The genomic and epidemiological virulence patterns of Salmonella enterica serovars in the United States.

ABSTRACT: The serovars of Salmonella enterica display dramatic differences in pathogenesis and host preferences. We developed a process (patent pending) for grouping Salmonella isolates and serovars by their public health risk. We collated a curated set of 12,337 S. enterica isolate genomes from human, beef, and bovine sources in the US. After annotating a virulence gene catalog for each isolate, we used unsupervised random forest methods to estimate the proximity (similarity) between isolates based upon the genomic presentation of putative virulence traits We then grouped isolates (virulence clusters) using hierarchical clustering (Ward's method), used non-parametric bootstrapping to assess cluster stability, and externally validated the clusters against epidemiological virulence measures from Food

SUBMITTER: Fenske GJ 

PROVIDER: S-EPMC10697515 | biostudies-literature | 2023

REPOSITORIES: biostudies-literature