About VFDB

The virulence factor database (VFDB) is an integrated and comprehensive online resource for curating information about virulence factors of bacterial pathogens. Since its inception in 2004, VFDB has been dedicated to providing up-to-date knowledge of VFs from various medically significant bacterial pathogens.
The motivation for constructing VFDB was twofold:
First, to provide in-depth coverage major virulence factors of the best-characterized bacterial pathogens, with the structure features, functions and mechanisms used by these pathogens to allow them to conquer new niches and to circumvent host defense mechanisms, and cause disease.
Second, to provide current knowledge of the wide variety of mechanisms used by bacterial pathogens for researchers to elucidate pathogenic mechanisms in bacterial diseases that are not yet well characterized and to develop new rational approaches to the treatment and prevention of infectious diseases.

Definitions

A bacterial pathogen is usually defined as any bacterium that has the capacity to cause disease. Its ability to cause disease is called pathogenicity.
Virulence provides a quantitative measure of the pathogenicity or the likelihood of causing disease.
Virulence factors refer to the properties (i.e., gene products) that enable a microorganism to establish itself on or within a host of a particular species and enhance its potential to cause disease. Virulence factors include bacterial toxins, cell surface proteins that mediate bacterial attachment, cell surface carbohydrates and proteins that protect a bacterium, and hydrolytic enzymes that may contribute to the pathogenicity of the bacterium.

About anti-virulence compounds

The rapid emergence of adaptive mutations and the widespread dissemination of antibiotic resistance genes have made infections caused by multidrug-resistant bacterial strains a serious public health threat. In addition, conventional antibiotics typically target essential cellular functions of bacteria, such as cell wall, replication, transcription and translation, which not only kill or inhibit bacterial pathogens but also disrupt commensal and beneficial microbiota, often leading to further clinical complications. Consequently, there is an urgent need for novel antibacterial strategies to combat drug-resistant bacterial infections.
Disarming bacterial pathogens by targeting virulence factors is a promising alternative to classic antibiotics. Compared to conventional strategies that target viability of bacteria, anti-virulence strategies may impose less selective pressure for the emergence of resistant strains, and even further diminish the risk of commensal bacteria elimination so as to be less harmful to the resident microbial flora. Anti-virulence compounds can be designed to target various bacterial VFs by preventing bacterial adhesion or biofilm formation, disrupting effector delivery systems, blocking quorum sensing, and attenuating virulence through global or specific gene expression regulation. With the deepening understanding of bacterial pathogenesis and advancements in computer-aided drug design methods, an increasing number of potential anti-virulence drug candidatessmall molecules have been discovered over the past decades.
To provide valuable reference resources for drug design, repurposing, and target selection, the VFDB has systematically collected public data on anti-virulence compounds through extensive literature mining, and further integrated this information with its existing knowledge of bacterial VFs. By cross-linking the current knowledge of bacterial VFs with information on relevant compounds, the VFDB aims to bridge the gap between chemists and microbiologists, providing crucial insights for the development of innovative and effective antibacterial therapies to combat bacterial infections and address antibiotic resistance.

About VF category

Traditional microbiological studies generally rely on laboratory bacterium isolation and cultivation, while recent NGS-based metagenomic analyses have revealed a large number of unculturable bacteria, the majority of which are yet uncharacterized. Thus, the in-depth mining of the panbacterial microbiome data in terms of pathogenesis requires a well-organized reference category of all established bacterial VFs from various known pathogens. However, the independent naming of homologous VFs in different bacteria leads to considerable confusion and hampers follow-up panbacterial analyses. Therefore, a well-defined classification scheme with a unified nomenclature is essential for future efficient data mining of bacterial VFs.
To better organize and present bacterial VFs in the database, the VFDB proposed an individual simplified classification scheme for each bacterial genus based on field conventions since inception in 2004. Nevertheless, the previous classification schemes of different bacteria are generally independent of each other, although they share certain similarities. Since the release of 2021, we introduced a general VF category applicable to various bacterial pathogens in the database and reorganized the VFDB dataset accordingly to make it readily applicable for future panbacterial data mining.
Since the majority of the current classifications of various bacterial VFs have proven very useful and durable for phylogenetic analyses, we have tried to maximally follow the existing conventions based on extensive literature mining. Thus, the newly proposed general classification scheme would be instantly familiar to and readily acceptable by traditional bacteriologists. However, unlike the previous scheme proposed in the 2012 release, which contains only four major bacterial VF categories (i.e., adhesion and invasion, secretion system, toxin, and iron acquisition), the newly established general classification scheme was designed to be a comprehensive system capable of covering all known bacterial VFs.
Please note the newly introduced VF category is a tentative scheme rather than a complete solution. Any comments or suggestions are welcome.

About VFanalyzer

The fast development of the third-generation sequencing technologies (i.e. Pacific Biosciences and Oxford Nanopore) in recent years enable the easy accessibility of complete/draft genomes of bacterial pathogens for the scientific community. However, it remains a challenge for microbiologists or physicians with limited bioinformatics skills to efficiently define and extract biologically relevant information from volumes of genomic data. Therefore, we recently developed an automatic and comprehensive platform for accurate bacterial VF identification, named VFanalyzer.
Instead of using simple BLAST searches, VFanalyzer first constructs orthologous groups within the query genome and pre-analyzed reference genomes from VFDB to avoid potential false positives due to paralogs. Then, it conducts iterative and exhaustive sequence similarity searches among the hierarchical pre-build datasets of VFDB to accurately identify potential untypical/strain-specific VFs. Finally, via a context-based data refinement process for VFs encoded by gene clusters, VFanalyzer can achieve relatively high specificity and sensitivity without manual curation.
Please note VFanalyzer are developed in JavaScript-rich manner, it may take a few minutes to load JS library for FIRST-TIME users, please wait with patience.

Term of use ( )

Access and use of VFDB are provided "AS IS" and without warranties of any kind either expressed or implied. By using this website, you agree that VFDB will not be liable for any losses or damages arising from your use of or reliance on the VFDB data, or other websites or information to which this website may be linked.
The contents of VFDB, including text, sequence and other material contained on the VFDB website ("VFDB data") are for research and educational purposes only. The VFDB data is not intended as a substitute for professional medical or clinical help, judgment or advice.
The VFDB data is freely available under the Creative Commons Attribution-NonCommercial (CC BY-NC) license version 4.0 for personal and public non-commercial, research or academic use by individuals at academic, government or non-profit institutions. Users intending to use VFDB data for commercial purposes should contact us via the official email.

Some of our authorized commercial users: