{"id":12427,"date":"2023-11-09T13:33:21","date_gmt":"2023-11-09T18:33:21","guid":{"rendered":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/?p=12427"},"modified":"2023-11-09T14:18:15","modified_gmt":"2023-11-09T19:18:15","slug":"pathogen-detection-shiga-toxin-subtype","status":"publish","type":"post","link":"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2023\/11\/09\/pathogen-detection-shiga-toxin-subtype\/","title":{"rendered":"NCBI Pathogen Detection Plays Key Role in Identification of a Novel Shiga Toxin Subtype"},"content":{"rendered":"<p><span data-contrast=\"auto\">Using the <\/span><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pathogens\/?utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=pathogen-detection-shiga-toxin-20231109\"><span data-contrast=\"none\">Pathogen Detection<\/span><\/a><span data-contrast=\"auto\"> pipeline, we recently found new Shiga toxin 2 (<\/span><i><span data-contrast=\"auto\">stx2<\/span><\/i><span data-contrast=\"auto\">) subtypes in isolates from the United States collected as part of the <\/span><a href=\"https:\/\/www.cdc.gov\/\"><span data-contrast=\"none\">Centers for Disease Control and Prevention (CDC)<\/span><\/a><span data-contrast=\"auto\"> routine disease surveillance. Our pipeline relies on <\/span><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pathogens\/antimicrobial-resistance\/AMRFinder\/?utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=pathogen-detection-shiga-toxin-20231109\"><span data-contrast=\"none\">AMRFinderPlus<\/span><\/a><span data-contrast=\"auto\"> to identify anti-microbial resistance (AMR), stress-resistance, and virulence genes. We screened over 60,000 <\/span><i><span data-contrast=\"auto\">E. coli<\/span><\/i><span data-contrast=\"auto\"> and <\/span><i><span data-contrast=\"auto\">Shigella <\/span><\/i><span data-contrast=\"auto\">genomes for Shiga toxin, a factor associated with food borne illness. These analysis results and full AMRFinderPlus results for now over 270,000 <\/span><i><span data-contrast=\"auto\">E. coli <\/span><\/i><span data-contrast=\"auto\">and <\/span><i><span data-contrast=\"auto\">Shigella<\/span><\/i><span data-contrast=\"auto\"> genomes are available in the <\/span><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pathogens\/microbigge\/\"><span data-contrast=\"none\">MicroBIGG-E<\/span><\/a><span data-contrast=\"auto\"> browser. <\/span><!--more--><\/p>\n<p><span data-contrast=\"auto\">To further classify and characterize the new subtypes we found, we collaborated with colleagues from the CDC, the <\/span><a href=\"https:\/\/www.fda.gov\/\"><span data-contrast=\"none\">U.S. Food and Drug Administration (FDA)<\/span><\/a><span data-contrast=\"auto\">, and an international group of Shiga toxin experts. Read our <\/span><a href=\"https:\/\/www.mdpi.com\/2076-2607\/11\/10\/2561\"><span data-contrast=\"none\">publication<\/span><\/a>,<span data-contrast=\"auto\"> also available as a free full-text article in <\/span><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC10608928\/?utm_source=ncbi_insights&amp;utm_medium=referral&amp;utm_campaign=pathogen-detection-shiga-toxin-20231109\"><span data-contrast=\"none\">PubMed Central (PMC)<\/span><\/a>, <span data-contrast=\"auto\">on discovering and characterizing these previously unknown Shiga toxin subtypes.<\/span><span data-ccp-props=\"{&quot;134233117&quot;:true,&quot;134233118&quot;:true,&quot;201341983&quot;:0,&quot;335559738&quot;:150,&quot;335559739&quot;:0,&quot;335559740&quot;:240}\">\u00a0<\/span><\/p>\n<p><span data-contrast=\"auto\">We are working with our collaborators to develop a <\/span><i><span data-contrast=\"auto\">stx <\/span><\/i><span data-contrast=\"auto\">typing scheme that incorporates our findings and will add this to Pathogen Detection resources in the near future. Stay tuned!<\/span><span data-ccp-props=\"{&quot;134233117&quot;:false,&quot;134233118&quot;:false,&quot;201341983&quot;:0,&quot;335559738&quot;:150,&quot;335559739&quot;:0,&quot;335559740&quot;:240}\">\u00a0<\/span><\/p>\n<p><b><span data-contrast=\"none\">Stay up to date<\/span><\/b><span data-contrast=\"none\">\u202f<\/span><span data-ccp-props=\"{&quot;134233117&quot;:false,&quot;134233118&quot;:false,&quot;201341983&quot;:0,&quot;335559738&quot;:150,&quot;335559739&quot;:0,&quot;335559740&quot;:240}\">\u00a0<\/span><\/p>\n<p><span data-contrast=\"none\">Follow us on social <\/span><a href=\"https:\/\/twitter.com\/ncbi\"><span data-contrast=\"none\">@NCBI<\/span><\/a><span data-contrast=\"none\">\u202fand\u202f<\/span><a href=\"https:\/\/public.govdelivery.com\/accounts\/USNLMOCPL\/subscriber\/new?topic_id=USNLMOCPL_52\"><span data-contrast=\"none\">join our mailing list<\/span><\/a><span data-contrast=\"none\">\u202fto keep up to date with\u202fNCBI Pathogen Detection\u202fand other NCBI news.\u202f\u202f<\/span><span data-ccp-props=\"{&quot;134233117&quot;:false,&quot;134233118&quot;:false,&quot;201341983&quot;:0,&quot;335559738&quot;:150,&quot;335559739&quot;:0,&quot;335559740&quot;:240}\">\u00a0<\/span><\/p>\n<p><b><span data-contrast=\"none\">Questions?<\/span><\/b><span data-contrast=\"none\">\u202f<\/span><span data-ccp-props=\"{&quot;134233117&quot;:false,&quot;134233118&quot;:false,&quot;201341983&quot;:0,&quot;335559738&quot;:150,&quot;335559739&quot;:0,&quot;335559740&quot;:240}\">\u00a0<\/span><\/p>\n<p><span data-contrast=\"none\">Please\u202f<\/span><a href=\"https:\/\/support.nlm.nih.gov\/support\/create-case\/\"><span data-contrast=\"none\">reach out to us<\/span><\/a><span data-contrast=\"none\">\u202fif you have questions or would like to provide feedback.<\/span><span data-ccp-props=\"{&quot;134233117&quot;:false,&quot;134233118&quot;:false,&quot;201341983&quot;:0,&quot;335559738&quot;:150,&quot;335559739&quot;:0,&quot;335559740&quot;:240}\">\u00a0<\/span><\/p>\n<p><span data-ccp-props=\"{&quot;201341983&quot;:0,&quot;335559739&quot;:160,&quot;335559740&quot;:259}\">\u00a0<\/span><\/p>\n","protected":false},"excerpt":{"rendered":"<p>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 &hellip; <a href=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2023\/11\/09\/pathogen-detection-shiga-toxin-subtype\/\" class=\"more-link\">Continue reading <span class=\"screen-reader-text\">NCBI Pathogen Detection Plays Key Role in Identification of a Novel Shiga Toxin Subtype<\/span> <span class=\"meta-nav\">&rarr;<\/span><\/a><\/p>\n","protected":false},"author":42204617,"featured_media":12429,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_coblocks_attr":"","_coblocks_dimensions":"","_coblocks_responsive_height":"","_coblocks_accordion_ie_support":"","jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_memberships_contains_paid_content":false,"footnotes":"","jetpack_publicize_message":"NCBI Pathogen Detection Plays Key Role in Identification of a Novel Shiga Toxin Subtype","jetpack_publicize_feature_enabled":true,"jetpack_social_post_already_shared":true,"jetpack_social_options":{"image_generator_settings":{"template":"highway","enabled":false},"version":2}},"categories":[2248],"tags":[20148090,140732360],"table_tags":[],"class_list":["post-12427","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-whats-new","tag-pathogen-detection","tag-pubmed-central-pmc"],"jetpack_publicize_connections":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v24.6 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>NCBI Pathogen Detection Plays Key Role in Identification of a Novel Shiga Toxin Subtype - NCBI Insights<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/ncbiinsights.ncbi.nlm.nih.gov\/2023\/11\/09\/pathogen-detection-shiga-toxin-subtype\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"NCBI Pathogen Detection Plays Key Role in Identification of a Novel Shiga Toxin Subtype - NCBI Insights\" \/>\n<meta property=\"og:description\" content=\"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. 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Our pipeline relies on AMRFinderPlus to identify anti-microbial resistance (AMR), stress-resistance, and virulence genes. 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