The EnteroBase user's guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny, and Escherichia core genomic diversity

EnteroBase is an integrated software environment that supports the identification of global population structures within several bacterial genera that include pathogens. Here, we provide an overview of how EnteroBase works, what it can do, and its future prospects. EnteroBase has currently assembled more than 300,000 genomes from Illumina short reads from Salmonella , Escherichia , Yersinia , Clostridioides , Helicobacter , Vibrio , and Moraxella and genotyped those assemblies by core genome multilocus sequence typing (cgMLST). Hierarchical clustering of cgMLST sequence types allows mapping a new bacterial strain to predefined population structures at multiple levels of resolution within a few hours after…

• W
  Wellcome

  Award: 202792/Z/16/Z
• WT
  Wellcome Trust

  Awards: 202792, 202792/Z/16/Z
• DF
  Directorate for Biological Sciences
• BA
  Biotechnology and Biological Sciences Research Council

  Awards: BB/L020319/1, BB/L020319/1, BBS/E/F/000PR10352