Year: 2024
Type: article
Abstract: 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.
Source: Nucleic Acids Research
DOI: 10.1093/nar/gkae902
Authors: Nigel P Dyer, Birgitta Päuker, Laura Baxter, Anshul Gupta, Boyke Bunk, Jörg Overmann, Margo Diricks, Viola Dreyer, Stefan Niemann, Kathryn E Holt, Mohammed Rahman, Paul E Brown, Richard Stark, Zhemin Zhou, Sascha Ott, Ulrich Nübel
Institutions: University of Warwick, German Center for Infection Research, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Technische Universität Braunschweig, Research Center Borstel - Leibniz Lung Center, London School of Hygiene & Tropical Medicine, Monash University, Soochow University
Language: English
Subfield: Food Science
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $4,192
Award: G8622962884
OpenAlex ID: W4403684406