SCCmecExtractor: a tool for extracting staphylococcal cassette chromosome elements from whole-genome sequences

Staphylococcal cassette chromosome (SCC) elements are mobile genetic elements that integrate at the rlmH gene and are predominantly responsible for methicillin resistance in staphylococci. Although staphylococcal cassette chromosome mec (SCCmec) typing tools exist, none can extract the element sequence itself or explicitly classify SCC elements that lack methicillin resistance genes. Here, we present SCCmecExtractor, a lightweight Python toolkit that identifies SCC element boundaries through degenerate attachment site (att) pattern matching, extracts complete elements from whole-genome assemblies and characterizes their mec and ccr gene content, providing SCCmec type classification where applicable. Benchmarking on 7,297 genomes spanning 70 species across Staphylococcus and Mammaliicoccus demonstrated 94.8% SCCmec type concordance with the sccmec tool [1] on 1,454 Staphylococcus aureus genomes, with all eight disagreements involving elements with multiple ccr complexes. The tool extracted 1,562 SCC elements from 1,454 S. aureus, 5,295 non-aureus Staphylococcus and 548 Mammaliicoccus genomes, achieving effective extraction rates (excluding assembly-limited genomes and those lacking valid ccr pairs) of 87.3% for S. aureus, 58.8% for non-aureus Staphylococcus and 61.9% for Mammaliicoccus. A hybrid detection module classifies extracted elements by similarity to 32 SCCmec type references, distinguishing canonical single-type elements, hybrid elements showing recombination-derived similarity to multiple types and multi-ccr elements consistent with structural tandem/nested elements. Notably, 616 of the 1,562 extracted elements (39.4%) were non-mec SCC elements lacking methicillin resistance genes, a class of mobile element often overlooked. Non-mec SCC prevalence increased from 12.2% in S. aureus to 55.6% in non-aureus Staphylococcus and 76.0% in Mammaliicoccus, revealing a substantial reservoir of SCC diversity beyond methicillin resistance. SCCmecExtractor is freely available via PyPI, Docker and Singularity under an MIT licence.