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Virulence factor activity relationships (VFARs): a bioinformatics perspective.

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Area of Science:

  • Microbiology
  • Bioinformatics
  • Environmental Science

Background:

  • Virulence factor activity relationships (VFARs), inspired by quantitative structure-activity relationships (QSARs), are proposed for assessing microbial risks in water safety.
  • The rapid expansion of genomic sequencing and bioinformatics tools has significantly enhanced the potential for VFAR-based analyses.

Purpose of the Study:

  • To review bioinformatics databases and tools for predicting microbial virulence and antimicrobial resistance.
  • To assess the current state and future potential of VFAR approaches in prioritizing microorganisms for water safety.

Main Methods:

  • Comprehensive review of over 20 bioinformatics databases and tools developed in the last decade.
  • Analysis of the capabilities of these tools in predicting virulence and antimicrobial resistance.
  • Evaluation of the integration of omics technologies for VFAR applications.

Main Results:

  • A majority of reviewed bioinformatics tools are specifically designed for or include modules for virulence/resistance determination.
  • The availability of extensive genomic data (over 241,000 bacterial genomes, 13,000 metagenomic projects) supports VFAR development.
  • Current omics tools are sufficiently developed for applying VFAR approaches, combined with other analyses, to rank organisms.

Conclusions:

  • VFAR approaches, supported by advanced bioinformatics and omics technologies, are capable of ranking and prioritizing microorganisms relevant to specific environmental niches.
  • Further development requires integrating data on co-occurrence, treatment response, environmental modulation of virulence, and economic impact, while addressing uncertainties.
  • Future research should focus on integrating activity, risk, and uncertainty measurements to enhance VFAR capabilities.