A comprehensive and high-quality collection of Escherichia coli genomes and their genes

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Horesh , G , Blackwell , G A , Tonkin-Hill , G , Corander , J , Heinz , E & Thomson , N R 2021 , ' A comprehensive and high-quality collection of Escherichia coli genomes and their genes ' , Microbial Genomics , vol. 7 , no. 2 , 000499 . https://doi.org/10.1099/mgen.0.000499

Title: A comprehensive and high-quality collection of Escherichia coli genomes and their genes
Author: Horesh, Gal; Blackwell, Grace A.; Tonkin-Hill, Gerry; Corander, Jukka; Heinz, Eva; Thomson, Nicholas R.
Contributor organization: Department of Mathematics and Statistics
Helsinki Institute for Information Technology
Jukka Corander / Principal Investigator
Biostatistics Helsinki
Date: 2021-02
Language: eng
Number of pages: 15
Belongs to series: Microbial Genomics
ISSN: 2057-5858
DOI: https://doi.org/10.1099/mgen.0.000499
URI: http://hdl.handle.net/10138/328629
Abstract: Escherichia coli 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, E. coli is considered a priority pathogen due to high levels of observed drug resistance. The diversity in the E. coli population is driven by high genome plasticity and a very large gene pool. All these have made E. coli one of the most well- studied organisms, as well as a commonly used laboratory strain. Today, there are thousands of sequenced E. coli 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 E. coli and Shigella genomes to provide a single, uniform, high- quality dataset. Shigella were included as they are considered specialized pathovars of E. coli. 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 E. coli lineages and the distribution and flow of genes in the E. coli population at a high resolution. The analysis we present emphasizes our lack of understanding of the true diversity of the E. coli species, and the biased nature of our current understanding of the genetic diversity of such a key pathogen.
Subject: antimicrobial resistance
Escherichia coli
horizontal gene transfer
1184 Genetics, developmental biology, physiology
Peer reviewed: Yes
Rights: cc_by
Usage restriction: openAccess
Self-archived version: publishedVersion

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