ArticlePhilosophical transactions of the Royal Society of London. Series B, Biological sciences2022
EnteroBase: hierarchical clustering of 100 000s of bacterial genomes into species/subspecies and populations.
Article in Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
37 citing papers in PubMed, 67 citations in OpenAlex.
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- Prevalence and genomic insights into Yersinia enterocolitica in Southeastern China (2008-2022).Applied microbiology and biotechnology · 2025Article
- Phenotypic and Genotypic Characterization of ESBL-, AmpC-, and Carbapenemase-ProducingAntibiotics (Basel, Switzerland) · 2025Article
- Lessons from 5 Years of Routine Whole-Genome Sequencing for Epidemiologic Surveillance of Shiga Toxin-Producing Escherichia coli, France, 2018-2022.Emerging infectious diseases · 2025Article
- Multi-country and intersectoral assessment of cluster congruence between pipelines for genomics surveillance of foodborne pathogens.Nature communications · 2025Article
- aurora: a machine learning gwas tool for analyzing microbial habitat adaptation.Genome biology · 2025Article
- Emergence and global spread of a dominant multidrug-resistant clade within Acinetobacter baumannii.Nature communications · 2025Article
- Re-evaluation of boundaries ofInternational journal of systematic and evolutionary microbiology · 2025Article
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- Microbe Profile:Microbiology (Reading, England) · 2025Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 1 institution in 1 country.
Funding
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
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.