Jump to main content
Jump to site search
PLANNED MAINTENANCE Close the message box

Scheduled maintenance work on Wednesday 22nd May 2019 from 11:00 AM to 1:00 PM (GMT).

During this time our website performance may be temporarily affected. We apologise for any inconvenience this might cause and thank you for your patience.

Issue 3, 2017
Previous Article Next Article

Virulence factor activity relationships (VFARs): a bioinformatics perspective

Author affiliations


Virulence factor activity relationships (VFARs) – a concept loosely based on quantitative structure–activity relationships (QSARs) for chemicals was proposed as a predictive tool for ranking risks due to microorganisms relevant to water safety. A rapid increase in sequencing capabilities and bioinformatics tools has significantly increased the potential for VFAR-based analyses. This review summarizes more than 20 bioinformatics databases and tools, developed over the last decade, along with their virulence and antimicrobial resistance prediction capabilities. With the number of bacterial whole genome sequences exceeding 241 000 and metagenomic analysis projects exceeding 13 000 and the ability to add additional genome sequences for few hundred dollars, it is evident that further development of VFARs is not limited by the availability of information at least at the genomic level. However, additional information related to co-occurrence, treatment response, modulation of virulence due to environmental and other factors, and economic impact must be gathered and incorporated in a manner that also addresses the associated uncertainties. Of the bioinformatics tools, a majority are either designed exclusively for virulence/resistance determination or equipped with a dedicated module. The remaining have the potential to be employed for evaluating virulence. This review focusing broadly on omics technologies and tools supports the notion that these tools are now sufficiently developed to allow the application of VFAR approaches combined with additional engineering and economic analyses to rank and prioritize organisms important to a given niche. Knowledge gaps do exist but can be filled with focused experimental and theoretical analyses that were unimaginable a decade ago. Further developments should consider the integration of the measurement of activity, risk, and uncertainty to improve the current capabilities.

Graphical abstract: Virulence factor activity relationships (VFARs): a bioinformatics perspective

Back to tab navigation

Publication details

The article was received on 20 Dec 2016, accepted on 14 Feb 2017 and first published on 15 Feb 2017

Article type: Critical Review
DOI: 10.1039/C6EM00689B
Environ. Sci.: Processes Impacts, 2017,19, 247-260

  •   Request permissions

    Virulence factor activity relationships (VFARs): a bioinformatics perspective

    H. Waseem, M. R. Williams, T. Stedtfeld, B. Chai, R. D. Stedtfeld, J. R. Cole, J. M. Tiedje and S. A. Hashsham, Environ. Sci.: Processes Impacts, 2017, 19, 247
    DOI: 10.1039/C6EM00689B

Search articles by author