Escherichia coli lineage deconvolution indexes for Themisto, mSWEEP/mGEMS, and demix_check
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2024-06-25, 2024-06-25
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Description
Escherichia coli lineage deconvolution indexes for Themisto, mSWEEP/mGEMS, and demix_check
This dataset contains the indexes used in a study conducted in Punjab, Pakistan that investigated E. coli colonisation diversity in healthy carriage with the use of CLED enrichment plates. The following files are included in the download:
Themisto v3 pseudoalignment index.
PopPUNK database.
Demix_check index.
Raw assembly data.
About
Version history
v0.1.1 (current version)
Added reference to the study.
v0.1.0
Added brief description with a few missing parts.
Distribution
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).
Citation
Khawaja, T., Mäklin, 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). https://doi.org/10.1038/s41467-024-49591-5
Methods briefly
Data
Assembly data included originates from the following studies:
Horesh G, et al., A comprehensive and high-quality collection of Escherichia coli genomes and their genes. Microbial Genomics 2021. doi: 10.1099/mgen.0.000499
Gladstone R, et al., Emergence and dissemination of antimicrobial resistance in Escherichia coli causing bloodstream infections in Norway in 2002–17: a nationwide, longitudinal, microbial population genomic study. The Lancet Microbe 2021. doi: 10.1016/S2666-5247(21)00031-8
Shao Y, et al., Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth. Nature 2019. 10.1038/s41586-019-1560-1
Snaith AE, et al. The highly diverse plasmid population found in Escherichia coli colonizing travellers to Laos and its role in antimicrobial resistance gene carriage. Microbial Genomics 2023. doi: 10.1099/mgen.0.001000
Habib A, et al. Dissemination of carbapenemase-producing Enterobacterales in the community of Rawalpindi, Pakistan. PLOS ONE 2022. doi: 10.1371/journal.pone.0270707
Runcharoen C, et al. Whole genome sequencing of ESBL-producing Escherichia coli isolated from patients, farm waste and canals in Thailand. Genome Medicine 2017. doi: 10.1186/s13073-017-0471-8
Musicha P, et al. Trends in antimicrobial resistance in bloodstream infection isolates at a large urban hospital in Malawi (1998–2016): a surveillance study. The Lancet Infectious Diseases 2017. doi: 10.1016/S1473-3099(17)30394-8
Themisto index construction
Assemblies were indexed with Themisto v3.0.0-rc using k-mer size 31 and the `--file-colors` option.
PopPUNK clustering
We followed the approach described in Mäklin et al. 2022 using PopPUNK v2.5.0.
Demix check indexing
The index was generated using the `setup_reference.sh` script from tmaklin/coreutils_demix_check.
Contact
Tommi Mäklin <tommi'at'maklin.fi>.