alisonmacfadyen/sccmecextractor repository overview

SCCmecExtractor

A containerised bioinformatics pipeline for extracting and typing SCCmec (Staphylococcal Cassette Chromosome mec) sequences from Staphylococcus and Mammaliicoccus whole genome sequencing data.

What's Included

This Docker image provides a complete environment with:

• https://github.com/oschwengers/bakta⁠ (v1.12.0) - Rapid bacterial genome annotation
• https://blast.ncbi.nlm.nih.gov/⁠ - Sequence similarity searching for rlmH, ccr and mec gene detection
• SCCmecExtractor - Python toolkit for identifying, extracting, and typing SCCmec elements based on attachment site detection

Quick Start

1. Download the Bakta Database

First, download the lightweight Bakta database (required for genome annotation):

docker run --rm -v /path/to/bakta_db:/data/bakta_db \
    alisonmacfadyen/sccmecextractor:latest \
    bakta_db download --output /data/bakta_db --type light

Note for Windows users: Replace /path/to/bakta_db with the full Windows path (e.g., C:/Users/YourUsername/bakta_db)

1. Run SCCmecExtractor

Annotate your genome:

docker run --rm \
    -v /path/to/bakta_db:/data/bakta_db \
    -v $PWD:/work \
    alisonmacfadyen/sccmecextractor:latest \
    bakta --db /data/bakta_db \
          --output output-dir \
          genome.fna.gz

Run the full pipeline (recommended):

docker run --rm \
    -v $PWD:/work \
    alisonmacfadyen/sccmecextractor:latest \
    sccmec-pipeline -f genome.fna -g genome.gff3 -o results/

Or run individual steps:

  # Identify att sites
  docker run --rm \
    -v $PWD:/work \
    alisonmacfadyen/sccmecextractor:latest \
    sccmec-locate-att -f genome.fna -g genome.gff3 -o att_sites.tsv

  # Extract SCCmec sequence
  docker run --rm \
    -v $PWD:/work \
    alisonmacfadyen/sccmecextractor:latest \
    sccmec-extract -f genome.fna -g genome.gff3 -a att_sites.tsv -s sccmec_output

  # Type the extracted element
  docker run --rm \
    -v $PWD:/work \
    alisonmacfadyen/sccmecextractor:latest \
    sccmec-type -f sccmec_output/genome_sccmec.fna -o typing_results.tsv

  # Generate a unified report
  docker run --rm \
    -v $PWD:/work \
    alisonmacfadyen/sccmecextractor:latest \
    sccmec-report -e extraction_report.tsv -t typing_results.tsv -o unified_report.tsv

Key Features

• Broad species support: Detects SCC elements in S. aureus, S. pseudintermedius, other non-aureus staphylococci as well as Mammaliicoccus species
• Expanded attachment site detection: 24 att site patterns including
• BLAST-based gene detection: Uses BLAST+ to identify rlmH, ccr recombinase genes and mec gene
• ccr-validated extraction: Elements are validated for the presence of cassette chromosome recombinase (ccr) genes, filtering out non-SCC elements such as Staphylococcal Cassette Islands (SCIs)
• Composite element detection: Identifies tandem SCC elements with validated inner and outer ccr regions
• SCCmec typing: Classifies elements by mec gene complex and ccr allotype

How It Works

1. Annotate your bacterial genome using Bakta
2. Identify canonical and divergent attachment (att) sites in the genome
3. Validate the presence of ccr recombinase genes within the predicted element
4. Extract the SCCmec sequence based on att site locations and rlmH gene context
5. Gene level typing of the extracted element (or WGS if extraction not possible) for mec and ccr gene content
6. Report unified results combining extraction and typing information

Documentation

• GitHub Repository: https://github.com/AlisonMacFadyen/SCCmecExtractor⁠
• Full Usage Guide: See the README on GitHub for detailed usage instructions and troubleshooting

Requirements

• Docker Desktop or Docker Engine
• Sufficient disk space for Bakta database (~1.5 GB for light version, ~5 GB for full version), if carrying out Bakta annotation

Citation

If you use this tool in your research, please cite:

MacFadyen, A.C. SCCmecExtractor: A toolkit for extracting SCCmec sequences from Staphylococcus and Mammliicoccus genomes. GitHub: https://github.com/AlisonMacFadyen/SCCmecExtractor⁠

License

MIT License - See https://github.com/AlisonMacFadyen/SCCmecExtractor/blob/main/LICENSE⁠ file for details

Support

For issues, questions, or contributions, please visit the https://github.com/AlisonMacFadyen/SCCmecExtractor⁠ or contact: [email protected]⁠