ArticleCommunications biology2021
Mash-based analyses of Escherichia coli genomes reveal 14 distinct phylogroups.
Article in Communications biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 75 papers.
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Who cites it
75 citing papers in PubMed.
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- Urinary Tract Infections: Molecular Determinants of Uropathogenicity and Their Translation into Contemporary Clinical Practice.International journal of molecular sciences · 2026Review
- Comparative genomic analysis ofMicrobiology spectrum · 2026Article
- Taxonomic Resolution of 16S rRNA, FastANI, Mash, and FastAAI across 30,495 Prokaryotic Type-Strain Genomes.bioRxiv : the preprint server for biology · 2026Article
- Annotating the pangenome reveals the diversity in the genetic basis for metabolic enzymes.Science advances · 2026Article
- In silico typing maps the natural diversity of Escherichia coli transporter-dependent capsules.Nature microbiology · 2026Article
- Comparative Genomics ofPathogens (Basel, Switzerland) · 2026Article
- Distinct genetic programs drive antibiotic resistance and intracellular invasion in emerging MRSA strains.mSystems · 2026Article
- Genome-based source attribution using a One HealthMicrobial genomics · 2026Article
- Identification of specific metabolic capacities associated with major extraintestinal pathogenicJournal of bacteriology · 2026Article
- The disputed identity ofmBio · 2026Article
- Structure of theMicrobiology spectrum · 2026Article
- Use of proximity ligation shotgun metagenomics to investigate the dynamics of plasmids and bacteriophages in the gut microbiome following fecal microbiota transplantation.Gut microbes · 2025Article
- Rare metabolic gene essentiality is a determinant of microniche adaptation in Eschherichia coli.PLoS pathogens · 2025Article
- Metabolic modeling of microbial communities in the chicken ceca reveals a landscape of competition and co-operation.Microbiome · 2025Article
- Contribution of maternal gut carriage to neonatal acquisition of extended-spectrum beta-lactamase-producing Enterobacterales in Madagascar and Cambodia.Nature communications · 2025Article
- Genomic characterization of azithromycin-resistant and extended-spectrum β-lactamase-producingJAC-antimicrobial resistance · 2025Article
- Large-scale genomic analysis reveals the distribution and diversity of type VI secretion systems inmSystems · 2025Article
- Phylogroup Homeostasis ofMicroorganisms · 2025Article
15 more citing papers are in PubMed but not listed here.
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7 authors.
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Abstract
In this study, more than one hundred thousand Escherichia coli and Shigella genomes were examined and classified. This is, to our knowledge, the largest E. coli genome dataset analyzed to date. A Mash-based analysis of a cleaned set of 10,667 E. coli genomes from GenBank revealed 14 distinct phylogroups. A representative genome or medoid identified for each phylogroup was used as a proxy to classify 95,525 unassembled genomes from the Sequence Read Archive (SRA). We find that most of the sequenced E. coli genomes belong to four phylogroups (A, C, B1 and E2(O157)). Authenticity of the 14 phylogroups is supported by several different lines of evidence: phylogroup-specific core genes, a phylogenetic tree constructed with 2613 single copy core genes, and differences in the rates of gene gain/loss/duplication. The methodology used in this work is able to reproduce known phylogroups, as well as to identify previously uncharacterized phylogroups in E. coli species.
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