Staphylococcus Plasmids Database

Overview This repository contains a curated FASTA database of plasmid-associated sequences identified in Staphylococcus aureus and related species.

Plasmids play a key role in the dissemination of virulence factors, antimicrobial resistance genes, and adaptive traits. Their detection is essential for genomic characterisation, particularly in food safety and public health contexts where horizontal gene transfer contributes to the spread of enterotoxin genes and other determinants.

Contents

• Staphylococcus_Plasmids.fasta: curated nucleotide sequences of Staphylococcus plasmids

Intended Use

This database is designed for:

• Whole genome sequencing (WGS) analysis
• Screening using BLAST+ or ABRicate
• Detection of plasmid-associated sequences and mobile genetic elements

Recommended Tools

• BLAST+ (blastn)
• ABRicate

Recommended Parameters

• Minimum identity: 80%
• Minimum coverage: 95%

These thresholds provide a balance between sensitivity and specificity for detecting plasmid-associated sequences across diverse Staphylococcus genomes.

Example Usage

BLAST+ makeblastdb -in Staphylococcus_Plasmids.fasta -dbtype nucl -out plasmid_db

blastn -query genome.fasta -db plasmid_db -out results.txt -outfmt “6 qseqid sseqid pident length qcovs evalue bitscore” -perc_identity 80

Filter results for coverage >=95%.

ABRicate abricate –db Staphylococcus_Plasmids genome.fasta > report.tab

Ensure the database is installed in the ABRicate database directory.

Interpretation

Detection of plasmid-associated sequences indicates the presence of mobile genetic elements that may carry virulence factors, antimicrobial resistance genes, or other adaptive traits.

Detection does not confirm plasmid structure, copy number, transferability, or gene expression. Results should be interpreted alongside assembly context, contig structure, and, where possible, plasmid reconstruction approaches.

Limitations

• Database is limited to currently curated plasmid sequences
• Novel or highly divergent plasmids may not be detected
• Fragmented assemblies may lead to partial or ambiguous hits
• Presence of plasmid sequences does not confirm functional activity or transfer potential

Curation Sequences were compiled from public databases and peer-reviewed literature, focusing on well-characterised Staphylococcus plasmids. Updates should follow transparent inclusion and validation criteria.

Versioning

Version: 1.0 Date: 2026-04-26

Citation If you use this database, cite both the associated publication and this repository.

Publication: 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.

Database: Staphylococcus Plasmids Database. GitHub repository. Available at: https://github.com/macgenomegue/Staphylococcus_Plasmids

Suggested citation format: Staphylococcus Plasmids Database (version 1.0). Available at: https://github.com/macgenomegue/Staphylococcus_Plasmids

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/