Welcome to BacSPaD, your comprehensive resource for bacterial strains pathogenicity data. Here’s a brief overview to help you get started:

Data Section

Perform keyword queries across all fields or specific fields. For instance, if you want to focus your analysis on certain species, genus, families, order, class or phylum select the corresponding metadata fields. You may also be eventually interested in selecting certain diseases using “disease category”, “disease subcategory”, and “isolation source” fields.

Use BV-BRC genome IDs to retrieve corresponding genomes and data files (e.g., proteomes, protein families) from the BV-BRC FTP website (https://www.bv-brc.org/docs/quick_references/ftp.html) as there demonstrated:

“Once you have copied the list of genome ids you are interested in a separate file “genome_list”, you can use the following one line shell script to read the list of genome ids from your file and download corresponding .fna files from the PATRIC FTP site. If you are interested in other file type, say .PATRIC.faa or .PATRIC.features.tab, simply replace .fna with that extension.

for i in ` cat genome_list `; do wget -qN “ftp://ftp.bvbrc.org/genomes/$i/$i.fna”; done

Dashboard

Interactive Visualizations: Explore top species and families, taxa distribution, associated disease categories and isolation sources, and a location map of all strains.

Molecular Biology

Genome Data: Visualize distributions of the number of plasmids, contigs, genome lengths, GC content (%), and number of coding sequences for both HP and NHP genomes.

Virulence Factors

Access information on virulence factors for the most prevalent clinical species, including gene name, gene frequency in HP and NHP strains, the associated BV-BRC genome ids and species names; as well as the number of associated strains, species, genus, and families.

About

Learn about BacSPaD’s utility for microbiology research and find contact information.

Citation

If you use BacSPaD, please cite it as follows:

Ribeiro, S., Chaumet, G., Alves, K., Nourikyan, J., Shi, L., Lavergne,J.-P., Mijakovic, I., de Bernard, S., & Buffat, L. (2024). BacSPaD: A robust bacterial strains’ pathogenicity resource based on integrated and curated genomic metadata. Preprints, 202407.0837.v1. https://doi.org/10.20944/preprints202407.0837.v1

Disclaimer: If you experience visualization issues in Google Chrome, please try using an alternative browser such as Firefox or Edge. Alternatively, you can try deactivating any potentially interfering extensions. If the issue persists, please contact us.

For further assistance, contact us at sara.ribeiro@altrabio.com.

Taxonomy

BacSPaD (Bacterial Strains Pathogenicity Dataset) is a pioneering resource developed to address the critical gap in accessible and reliable data on bacterial pathogenicity at the strain level. This manually curated dataset integrates comprehensive genomic metadata to provide researchers with annotations on the pathogenic potential of bacterial strains. We leveraged metadata from esteemed sources and enhanced it with meticulous manual reviews of relevant scientific literature. Our dataset features pathogenicity annotations for 5,992 high-quality and complete genomes, identifying strains as either pathogenic (HP) or non-pathogenic (NHP) to humans. This open-access resource serves as an invaluable tool for researchers engaged in studying bacterial pathogenesis and developing computational tools for pathogenicity prediction. By providing a clear, searchable interface, BacSPaD enables users to download the data and query metadata fields in the section ‘Data’, and ‘Virulence Factors’ and visualize associated statistics in the section ‘Dashboard’ and ‘Molecular Biology’. Whether for academic research, public health surveillance, or the development of novel therapeutic strategies, BacSPaD offers a structured and reliable foundation for enhancing our understanding of bacterial interactions and their implications on human health. This work is part of the PEST-BIN European consortium (https://www.sysbio.se/pest-bin_eu/), which aims to enhance understanding of bacterial pathogenicity.

Contacts:
  • sara.ribeiro@altrabio.com
  • guillaume.chaumet@altrabio.com
  • contactus@altrabio.com