ArticlePLoS genetics2016
Combined Analysis of Variation in Core, Accessory and Regulatory Genome Regions Provides a Super-Resolution View into the Evolution of Bacterial Populations.
Article in PLoS genetics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 119 papers, 2 of them syntheses that pooled it.
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Who cites it
119 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Meta-analysis of Pandemic Escherichia coli ST131 Plasmidome Proves Restricted Plasmid-clade Associations.Scientific reports · 2020Pooled it
- Global Extraintestinal Pathogenic Escherichia coli (ExPEC) Lineages.Clinical microbiology reviews · 2019Pooled it
- Resistance potentiators: Evolutionary catalysts of antibiotic resistance.PLoS biology · 2026Article
- Tracking Extended-Spectrum β-Lactamase-ProducingAntibiotics (Basel, Switzerland) · 2026Article
- Pathogenomics of multidrug-resistant Escherichia coli from bloodstream infections in South Africa.BMC medical genomics · 2026Article
- Genomic perplexity and the evolution of context-dependent function.Molecular biology and evolution · 2026Article
- Comparative Pan- and Phylo-Genomic Analysis of Ideonella and Thermobifida Strains: Dissemination of Biodegradation Potential and Genomic Divergence.Biochemical genetics · 2026Article
- Pathogenic potential and phylogenomic analysis ofMicrobial genomics · 2026Article
- Pangenome dynamics and population structure of the zoonotic pathogen Salmonella enterica serotype Hadar.Nature communications · 2026Article
- Genomic and functional characterization of the L‑sorbose phosphotransferase system in high-riskmSystems · 2026Article
- Genetic landscape of Borrelia burgdorferi sensu stricto in Canada: a study of genetic diversity.Scientific reports · 2025Article
- Basic reproduction number varies markedly between closely related pandemic Escherichia coli clones.Nature communications · 2025Article
- Escherichia coli phylogeny drives co-amoxiclav resistance through variable expression of TEM-1 beta-lactamase.Nature communications · 2025Article
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- De novo mutations mediate phenotypic switching in an opportunistic human lung pathogen.Nature communications · 2025Article
- Linkage-based ortholog refinement in bacterial pangenomes with CLARC.Nucleic acids research · 2025Article
- Comparative Genomic Analysis of TwoMicroorganisms · 2025Article
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- High intra-laboratory reproducibility of nanopore sequencing in bacterial species underscores advances in its accuracy.Microbial genomics · 2025Article
- Characterization of antibiotic determinants and heavy metal resistance genes inMicrobial genomics · 2025Article
59 more citing papers are in PubMed but not listed here.
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Authors and funding
21 authors.
Funding
Abstract
The use of whole-genome phylogenetic analysis has revolutionized our understanding of the evolution and spread of many important bacterial pathogens due to the high resolution view it provides. However, the majority of such analyses do not consider the potential role of accessory genes when inferring evolutionary trajectories. Moreover, the recently discovered importance of the switching of gene regulatory elements suggests that an exhaustive analysis, combining information from core and accessory genes with regulatory elements could provide unparalleled detail of the evolution of a bacterial population. Here we demonstrate this principle by applying it to a worldwide multi-host sample of the important pathogenic E. coli lineage ST131. Our approach reveals the existence of multiple circulating subtypes of the major drug-resistant clade of ST131 and provides the first ever population level evidence of core genome substitutions in gene regulatory regions associated with the acquisition and maintenance of different accessory genome elements.
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