{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T20:07:22Z","timestamp":1792786042988,"version":"4.5.0"},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2024,10,23]],"date-time":"2024-10-23T00:00:00Z","timestamp":1729641600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"PATH-SAFE"},{"name":"HM Treasury"},{"name":"Global Health EDCTP3"},{"DOI":"10.13039\/501100000780","name":"European Union","doi-asserted-by":"publisher","award":["PANGenS"],"award-info":[{"award-number":["PANGenS"]}],"id":[{"id":"10.13039\/501100000780","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100009139","name":"German Center for Infection Research","doi-asserted-by":"publisher","award":["TI 12.901\/12.902"],"award-info":[{"award-number":["TI 12.901\/12.902"]}],"id":[{"id":"10.13039\/100009139","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,1,6]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>This paper presents an update on the content, accessibility and analytical tools of the EnteroBase platform for web-based pathogen genome analysis. EnteroBase provides manually curated databases of genome sequence data and associated metadata from currently\u00a0&amp;gt;1.1 million bacterial isolates, more recently including Streptococcus spp. and Mycobacterium tuberculosis, in addition to Salmonella,Escherichia\/Shigella,Clostridioides,Vibrio,Helicobacter,YersiniaandMoraxella. We have implemented the genome-based detection of antimicrobial resistance determinants and the new bubble plot graphical tool for visualizing bacterial genomic population structures, based on pre-computed hierarchical clusters. Access to data and analysis tools is provided through an enhanced graphical user interface and a new application programming interface (RESTful API). EnteroBase is now being developed and operated by an international consortium, to accelerate the development of the platform and ensure the longevity of the resources built. EnteroBase can be accessed at https:\/\/enterobase.warwick.ac.uk as well as https:\/\/enterobase.dsmz.de.<\/jats:p>","DOI":"10.1093\/nar\/gkae902","type":"journal-article","created":{"date-parts":[[2024,10,14]],"date-time":"2024-10-14T07:18:42Z","timestamp":1728890322000},"page":"D757-D762","source":"Crossref","is-referenced-by-count":73,"title":["EnteroBase in 2025: exploring the genomic epidemiology of bacterial pathogens"],"prefix":"10.1093","volume":"53","author":[{"given":"Nigel\u00a0P","family":"Dyer","sequence":"first","affiliation":[{"name":"Bioinformatics & Digital Health Services, Research Technology Platforms, University of Warwick , Gibbet Hill Campus, Coventry CV4 7AL ,","place":["UK"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0009-8996-0844","authenticated-orcid":false,"given":"Birgitta","family":"P\u00e4uker","sequence":"additional","affiliation":[{"name":"Leibniz Institute DSMZ, Germany\u2014German Collection of Microorganisms and Cell Cultures , Inhoffenstr. 7B, 38124 Braunschweig ,","place":["Germany"]},{"name":"German Center for Infection Research (DZIF), partner site Braunschweig-Hannover , Inhoffenstr. 7, 38124 Braunschweig ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laura","family":"Baxter","sequence":"additional","affiliation":[{"name":"Bioinformatics & Digital Health Services, Research Technology Platforms, University of Warwick , Gibbet Hill Campus, Coventry CV4 7AL ,","place":["UK"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-4827-8057","authenticated-orcid":false,"given":"Anshul","family":"Gupta","sequence":"additional","affiliation":[{"name":"Leibniz Institute DSMZ, Germany\u2014German Collection of Microorganisms and Cell Cultures , Inhoffenstr. 7B, 38124 Braunschweig 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,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Margo","family":"Diricks","sequence":"additional","affiliation":[{"name":"Research Center Borstel, Leibniz Lung Center ,\u00a0Parkallee 1, 23845 Borstel ,","place":["Germany"]},{"name":"German Center for Infection Research (DZIF), partner site Hamburg-L\u00fcbeck-Borstel-Riems , Parkallee 1, 23845 Borstel ,","place":["Germany"]},{"name":"National and WHO Supranational Reference Laboratory for Mycobacteria, Research Center Borstel ,\u00a0Parkallee 1, 23845 Borstel,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Viola","family":"Dreyer","sequence":"additional","affiliation":[{"name":"Research Center Borstel, Leibniz Lung Center ,\u00a0Parkallee 1, 23845 Borstel ,","place":["Germany"]},{"name":"German Center for Infection Research (DZIF), partner site Hamburg-L\u00fcbeck-Borstel-Riems , Parkallee 1, 23845 Borstel ,","place":["Germany"]},{"name":"National and WHO Supranational Reference Laboratory for Mycobacteria, Research Center Borstel ,\u00a0Parkallee 1, 23845 Borstel,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stefan","family":"Niemann","sequence":"additional","affiliation":[{"name":"Research Center Borstel, Leibniz Lung Center ,\u00a0Parkallee 1, 23845 Borstel ,","place":["Germany"]},{"name":"German Center for Infection Research (DZIF), partner site Hamburg-L\u00fcbeck-Borstel-Riems , Parkallee 1, 23845 Borstel ,","place":["Germany"]},{"name":"National and WHO Supranational Reference Laboratory for Mycobacteria, Research Center Borstel ,\u00a0Parkallee 1, 23845 Borstel,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kathryn\u00a0E","family":"Holt","sequence":"additional","affiliation":[{"name":"Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine ,15-17 Tavistock Pl, London WC1H 9SH,","place":["UK"]},{"name":"Department of Infectious Diseases, School of Translational Medicine, Monash University , 45 Kanooka Grove, Clayton VIC 3168,","place":["Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mohammed","family":"Rahman","sequence":"additional","affiliation":[{"name":"Bioinformatics & Digital Health Services, Research Technology Platforms, University of Warwick , Gibbet Hill Campus, Coventry CV4 7AL ,","place":["UK"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paul\u00a0E","family":"Brown","sequence":"additional","affiliation":[{"name":"Bioinformatics & Digital Health Services, Research Technology Platforms, University of Warwick , Gibbet Hill Campus, Coventry CV4 7AL ,","place":["UK"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Richard","family":"Stark","sequence":"additional","affiliation":[{"name":"Bioinformatics & Digital Health Services, Research Technology Platforms, University of Warwick , 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