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Virulence factor activity relationships (VFARs): a bioinformatics perspective

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Inside back cover

Back cover

Environmental Science: Processes & Impacts Vol - 19 Issue - 2

Environmental Science: Processes & Impacts Vol - 19 Issue - 1

Environmental Science: Processes & Impacts Vol -18

Virulence factor activity relationships (VFARs): a bioinformatics perspective

Content Provider	Royal Society of Chemistry (RSC)
Author	Waseem, Hassan Stedtfeld, Robert D. Stedtfeld, Tiffany Williams, Maggie R. Tiedje, James M. Hashsham, Syed A. Cole, James R. Chai, Benli
Copyright Year	2017
Abstract	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.
Starting Page	247
Ending Page	260
Page Count	14
File Format	HTM / HTML PDF
ISSN	20507887
Volume Number	19
Issue Number	3
Journal	Environmental Science: Processes & Impacts
DOI	10.1039/c6em00689b
Language	English
Publisher	Royal Society of Chemistry
Access Restriction	Open
Subject Keyword	VFAR Virulence factor Bioinformatics Virulence Antimicrobial resistance Genomics
Content Type	Text
Resource Type	Article
Subject	Environmental Chemistry Public Health, Environmental and Occupational Health Management, Monitoring, Policy and Law

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