Development of a Virulence Factor Biochip and its Validation for Microbial Risk Assessment in Drinking Water

EPA Grant Number: R831628
Title: Development of a Virulence Factor Biochip and its Validation for Microbial Risk Assessment in Drinking Water
Investigators: Rose, Joan B. , Whittam, Thomas S. , Gulari, Erdogan , Hashsham, Syed
Institution: Michigan State University , University of Michigan
EPA Project Officer: Hiscock, Michael
Project Period: November 1, 2004 through October 31, 2007 (Extended to April 30, 2009)
Project Amount: $600,000
RFA: Microbial Risk in Drinking Water (2003) RFA Text |  Recipients Lists
Research Category: Drinking Water , Water


The concept of using genetic databases for identifying microbial risks in water, coined as Virulence-factor Activity Relationships (VFARs) was first developed by The Committee on Drinking Water Contaminants, National Research Council, as an approach to screen microorganisms for their occurrence in water and/or their ability to cause harm and waterborne disease. We are currently developing a bioinformatics pilot program for the assessment of VFARs and have developed a biochip known as GeneScreen for the detection of E. coli bacteria exploiting the sequence variability inherent in 16S and 23S rRNAs, spacer region, and virulence and functional genes which can provide identification (taxonomy) to the genus and species, as well as pathogenicity and potential risk. Here we propose to develop and validate a high density biochip for some 15 groups or genera/species of targeted bacteria and viruses, some of which are on the CCL and others important for the assessment of the microbial safety of water. We will target traditional indicator organisms, pathogenic bacterial strains and viruses, as well as key virulence factors. Specific goals will include: selection of gene targets to encompass the microorganisms of interest to water safety; designing probes to uniquely identify each of the above microorganisms and provide reliable detection; synthesize microfluidic biochips containing the above set of probes in replicate with positive and negative controls (biochip synthesis); validate and field-test the synthesized biochips using standard individual targets, appropriate target mixtures, and field samples (validation and field-testing); and undertake a pilot risk analysis of a water system(s) testing a variety of computational approaches for interpreting the results of the biochip (analysis). Our team has focused on developing and using microarrays for various environmental applications and has established standard protocols critical to probe design and data analysis.

Publications and Presentations:

Publications have been submitted on this project: View all 14 publications for this project

Journal Articles:

Journal Articles have been submitted on this project: View all 4 journal articles for this project

Supplemental Keywords:

microarray, waterborne disease, enteric viruses, noroviruses, CCL, E coli, legionella, RFA, Health, Scientific Discipline, PHYSICAL ASPECTS, Water, Ecosystem Protection/Environmental Exposure & Risk, Environmental Chemistry, Health Risk Assessment, Risk Assessments, Monitoring/Modeling, Environmental Monitoring, Physical Processes, Drinking Water, microbial contamination, monitoring, measurement , microbial risk assessment, biochip, microbiological organisms, detection, exposure and effects, virulence factor activity relationships, virulence factor biochip, exposure, bacteria monitoring, other - risk assessment, E. Coli, human exposure, microbial risk management, measurement, microorganism, drinking water contaminants, assessment technology, other - risk management

Progress and Final Reports:

  • 2005 Progress Report
  • 2006 Progress Report
  • 2007 Progress Report
  • 2008 Progress Report
  • Final