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EnteroBase : Hierarchical clustering of 100,000s of bacterial genomes into species/sub-species and populations
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Achtman, Mark, Zhou, Zhemin, Charlesworth, Jane and Baxter, Laura (2022) EnteroBase : Hierarchical clustering of 100,000s of bacterial genomes into species/sub-species and populations. Philosophical Transactions of the Royal Society B: Biological Sciences, 377 (1861). 20210240. doi:10.1098/rstb.2021.0240 ISSN 0962-8436.
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WRAP-EnteroBase-hierarchical-clustering-100000s-bacterial-genomes-species-sub-species-populations-2022.pdf - Accepted Version Embargoed item. Restricted access to Repository staff only - Requires a PDF viewer. Download (9Mb) |
Official URL: https://doi.org/10.1098/rstb.2021.0240
Abstract
The definition of bacterial species is traditionally a taxonomic issue while bacterial populations are identified by population genetics. These assignments are species specific, and depend on the practitioner. Legacy multilocus sequence typing is commonly used to identify sequence types (STs) and clusters (ST Complexes). However, these approaches are not adequate for the millions of genomic sequences from bacterial pathogens that have been generated since 2012. EnteroBase (http://enterobase.warwick.ac.uk) automatically clusters core genome MLST allelic profiles into hierarchical clusters (HierCC) after assembling annotated draft genomes from short read sequences. HierCC clusters span core sequence diversity from the species level down to individual transmission chains. Here we evaluate HierCC’s ability to correctly assign 100,000s of genomes to the species/subspecies and population levels for Salmonella, Escherichia, Clostridoides, Yersinia, Vibrio and Streptococcus. HierCC assignments were more consistent with maximum-likelihood super-trees of core SNPs or presence/absence of accessory genes than classical taxonomic assignments or 95% ANI. However, neither HierCC nor ANI were uniformly consistent with classical taxonomy of Streptococcus. HierCC was also consistent with legacy eBGs/ST Complexes in Salmonella or Escherichia and with O serogroups in Salmonella. Thus, EnteroBase HierCC supports the automated 36 identification of and assignment to species/subspecies and populations for multiple genera.
| Item Type: | Journal Article | ||||||||
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| Subjects: | Q Science > QH Natural history Q Science > QR Microbiology |
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| Divisions: | Faculty of Science, Engineering and Medicine > Medicine > Warwick Medical School | ||||||||
| Library of Congress Subject Headings (LCSH): | Bacterial genomes, Salmonella -- Genetics, Escherichia -- Genetics, Yersinia -- Genetics, Vibrio -- Genetics, Streptococcus -- Genetics | ||||||||
| Journal or Publication Title: | Philosophical Transactions of the Royal Society B: Biological Sciences | ||||||||
| Publisher: | The Royal Society Publishing | ||||||||
| ISSN: | 0962-8436 | ||||||||
| Official Date: | 10 October 2022 | ||||||||
| Dates: |
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| Volume: | 377 | ||||||||
| Number: | 1861 | ||||||||
| Article Number: | 20210240 | ||||||||
| DOI: | 10.1098/rstb.2021.0240 | ||||||||
| Status: | Peer Reviewed | ||||||||
| Publication Status: | Published | ||||||||
| Reuse Statement (publisher, data, author rights): | You retain the right to use the Article in the following ways, provided that you acknowledge the Definitive Published Version of the article by placing the full bibliographic reference and URL of the relevant journal homepage close to the title of the article | ||||||||
| Access rights to Published version: | Open Access (Creative Commons) | ||||||||
| Date of first compliant deposit: | 25 March 2022 | ||||||||
| Date of first compliant Open Access: | 28 March 2022 | ||||||||
| RIOXX Funder/Project Grant: |
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