EnteroBase in 2025: exploring the genomic epidemiology of bacterial pathogens.

Journal

Nucleic acids research
ISSN: 1362-4962
Titre abrégé: Nucleic Acids Res
Pays: England
ID NLM: 0411011

Informations de publication

Date de publication:
23 Oct 2024
Historique:
accepted: 14 10 2024
revised: 25 09 2024
received: 13 08 2024
medline: 23 10 2024
pubmed: 23 10 2024
entrez: 23 10 2024
Statut: aheadofprint

Résumé

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.

Identifiants

DOI: 10.1093/nar/gkae902 PMID: 39441072
pubmed: 39441072
pii: 7832345
doi: 10.1093/nar/gkae902
pii:
doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Subventions

Organisme : PATH-SAFE
Organisme : HM Treasury
Organisme : Global Health EDCTP3
Organisme : European Union
ID : PANGenS
Organisme : German Center for Infection Research
ID : TI 12.901/12.902

Informations de copyright

© The Author(s) 2024. Published by Oxford University Press on behalf of Nucleic Acids Research.

Auteurs

Nigel P Dyer (NP)

Bioinformatics & Digital Health Services, Research Technology Platforms, University of Warwick, Gibbet Hill Campus, Coventry CV4 7AL, UK.

Birgitta Päuker (B)

Leibniz Institute DSMZ, Germany-German Collection of Microorganisms and Cell Cultures, Inhoffenstr. 7B, 38124 Braunschweig, Germany.
German Center for Infection Research (DZIF), partner site Braunschweig-Hannover, Inhoffenstr. 7, 38124 Braunschweig, Germany.
ORCID: 0009-0009-8996-0844

Laura Baxter (L)

Bioinformatics & Digital Health Services, Research Technology Platforms, University of Warwick, Gibbet Hill Campus, Coventry CV4 7AL, UK.

Anshul Gupta (A)

Leibniz Institute DSMZ, Germany-German Collection of Microorganisms and Cell Cultures, Inhoffenstr. 7B, 38124 Braunschweig, Germany.
ORCID: 0009-0005-4827-8057

Boyke Bunk (B)

Leibniz Institute DSMZ, Germany-German Collection of Microorganisms and Cell Cultures, Inhoffenstr. 7B, 38124 Braunschweig, Germany.

Jörg Overmann (J)

Leibniz Institute DSMZ, Germany-German Collection of Microorganisms and Cell Cultures, Inhoffenstr. 7B, 38124 Braunschweig, Germany.
German Center for Infection Research (DZIF), partner site Braunschweig-Hannover, Inhoffenstr. 7, 38124 Braunschweig, Germany.
Technical University of Braunschweig, Institute of Microbiology, Spielmannstr. 7, 38106 Braunschweig, Germany.

Margo Diricks (M)

Research Center Borstel, Leibniz Lung Center, Parkallee 1, 23845 Borstel, Germany.
German Center for Infection Research (DZIF), partner site Hamburg-Lübeck-Borstel-Riems, Parkallee 1, 23845 Borstel, Germany.
National and WHO Supranational Reference Laboratory for Mycobacteria, Research Center Borstel, Parkallee 1, 23845 Borstel, Germany.

Viola Dreyer (V)

Research Center Borstel, Leibniz Lung Center, Parkallee 1, 23845 Borstel, Germany.
German Center for Infection Research (DZIF), partner site Hamburg-Lübeck-Borstel-Riems, Parkallee 1, 23845 Borstel, Germany.
National and WHO Supranational Reference Laboratory for Mycobacteria, Research Center Borstel, Parkallee 1, 23845 Borstel, Germany.

Stefan Niemann (S)

Research Center Borstel, Leibniz Lung Center, Parkallee 1, 23845 Borstel, Germany.
German Center for Infection Research (DZIF), partner site Hamburg-Lübeck-Borstel-Riems, Parkallee 1, 23845 Borstel, Germany.
National and WHO Supranational Reference Laboratory for Mycobacteria, Research Center Borstel, Parkallee 1, 23845 Borstel, Germany.

Kathryn E Holt (KE)

Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine,15-17 Tavistock Pl, LondonWC1H 9SH, UK.
Department of Infectious Diseases, School of Translational Medicine, Monash University, 45 Kanooka Grove, Clayton VIC 3168, Australia.

Mohammed Rahman (M)

Bioinformatics & Digital Health Services, Research Technology Platforms, University of Warwick, Gibbet Hill Campus, Coventry CV4 7AL, UK.

Paul E Brown (PE)

Bioinformatics & Digital Health Services, Research Technology Platforms, University of Warwick, Gibbet Hill Campus, Coventry CV4 7AL, UK.

Richard Stark (R)

Bioinformatics & Digital Health Services, Research Technology Platforms, University of Warwick, Gibbet Hill Campus, Coventry CV4 7AL, UK.

Zhemin Zhou (Z)

Soochow University, Pasteurien College, No. 199 Ren'ai Road, Suzhou, Jiangsu 215123, China.

Sascha Ott (S)

Bioinformatics & Digital Health Services, Research Technology Platforms, University of Warwick, Gibbet Hill Campus, Coventry CV4 7AL, UK.
ORCID: 0000-0002-5411-8114

Ulrich Nübel (U)

Leibniz Institute DSMZ, Germany-German Collection of Microorganisms and Cell Cultures, Inhoffenstr. 7B, 38124 Braunschweig, Germany.
German Center for Infection Research (DZIF), partner site Braunschweig-Hannover, Inhoffenstr. 7, 38124 Braunschweig, Germany.
Technical University of Braunschweig, Institute of Microbiology, Spielmannstr. 7, 38106 Braunschweig, Germany.
ORCID: 0000-0003-3131-1656

Classifications MeSH