Staphylococcus SaPIs Database
Overview
This repository contains a curated FASTA database of Staphylococcal Pathogenicity Islands (SaPIs) for use in genomic screening of Staphylococcus aureus and related species.
SaPIs are mobile genetic elements that frequently carry virulence determinants, including enterotoxin genes. Their detection is critical for risk characterisation of enterotoxigenic strains in food safety and public health contexts.
Contents Staphylococcus_SaPIs.fasta: curated nucleotide sequences of SaPIs
Intended Use
This database is designed for:
- Whole genome sequencing (WGS) analysis
- Screening using BLAST+ or ABRicate
- Detection of SaPI-associated virulence regions
Recommended Tools
- BLAST+ (blastn)
- ABRicate
Recommended Parameters
- Minimum identity: 80 percent
- Minimum coverage: 95 percent
These thresholds balance sensitivity and specificity for detection of SaPI regions across diverse Staphylococcus genomes.
Example Usage
BLAST+ makeblastdb -in Staphylococcus_SaPIs.fasta -dbtype nucl -out SaPIs_db blastn -query genome.fasta \
-db SaPIs_db
-out results.txt
-outfmt "6 qseqid sseqid pident length qcovs evalue bitscore"
-perc_identity 80
Filter results for coverage >=95 percent.
ABRicate abricate --db Staphylococcus_SaPIs genome.fasta > report.tab
Ensure database is installed in ABRicate database directory.
Interpretation Detection of SaPI sequences indicates the presence of mobile genetic elements associated with virulence. This includes potential carriage of enterotoxin genes. Detection does not confirm gene expression or toxin production.
Limitations
- Database is limited to currently curated sequences
- Novel or highly divergent SaPIs may not be detected
- Results depend on assembly quality and completeness
Curation
Sequences were compiled from public databases and literature. Details of inclusion criteria and sources should be documented if expanded.
Versioning
Version: 1.0 Date: 2026-04-30
Citation
If you use this database, cite: Staphylococcus SaPIs Database. GitHub repository. Available at: https://github.com/macgenomegue/Staphylococcus_SaPIs
Suggested citation format Staphylococcus SaPIs Database (version 1.0). Available at: https://github.com/macgenomegue/Staphylococcus_SaPIs Macori G, Bellio A, Bianchi DM, Chiesa F, Gallina S, Romano A, Zuccon F, Cabrera-Rubio R, Cauquil A, Merda D, Auvray F. Genome-wide profiling of enterotoxigenic Staphylococcus aureus strains used for the production of naturally contaminated cheeses. Genes. 2019 Dec 27;11(1):33. Contact
Maintainer: [Guerrino Macori] Institution: [University College Dublin]
License This database is licensed under the Creative Commons Attribution 4.0 International License (CC BY 4.0). Full licence text: https://creativecommons.org/licenses/by/4.0/