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The user’s guide to comparative genomics with EnteroBase, including case studies on transmissions of micro-clades of Salmonella , the phylogeny of ancient and modern Yersinia pestis genomes, and the core genomic diversity of all Escherichia

https://doi.org/10.1101/613554
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What this work says

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

inferredcites →https://doi.org/10.1002/ece3.3924openalex-snapshot
Ancient pathogen DNA in human teeth and petrous bones
inferredcites →https://doi.org/10.1007/978-3-319-89929-9_15openalex-snapshot
Accurate Reconstruction of Microbial Strains from Metagenomic Sequencing Using Representative Reference Genomes
inferredcites →https://doi.org/10.1007/978-3-642-18472-7_26openalex-snapshot
Inference of Large Phylogenies Using Neighbour-Joining
inferredcites →https://doi.org/10.1016/j.anaerobe.2019.01.002openalex-snapshot
Genomic analysis of three Clostridioides difficile isolates from urban water sources
inferredcites →https://doi.org/10.1016/j.cell.2015.10.009openalex-snapshot
Early Divergent Strains of Yersinia pestis in Eurasia 5,000 Years Ago
inferredcites →https://doi.org/10.1016/j.chom.2016.05.012openalex-snapshot
Historical Y. pestis Genomes Reveal the European Black Death as the Source of Ancient and Modern Plague Pandemics
inferredcites →https://doi.org/10.1016/j.cub.2018.05.058openalex-snapshot
Pan-genome Analysis of Ancient and Modern Salmonella enterica Demonstrates Genomic Stability of the Invasive Para C Lineage for Millennia
inferredcites →https://doi.org/10.1016/j.resmic.2009.10.002openalex-snapshot
Supplement 2003–2007 (No. 47) to the White-Kauffmann-Le Minor scheme
inferredcites →https://doi.org/10.1016/j.resmic.2014.07.004openalex-snapshot
Supplement 2008–2010 (no. 48) to the White–Kauffmann–Le Minor scheme
inferredcites →https://doi.org/10.1016/s0007-1935(17)33996-9openalex-snapshot
Salmonella Infection in Badgers in The South West of England
inferredcites →https://doi.org/10.1016/s0022-2836(05)80360-2openalex-snapshot
Basic Local Alignment Search Tool
inferredcites →https://doi.org/10.1016/s1473-3099(13)70323-2openalex-snapshot
Yersinia pestis and the Plague of Justinian 541–543 AD: a genomic analysis
inferredcites →https://doi.org/10.1016/s1567-1348(02)00089-8openalex-snapshot
Salmonella typhi, the causative agent of typhoid fever, is approximately 50,000 years old
inferredcites →https://doi.org/10.1038/35097083openalex-snapshot
Genome sequence of Yersinia pestis, the causative agent of plague
inferredcites →https://doi.org/10.1038/nature10549openalex-snapshot
A draft genome of Yersinia pestis from victims of the Black Death
inferredcites →https://doi.org/10.1038/ncomms12827openalex-snapshot
An extended genotyping framework for Salmonella enterica serovar Typhi, the cause of human typhoid
inferredcites →https://doi.org/10.1038/ng.705openalex-snapshot
Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity
inferredcites →https://doi.org/10.1038/nrmicro3093openalex-snapshot
MLST revisited: the gene-by-gene approach to bacterial genomics
inferredcites →https://doi.org/10.1038/s41467-018-04550-9openalex-snapshot
Analysis of 3800-year-old Yersinia pestis genomes suggests Bronze Age origin for bubonic plague
inferredcites →https://doi.org/10.1038/s41467-019-12154-0openalex-snapshot
Phylogeography of the second plague pandemic revealed through analysis of historical Yersinia pestis genomes
inferredcites →https://doi.org/10.1038/s41586-018-0094-2openalex-snapshot
137 ancient human genomes from across the Eurasian steppes
inferredcites →https://doi.org/10.1073/pnas.1015622108openalex-snapshot
Genome sequencing of environmental Escherichia coli expands understanding of the ecology and speciation of the model bacterial species
inferredcites →https://doi.org/10.1073/pnas.1107176108openalex-snapshot
Genomic anatomy of Escherichia coli O157:H7 outbreaks
inferredcites →https://doi.org/10.1073/pnas.1205750110openalex-snapshot
Historical variations in mutation rate in an epidemic pathogen, Yersinia pestis
inferredcites →https://doi.org/10.1073/pnas.1411012111openalex-snapshot
Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever
inferredcites →https://doi.org/10.1073/pnas.1416707112openalex-snapshot
Patterns of genome evolution that have accompanied host adaptation in Salmonella
inferredcites →https://doi.org/10.1073/pnas.180094797openalex-snapshot
Multiple independent origins of Shigella clones of Escherichia coli and convergent evolution of many of their characteristics
inferredcites →https://doi.org/10.1073/pnas.1812865115openalex-snapshot
Integrative approach using Yersinia pestis genomes to revisit the historical landscape of plague during the Medieval Period
inferredcites →https://doi.org/10.1073/pnas.1820447116openalex-snapshot
Ancient Yersinia pestis genomes from across Western Europe reveal early diversification during the First Pandemic (541–750)
inferredcites →https://doi.org/10.1073/pnas.95.6.3140openalex-snapshot
Multilocus sequence typing: A portable approach to the identification of clones within populations of pathogenic microorganisms
inferredcites →https://doi.org/10.1093/bioinformatics/btq461openalex-snapshot
Search and clustering orders of magnitude faster than BLAST
inferredcites →https://doi.org/10.1093/bioinformatics/btu033openalex-snapshot
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
inferredcites →https://doi.org/10.1093/bioinformatics/bty191openalex-snapshot
Minimap2: pairwise alignment for nucleotide sequences
inferredcites →https://doi.org/10.1093/molbev/msw170openalex-snapshot
A High-CoverageYersinia pestisGenome from a Sixth-Century Justinianic Plague Victim
inferredcites →https://doi.org/10.1093/nar/gkv1276openalex-snapshot
GenBank
inferredcites →https://doi.org/10.1098/rspb.1998.0429openalex-snapshot
Movement of badgers (Meles meles) in a high–density population: individual, population and disease effects
inferredcites →https://doi.org/10.1099/ijs.0.000228openalex-snapshot
Escherichia marmotae sp. nov., isolated from faeces of Marmota himalayana
inferredcites →https://doi.org/10.1099/mgen.0.000070openalex-snapshot
Phylogenetic structure of European Salmonella Enteritidis outbreak correlates with national and international egg distribution network
inferredcites →https://doi.org/10.1099/mgen.0.000093openalex-snapshot
Microreact: visualizing and sharing data for genomic epidemiology and phylogeography
inferredcites →https://doi.org/10.1099/mgen.0.000151openalex-snapshot
Comprehensive assessment of the quality of Salmonella whole genome sequence data available in public sequence databases using the Salmonella in silico Typing Resource (SISTR)
inferredcites →https://doi.org/10.1099/mgen.0.000192openalex-snapshot
ClermonTyping: an easy-to-use and accurate in silico method for Escherichia genus strain phylotyping
inferredcites →https://doi.org/10.1099/mic.0.055459-0openalex-snapshot
Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strain
inferredcites →https://doi.org/10.1101/317610openalex-snapshot
Easily phylotyping E. coli via the EzClermont web app and command-line tool
inferredcites →https://doi.org/10.1101/727230openalex-snapshot
Global genomic population structure of Clostridioides difficile
inferredcites →https://doi.org/10.1101/781724openalex-snapshot
Escherichia ruysiae sp. nov., isolated from an international traveller
inferredcites →https://doi.org/10.1101/gr.232397.117openalex-snapshot
GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens
inferredcites →https://doi.org/10.1101/gr.6122607openalex-snapshot
The rise and spread of a new pathogen: Seroresistant Moraxella catarrhalis
inferredcites →https://doi.org/10.1111/1365-2656.12743openalex-snapshot
Wildlife disease ecology from the individual to the population: Insights from a long‐term study of a naturally infected European badger population
inferredcites →https://doi.org/10.1111/1758-2229.12019openalex-snapshot
The C lermont E scherichia coli phylo‐typing method revisited: improvement of specificity and detection of new phylo‐groups
inferredcites →https://doi.org/10.1111/j.1365-2958.2006.05172.xopenalex-snapshot
Sex and virulence in Escherichia coli : an evolutionary perspective
inferredcites →https://doi.org/10.1111/j.1462-2920.2011.02588.xopenalex-snapshot
Population structure of the Yersinia pseudotuberculosis complex according to multilocus sequence typing
inferredcites →https://doi.org/10.1111/zph.12571openalex-snapshot
Salmonella enterica serovar Kentucky recovered from human clinical cases in Maryland, USA (2011–2015)
inferredcites →https://doi.org/10.1128/aem.01262-09openalex-snapshot
Cryptic Lineages of the Genus Escherichia
inferredcites →https://doi.org/10.1128/aem.01746-19openalex-snapshot
SeqSero2: Rapid and Improved Salmonella Serotype Determination Using Whole-Genome Sequencing Data
inferredcites →https://doi.org/10.1128/aem.02554-10openalex-snapshot
Genome Signatures of Escherichia coli O157:H7 Isolates from the Bovine Host Reservoir
inferredcites →https://doi.org/10.1128/aem.69.7.4312-4315.2003openalex-snapshot
Nontyphoidal Salmonellae in United Kingdom Badgers: Prevalence and Spatial Distribution
inferredcites →https://doi.org/10.1128/jb.157.2.690-693.1984openalex-snapshot
Standard reference strains of Escherichia coli from natural populations
inferredcites →https://doi.org/10.1128/jb.186.5.1518-1530.2004openalex-snapshot
eBURST: Inferring Patterns of Evolutionary Descent among Clusters of Related Bacterial Genotypes from Multilocus Sequence Typing Data
inferredcites →https://doi.org/10.1128/jcm.00737-17openalex-snapshot
Development of a Web Tool for Escherichia coli Subtyping Based on fimH Alleles
inferredcites →https://doi.org/10.1128/jcm.01796-09openalex-snapshot
Multilocus Sequence Typing of Clostridium difficile
inferredcites →https://doi.org/10.1128/jcm.02395-14openalex-snapshot
Use of Whole-Genus Genome Sequence Data To Develop a Multilocus Sequence Typing Tool That Accurately Identifies Yersinia Isolates to the Species and Subspecies Levels
inferredcites →https://doi.org/10.1128/mbio.00470-18openalex-snapshot
Escherichia coli ST131- H 22 as a Foodborne Uropathogen
inferredcites →https://doi.org/10.1128/mbio.00527-16openalex-snapshot
What’s in a Name? Species-Wide Whole-Genome Sequencing Resolves Invasive and Noninvasive Lineages of Salmonella enterica Serotype Paratyphi B
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/10.1128/mbio.02303-18openalex-snapshot
Salmonella enterica Phylogeny Based on Whole-Genome Sequencing Reveals Two New Clades and Novel Patterns of Horizontally Acquired Genetic Elements
inferredcites →https://doi.org/10.1186/s13073-017-0480-7openalex-snapshot
Public health surveillance in the UK revolutionises our understanding of the invasive Salmonella Typhimurium epidemic in Africa
inferredcites →https://doi.org/10.1371/journal.pgen.1003471openalex-snapshot
Neutral Genomic Microevolution of a Recently Emerged Pathogen, Salmonella enterica Serovar Agona
inferredcites →https://doi.org/10.1371/journal.pgen.1004874openalex-snapshot
Distinct Genealogies for Plasmids and Chromosome
inferredcites →https://doi.org/10.1371/journal.pgen.1007261openalex-snapshot
A genomic overview of the population structure of Salmonella
inferredcites →https://doi.org/10.1371/journal.pone.0022751openalex-snapshot
Prospective Genomic Characterization of the German Enterohemorrhagic Escherichia coli O104:H4 Outbreak by Rapid Next Generation Sequencing Technology
inferredcites →https://doi.org/10.1371/journal.pone.0048022openalex-snapshot
Transforming Microbial Genotyping: A Robotic Pipeline for Genotyping Bacterial Strains
inferredcites →https://doi.org/10.1371/journal.pone.0112963openalex-snapshot
Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement
inferredcites →https://doi.org/10.1371/journal.pone.0147101openalex-snapshot
The Salmonella In Silico Typing Resource (SISTR): An Open Web-Accessible Tool for Rapidly Typing and Subtyping Draft Salmonella Genome Assemblies
inferredcites →https://doi.org/10.1371/journal.pone.0187230openalex-snapshot
Yersinia pestis strains of ancient phylogenetic branch 0.ANT are widely spread in the high-mountain plague foci of Kyrgyzstan
inferredcites →https://doi.org/10.1371/journal.pone.0213039openalex-snapshot
GenomeGraphR: A user-friendly open-source web application for foodborne pathogen whole genome sequencing data integration, analysis, and visualization
inferredcites →https://doi.org/10.1371/journal.ppat.1002776openalex-snapshot
Multilocus Sequence Typing as a Replacement for Serotyping in Salmonella enterica
inferredcites →https://doi.org/10.2807/1560-7917.es.2019.24.13.1900161openalex-snapshot
Outbreak of Salmonella enterica serotype Poona in infants linked to persistent Salmonella contamination in an infant formula manufacturing facility, France, August 2018 to February 2019
inferredcites →https://doi.org/10.3389/fmicb.2018.01106openalex-snapshot
Phylogeny and Classification of Yersinia pestis Through the Lens of Strains From the Plague Foci of Commonwealth of Independent States
inferredcites →https://doi.org/10.4000/afriques.2125openalex-snapshot
Putting Africa on the Black Death map: Narratives from genetics and history
inferredcites →https://doi.org/10.7554/elife.12994openalex-snapshot
Eighteenth century Yersinia pestis genomes reveal the long-term persistence of an historical plague focus

What points at this work

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

inferred← citeshttps://doi.org/10.1007/s10096-021-04164-yopenalex-snapshot
Outbreak of Central American born Shigella sonnei in two youth camps in Belgium in the summer of 2019
inferred← citeshttps://doi.org/10.1038/s41598-019-54004-5openalex-snapshot
An Escherichia coli ST131 pangenome atlas reveals population structure and evolution across 4,071 isolates
inferred← citeshttps://doi.org/10.1038/s41598-020-61254-1openalex-snapshot
Genome-based Salmonella serotyping as the new gold standard
inferred← citeshttps://doi.org/10.1038/s41598-020-71207-3openalex-snapshot
Impact of DNA extraction on whole genome sequencing analysis for characterization and relatedness of Shiga toxin-producing Escherichia coli isolates
inferred← citeshttps://doi.org/10.1073/pnas.1903797116openalex-snapshot
The Justinianic Plague: An inconsequential pandemic?
inferred← citeshttps://doi.org/10.1099/mgen.0.000428openalex-snapshot
Genomic diversity of Escherichia coli isolates from non-human primates in the Gambia
inferred← citeshttps://doi.org/10.1099/mgen.0.000782openalex-snapshot
Use of genomics to explore AMR persistence in an outdoor pig farm with low antimicrobial usage
inferred← citeshttps://doi.org/10.1099/mgen.0.001116openalex-snapshot
The advantage of intergenic regions as genomic features for machine-learning-based host attribution of Salmonella Typhimurium from the USA
inferred← citeshttps://doi.org/10.1101/2021.10.28.466354openalex-snapshot
Systems-based approach for optimization of a scalable bacterial ST mapping assembly-free algorithm
inferred← citeshttps://doi.org/10.1101/2021.12.15.472871openalex-snapshot
Matchtigs: minimum plain text representation of kmer sets
inferred← citeshttps://doi.org/10.1101/2022.04.06.487395openalex-snapshot
A multidrug-resistant Salmonella enterica Typhimurium DT104 complex lineage circulating among humans and cattle in the United States lost the ability to produce pertussis-like toxin ArtAB
inferred← citeshttps://doi.org/10.1101/317610openalex-snapshot
Easily phylotyping E. coli via the EzClermont web app and command-line tool
inferred← citeshttps://doi.org/10.1101/727230openalex-snapshot
Global genomic population structure of Clostridioides difficile
inferred← citeshttps://doi.org/10.1101/806208openalex-snapshot
Can genome-based analysis be the new gold-standard for routine Salmonella serotyping?
inferred← citeshttps://doi.org/10.1101/gr.277615.122openalex-snapshot
Extremely fast construction and querying of compacted and colored de Bruijn graphs with GGCAT
inferred← citeshttps://doi.org/10.1128/aem.00814-20openalex-snapshot
Municipal Wastewater Surveillance Revealed a High Community Disease Burden of a Rarely Reported and Possibly Subclinical Salmonella enterica Serovar Derby Strain
inferred← citeshttps://doi.org/10.1128/ecosalplus.esp-0015-2019openalex-snapshot
Escherichia albertiiPathogenesis
inferred← citeshttps://doi.org/10.1128/msystems.01212-21openalex-snapshot
F Plasmid Lineages in Escherichia coli ST95: Implications for Host Range, Antibiotic Resistance, and Zoonoses
inferred← citeshttps://doi.org/10.1186/s13059-020-02135-8openalex-snapshot
Bifrost: highly parallel construction and indexing of colored and compacted de Bruijn graphs
inferred← citeshttps://doi.org/10.1186/s13059-023-02968-zopenalex-snapshot
Matchtigs: minimum plain text representation of k-mer sets
inferred← citeshttps://doi.org/10.1186/s42522-020-0010-1openalex-snapshot
Typing methods based on whole genome sequencing data
inferred← citeshttps://doi.org/10.2807/1560-7917.es.2019.24.22.1900305openalex-snapshot
Outbreak of Shiga toxin-producing Escherichia coli (STEC) O26 paediatric haemolytic uraemic syndrome (HUS) cases associated with the consumption of soft raw cow’s milk cheeses, France, March to May 2019
inferred← citeshttps://doi.org/10.3389/fmicb.2025.1635769openalex-snapshot
Prevalence, sequence diversity, and amplification of an IS-associated enterotoxin gene, astA, in Escherichia coli
inferred← citeshttps://doi.org/10.3389/fpubh.2019.00309openalex-snapshot
Development and Implementation of Whole Genome Sequencing-Based Typing Schemes for Clostridioides difficile
inferred← citeshttps://doi.org/10.3390/foods9081030openalex-snapshot
The Benefits of Whole Genome Sequencing for Foodborne Outbreak Investigation from the Perspective of a National Reference Laboratory in a Smaller Country
inferred← citeshttps://doi.org/10.3390/microorganisms11061513openalex-snapshot
Whole Genome Sequencing of Avian Pathogenic Escherichia coli Causing Bacterial Chondronecrosis and Osteomyelitis in Australian Poultry
inferred← citeshttps://doi.org/10.3390/microorganisms8091336openalex-snapshot
Emergence of Resistance to Fluoroquinolones and Third-Generation Cephalosporins in Salmonella Typhi in Lahore, Pakistan
inferred← citeshttps://doi.org/10.3390/toxins12020067openalex-snapshot
Shiga Toxin-Associated Hemolytic Uremic Syndrome: A Narrative Review
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