Expanding E. coli Virulence Database

To supplement VirulenceFinder's existing E. coli virulence gene database as of study onset (101 genes, 936 alleles), a supplemental ExPEC FASTA database containing a selection of diverse ExPEC-associated genes was constructed. Genes were identified as candidates for inclusion based on the genes used in the two main established operational definitions for ExPEC and UPEC (4 (link), 5 (link)) and recommendations from expert colleagues (authors J. R. Johnson and B. D. Johnston as well as Erick Denamur [INSERM, Universités Paris Diderot et Paris Nord, France] and David M. Gordon [Ecology and Evolution, Research School of Biology, the Australian National University, Acton, Australia]). As a proof of concept, the database was validated first by comparing PCR virulence genotyping results obtained in previous studies for nine control strains (6 (link)) with the virulence genes predicted here in silico for the same nine strains by using the revised VirulenceFinder to analyze the WGS data of these strain. A second evaluation was done by comparing (previous and new) PCR virulence genotyping results for 288 clinical and fecal strains of human origin that had been classified previously as ExPEC_JJ versus non-ExPEC_JJ (11 (link)) with the virulence genes predicted here by applying the revised VirulenceFinder to the WGS data of these strains. Finally, using WGS-based pathotype classifications as derived using the revised VirulenceFinder, the ExPEC_JJ/non-ExPEC_JJ status of these 288 strains was compared with their UPEC_HM/non-UPEC_HM status.