1887

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Volume 7, Issue 2

A comprehensive and high-quality collection of genomes and their genes Open Access

Abstract

is a highly diverse organism that includes a range of commensal and pathogenic variants found across a range of niches and worldwide. In addition to causing severe intestinal and extraintestinal disease, is considered a priority pathogen due to high levels of observed drug resistance. The diversity in the population is driven by high genome plasticity and a very large gene pool. All these have made one of the most well-studied organisms, as well as a commonly used laboratory strain. Today, there are thousands of sequenced genomes stored in public databases. While data is widely available, accessing the information in order to perform analyses can still be a challenge. Collecting relevant available data requires accessing different sources, where data may be stored in a range of formats, and often requires further manipulation and processing to apply various analyses and extract useful information. In this study, we collated and intensely curated a collection of over 10 000 and genomes to provide a single, uniform, high-quality dataset. were included as they are considered specialized pathovars of . We provide these data in a number of easily accessible formats that can be used as the foundation for future studies addressing the biological differences between lineages and the distribution and flow of genes in the population at a high resolution. The analysis we present emphasizes our lack of understanding of the true diversity of the species, and the biased nature of our current understanding of the genetic diversity of such a key pathogen.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): antimicrobial resistance , Escherichia coli , horizontal gene transfer , pan-genome and Shigella
Funding
This study was supported by the:
  • European Research Council () (Award 742158)
    • Principle Award Recipient: JukkaCorander
  • Wellcome Trust PhD Scholarship Grant (Award 204016)
    • Principle Award Recipient: GerryTonkin-Hill
  • Wellcome Sanger Institute PhD Studentship (Award NA)
    • Principle Award Recipient: GalHoresh
  • Wellcome Sanger Institute (Award 206194)
    • Principle Award Recipient: NotApplicable
© 2021 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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2021-01-08
2024-04-25
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A comprehensive and high-quality collection of Escherichia coli genomes and their genes
M Gen 7, 000499 (2021); https://doi.org/10.1099/mgen.0.000499
/content/journal/mgen/10.1099/mgen.0.000499
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