The US Environmental Protection Agency (USEPA) is currently using several approaches to ascertain the long-term and short-term utility of the Virulence Factor Associated Relationships (VFARs) concept for evaluating CCL organisms and for identifying currently unknown pathogens from the environment. A data mining effort has been funded to find common DNA sequences among diverse species of pathogenic bacteria. One research approach uses proteomics to examine and compare gene products from virulent and avirulent isolates of Aeromonas that are growing in cell culture. Another approach, which will be accomplished through an Interagency Agreement, will compare gene products and genes in Cryptosporidium strains that cause illness in humans with those from Cryptosporidium isolates that are avirulent in humans. Other protozoan species that infect humans will then be examined for genes that are analogous to those associated with those Cryptosporidium strains that are virulent to humans. The most creative approach that the USEPA is currently using compares the responses of mammalian cells to pathogenic strains of Aeromonas to the responses observed with avirulent strains from the same genus. If the responses are significantly different, this approach should eliminate the need to identify the entire array of genes necessary for virulence in order to distinguish between virulent and avirulent isolates. This approach will accurately characterize as avirulent those strains that carry one or more virulence genes but do not express them. In addition, this approach will screen newly discovered microorganisms for virulence potential. The preliminary results obtained from these in-house studies are promising. Neonatal mice were challenged with a virulent isolate of A. hydrophila and an avirulent isolate of A. caviae. Five hours later microarrays were used to measure host mRNA responses. The differences were dramatic; over 400 genes were up-regulated after exposure of the host to the virulent strain, whereas only 28 host genes were up-regulated after exposure to the avirulent strain. Furthermore, many of the genes that were induced by the virulent isolate were genes that are associated with immune responses. These experiments will be repeated using tissue culture and eventually using other genera of pathogens.