Escherichia coli lineage deconvolution indexes for Themisto, mSWEEP/mGEMS, and demix_check

<h2><strong><em>Escherichia coli</em> lineage deconvolution indexes for Themisto, mSWEEP/mGEMS, and demix_check</strong></h2> <p>This dataset contains the indexes used in a study conducted in Punjab, Pakistan that investigated <em>E. coli</em> colonisation diversity in healthy carriage with the use of CLED enrichment plates. The following files are included in the download:</p> <ul> <li>Themisto v3 pseudoalignment index.</li> <li>PopPUNK database.</li> <li>Demix_check index.</li> <li>Raw assembly data.</li> </ul> <h3><strong>About</strong></h3> <h4><strong>Version history</strong></h4> <p><strong>v0.1.1 (current version)</strong></p> <ul> <li>Added reference to the study.</li> </ul> <p><strong>v0.1.0</strong></p> <ul> <li>Added brief description with a few missing parts.</li> </ul> <h4><strong>Distribution</strong></h4> <p>These files are made available under a CC-BY 4.0 license. If you use these assemblies in your study please cite the source as appropriate (study will be added in a later version).</p> <h4><strong>Citation</strong></h4> <p>Khawaja, T., M&auml;klin, T., Kallonen, T. et al. Deep sequencing of _Escherichia coli_ exposes colonisation diversity and impact of antibiotics in Punjab, Pakistan. Nature Communications 15, 5196 (2024). <a href="https://doi.org/10.1038/s41467-024-49591-5">https://doi.org/10.1038/s41467-024-49591-5</a></p> <h3><strong>Methods briefly</strong></h3> <h4><strong>Data</strong></h4> <p>Assembly data included originates from the following studies:</p> <ul> <li>Horesh G, et al., A comprehensive and high-quality collection of <em>Escherichia coli</em> genomes and their genes. <em>Microbial Genomics</em> 2021. doi: <a href="https://doi.org/10.1099/mgen.0.000499">10.1099/mgen.0.000499</a></li> <li>Gladstone R, et al., Emergence and dissemination of antimicrobial resistance in <em>Escherichia coli</em> causing bloodstream infections in Norway in 2002&ndash;17: a nationwide, longitudinal, microbial population genomic study. <em>The Lancet Microbe</em> 2021. doi: <a href="https://doi.org/10.1016/S2666-5247(21)00031-8">10.1016/S2666-5247(21)00031-8</a></li> <li>Shao Y, et al., Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth. <em>Nature</em> 2019. <a href="https://doi.org/10.1038/s41586-019-1560-1">10.1038/s41586-019-1560-1</a></li> <li>Snaith AE, et al. The highly diverse plasmid population found in <em>Escherichia coli</em> colonizing travellers to Laos and its role in antimicrobial resistance gene carriage. <em>Microbial Genomics</em> 2023. doi: <a href="https://doi.org/10.1099/mgen.0.001000">10.1099/mgen.0.001000</a></li> <li>Habib A, et al. Dissemination of carbapenemase-producing Enterobacterales in the community of Rawalpindi, Pakistan. <em>PLOS ONE</em> 2022. doi: <a href="https://doi.org/10.1371/journal.pone.0270707">10.1371/journal.pone.0270707</a></li> <li>Runcharoen C, et al. Whole genome sequencing of ESBL-producing <em>Escherichia coli</em> isolated from patients, farm waste and canals in Thailand. <em>Genome Medicine</em> 2017. doi: <a href="https://doi.org/10.1186/s13073-017-0471-8">10.1186/s13073-017-0471-8</a></li> <li>Musicha P, et al. Trends in antimicrobial resistance in bloodstream infection isolates at a large urban hospital in Malawi (1998&ndash;2016): a surveillance study. <em>The Lancet Infectious Diseases</em> 2017. doi: <a href="https://doi.org/10.1016/S1473-3099(17)30394-8">10.1016/S1473-3099(17)30394-8</a></li> </ul> <h4><strong>Themisto index construction</strong></h4> <p>Assemblies were indexed with <a href="https://github.com/algbio/themisto">Themisto</a> v3.0.0-rc using <em>k</em>-mer size 31 and the `--file-colors` option.</p> <h4><strong>PopPUNK clustering</strong></h4> <p>We followed the approach described in <a href="https://doi.org/10.1038/s41467-022-35178-5">M&auml;klin et al. 2022</a> using <a href="https://github.com/bacpop/poppunk">PopPUNK</a> v2.5.0.</p> <h4><strong>Demix check indexing</strong></h4> <p>The index was generated using the `setup_reference.sh` script from <a href="https://github.com/tmaklin/coreutils_demix_check">tmaklin/coreutils_demix_check</a>.</p> <h3><strong>Contact</strong></h3> <p>Tommi M&auml;klin &lt;tommi'at'maklin.fi&gt;.</p>