Human polymicrobial infections, The Lancet, vol.365, issue.9455, pp.253-255, 2005. ,
DOI : 10.1016/S0140-6736(05)70155-0
SUMMARY, Epidemiology and Infection, vol.13, issue.03, pp.531-539, 1991. ,
DOI : 10.1016/S0022-2836(75)80083-0
Epidemiology Of Chronic Pseudomonas aeruginosa Infections In Cystic Fibrosis, Journal of Infectious Diseases, vol.170, issue.6, pp.1616-1621, 1994. ,
DOI : 10.1093/infdis/170.6.1616
Molecular Epidemiology of Pseudomonas aeruginosa Colonization in a Burn Unit: Persistence of a Multidrug-Resistant Clone and a Silver Sulfadiazine-Resistant Clone, Journal of Clinical Microbiology, vol.41, issue.3, pp.1192-1202, 2003. ,
DOI : 10.1128/JCM.41.3.1192-1202.2003
Helicobacter pylori genetic diversity within the gastric niche of a single human host, Proceedings of the National Academy of Sciences, vol.98, issue.25, pp.14625-14630, 2001. ,
DOI : 10.1073/pnas.251551698
Phenotypic and genomic variation among Staphylococcus epidermidis strains infecting joint prostheses, J Clin Microbiol, vol.37, pp.1306-1312, 1999. ,
Polyclonal Staphylococcal Endocarditis Caused by Genetic Variability, Clinical Infectious Diseases, vol.31, issue.1, pp.24-30, 2000. ,
DOI : 10.1086/313915
Patients with Active Tuberculosis often Have Different Strains in the Same Sputum Specimen, American Journal of Respiratory and Critical Care Medicine, vol.169, issue.5, pp.610-614, 2004. ,
DOI : 10.1164/rccm.200305-714OC
Genetic Diversity among Strains of Mycobacterium avium Causing Monoclonal and Polyclonal Bacteremia in Patients with AIDS, Journal of Infectious Diseases, vol.167, issue.6, pp.1384-1390, 1993. ,
DOI : 10.1093/infdis/167.6.1384
Isolates from Blood Cultures: Prevalence of Genotypic Variation and Polyclonal Bacteremia, Clinical Infectious Diseases, vol.33, issue.8, pp.1317-1323, 2001. ,
DOI : 10.1086/322673
EXPERIMENTAL EVIDENCE FOR SYMPATRIC ECOLOGICAL DIVERSIFICATION DUE TO FREQUENCY-DEPENDENT COMPETITION IN ESCHERICHIA COLI, Evolution, vol.16, issue.3, pp.245-260, 2004. ,
DOI : 10.1111/j.0014-3820.2004.tb01642.x
Repeated evolution of an acetate-crossfeeding polymorphism in long-term populations of Escherichia coli, Molecular Biology and Evolution, vol.15, issue.7, pp.789-797, 1998. ,
DOI : 10.1093/oxfordjournals.molbev.a025984
Evolution of cooperation and conflict in experimental bacterial populations, Nature, vol.425, issue.6953, pp.72-74, 2003. ,
DOI : 10.1038/nature01906
Long-Term Experimental Evolution in Escherichia coli. VIII. Dynamics of a Balanced Polymorphism, The American Naturalist, vol.155, issue.1, pp.24-35, 2000. ,
DOI : 10.2307/3079013
URL : https://hal.archives-ouvertes.fr/hal-00173266
Clonal Adaptive Radiation in a Constant Environment, Science, vol.313, issue.5786, pp.514-517, 2006. ,
DOI : 10.1126/science.1129865
Maintaining a healthy SPANC balance through regulatory and mutational adaptation, Molecular Microbiology, vol.176, issue.1, pp.1-8, 2005. ,
DOI : 10.1111/j.1365-2958.2005.04649.x
Signal Transduction and Regulatory Mechanisms Involved in Control of the ??S (RpoS) Subunit of RNA Polymerase, Microbiology and Molecular Biology Reviews, vol.66, issue.3, pp.373-395, 2002. ,
DOI : 10.1128/MMBR.66.3.373-395.2002
Cooperation and competition in pathogenic bacteria, Nature, vol.33, issue.7003, pp.1024-1027, 2004. ,
DOI : 10.1038/414751a
URL : https://www.era.lib.ed.ac.uk/bitstream/1842/698/2/West_S.pdf
Shared themes of antigenic variation and virulence in bacterial, protozoal, and fungal infections, Microbiol Mol Biol Rev, vol.61, pp.281-293, 1997. ,
The population genetics of commensal Escherichia coli, Nature Reviews Microbiology, vol.75, issue.3, pp.207-217, 2010. ,
DOI : 10.1038/nrmicro2298
Pathogenic Escherichia coli, Nature Reviews Microbiology, vol.63, issue.2, pp.123-140, 2004. ,
DOI : 10.1128/IAI.69.1.315-324.2001
Medical and economic impact of extraintestinal infections due to Escherichia coli: focus on an increasingly important endemic problem, Microbes and Infection, vol.5, issue.5, pp.449-456, 2003. ,
DOI : 10.1016/S1286-4579(03)00049-2
Genetic diversity and structure in Escherichia coli populations, Science, vol.210, issue.4469, pp.545-547, 1980. ,
DOI : 10.1126/science.6999623
Sex in Escherichia coli does not disrupt the clonal structure of the population: evidence from random amplified polymorphic DNA and restriction-fragment-length polymorphism, Journal of Molecular Evolution, vol.18, issue.4, pp.440-448, 1995. ,
DOI : 10.1007/BF00160315
Phylogenetic distribution of branched RNA-linked multicopy single-stranded DNA among natural isolates of Escherichia coli., Journal of Bacteriology, vol.172, issue.11, pp.6175-6181, 1990. ,
DOI : 10.1128/jb.172.11.6175-6181.1990
Decreasing the effects of horizontal gene transfer on bacterial phylogeny: the Escherichia coli case study, Molecular Phylogenetics and Evolution, vol.30, issue.1, pp.243-250, 2004. ,
DOI : 10.1016/S1055-7903(03)00181-7
The link between phylogeny and virulence in Escherichia coli extraintestinal infection, Infect Immun, vol.67, pp.546-553, 1999. ,
A Specific Genetic Background Is Required for Acquisition and Expression of Virulence Factors in Escherichia coli, Molecular Biology and Evolution, vol.21, issue.6, pp.1085-1094, 2004. ,
DOI : 10.1093/molbev/msh118
Interpreting chromosomal DNA restriction patterns produced by pulsed-field gel electrophoresis: criteria for bacterial strain typing, J Clin Microbiol, vol.33, pp.2233-2239, 1995. ,
Escherichia coli molecular phylogeny using the incongruence length difference test, Molecular Biology and Evolution, vol.15, issue.12, pp.1685-1695, 1998. ,
DOI : 10.1093/oxfordjournals.molbev.a025895
URL : http://mbe.oxfordjournals.org/cgi/content/short/15/12/1685
Isolates, in Relation to Accessory Traits, Phylogenetic Group, and Ecological Source, The Journal of Infectious Diseases, vol.194, issue.8, pp.1141-1150, 2006. ,
DOI : 10.1086/507305
Molecular Mechanisms of Antibacterial Multidrug Resistance, Cell, vol.128, issue.6, pp.1037-1050, 2007. ,
DOI : 10.1016/j.cell.2007.03.004
High Frequency of Mutator Strains among Human Uropathogenic Escherichia coli Isolates, Journal of Bacteriology, vol.184, issue.2, pp.605-609, 2002. ,
DOI : 10.1128/JB.184.2.605-609.2002
Evolution of mutation rates in bacteria, Molecular Microbiology, vol.21, issue.4, pp.820-827, 2006. ,
DOI : 10.1099/mic.0.27230-0
Mutators, population size, adaptive landscape and the adaptation of asexual populations of bacteria, Genetics, vol.152, pp.485-493, 1999. ,
Microbial competition: Escherichia coli mutants that take over stationary phase cultures, Science, vol.259, issue.5102, pp.1757-1760, 1993. ,
DOI : 10.1126/science.7681219
Genetic architecture of thermal adaptation in Escherichia coli, Proceedings of the National Academy of Sciences, vol.98, issue.2, pp.525-530, 2001. ,
DOI : 10.1073/pnas.98.2.525
Phenotype MicroArrays for High-Throughput Phenotypic Testing and Assay of Gene Function, Genome Research, vol.11, issue.7, pp.1246-1255, 2001. ,
DOI : 10.1101/gr.186501
A Regulatory Trade-Off as a Source of Strain Variation in the Species Escherichia coli, Journal of Bacteriology, vol.186, issue.17, pp.5614-5620, 2004. ,
DOI : 10.1128/JB.186.17.5614-5620.2004
Crl Activates Transcription Initiation of RpoS-Regulated Genes Involved in the Multicellular Behavior of Salmonella enterica Serovar Typhimurium, Journal of Bacteriology, vol.188, issue.11, pp.3983-3994, 2006. ,
DOI : 10.1128/JB.00033-06
Characterization of the rdar morphotype, a multicellular behaviour in Enterobacteriaceae, Cellular and Molecular Life Sciences, vol.62, issue.11, pp.1234-1246, 2005. ,
DOI : 10.1007/s00018-005-4557-x
Mechanisms Causing Rapid and Parallel Losses of Ribose Catabolism in Evolving Populations of Escherichia coli B, Journal of Bacteriology, vol.183, issue.9, pp.2834-2841, 2001. ,
DOI : 10.1128/JB.183.9.2834-2841.2001
Transcriptional Expression of Escherichia coli Glutamate-Dependent Acid Resistance Genes gadA and gadBC in an hns rpoS Mutant, Journal of Bacteriology, vol.185, issue.15, pp.4644-4647, 2003. ,
DOI : 10.1128/JB.185.15.4644-4647.2003
The Small Noncoding DsrA RNA Is an Acid Resistance Regulator in Escherichia coli, Journal of Bacteriology, vol.186, issue.18, pp.6179-6185, 2004. ,
DOI : 10.1128/JB.186.18.6179-6185.2004
outer membrane protein expression during experimental infection of rhesus macaques, Proceedings of the National Academy of Sciences, vol.101, issue.7, pp.2106-2111, 2004. ,
DOI : 10.1073/pnas.0308573100
Induction of bacteremia in newborn rats by Escherichia coli K1 is correlated with only certain O (lipopolysaccharide) antigen types, Infect Immun, vol.39, pp.599-608, 1983. ,
Haemophilus influenzae bacteremia and meningitis resulting from survival of a single organism, Proceedings of the National Academy of Sciences, vol.75, issue.3, pp.1534-1536, 1978. ,
DOI : 10.1073/pnas.75.3.1534
Bacterial Colonization and Infection Resulting from Multiplication of a Single Organism, Clinical Infectious Diseases, vol.9, issue.3, pp.488-493, 1987. ,
DOI : 10.1093/clinids/9.3.488
Nasal Carriage, The Journal of Infectious Diseases, vol.196, issue.7, pp.1068-1075, 2007. ,
DOI : 10.1086/520934
High and low UV-dose responses in SOS-induction of the precise excision of transposons Tn1, Tn5 and Tn10 in Escherichia coli, Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, vol.401, issue.1-2, pp.179-191, 1998. ,
DOI : 10.1016/S0027-5107(98)00007-4
The SOS Response Controls Integron Recombination, Science, vol.324, issue.5930, p.1034, 2009. ,
DOI : 10.1126/science.1172914
URL : https://hal.archives-ouvertes.fr/hal-00409031
Quinolones Induce Partial or Total Loss of Pathogenicity Islands in Uropathogenic Escherichia coli by SOS-Dependent or -Independent Pathways, Respectively, Antimicrobial Agents and Chemotherapy, vol.50, issue.2, pp.649-653, 2006. ,
DOI : 10.1128/AAC.50.2.649-653.2006
Genes under positive selection in Escherichia coli, Genome Research, vol.17, issue.9, pp.1336-1343, 2007. ,
DOI : 10.1101/gr.6254707
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1950902
Genetic Basis of Evolutionary Adaptation by Escherichia coli to Stressful Cycles of Freezing, Thawing and Growth, Genetics, vol.180, issue.1, pp.431-443, 2008. ,
DOI : 10.1534/genetics.108.091330
URL : https://hal.archives-ouvertes.fr/hal-00330443
Mechanisms of Maintenance of Species Diversity, Annual Review of Ecology and Systematics, vol.31, issue.1, pp.343-366, 2000. ,
DOI : 10.1146/annurev.ecolsys.31.1.343
Complexity and Diversity, Science, vol.328, issue.5977, pp.494-497, 2010. ,
DOI : 10.1126/science.1187468
rpoS Gene Function Is a Disadvantage for Escherichia coli BJ4 during Competitive Colonization of the Mouse Large Intestine, Infection and Immunity, vol.68, issue.5, pp.2518-2524, 2000. ,
DOI : 10.1128/IAI.68.5.2518-2524.2000
The alternative sigma factor katF (rpoS) regulates Salmonella virulence., Proceedings of the National Academy of Sciences, vol.89, issue.24, pp.11978-11982, 1992. ,
DOI : 10.1073/pnas.89.24.11978
Cooperation, virulence and siderophore production in bacterial parasites, Proceedings of the Royal Society B: Biological Sciences, vol.270, issue.1510, pp.37-44, 2003. ,
DOI : 10.1098/rspb.2002.2209
Study of pyoverdine type and production by Pseudomonas aeruginosa isolated from cystic fibrosis patients: prevalence of type II pyoverdine isolates and accumulation of pyoverdine-negative mutations, Archives of Microbiology, vol.175, issue.5, pp.384-388, 2001. ,
DOI : 10.1007/s002030100278
Horizontal Gene Transfer of the Secretome Drives the Evolution of Bacterial Cooperation and Virulence, Current Biology, vol.19, issue.20, pp.1683-1691, 2009. ,
DOI : 10.1016/j.cub.2009.08.056
Prisoner's dilemma in an RNA virus, Nature, vol.398, issue.6726, pp.441-443, 1999. ,
DOI : 10.1038/18913
Large-Scale Population Structure of Human Commensal Escherichia coli Isolates, Applied and Environmental Microbiology, vol.70, issue.9, pp.5698-5700, 2004. ,
DOI : 10.1128/AEM.70.9.5698-5700.2004
Antimicrobial susceptibility on solid media, Antibiotics in laboratory medicine, pp.8-60, 2005. ,
Editorial Response: Coagulase-Negative Staphylococcal Infections: A Diagnostic and Therapeutic Challenge, Clinical Infectious Diseases, vol.31, issue.1, pp.31-33, 2000. ,
DOI : 10.1086/313894
Distribution of repetitive DNA sequences in eubacteria and application to finerpriting of bacterial enomes, Nucleic Acids Research, vol.19, issue.24, pp.6823-6831, 1991. ,
DOI : 10.1093/nar/19.24.6823
Epidemiological typing of extended-spectrum ??-lactamase-producing Klebsiella pneumoniae isolates responsible for five outbreaks in a university hospital, Journal of Hospital Infection, vol.36, issue.1, pp.23-36, 1997. ,
DOI : 10.1016/S0195-6701(97)90088-8
Evolution of extended-spectrum beta-lactam resistance (SHV-8) in a strain of Escherichia coli during multiple episodes of bacteremia, Antimicrob Agents Chemother, vol.41, pp.647-653, 1997. ,
Outer membrane permeability in Pseudomonas aeruginosa: comparison of a wild-type with an antibiotic-supersusceptible mutant., Antimicrobial Agents and Chemotherapy, vol.21, issue.2, pp.299-309, 1982. ,
DOI : 10.1128/AAC.21.2.299
DD-HDS: A Method for Visualization and Exploration of High-Dimensional Data, IEEE Transactions on Neural Networks, vol.18, issue.5, pp.1265-1279, 2007. ,
DOI : 10.1109/TNN.2007.891682
URL : https://hal.archives-ouvertes.fr/inserm-00250168
Characterization of the acid resistance phenotype and rpoS alleles of shiga-like toxin-producing Escherichia coli, Infect Immun, vol.64, pp.2808-2811, 1996. ,
Identification and molecular analysis of glgS, a novel growth-phase-regulated and rpoS-dependent gene involved in glycogen synthesis in Escherichia coli, Molecular Microbiology, vol.583, issue.14, pp.1877-1886, 1992. ,
DOI : 10.1016/0968-0004(91)90071-3
) regulon, Molecular Microbiology, vol.63, issue.1, pp.149-160, 1996. ,
DOI : 10.1016/0264-410X(92)90392-W
Technical improvements in two-dimensional electrophoresis increase the level of genetic variation detected in wheat-seedling proteins, Electrophoresis, vol.80, issue.1, pp.52-54, 1986. ,
DOI : 10.1002/elps.1150070108
An efficient solubilization buffer for plant proteins focused in immobilized pH gradients, PROTEOMICS, vol.3, issue.7, pp.1299-1302, 2003. ,
DOI : 10.1002/pmic.200300450
Elimination of point streaking on silver stained two-dimensional gels by addition of iodoacetamide to the equilibration buffer, Electrophoresis, vol.129, issue.2, pp.122-124, 1987. ,
DOI : 10.1002/elps.1150080207
A two-dimensional proteome map of maize endosperm, Phytochemistry, vol.65, issue.11, pp.1609-1618, 2004. ,
DOI : 10.1016/j.phytochem.2004.04.035
MaGe: a microbial genome annotation system supported by synteny results, Nucleic Acids Research, vol.34, issue.1, pp.53-65, 2006. ,
DOI : 10.1093/nar/gkj406
SSAHA: A Fast Search Method for Large DNA Databases, Genome Research, vol.11, issue.10, pp.1725-1729, 2001. ,
DOI : 10.1101/gr.194201
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs, Genome Research, vol.18, issue.5, pp.821-829, 2008. ,
DOI : 10.1101/gr.074492.107
Constraints on microbial metabolism drive evolutionary diversification in homogeneous environments, Journal of Evolutionary Biology, vol.97, issue.5, pp.1882-1889, 2007. ,
DOI : 10.1111/j.1420-9101.2007.01376.x
Grown Planktonically and as Biofilm, Journal of Proteome Research, vol.7, issue.11, pp.4659-4669, 2008. ,
DOI : 10.1021/pr8001723
Control of RpoS in global gene expression of Escherichia coli in minimal media, Molecular Genetics and Genomics, vol.180, issue.Suppl 1, pp.19-33, 2009. ,
DOI : 10.1007/s00438-008-0389-3
Effect ofrpoS gene knockout on the metabolism ofEscherichia coli during exponential growth phase and early stationary phase based on gene expressions, enzyme activities and intracellular metabolite concentrations, Biotechnology and Bioengineering, vol.7, issue.3, pp.585-595, 2006. ,
DOI : 10.1002/bit.20858
??S-Dependent Gene Expression at the Onset of Stationary Phase in Escherichia coli: Function of ??S-Dependent Genes and Identification of Their Promoter Sequences, Journal of Bacteriology, vol.186, issue.21, pp.7186-7195, 2004. ,
DOI : 10.1128/JB.186.21.7186-7195.2004
RNA Polymerase, Annual Review of Microbiology, vol.54, issue.1, pp.499-518, 2000. ,
DOI : 10.1146/annurev.micro.54.1.499