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The usual suspects: databases of virulence factors in Bacteria

J. Harry Caufield

Bacteria have earned much of their reputation. Despite their close relationship with humanity, whether in our microbiomes or in our food and beverages, various bacterial species still pose a threat to our society. Luckily, genomics allows us to quickly compare virulent bacterial strains with more temperate ones. The result is more data, and where there's data, there's eventually a database.

Here are a few on the subject:

PATRIC - The Pathosystems Resource Integration Center
Most recently, PATRIC has added a manually literature and database-curated set of virulence factors from six big-name bacterial pathogen genera, including Mycobacterium and Listeria. They now specifically detail virulence factors for ten different pathogen species. Many of these are virulence factor homologs identified by protein BLAST.

PATRIC doesn't make it easy to just get virulence factors, but if you're on an organism page, hit the Specialty Genes tab and then click the Virulence Factor checkbox on the left to filter.
Listeria. Always clean your vegetables.
A recent citation: Mao, C. et al. Curation, integration and visualization of bacterial virulence factors in PATRIC. Bioinformatics 31, 252–8 (2015).

VFDB
Oh, wait, this one's included in PATRIC now as far as I can tell. Its last major release was in 2012.

PAI DB
This database is a bit different: it contains pathogenicity islands rather than just virulence factors. Pathogenicity islands are rich in virulence factors and all manner of other novel genes, so they're important to consider in any discussion of virulence factors. PAI DB appears to be actively updated and even contains a pathogenicity island search function (PAI Finder) though it's just based on BLASTing against known islands and virulence genes.

Their logo is perfect.

A recent citation: Yoon, S. H., Park, Y.-K. & Kim, J. F. PAIDB v2.0: exploration and analysis of pathogenicity and resistance islands. Nucleic Acids Res gku985– (2014). doi:10.1093/nar/gku985

MVirDB
A database with some overlap between PATRIC, MvirDB doesn't look like much and I'm not sure if it's actively maintained. That being said, it's essentially just a few tables, accessible through the download links on the left of the page. MVirDB unifies some smaller databases so it may contain completely unique sets of annotations.

Uniprot
OK, it's not explicitly a database of virulence factors. It's easy to sort it by GO terms, though, like the term for pathogenesis. That GO term has a keyword in Uniprot and you can search for it by dropping this in the search box: "keyword:"Virulence [KW-0843]"". The results can be filtered down to the reviewed Swiss-Prot set for a subset of reliable virulence factors.

Try it yourself!

The NCBI databases don't make it quite this easy, but linking through the Biosystems database seems to help. Here's an example.