Using the Pathogen Detection pipeline, we recently found new Shiga toxin 2 (stx2) subtypes in isolates from the United States collected as part of the Centers for Disease Control and Prevention (CDC) routine disease surveillance. Our pipeline relies on AMRFinderPlus to identify anti-microbial resistance (AMR), stress-resistance, and virulence genes. We screened over 60,000 E. coli and Shigella genomes for Shiga toxin, a factor associated with food borne illness. These analysis results and full AMRFinderPlus results for now over 270,000 E. coli and Shigella genomes are available in the MicroBIGG-E browser.
To further classify and characterize the new subtypes we found, we collaborated with colleagues from the CDC, the U.S. Food and Drug Administration (FDA), and an international group of Shiga toxin experts. Read our publication, also available as a free full-text article in PubMed Central (PMC), on discovering and characterizing these previously unknown Shiga toxin subtypes.
We are working with our collaborators to develop a stx typing scheme that incorporates our findings and will add this to Pathogen Detection resources in the near future. Stay tuned!
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