EnteroBase in 2025: exploring the genomic epidemiology of bacterial pathogens
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 >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.
Authors
- Nigel Dyer (ORCID: https://orcid.org/0000-0001-6158-0510)
- Margo Diricks (ORCID: https://orcid.org/0000-0002-5428-1456)
- Richard Stark (ORCID: https://orcid.org/0000-0001-5676-7604)
- Ulrich Nübel (ORCID: https://orcid.org/0000-0003-3131-1656)
- Sascha Ott
- Mohammed M. Rahman (ORCID: https://orcid.org/0000-0003-2229-5121)
- Jörg Overmann (ORCID: https://orcid.org/0000-0003-3909-7201)
- Stefan Niemann (ORCID: https://orcid.org/0000-0002-6604-0684)
- Arpana Gupta (ORCID: https://orcid.org/0000-0002-1669-9624)
- Boyke Bunk (ORCID: https://orcid.org/0000-0002-8420-8161)
- Paul E. Brown (ORCID: https://orcid.org/0000-0002-8764-4583)
- Laura Baxter (ORCID: https://orcid.org/0000-0003-3287-7547)
- Kathryn E. Holt (ORCID: https://orcid.org/0000-0003-3949-2471)
- Zhemin Zhou (ORCID: https://orcid.org/0000-0001-9783-0366)
- Birgitta Päuker
- Viola Dreyer
Institutions
- Soochow University (CN)
- University of Warwick (GB)
- London School of Hygiene & Tropical Medicine (GB)
- German Center for Infection Research (DE)
- Czech Academy of Sciences, Institute of Microbiology (CZ)
- Research Center Borstel - Leibniz Lung Center (DE)
- Monash University (AU)
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures (DE)
- Technische Universität Braunschweig (DE)
Publication Details
- Journal
- Nucleic Acids Research
- Published
- 2024-10-14
- DOI
- https://doi.org/10.1093/nar/gkae902
- Citations
- 40
- Primary Topic
- Bacterial Identification and Susceptibility Testing
- Type
- article
- Field-Weighted Citation Impact
- 15.24
Funders
- Deutsches Zentrum für Infektionsforschung
- Government of the United Kingdom
- University of Warwick
- European Commission
- Leibniz-Gemeinschaft
- European and Developing Countries Clinical Trials Partnership