We have expanded the Reference Gene Catalog8 (link) to include genetic elements related to stress response and virulence genes; these expansions can be visualized in the Reference Gene Catalog Browser (https://www.ncbi.nlm.nih.gov/pathogens/refgene/ ). One reason we expanded AMRFinderPlus is to understand the linkages between AMR genes and stress response and virulence genes in food-borne pathogens; thus, the stress response and virulence genes included in the Reference Gene Catalog are composed primarily of E. coli-related genes derived primarily from González-Escalona et al.23 (link) as well as BacMet24 (link), but also have been supplemented by manual curation efforts for other taxa. Stx gene nomenclature adopts the system of Scheutz et al.25 (link) and the intimin (eae) gene nomenclature uses existing designations in the literature26 (link),27 (link). Genes are incorporated only if there is literature supporting the function of that protein or closely related sequences that meet the identification criteria. As a major focus of our work is to improve NCBI’s Pathogen Detection system16 (link), we excluded genes that belonged to organisms not deemed clinically relevant. To remove ‘housekeeping’ proteins that were universally found in one or more taxa in the Pathogen Detection system, sequences were not included if they were found at a frequency of greater than 95% in a survey of 58,531 RefSeq bacterial assemblies belonging to any of the following species: Acinetobacter, Campylobacter, Citrobacter, Enterococcus, Enterobacter, Escherichia/Shigella, Klebsiella, Listeria, Salmonella, Staphylococcus, Pseudomonas, and Vibrio. If genes of particular interest in foodborne pathogens exceeded this threshold, they were excluded in the taxa where they appear to be nearly universal (see “Identifying genomic elements” below). In addition, genes with misidentified functions, such as copper-binding proteins that use copper as a co-factor yet do not confer resistance to copper, also were excluded. As we continue to expand the database, we use similar criteria when adding genes.
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