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Signatures of negative frequency dependent selection in colonisation factors and the evolution of a multi-drug resistant lineage of Escherichia coli

https://doi.org/10.1101/400374
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1016/j.ijmm.2011.09.006openalex-snapshot
What defines extraintestinal pathogenic Escherichia coli?
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Import and spread of extended-spectrum β-lactamase-producing Enterobacteriaceae by international travellers (COMBAT study): a prospective, multicentre cohort study
inferredcites →https://doi.org/10.1038/nature09415openalex-snapshot
Gut inflammation provides a respiratory electron acceptor for Salmonella
inferredcites →https://doi.org/10.1038/ncomms6471openalex-snapshot
Diversification of bacterial genome content through distinct mechanisms over different timescales
inferredcites →https://doi.org/10.1038/nrmicro.2015.29openalex-snapshot
'Add, stir and reduce': Yersinia spp. as model bacteria for pathogen evolution
inferredcites →https://doi.org/10.1038/nrmicro884openalex-snapshot
Genomic islands in pathogenic and environmental microorganisms
inferredcites →https://doi.org/10.1038/nrurol.2010.190openalex-snapshot
The epidemiology of urinary tract infection
inferredcites →https://doi.org/10.1038/s41559-017-0337-xopenalex-snapshot
Frequency-dependent selection in vaccine-associated pneumococcal population dynamics
inferredcites →https://doi.org/10.1038/srep35285openalex-snapshot
The cytochrome bd-I respiratory oxidase augments survival of multidrug-resistant Escherichia coli during infection
inferredcites →https://doi.org/10.1073/pnas.1322678111openalex-snapshot
Global dissemination of a multidrug resistant Escherichia coli clone
inferredcites →https://doi.org/10.1073/pnas.1415959112openalex-snapshot
Host-specific induction of Escherichia coli fitness genes during human urinary tract infection
inferredcites →https://doi.org/10.1073/pnas.1606324113openalex-snapshot
Siderophore vaccine conjugates protect against uropathogenic Escherichia coli urinary tract infection
inferredcites →https://doi.org/10.1073/pnas.1617849114openalex-snapshot
Evolution of antibiotic resistance is linked to any genetic mechanism affecting bacterial duration of carriage
inferredcites →https://doi.org/10.1074/jbc.m611502200openalex-snapshot
Functional Genomic Studies of Uropathogenic Escherichia coli and Host Urothelial Cells when Intracellular Bacterial Communities Are Assembled
inferredcites →https://doi.org/10.1086/282825openalex-snapshot
Partitioning of Resources and the Outcome of Interspecific Competition: A Model and Some General Considerations
inferredcites →https://doi.org/10.1093/bioinformatics/bti191openalex-snapshot
RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees
inferredcites →https://doi.org/10.1093/bioinformatics/btl158openalex-snapshot
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
inferredcites →https://doi.org/10.1093/bioinformatics/bts507openalex-snapshot
MEGA-CC: computing core of molecular evolutionary genetics analysis program for automated and iterative data analysis
inferredcites →https://doi.org/10.1093/bioinformatics/btu153openalex-snapshot
Prokka: rapid prokaryotic genome annotation
inferredcites →https://doi.org/10.1093/bioinformatics/btv421openalex-snapshot
Roary: rapid large-scale prokaryote pan genome analysis
inferredcites →https://doi.org/10.1093/gbe/evt038openalex-snapshot
The Evolutionary Path to Extraintestinal Pathogenic, Drug-Resistant Escherichia coli Is Marked by Drastic Reduction in Detectable Recombination within the Core Genome
inferredcites →https://doi.org/10.1093/jac/dkr349openalex-snapshot
Molecular epidemiology of extraintestinal pathogenic Escherichia coli isolates from a regional cohort of elderly patients highlights the prevalence of ST131 strains with increased antimicrobial resistance in both community and hospital care settings
inferredcites →https://doi.org/10.1093/jac/dkr585openalex-snapshot
Genomic analysis uncovers a phenotypically diverse but genetically homogeneous Escherichia coli ST131 clone circulating in unrelated urinary tract infections
inferredcites →https://doi.org/10.1093/molbev/msx148openalex-snapshot
Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper
inferredcites →https://doi.org/10.1093/nar/gkh340openalex-snapshot
MUSCLE: multiple sequence alignment with high accuracy and high throughput
inferredcites →https://doi.org/10.1099/mgen.0.000030openalex-snapshot
Directional gene flow and ecological separation in Yersinia enterocolitica
inferredcites →https://doi.org/10.1099/mgen.0.000220openalex-snapshot
PANINI: Pangenome Neighbour Identification for Bacterial Populations
inferredcites →https://doi.org/10.1101/gr.074492.107openalex-snapshot
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
inferredcites →https://doi.org/10.1101/gr.180190.114openalex-snapshot
Large-scale genomic sequencing of extraintestinal pathogenic Escherichia coli strains
inferredcites →https://doi.org/10.1101/gr.216606.116openalex-snapshot
Systematic longitudinal survey of invasive Escherichia coli in England demonstrates a stable population structure only transiently disturbed by the emergence of ST131
inferredcites →https://doi.org/10.1111/1469-0691.12028openalex-snapshot
The changing epidemiology of bacteraemias in Europe: trends from the European Antimicrobial Resistance Surveillance System
inferredcites →https://doi.org/10.1111/j.0014-3820.2004.tb01642.xopenalex-snapshot
EXPERIMENTAL EVIDENCE FOR SYMPATRIC ECOLOGICAL DIVERSIFICATION DUE TO FREQUENCY-DEPENDENT COMPETITION IN ESCHERICHIA COLI
inferredcites →https://doi.org/10.1111/j.1462-5822.2007.00952.xopenalex-snapshot
Development of intracellular bacterial communities of uropathogenicEscherichia colidepends on type 1 pili
inferredcites →https://doi.org/10.1126/science.1084550openalex-snapshot
Intracellular Bacterial Biofilm-Like Pods in Urinary Tract Infections
inferredcites →https://doi.org/10.1126/science.1218198openalex-snapshot
Population Genomics of Early Events in the Ecological Differentiation of Bacteria
inferredcites →https://doi.org/10.1126/science.280.5365.912openalex-snapshot
Chaos, Persistence, and Evolution of Strain Structure in Antigenically Diverse Infectious Agents
inferredcites →https://doi.org/10.1128/aac.01763-10openalex-snapshot
Characteristics of NDM-1-Producing Escherichia coli Isolates That Belong to the Successful and Virulent Clone ST131
inferredcites →https://doi.org/10.1128/aac.02824-14openalex-snapshot
A New Clone Sweeps Clean: the Enigmatic Emergence of Escherichia coli Sequence Type 131
inferredcites →https://doi.org/10.1128/cmr.00116-14openalex-snapshot
The Role of Epidemic Resistance Plasmids and International High-Risk Clones in the Spread of Multidrug-Resistant Enterobacteriaceae
inferredcites →https://doi.org/10.1128/jb.187.4.1430-1440.2005openalex-snapshot
The Flag-2 Locus, an Ancestral Gene Cluster, Is Potentially Associated with a Novel Flagellar System from Escherichia coli
inferredcites →https://doi.org/10.1128/mbio.00347-16openalex-snapshot
Sequential Acquisition of Virulence and Fluoroquinolone Resistance Has Shaped the Evolution of Escherichia coli ST131
inferredcites →https://doi.org/10.1128/mbio.00377-13openalex-snapshot
The Epidemic of Extended-Spectrum-β-Lactamase-Producing Escherichia coli ST131 Is Driven by a Single Highly Pathogenic Subclone, H 30-Rx
inferredcites →https://doi.org/10.1128/mbio.02162-15openalex-snapshot
Evolutionary History of the Global Emergence of the Escherichia coli Epidemic Clone ST131
inferredcites →https://doi.org/10.1186/1471-2105-9-539openalex-snapshot
Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations
inferredcites →https://doi.org/10.1186/1471-2164-15-830openalex-snapshot
Comparative genome analysis identifies few traits unique to the Escherichia coli ST131 H30Rx clade and extensive mosaicism at the capsule locus
inferredcites →https://doi.org/10.1371/journal.pgen.1003716openalex-snapshot
Combining Quantitative Genetic Footprinting and Trait Enrichment Analysis to Identify Fitness Determinants of a Bacterial Pathogen
inferredcites →https://doi.org/10.1371/journal.pgen.1006280openalex-snapshot
Combined Analysis of Variation in Core, Accessory and Regulatory Genome Regions Provides a Super-Resolution View into the Evolution of Bacterial Populations
inferredcites →https://doi.org/10.1371/journal.pone.0088374openalex-snapshot
Phenotypic Microarrays Suggest Escherichia coli ST131 Is Not a Metabolically Distinct Lineage of Extra-Intestinal Pathogenic E. coli
inferredcites →https://doi.org/10.1371/journal.pone.0108642openalex-snapshot
AcrB, AcrD, and MdtABC Multidrug Efflux Systems Are Involved in Enterobactin Export in Escherichia coli
inferredcites →https://doi.org/10.1371/journal.ppat.1003788openalex-snapshot
Genome-Wide Detection of Fitness Genes in Uropathogenic Escherichia coli during Systemic Infection
inferredcites →https://doi.org/10.2807/1560-7917.es.2016.21.42.30376openalex-snapshot
Prolonged colonisation with Escherichia coli O25:ST131 versus other extended-spectrum beta-lactamase-producing E. coli in a long-term care facility with high endemic level of rectal colonisation, the Netherlands, 2013 to 2014
inferredcites →https://doi.org/10.3201/eid1910.130309openalex-snapshot
Multidrug-ResistantEscherichia coliBacteremia
inferredcites →https://doi.org/10.48550/arxiv.1407.4443openalex-snapshot
On the Complexity of Best Arm Identification in Multi-Armed Bandit Models
inferredcites →https://doi.org/10.48550/arxiv.1501.03291openalex-snapshot
Bayesian Optimization for Likelihood-Free Inference of Simulator-Based Statistical Models

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1038/s41396-020-00867-wopenalex-snapshot
Negative frequency-dependent selection and asymmetrical transformation stabilise multi-strain bacterial population structures
inferred← citeshttps://doi.org/10.1038/s41564-019-0651-yopenalex-snapshot
Designing ecologically optimized pneumococcal vaccines using population genomics
inferred← citeshttps://doi.org/10.1038/s41588-019-0417-8openalex-snapshot
Atlas of group A streptococcal vaccine candidates compiled using large-scale comparative genomics
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