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

Abstract

Escherichia coli is a highly diverse organism which 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 specialised pathovars of E. coli. We provide these data in a number of easily accessible formats which 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 emphasises 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. Author NotesAll supporting data have been provided within the article or through supplementary data files. All supporting code is provided in the git repository https://github.com/ghoresh11/ecoli_genome_collection. Significance as a BioResource to the communityAs of today, there are more than 140,000 E. coli genomes available on public databases. While data is widely available, collating the data and extracting meaningful information from it often requires multiple steps, computational resources and expert knowledge. Here, we collate a high quality and comprehensive set of over 10,000 E. coli genomes, isolated from human hosts, into a set of manageable files that offer an accessible and usable snapshot of the currently available genome data, linked to a minimal data quality standard. The data provided includes a detailed synopsis of the main lineages present, including their antimicrobial and virulence profiles, their complete gene content, and all the associated metadata for each genome. This includes a database which enables the user to compare newly sequenced isolates against the assembled genomes. Additionally, we provide a searchable index which allows the user to query any DNA sequence against the assemblies of the collection. This collection paves the path for many future studies, including those investigating the differences between E. coli lineages, following the evolution of different genes in the E. coli pan-genome and exploring the dynamics of horizontal gene transfer in this important organism. Data SummaryO_LIThe complete aggregated metadata of 10,146 high quality genomes isolated from human hosts (doi.org/10.6084/m9.figshare.12514883, File F1). C_LIO_LIA PopPUNK database which can be used to query any genome and examine its context relative to this collection (Deposited to doi.org/10.6084/m9.figshare.12650834). C_LIO_LIA BIGSI index of all the genomes which can be used to easily and quickly query the genomes for any DNA sequence of 61 bp or longer (Deposited to doi.org/10.6084/m9.figshare.12666497). C_LIO_LIDescription and complete profiling the 50 largest lineages which represent the majority of publicly available human-isolated E. coli genomes (doi.org/10.6084/m9.figshare.12514883, File F2). Phylogenetic trees of representative genomes of these lineages, presented in this manuscript, are also provided (doi.org/10.6084/m9.figshare.12514883, Files tree_500.nwk and tree_50.nwk). C_LIO_LIThe complete pan-genome of the 50 largest lineages which includes: O_LIA FASTA file containing a single representative sequence of each gene of the gene pool (doi.org/10.6084/m9.figshare.12514883, File F3). C_LIO_LIComplete gene presence-absence across all isolates (doi.org/10.6084/m9.figshare.12514883, File F4). C_LIO_LIThe frequency of each gene within each of the lineages (doi.org/10.6084/m9.figshare.12514883, File F5). C_LIO_LIThe representative sequences from each lineage for all the genes (doi.org/10.6084/m9.figshare.12514883, File F6). C_LI C_LI