45,671 Escherichia coli genomes

<h1>45,671&nbsp;<em>Escherichia coli</em> genomes</h1> <p>This upload contains 45,671 high-quality&nbsp;<em>E. coli</em> assemblies collected from multiple sources with emphasis on improving coverage of commensal <em>E. coli</em> and adding more sequences from underrepresented countries.</p> <p>The assemblies are compressed using the <a href="https://github.com/refresh-bio/agc">Assembled Genomes Compressor AGC</a> which achieves a &gt;10x better compression ratio over plain gzip and allows quick retrieval of one or more sequences. Instructions for decompressing the files are provided below.</p> <h2>Usage</h2> <h3>Extracting the AGC archive</h3> <ul> <li>Install AGC version 3.0 or newer from bioconda or by downloading a precompiled binary from <a href="https://github.com/refresh-bio/agc/releases">https://github.com/refresh-bio/agc/releases</a>.</li> <li>Run `agc listset 45k_E_coli_genomes.agc &gt; 45k_E_coli_genomes_filenames.txt` to list the assemblies in the archive.</li> <li>To extract a single assembly, run `agc getset -p -o assembly_name.fa 45k_E_coli_genomes.agc assembly_name.fa`.</li> <li>To extract all assemblies, run `cat 45k_E_coli_genomes_filenames.txt | xargs -I {} agc getset&nbsp; -o {} -p 45k_E_coli_genomes.agc {}` <ul> <li><strong>warning</strong> extracting the whole archive this way will take ~240GB disk space.</li> <li><strong>note</strong>&nbsp;remember to use the `-p` toggle with agc to reduce the runtime.</li> <li><strong>parallelise</strong> the extraction by running `parallel -j &lt;number of threads&gt; 'agc getset -o {} -t 1 -p 45k_E_coli_genomes.agc {}' &lt; 45k_E_coli_genomes_filenames.txt`.</li> </ul> </li> </ul> <h3>Metadata</h3> <p>The file `45k_E_coli_metadata.tsv` details which multilocus sequence type (ST) and clonal complex (CC) the assemblies belong to, assigned using the ecoli#1 scheme in <a href="https://github.com/EnzoAndree/FastMLST">fastmlst v0.0.15</a>, the phylogroup the ST belongs to according to <a href="https://doi.org/10.1099/mgen.0.000499">Horesh et al. (2021)</a>, and the presence of at least 17 of the 19 pks island genes (pks+) and/or the clbS gene encoding the colibactin self-resistance protein ClbS which were determined using the <a href="https://github.com/tmaklin/clbtype">clbtype</a> scripts.</p> <h3>Distribution</h3> <p>You are free to use the assemblies, provided that the sources are cited accordingly.</p> <h3>Citation</h3> <p>This collection was first published as part of the study "Geographical variation in the incidence of colorectal cancer and urinary tract cancer is associated with population exposure to colibactin-producing <em>Escherichia coli</em>" in <em>Lancet Microbe</em>&nbsp;on 5 December 2024, doi:&nbsp;<a href="https://doi.org/10.1016/j.lanmic.2024.101015">10.1016/j.lanmic.2024.101015</a>.</p> <h2>Methods</h2> <h3>Definition of&nbsp;<em>Escherichia coli</em></h3> <p>In the context of these files,&nbsp;<em>E. coli</em> is defined as all assemblies belonging to the same 97% pangenome average nucleotide identity (panANI) cluster which is comparable to the more traditional definition of a bacterial species as 95% ANI clusters. This definition is consistent with the one provided in <a href="https://gtdb.ecogenomic.org/">GTDB Release 09-RS220 (24th April 2024)</a>.</p> <p>The 97%-panANI clusters were defined by running&nbsp;<a href="https://github.com/tmaklin/panaani">panaani v0.1.0</a> on the quality filtered source data referenced below.</p> <h3>Source data</h3> <p>Assemblies from the following studies were considered for inclusion:</p> <ul> <li>661k genomes collection from&nbsp;<a href="https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3001421https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3001421">Blackwell et al. 2021</a></li> <li>Avian&nbsp;<em>E. coli</em> <a href="https://www.nature.com/articles/s41467-021-20988-w">genomes</a></li> <li>Bin-assembled <em>E. coli</em> from <a href="https://doi.org/10.1016/j.cell.2022.10.011">Bangladesh</a>, <a href="https://doi.org/10.1016/j.cell.2022.11.023">Finland</a>, <a href="https://www.nature.com/articles/s41467-024-49591-5">Pakistan</a>, <a href="https://www.nature.com/articles/s41586-019-1560-1">UK</a>, <a href="https://www.nature.com/articles/s41467-023-36135-6">Zimbabwe</a></li> <li>Carbapenemase producing&nbsp;<em>E. coli</em> from <a href="https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2023.28.27.2200774">Norwegian travellers</a></li> <li><em>E. coli</em> genomes from <a href="../records/12528310">a previous index</a></li> <li><em>E. coli</em> isolated from inpatients in <a href="https://link.springer.com/article/10.1186/s13756-018-0361-x">Tanzania</a></li> <li><em>E. coli</em> from various sources in <a href="https://www.nature.com/articles/s41564-022-01079-y">Kenya</a></li> <li><em>E. coli</em> from a one health study in <a href="https://www.thelancet.com/journals/lanmic/article/PIIS2666-5247(23)00208-2/fulltext">Ghana</a></li> <li><em>E. coli</em> from bloodstream infections in <a href="https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000863">Nigeria</a></li> <li>Enteropathogenic&nbsp;<em>E. col</em><em>i&nbsp;</em>from <a href="https://www.nature.com/articles/s41564-018-0217-4#Sec10">Sub-Saharan Africa and South Asia</a></li> <li>Enteropathogenic&nbsp;<em>E. coli</em> isolated from cattle in <a href="https://www.sciencedirect.com/science/article/pii/S0168160522000265#s0050">South Africa</a></li> <li>ESBL positive <em>E. coli</em> from <a href="https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2021.752883/full">Benin</a></li> <li>ESBL producing&nbsp;<em>E. coli</em> and&nbsp;<em>Klebsiella</em> from rats in <a href="https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2018.00150/full">Guinea</a></li> <li>ESBL producing&nbsp;<em>E. coli</em> from European soldiers deployed in <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10198576/">Mali</a></li> <li>ESBL producing<em> E. coli</em> from <a href="https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.001035">Malawi</a></li> <li>GTDB representative genomes from&nbsp;<a href="https://data.gtdb.ecogenomic.org/releases/release214/">Release 214</a></li> <li>Livestock&nbsp;<em>E. coli</em> from <a href="https://journals.asm.org/doi/full/10.1128/mbio.02693-18">England</a></li> <li>Metagenome-assembled genome from <a href="https://www.cell.com/cell/fulltext/S0092-8674(23)00597-4">Hadza hunter-gatherers</a></li> <li>Mgnify&nbsp;<a href="https://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/chicken-gut/v1.0/">chicken gut v1.0</a></li> <li>Mgnify <a href="https://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/cow-rumen/v1.0/">cow rumen v1.0</a></li> <li>Mgnify <a href="https://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v2.0.1/">human gut v2.0.1</a></li> <li>Mgnify <a href="https://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-oral/v1.0/">human oral v1.0</a></li> <li>Mgnify <a href="https://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-vaginal/">human vaginal v1.0</a></li> <li>Mgnify <a href="https://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/pig-gut/">pig gut v1.0</a></li> <li>One health study in the <a href="https://www.sciencedirect.com/science/article/pii/S2352771423000381">US</a></li> <li><em>Salmonella</em> genomes from water in <a href="https://www.nature.com/articles/s41598-022-08200-5">Lake Victoria</a></li> </ul> <h3>Quality filtering</h3> <p>An assembly met the criteria for high-quality if the following conditions were met:</p> <ul> <li><a href="https://github.com/Ecogenomics/CheckM">checkm v1.2.2</a>&nbsp;completeness &gt;=90%</li> <li><a href="https://github.com/Ecogenomics/CheckM">checkm v1.2.2</a> contamination &lt;= 10%</li> <li><a href="https://github.com/grp-bork/gunc">gunc v1.0.5</a> chimerism analysis score "pass"</li> </ul>