
• mec gene and mobile element analysis: Detects presence and context of mecA and mecC genes and associated mobile genetic elements to track staphylococcal adaptation across hospitals, communities, and livestock.

Methodology:

Analyzes whole-genome sequencing data using BLAST-based and k-mer-based gene detection to identify and type SCCmec elements.