The indigenous gastrointestinal microflora, Trends Microbiol, vol.4, issue.11, pp.430-435, 1996. ,
The distribution and genetic structure of Escherichia coli in Australian vertebrates: host and geographic effects, Microbiology, vol.149, p.14663089, 2003. ,
The population genetics of commensal Escherichia coli, Nat Rev Microbiol, vol.8, issue.3, pp.207-224, 2010. ,
Presence and growth of naturalized Escherichia coli in temperate soils from Lake Superior watersheds, Appl Environ Microbiol, vol.72, issue.1, p.1352292, 2006. ,
Escherichia coli in the Environment: Implications for Water Quality and Human Health, Microbes Environ, vol.23, issue.2, pp.101-109, 2008. ,
Survival of Escherichia coli in the environment: fundamental and public health aspects, ISME J, vol.5, issue.2, p.3105702, 2011. ,
Evidence for coexistence of distinct Escherichia coli populations in various aquatic environments and their survival in estuary water, Appl Environ Microbiol, vol.79, issue.15, p.3719502, 2013. ,
Escherichia coli: virulence mechanisms of a versatile pathogen, 2002. ,
Pathogenic Escherichia coli, Nat Rev Microbiol, vol.2, issue.2, pp.123-163, 2004. ,
Sex and virulence in Escherichia coli: an evolutionary perspective, Mol Microbiol, vol.60, issue.5, p.1557465, 2006. ,
URL : https://hal.archives-ouvertes.fr/hal-00174910
Molecular mechanisms of Escherichia coli pathogenicity, Nat Rev Microbiol, vol.8, issue.1, pp.26-38, 2010. ,
coli as an all-rounder: the thin line between commensalism and pathogenicity, Curr Top Microbiol Immunol, vol.358, pp.3-32, 2013. ,
Diarrheagenic Escherichia coli, Braz J Microbiol, vol.47, p.5156508, 2016. ,
Escherichia coli: an old friend with new tidings, FEMS Microbiol Rev, vol.40, issue.4, pp.437-63, 2016. ,
Attributable deaths and disability-adjusted life-years caused by infections with antibiotic-resistant bacteria in the EU and the European Economic Area in 2015: a population-level modelling analysis, Lancet Infect Dis, vol.19, issue.1, p.6300481, 2019. ,
The evolution of the Escherichia coli phylogeny, Infect Genet Evol, vol.12, issue.2, pp.214-240, 2012. ,
Standard reference strains of Escherichia coli from natural populations, J Bacteriol, vol.157, issue.2, p.215307, 1984. ,
Impact of homologous and non-homologous recombination in the genomic evolution of Escherichia coli, BMC Genomics, vol.13, p.3505186, 2012. ,
Recombinant transfer in the basic genome of Escherichia coli, Proc Natl Acad Sci U S A, vol.112, issue.29, pp.9070-9075, 2015. ,
ClermonTyping: an easy-to-use and accurate in silico method for Escherichia genus strain phylotyping, Microb Genom, vol.4, issue.7, p.6113867, 2018. ,
Insights into the evolution of pathogenicity of Escherichia coli from genomic analysis of intestinal E. coli of Marmota himalayana in Qinghai-Tibet plateau of China, Emerg Microbes Infect, vol.5, issue.12, p.520916, 2016. ,
Characteristics of human intestinal Escherichia coli with changing environments, Environ Microbiol, vol.10, issue.8, p.18459976, 2008. ,
Commensal Escherichia coli isolates are phylogenetically distributed among geographically distinct human populations. Microbiology, vol.147, pp.1671-1677, 2001. ,
Phenotypic and genotypic characterization of encapsulated Escherichia coli isolated from blooms in two Australian lakes, Environ Microbiol, vol.7, issue.5, pp.631-671, 2005. ,
Genetic diversity and population structure of Escherichia coli isolated from freshwater beaches, Environ Microbiol, vol.9, issue.9, p.17686024, 2007. ,
Influence of hydrological conditions on the Escherichia coli population structure in the water of a creek on a rural watershed, BMC Microbiol, vol.10, p.222, 2010. ,
URL : https://hal.archives-ouvertes.fr/inserm-00663723
Pathogenic Escherichia coli found in sewage treatment plants and environmental waters, Appl Environ Microbiol, vol.78, issue.16, p.3406122, 2012. ,
The link between phylogeny and virulence in Escherichia coli extraintestinal infection, Infect Immun, vol.67, issue.2, p.96353, 1999. ,
Phylogenetic distribution of extraintestinal virulenceassociated traits in Escherichia coli, J Infect Dis, vol.183, issue.1, pp.78-88, 2001. ,
Extraintestinal pathogenic Escherichia coli strains of avian and human origin: link between phylogenetic relationships and common virulence patterns, J Clin Microbiol, vol.45, issue.10, pp.3366-76, 2007. ,
URL : https://hal.archives-ouvertes.fr/hal-02664790
Pandemic lineages of extraintestinal pathogenic Escherichia coli, Clin Microbiol Infect, vol.20, issue.5, pp.380-90, 2014. ,
Worldwide Phylogenetic Group Patterns of Escherichia coli from Commensal Human and Wastewater Treatment Plant Isolates, Front Microbiol, vol.8, p.2512, 2017. ,
, PubMed Central
The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates, J Bacteriol, vol.190, issue.20, p.2566221, 2008. ,
Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths, PLoS Genet, vol.5, issue.1, p.2617782, 2009. ,
URL : https://hal.archives-ouvertes.fr/hal-00390293
Comparison of 61 sequenced Escherichia coli genomes, Microb Ecol, vol.60, issue.4, pp.708-728, 2010. ,
, , p.2974192
Insights from 20 years of bacterial genome sequencing, Funct Integr Genomics, vol.15, issue.2, pp.141-61, 2015. ,
Global dissemination of a multidrug resistant Escherichia coli clone, Proc Natl Acad Sci, vol.111, issue.15, pp.5694-5703, 2014. ,
Comparative genomics: the bacterial pan-genome, Curr Opin Microbiol, vol.11, issue.5, pp.472-479, 2008. ,
5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences, Nucleic Acids Res, vol.44, issue.D1, p.4702882, 2016. ,
, Draft Genome Sequences of the Escherichia coli Reference (ECOR) Collection. Microbiol Resour Announc, vol.7, issue.14, p.6256646, 2018.
Stratified reconstruction of ancestral Escherichia coli diversification, BMC Genomics, vol.20, issue.1, p.6896753, 2019. ,
A survey of bacterial insertion sequences using IScan, Nucleic Acids Res, vol.35, issue.16, pp.5284-93, 2007. ,
Causes of insertion sequences abundance in prokaryotic genomes, Mol Biol Evol, vol.24, issue.4, pp.969-81, 2007. ,
Pervasive domestication of defective prophages by bacteria, Proc Natl Acad Sci U S A, vol.111, issue.33, p.4143005, 2014. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01374961
VirSorter: mining viral signal from microbial genomic data, PeerJ, vol.3, p.4451026, 2015. ,
URL : https://hal.archives-ouvertes.fr/hal-01557667
PlaScope: a targeted approach to assess the plasmidome from genome assemblies at the species level, Microb Genom, vol.4, issue.9, 2018. ,
URL : https://hal.archives-ouvertes.fr/cea-02291353
Key components of the eight classes of type IV secretion systems involved in bacterial conjugation or protein secretion, Nucleic Acids Res, vol.42, issue.9, pp.5715-5742, 2014. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01374962
, , p.4027160
Host Range and Genetic Plasticity Explain the Coexistence of Integrative and Extrachromosomal Mobile Genetic Elements, Mol Biol Evol, vol.35, issue.11, p.2850, 2018. ,
URL : https://hal.archives-ouvertes.fr/pasteur-02098387
ISfinder: the reference centre for bacterial insertion sequences, Nucleic Acids Res, vol.34, p.1347377, 2006. ,
URL : https://hal.archives-ouvertes.fr/hal-00021179
Identification and analysis of integrons and cassette arrays in bacterial genomes, Nucleic Acids Res, vol.44, issue.10, p.4889954, 2016. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01374968
Integrons: Vehicles and pathways for horizontal dissemination in bacteria, Mob Genet Elements, vol.2, issue.5, p.3575428, 2012. ,
Core and panmetabolism in Escherichia coli, J Bacteriol, vol.193, issue.6, p.3067614, 2011. ,
URL : https://hal.archives-ouvertes.fr/hal-02646830
Interactions between genotype and environment drive the metabolic phenotype within Escherichia coli isolates, Environ Microbiol, vol.18, issue.1, pp.100-117, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01506467
Biodegradation of aromatic compounds by Escherichia coli, Microbiol Mol Biol Rev, vol.65, issue.4, p.99040, 2001. ,
Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments, Proc Natl Acad Sci U S A, vol.110, issue.50, p.3864276, 2013. ,
Phylogenetic distribution of traits associated with plant colonization in Escherichia coli, Environ Microbiol, vol.15, issue.2, p.22934605, 2013. ,
VFDB 2016: hierarchical and refined dataset for big data analysis-10 years on, Nucleic Acids Res, vol.44, issue.D1, p.4702877, 2016. ,
, Colicin biology. Microbiol Mol Biol Rev, vol.71, issue.1, pp.158-229, 2007.
,
BAGEL3: Automated identification of genes encoding bacteriocins and (non-)bactericidal posttranslationally modified peptides, Nucleic Acids Res, vol.41, p.3692055, 2013. ,
Environmental Escherichia coli: ecology and public health implications-a review, J Appl Microbiol, vol.123, issue.3, pp.570-81, 2017. ,
Investigating the Relatedness of Enteroinvasive Escherichia coli to Other E. coli and Shigella Isolates by Using Comparative Genomics, Infect Immun, vol.84, issue.8, p.4962626, 2016. ,
Evolutionary History of the Global Emergence of the Escherichia coli Epidemic Clone ST131, MBio, vol.7, issue.2, p.4807372, 2016. ,
Comparative Genomic Analysis of Globally Dominant ST131 Clone with Other Epidemiologically Successful Extraintestinal Pathogenic Escherichia coli (ExPEC) Lineages, MBio, vol.8, issue.5, p.5654935, 2017. ,
Fine-Scale Structure Analysis Shows Epidemic Patterns of Clonal Complex 95, a Cosmopolitan Escherichia coli Lineage Responsible for Extraintestinal Infection, mSphere, vol.2, issue.3, p.5451516, 2017. ,
Phylogenomic Analysis of Extraintestinal Pathogenic Escherichia coli Sequence Type 1193, an Emerging Multidrug-Resistant Clonal Group, Antimicrob Agents Chemother, vol.63, issue.1, p.6325179, 2019. ,
Diversity and Population Overlap between Avian and Human Escherichia coli Belonging to Sequence Type 95. mSphere, vol.4, p.6336079, 2019. ,
Genome dynamics and its impact on evolution of Escherichia coli, Med Microbiol Immunol, vol.199, issue.3, pp.145-54, 2010. ,
Horizontal gene transfer in human pathogens, Crit Rev Microbiol, vol.41, issue.1, pp.101-109, 2015. ,
Gene flow, mobile genetic elements and the recruitment of antibiotic resistance genes into Gram-negative pathogens, FEMS Microbiol Rev, vol.35, issue.5, pp.790-819, 2011. ,
Dissemination of Antimicrobial Resistance in Microbial Ecosystems through, Horizontal Gene Transfer. Front Microbiol, vol.7, p.4759269, 2016. ,
A population genomics approach to exploiting the accessory 'resistome' of Escherichia coli, Microb Genom, vol.3, issue.4, p.5506381, 2017. ,
Horizontal gene transfer overrides mutation in Escherichia coli colonizing the mammalian gut, Proc Natl Acad Sci, vol.116, issue.36, p.6731689, 2019. ,
Estimating variation within the genes and inferring the phylogeny of 186 sequenced diverse Escherichia coli genomes, BMC Genomics, vol.13, p.3575317, 2012. ,
Global Extraintestinal Pathogenic Escherichia coli (ExPEC) Lineages, Clin Microbiol Rev, vol.32, issue.3, p.6589867, 2019. ,
Testing the infinitely many genes model for the evolution of the bacterial core genome and pangenome, Mol Biol Evol, vol.29, issue.11, pp.3413-3438, 2012. ,
Two fundamentally different classes of microbial genes, Nat Microbiol, vol.2, p.16208, 2016. ,
Prophages in marine bacteria: dangerous molecular time bombs or the key to survival in the seas?, ISME J, vol.2, issue.6, pp.579-89, 2008. ,
Estimating the fitness effect of an insertion sequence, J Math Biol, vol.66, issue.1-2, p.22252506, 2013. ,
Fitness Costs of Plasmids: a Limit to, Plasmid Transmission. Microbiol Spectr, vol.5, issue.5, 2017. ,
Deletional bias and the evolution of bacterial genomes, Trends Genet, vol.17, issue.10, pp.2447-2454, 2001. ,
Where are the pseudogenes in bacterial genomes?, Trends Microbiol, vol.9, issue.11, p.11825713, 2001. ,
, Evolutionary Ecology of Prokaryotic Immune Mechanisms. Microbiol Mol Biol Rev, vol.80, issue.3, pp.745-63, 2016.
Pneumococcal Capsule Synthesis Locus cps as Evolutionary Hotspot with Potential to Generate Novel Serotypes by Recombination, Mol Biol Evol, vol.34, issue.10, p.5850285, 2017. ,
Genetic and life-history traits associated with the distribution of prophages in bacteria, ISME J, vol.10, issue.11, pp.2744-54, 2016. ,
Pathogenicity islands of virulent bacteria: structure, function and impact on microbial evolution, Mol Microbiol, vol.23, issue.6, p.9106201, 1997. ,
Bacteriophage-mediated spread of bacterial virulence genes, Curr Opin Microbiol, vol.23, pp.171-179, 2015. ,
The chromosomal accommodation and domestication of mobile genetic elements, Curr Opin Microbiol, vol.22, pp.22-31, 2014. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01122287
Ecology drives a global network of gene exchange connecting the human microbiome, Nature, vol.480, issue.7376, pp.241-245, 2011. ,
Mobile genes in the human microbiome are structured from global to individual scales, Nature, vol.535, issue.7612, p.4983458, 2016. ,
Reductive genome evolution at both ends of the bacterial population size spectrum, Nat Rev Microbiol, vol.12, issue.12, pp.841-50, 2014. ,
Genome reduction in an abundant and ubiquitous soil bacterium 'Candidatus Udaeobacter copiosus, Nat Microbiol, vol.2, p.16198, 2016. ,
Comparative genomics of Crohn's disease-associated adherent-invasive Escherichia coli, Gut, vol.66, issue.8, pp.1382-1391, 2017. ,
Genetic Attributes of E. coli Isolates from Chlorinated Drinking Water, PLoS One, vol.12, issue.1, 2017. ,
Prokka: rapid prokaryotic genome annotation, Bioinformatics, vol.30, issue.14, pp.2068-2077, 2014. ,
In silico serotyping of E. coli from short read data identifies limited novel O-loci but extensive diversity of O:H serotype combinations within and between pathogenic lineages, Microb Genom, vol.2, issue.7, p.5343136, 2016. ,
PopGenome: an efficient Swiss army knife for population genomic analyses in R, Mol Biol Evol, vol.31, issue.7, p.4069620, 2014. ,
Shifting the genomic gold standard for the prokaryotic species definition, Proc Natl Acad Sci U S A, vol.106, issue.45, p.2776425, 2009. ,
Mash: fast genome and metagenome distance estimation using MinHash, Genome Biol, vol.17, issue.1, p.4915045, 2016. ,
MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets, Nat Biotechnol, vol.35, issue.11, pp.1026-1034, 2017. ,
Clustering huge protein sequence sets in linear time, Nat Commun, vol.9, issue.1, p.2542, 2018. ,
micropan: an R-package for microbial pan-genomics, BMC Bioinformatics, vol.16, p.4375852, 2015. ,
Parallelization of MAFFT for large-scale multiple sequence alignments, Bioinformatics, vol.34, issue.14, p.6041967, 2018. ,
A probabilistic model of local sequence alignment that simplifies statistical significance estimation, PLoS Comput Biol, vol.4, issue.5, p.1000069, 2008. ,
Accelerated Profile HMM Searches, PLoS Comput Biol, vol.7, issue.10, 2011. ,
Prospects for building large timetrees using molecular data with incomplete gene coverage among species, Mol Biol Evol, vol.31, issue.9, p.4137717, 2014. ,
Bacterial phylogenetic reconstruction from whole genomes is robust to recombination but demographic inference is not, mBio, vol.5, issue.6, p.4251999, 2014. ,
The Impact of Selection, Gene Conversion, and Biased Sampling on the Assessment of Microbial Demography, Mol Biol Evol, vol.33, issue.7, pp.1711-1736, 2016. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01374966
IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies, Mol Biol Evol, vol.32, issue.1, p.4271533, 2015. ,
UFBoot2: Improving the Ultrafast Bootstrap Approximation, Mol Biol Evol, vol.35, issue.2, p.5850222, 2018. ,
Genome sequencing of environmental Escherichia coli expands understanding of the ecology and speciation of the model bacterial species, Proc Natl Acad Sci U S A, vol.108, issue.17, p.3084108, 2011. ,
ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R, Bioinformatics, 2018. ,
URL : https://hal.archives-ouvertes.fr/ird-01920132
Genome phylogeny based on gene content, Nat Genet, vol.21, issue.1, pp.108-118, 1999. ,
Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood, Bioinformatics, vol.26, issue.15, pp.1910-1912, 2010. ,
Regulation of genetic flux between bacteria by restriction-modification systems, Proc Natl Acad Sci U S A, vol.113, issue.20, p.4878467, 2016. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01374969
Rapid scoring of genes in microbial pan-genome-wide association studies with Scoary, Genome Biol, vol.17, issue.1, p.5124306, 2016. ,
Applied Regression Analysis, 1998. ,
MacSyFinder: a program to mine genomes for molecular systems with an application to CRISPR-Cas systems, PLoS One, vol.9, issue.10, p.110726, 2014. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01080418
The repertoire of ICE in prokaryotes underscores the unity, diversity, and ubiquity of conjugation, PLoS Genet, vol.7, issue.8, p.3158045, 2011. ,
URL : https://hal.archives-ouvertes.fr/pasteur-00647077
Abundance and co-occurrence of extracellular capsules increase environmental breadth: Implications for the emergence of pathogens, PLoS Pathog, vol.13, issue.7, p.5542703, 2017. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01578349
Identification of acquired antimicrobial resistance genes, J Antimicrob Chemother, vol.67, issue.11, p.3468078, 2012. ,
ARG-ANNOT, a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes, Antimicrob Agents Chemother, vol.58, issue.1, pp.212-232, 2014. ,
, , p.3910750