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The population genetics of commensal Escherichia coli

Tenaillon, Olivier, Skurnik, David, Picard, Bertrand, Denamur, Erick·2010·Nature Reviews Microbiology

DOI 10.1038/nrmicro2298

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Prokaryotes: The unseen majority
Whitman, W. B., Coleman, D. C., & Wiebe, W. J. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.12.6578 · Cited by 4,871 · cited 1×
“In the wild its total population size has been estimated to be 10 20 (Ref”
Background
Escherichia Coli and Salmonella: Typhimurium Cellular and Molecular Biology
Neidhardt, F. C., & Ingraham, J. L. (1987) · Medical Entomology and Zoology · Cited by 4,089
Lateral gene transfer and the nature of bacterial innovation
Ochman, H., Lawrence, J. G., & Groisman, E. A. (2000) · Nature · doi:10.1038/35012500 · Cited by 3,816
Evolution of mammals and their gut microbes
Ley, R. E., Hamady, M., Lozupone, C., Turnbaugh, P. J., Ramey, R. R., Bircher, J. S., Schlegel, M. L., Tucker, T. A., Schrenzel, M. D., Knight, R., et al. (2008) · Science · doi:10.1126/science.1155725 · Cited by 3,747
Approximate Bayesian computation in population genetics
Beaumont, M. A., Zhang, W., & Balding, D. J. (2002) · Genetics · doi:10.1093/genetics/162.4.2025 · Cited by 2,932
Cases in which Parsimony or Compatibility Methods will be Positively Misleading
Felsenstein, J. (1978) · Systematic Biology · doi:10.1093/sysbio/27.4.401 · Cited by 2,896
Rapid and Simple Determination of the Escherichia coli Phylogenetic Group
Clermont, O., Bonacorsi, S., & Bingen, E. (2000) · Applied and Environmental Microbiology · doi:10.1128/aem.66.10.4555-4558.2000 · Cited by 2,645
Factors influencing the composition of the intestinal microbiota in early infancy
Penders, J., Thijs, C., Vink, C., Stelma, F. F., Snijders, B., Kummeling, I., van den Brandt, P. A., & Stobberingh, E. E. (2006) · PEDIATRICS · doi:10.1542/peds.2005-2824 · Cited by 2,232
Cases in which parsimony or compatibility methods will be positively misleading.
Felsenstein, J. (1978) · Systematic Zoology · doi:10.2307/2412923 · Cited by 2,230
The impact of next-generation sequencing technology on genetics
Mardis, E. R. (2008) · Trends in Genetics · doi:10.1016/j.tig.2007.12.007 · Cited by 2,053
Sex and virulence in Escherichia coli: an evolutionary perspective
Wirth, T., Falush, D., Lan, R., Colles, F., Mensa, P., Wieler, L. H., Karch, H., Reeves, P. R., Maiden, M. C. J., Ochman, H., et al. (2006) · Molecular Microbiology · doi:10.1111/j.1365-2958.2006.05172.x · Cited by 2,025
How clonal are bacteria?
Smith, J. M., Smith, N. H., O'Rourke, M., & Spratt, B. G. (1993) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.90.10.4384 · Cited by 1,802
Local dispersal promotes biodiversity in a real-life game of rock–paper–scissors
Kerr, B., Riley, M. A., Feldman, M. W., & Bohannan, B. J. M. (2002) · Nature · doi:10.1038/nature00823 · Cited by 1,623
The global burden of diarrhoeal disease, as estimated from studies published between 1992 and 2000.
Kosek, M. N., Bern, C., & Guerrant, R. L. (2003) · Europe PMC (PubMed Central) · Cited by 1,617
Population genomics of domestic and wild yeasts
Liti, G., Carter, D. M., Moses, A. M., Warringer, J., Parts, L., James, S. A., Davey, R. P., Roberts, I. N., Burt, A., Koufopanou, V., et al. (2009) · Nature · doi:10.1038/nature07743 · Cited by 1,392
Methods of multilocus enzyme electrophoresis for bacterial population genetics and systematics
Selander, R. K., Caugant, D. A., Ochman, H., Musser, J. M., Gilmour, M. N., & Whittam, T. S. (1986) · Applied and Environmental Microbiology · doi:10.1128/aem.51.5.873-884.1986 · Cited by 1,385
Pathogenicity Islands and the Evolution of Microbes
Hacker, J., & Kaper, J. B. (2000) · Annual Review of Microbiology · doi:10.1146/annurev.micro.54.1.641 · Cited by 1,303
Organised Genome Dynamics in the Escherichia coli Species Results in Highly Diverse Adaptive Paths
Touchon, M., Hoede, C., Tenaillon, O., Barbe, V., Baeriswyl, S., Bidet, P., Bingen, E., Bonacorsi, S., Bouchier, C., Bouvet, O., et al. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000344 · Cited by 1,181
Self-citation
The indigenous gastrointestinal microflora
Berg, R. (1996) · Trends in Microbiology · doi:10.1016/0966-842x(96)10057-3 · Cited by 1,153 · cited 1×
“coli , a Gram-negative, non-sporulating facultative anaerobe, is an inhabitant of the intestines and faeces of warm-blooded animals and reptile”
Background
A Primitive T Cell-Independent Mechanism of Intestinal Mucosal IgA Responses to Commensal Bacteria
Macpherson, A. J., Gatto, D., Sainsbury, E., Harriman, G. R., Hengartner, H., & Zinkernagel, R. M. (2000) · Science · doi:10.1126/science.288.5474.2222 · Cited by 1,113
Integrons: agents of bacterial evolution
Mazel, D. (2006) · Nature Reviews Microbiology · doi:10.1038/nrmicro1462 · Cited by 1,107
The Pangenome Structure of Escherichia coli: Comparative Genomic Analysis of E. coli Commensal and Pathogenic Isolates
Rasko, D. A., Rosovitz, M. J., Myers, G. S. A., Mongodin, E. F., Fricke, W. F., Gajer, P., Crabtree, J., Sebaihia, M., Thomson, N. R., Chaudhuri, R., et al. (2008) · Journal of Bacteriology · doi:10.1128/jb.00619-08 · Cited by 879
Standard reference strains of Escherichia coli from natural populations
Ochman, H., & Selander, R. K. (1984) · Journal of Bacteriology · doi:10.1128/jb.157.2.690-693.1984 · Cited by 807
Medical and economic impact of extraintestinal infections due to Escherichia coli: focus on an increasingly important endemic problem
Russo, T. A., & Johnson, J. R. (2003) · Microbes and Infection · doi:10.1016/s1286-4579(03)00049-2 · Cited by 801
Inference of Bacterial Microevolution Using Multilocus Sequence Data
Didelot, X., & Falush, D. (2007) · Genetics · doi:10.1534/genetics.106.063305 · Cited by 645
Multilocus sequence typing
Enright, M. C., & Spratt, B. G. (1999) · Trends in Microbiology · doi:10.1016/s0966-842x(99)01609-1 · Cited by 644
Structured habitats and the evolution of anticompetitor toxins in bacteria.
Chao, L., & Levin, B. R. (1981) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.78.10.6324 · Cited by 562
Phylogenetic distribution of branched RNA-linked multicopy single-stranded DNA among natural isolates of Escherichia coli
Herzer, P. J., Inouye, S., Inouye, M., & Whittam, T. S. (1990) · Journal of Bacteriology · doi:10.1128/jb.172.11.6175-6181.1990 · Cited by 533
Carbon nutrition of Escherichia coli in the mouse intestine
Chang, D.-E., Smalley, D. J., Tucker, D. L., Leatham, M. P., Norris, W. E., Stevenson, S. J., Anderson, A. B., Grissom, J. E., Laux, D. C., Cohen, P. S., et al. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0307888101 · Cited by 512
Parallel evolution of virulence in pathogenic Escherichia coli
Reid, S. D., Herbelin, C. J., Bumbaugh, A. C., Selander, R. K., & Whittam, T. S. (2000) · Nature · doi:10.1038/35017546 · Cited by 507
Colonization resistance
Vollaard, E. J., & Clasener, H. A. (1994) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.38.3.409 · Cited by 478
Comprehensive polymorphism survey elucidates population structure of Saccharomyces cerevisiae
Schacherer, J., Shapiro, J. A., Ruderfer, D. M., & Kruglyak, L. (2009) · Nature · doi:10.1038/nature07670 · Cited by 453
Genetic Diversity and Structure in Escherichia coli Populations
Selander, R. K., & Levin, B. R. (1980) · Science · doi:10.1126/science.6999623 · Cited by 418
Recombination in Escherichia coli and the definition of biological species
Dykhuizen, D. E., & Green, L. (1991) · Journal of Bacteriology · doi:10.1128/jb.173.22.7257-7268.1991 · Cited by 394
Clonal Divergence in Escherichia coli as a Result of Recombination, Not Mutation
Guttman, D. S., & Dykhuizen, D. E. (1994) · Science · doi:10.1126/science.7973728 · Cited by 385
The distribution and genetic structure of Escherichia coli in Australian vertebrates: host and geographic effects
Gordon, D. M., & Cowling, A. (2003) · Microbiology · doi:10.1099/mic.0.26486-0 · Cited by 383
Phylogenetic and genomic diversity of human bacteremic Escherichia coli strains
Jaureguy, F., Landraud, L., Passet, V., Diancourt, L., Frapy, E., Guigon, G., Carbonnelle, E., Lortholary, O., Clermont, O., Denamur, E., et al. (2008) · BMC Genomics · doi:10.1186/1471-2164-9-560 · Cited by 380
Self-citation
A Specific Genetic Background Is Required for Acquisition and Expression of Virulence Factors in Escherichia coli
Escobar-Páramo, P., Clermont, O., Blanc-Potard, A.-B., Bui, H., Le Bouguénec, C., & Denamur, E. (2004) · Molecular Biology and Evolution · doi:10.1093/molbev/msh118 · Cited by 356
Self-citation
Complete Genome Sequence and Comparative Genome Analysis of Enteropathogenic Escherichia coli O127:H6 Strain E2348/69
Iguchi, A., Thomson, N. R., Ogura, Y., Saunders, D., Ooka, T., Henderson, I. R., Harris, D., Asadulghani, M., Kurokawa, K., Dean, P., et al. (2009) · Journal of Bacteriology · doi:10.1128/jb.01238-08 · Cited by 334
Commensal Escherichia coli isolates are phylogenetically distributed among geographically distinct human populations
Duriez, P., Clermont, O., Bonacorsi, S., Bingen, E., Chaventré, A., Elion, J., Picard, B., & Denamur, E. (2001) · Microbiology · doi:10.1099/00221287-147-6-1671 · Cited by 325
Self-citation
In the News
(2009) · Nature Reviews Microbiology · doi:10.1038/nrmicro2122 · Cited by 320
Survival and Implantation of Escherichia coli in the Intestinal Tract
Freter, R., Brickner, H., Fekete, J., Vickerman, M. M., & Carey, K. E. (1983) · Infection and Immunity · doi:10.1128/iai.39.2.686-703.1983 · Cited by 318
The Serology of the Coli Group
Kauffmann, F. (1947) · The Journal of Immunology · doi:10.4049/jimmunol.57.1.71 · Cited by 318
Escherichia coli Habitats, Cell Types, and Molecular Mechanisms of Gene Control
Savageau, M. A. (1983) · The American Naturalist · doi:10.1086/284168 · Cited by 314
Application of 'next-generation' sequencing technologies to microbial genetics
MacLean, D., Jones, J. D. G., & Studholme, D. J. (2009) · Nature Reviews Microbiology · doi:10.1038/nrmicro2088 · Cited by 293
Assigning Escherichia coli strains to phylogenetic groups: multi‐locus sequence typing versus the PCR triplex method
Gordon, D. M., Clermont, O., Tolley, H., & Denamur, E. (2008) · Environmental Microbiology · doi:10.1111/j.1462-2920.2008.01669.x · Cited by 290
Self-citation
The MatP/matS Site-Specific System Organizes the Terminus Region of the E. coli Chromosome into a Macrodomain
Mercier, R., Petit, M.-A., Schbath, S., Robin, S., El Karoui, M., Boccard, F., & Espéli, O. (2008) · Cell · doi:10.1016/j.cell.2008.08.031 · Cited by 288
What’s for Dinner?: Entner-Doudoroff Metabolism in Escherichia coli
Peekhaus, N., & Conway, T. (1998) · Journal of Bacteriology · doi:10.1128/jb.180.14.3495-3502.1998 · Cited by 288
GENETIC DIVERSITY AND TEMPORAL VARIATION IN THE E. COLI POPULATION OF A HUMAN HOST
Caugant, D. A., Levin, B. R., & Selander, R. K. (1981) · Genetics · doi:10.1093/genetics/98.3.467 · Cited by 282
Escherichia coli serotyping and disease in man and animals
Ørskov, F., & Ørskov, I. (1992) · Canadian Journal of Microbiology · doi:10.1139/m92-115 · Cited by 277
Cryptic Lineages of the Genus Escherichia
Walk, S. T., Alm, E. W., Gordon, D. M., Ram, J. L., Toranzos, G. A., Tiedje, J. M., & Whittam, T. S. (2009) · Applied and Environmental Microbiology · doi:10.1128/aem.01262-09 · Cited by 273
Extraintestinal Virulence Is a Coincidental By-Product of Commensalism in B2 Phylogenetic Group Escherichia coli Strains
Le Gall, T., Clermont, O., Gouriou, S., Picard, B., Nassif, X., Denamur, E., & Tenaillon, O. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm172 · Cited by 262
Self-citation
The Evolution and Maintenance of Virulence in Microparasites
(1996) · Emerging Infectious Diseases · doi:10.3201/eid0202.960203 · Cited by 248
Large-Scale Population Structure of Human Commensal Escherichia coli Isolates
Escobar-Páramo, P., Grenet, K., Le Menac'h, A., Rode, L., Salgado, E., Amorin, C., Gouriou, S., Picard, B., Rahimy, M. C., Andremont, A., et al. (2004) · Applied and Environmental Microbiology · doi:10.1128/aem.70.9.5698-5700.2004 · Cited by 243
Self-citation
Effect of human vicinity on antimicrobial resistance and integrons in animal faecal Escherichia coli
Skurnik, D. (2006) · Journal of Antimicrobial Chemotherapy · doi:10.1093/jac/dkl122 · Cited by 243
Self-citation
Identification of forces shaping the commensal Escherichia coli genetic structure by comparing animal and human isolates
Escobar‐Páramo, P., Le Menac’h, A., Le Gall, T., Amorin, C., Gouriou, S., Picard, B., Skurnik, D., & Denamur, E. (2006) · Environmental Microbiology · doi:10.1111/j.1462-2920.2006.01077.x · Cited by 236
Self-citation
NUMBERS OF ENTEROCOCCI IN WATER, SEWAGE, AND FECES DETERMINED BY THE MEMBRANE FILTER TECHNIQUE WITH AN IMPROVED MEDIUM
Slanetz, L. W., & Bartley, C. H. (1957) · Journal of Bacteriology · doi:10.1128/jb.74.5.591-595.1957 · Cited by 233
SpecialEscherichia coli serotypes among enterotoxigenic strains from diarrhoea in adults and children
Ørskov, F., Ørskov, I., Evans, D. J., Sack, R. B., Sack, D. A., & Wadström, T. (1976) · Medical Microbiology and Immunology · doi:10.1007/bf02121318 · Cited by 226
Respiration of Escherichia coli in the Mouse Intestine
Jones, S. A., Chowdhury, F. Z., Fabich, A. J., Anderson, A., Schreiner, D. M., House, A. L., Autieri, S. M., Leatham, M. P., Lins, J. J., Jorgensen, M., et al. (2007) · Infection and Immunity · doi:10.1128/iai.00484-07 · Cited by 223
Distribution of chromosome length variation in natural isolates of Escherichia coli
Bergthorsson, U., & Ochman, H. (1998) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a025847 · Cited by 220
Escherichia coli strains colonising the gastrointestinal tract protect germfree mice against Salmonella typhimurium infection
Hudault, S. (2001) · Gut · doi:10.1136/gut.49.1.47 · Cited by 216
Escherichia coli molecular phylogeny using the incongruence length difference test
Lecointre, G., Rachdi, L., Darlu, P., & Denamur, E. (1998) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a025895 · Cited by 209
Self-citation
Molecular evolution of the Escherichia coli chromosome. II. Clonal segments.
Milkman, R., & Stoltzfus, A. (1988) · Genetics · doi:10.1093/genetics/120.2.359 · Cited by 197
Spatial distribution of Escherichia coli in the mouse large intestine inferred from rRNA in situ hybridization
Poulsen, L. K., Lan, F., Kristensen, C. S., Hobolth, P., Molin, S., & Krogfelt, K. A. (1994) · Infection and Immunity · doi:10.1128/iai.62.11.5191-5194.1994 · Cited by 192
Electrophoretic Variation in Escherichia coli from Natural Sources
Milkman, R. (1973) · Science · doi:10.1126/science.182.4116.1024 · Cited by 190
Evidence for clonal population structure in Escherichia coli.
Ochman, H., & Selander, R. K. (1984) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.81.1.198 · Cited by 190
Genetic Structure of Natural Populations of Escherichia coli in Wild Hosts on Different Continents
Souza, V., Rocha, M., Valera, A., & Eguiarte, L. E. (1999) · Applied and Environmental Microbiology · doi:10.1128/aem.65.8.3373-3385.1999 · Cited by 190
Escherichia coli Strains Belonging to Phylogenetic Group B2 Have Superior Capacity to Persist in the Intestinal Microflora of Infants
Nowrouzian, F. L., Wold, A. E., & Adlerberth, I. (2005) · The Journal of Infectious Diseases · doi:10.1086/427996 · Cited by 189
PERSISTENCE OF INDIVIDUAL STRAINS OF ESCHERICHIA COLI IN THE INTESTINAL TRACT OF MAN
Sears, H. J., Brownlee, I., & Uchiyama, J. K. (1950) · Journal of Bacteriology · doi:10.1128/jb.59.2.293-301.1950 · Cited by 181
Escherichia coli in Infants' Intestinal Microflora: Colonization Rate, Strain Turnover, and Virulence Gene Carriage
Nowrouzian, F., Hesselmar, B., Saalman, R., Strannegård, I.-L., Åberg, N., Wold, A. E., & Adlerberth, I. (2003) · Pediatric Research · doi:10.1203/01.pdr.0000069843.20655.ee · Cited by 176
Enhanced persistence in the colonic microbiota of Escherichia coli strains belonging to phylogenetic group B2: role of virulence factors and adherence to colonic cells
Nowrouzian, F. L., Adlerberth, I., & Wold, A. E. (2006) · Microbes and Infection · doi:10.1016/j.micinf.2005.10.011 · Cited by 164
Multiple-Host Sharing, Long-Term Persistence, and Virulence of Escherichia coli Clones from Human and Animal Household Members
Johnson, J. R., Clabots, C., & Kuskowski, M. A. (2008) · Journal of Clinical Microbiology · doi:10.1128/jcm.00980-08 · Cited by 161
Protozoan predation, diversifying selection, and the evolution of antigenic diversity in Salmonella
Wildschutte, H., Wolfe, D. M., Tamewitz, A., & Lawrence, J. G. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0404028101 · Cited by 154
Molecular evolution of the Escherichia coli chromosome. III. Clonal frames.
Milkman, R., & Bridges, M. M. (1990) · Genetics · doi:10.1093/genetics/126.3.505 · Cited by 150
Escherichia coliColonization Patterns among Human Household Members and Pets, with Attention to Acute Urinary Tract Infection
Johnson, J. R., Owens, K., Gajewski, A., & Clabots, C. (2008) · The Journal of Infectious Diseases · doi:10.1086/524844 · Cited by 148
CD16 promotes Escherichia coli sepsis through an FcRγ inhibitory pathway that prevents phagocytosis and facilitates inflammation
da Silva, F. P., Aloulou, M., Skurnik, D., Benhamou, M., Andremont, A., Velasco, I. T., Chiamolera, M., Verbeek, J. S., Launay, P., & Monteiro, R. C. (2007) · Nature Medicine · doi:10.1038/nm1665 · Cited by 146
Self-citation
Grazing protozoa and the evolution of the Escherichia coli O157:H7 Shiga toxin-encoding prophage
Steinberg, K. M., & Levin, B. R. (2007) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2007.0245 · Cited by 146
Genetic diversity in relation to serotype in Escherichia coli
Caugant, D. A., Levin, B. R., Ørskov, I., Ørskov, F., Edén, C. S., & Selander, R. K. (1985) · Infection and Immunity · doi:10.1128/iai.49.2.407-413.1985 · Cited by 145
Nucleotide polymorphism and evolution in the glyceraldehyde-3-phosphate dehydrogenase gene (gapA) in natural populations of Salmonella and Escherichia coli.
Nelson, K., Whittam, T. S., & Selander, R. K. (1991) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.88.15.6667 · Cited by 145
Role of Escherichia coli O157:H7 Virulence Factors in Colonization at the Bovine Terminal Rectal Mucosa
Sheng, H., Lim, J. Y., Knecht, H. J., Li, J., & Hovde, C. J. (2006) · Infection and Immunity · doi:10.1128/iai.00406-06 · Cited by 144
Resident Colonic Escherichia coli Strains Frequently Display Uropathogenic Characteristics
Wold, A. E., Caugant, D. A., Lidin-Janson, G., de Man, P., & Svanborg, C. (1992) · The Journal of Infectious Diseases · doi:10.1093/infdis/165.1.46 · Cited by 143
Both Urinary and Rectal Escherichia coli Isolates Are Dominated by Strains of Phylogenetic Group B2
Zhang, L., Foxman, B., & Marrs, C. F. (2002) · Journal of Clinical Microbiology · doi:10.1128/jcm.40.11.3951-3955.2002 · Cited by 143
Molecular and evolutionary relationships among enteric bacteria
Lawrence, J. G., Ochman, H., & Hartl, D. L. (1991) · Journal of General Microbiology · doi:10.1099/00221287-137-8-1911 · Cited by 135
Escherichia coli Strains from Pregnant Women and Neonates: Intraspecies Genetic Distribution and Prevalence of Virulence Factors
Watt, S., Lanotte, P., Méreghetti, L., Moulin-Schouleur, M., Picard, B., & Quentin, R. (2003) · Journal of Clinical Microbiology · doi:10.1128/jcm.41.5.1929-1935.2003 · Cited by 130
Self-citation
Determination of Escherichia coli O types by allele-specific polymerase chain reaction: application to the O types involved in human septicemia
Clermont, O., Johnson, J. R., Menard, M. L., & Denamur, É. (2006) · Diagnostic Microbiology and Infectious Disease · doi:10.1016/j.diagmicrobio.2006.08.007 · Cited by 130
Phenotypic and genotypic characterization of encapsulated Escherichia coli isolated from blooms in two Australian lakes
Power, M. L., Littlefield‐Wyer, J., Gordon, D. M., Veal, D. A., & Slade, M. B. (2005) · Environmental Microbiology · doi:10.1111/j.1462-2920.2005.00729.x · Cited by 128
Sex in Escherichia coli does not disrupt the clonal structure of the population: evidence from random amplified polymorphic DNA and restriction-fragment-length polymorphism
Desjardins, P., Picard, B., Kaltenboeck, B., Élion, J., & Denamurl, E. (1995) · Journal of Molecular Evolution · doi:10.1007/bf00160315 · Cited by 121
Self-citation
Integron-Associated Antibiotic Resistance and Phylogenetic Grouping of Escherichia coli Isolates from Healthy Subjects Free of Recent Antibiotic Exposure
Skurnik, D., Menach, A. L., Zurakowski, D., Mazel, D., Courvalin, P. M., Denamur, É., Andremont, A., & Ruimy, R. (2005) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.49.7.3062-3065.2005 · Cited by 119
Self-citation
FURTHER OBSERVATIONS ON THE PERSISTENCE OF INDIVIDUAL STRAINS OF ESCHERICHIA COLI IN THE INTESTINAL TRACT OF MAN
Sears, H. J., & Brownlee, I. (1952) · Journal of Bacteriology · doi:10.1128/jb.63.1.47-57.1952 · Cited by 115
Evidence for a human‐specific Escherichia coli clone
Clermont, O., Lescat, M., O'Brien, C. L., Gordon, D. M., Tenaillon, O., & Denamur, É. (2008) · Environmental Microbiology · doi:10.1111/j.1462-2920.2007.01520.x · Cited by 111
Self-citation
Vaginal Escherichia coli share common virulence factor profiles, serotypes and phylogeny with other extraintestinal E. coli
Obata‐Yasuoka, M., Ba‐Thein, W., Tsukamoto, T., Yoshikawa, H., & Hayashi, H. (2002) · Microbiology · doi:10.1099/00221287-148-9-2745 · Cited by 108
Role of Intraspecies Recombination in the Spread of Pathogenicity Islands within the Escherichia coli Species
Schubert, S., Darlu, P., Clermont, O., Wieser, A., Magistro, G., Hoffmann, C., Weinert, K., Tenaillon, O., Matić, I., & Denamur, É. (2009) · PLoS Pathogens · doi:10.1371/journal.ppat.1000257 · Cited by 107
Self-citation
Heterogeneity of genome sizes among natural isolates of Escherichia coli
Bergthorsson, U., & Ochman, H. (1995) · Journal of Bacteriology · doi:10.1128/jb.177.20.5784-5789.1995 · Cited by 107
Nucleotide sequences of the gnd genes from nine natural isolates of Escherichia coli: evidence of intragenic recombination as a contributing factor in the evolution of the polymorphic gnd locus
Bisercic, M., Feutrier, J., & Reeves, P. R. (1991) · Journal of Bacteriology · doi:10.1128/jb.173.12.3894-3900.1991 · Cited by 105
Population Structure and Resistance Genes in Antibiotic-Resistant Bacteria from a Remote Community with Minimal Antibiotic Exposure
Pallecchi, L., Lucchetti, C., Bartoloni, A., Bartalesi, F., Mantella, A., Gamboa, H., Carattoli, A., Paradisi, F., & Rossolini, G. M. (2007) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.01101-06 · Cited by 103
Influence of the age and sex of human hosts on the distribution of Escherichia coli ECOR groups and virulence traits
Gordon, D. M., Stern, S., & Collignon, P. (2005) · Microbiology · doi:10.1099/mic.0.27425-0 · Cited by 103
Complete Genome Sequence and Comparative Analysis of the Wild-type Commensal Escherichia coli Strain SE11 Isolated from a Healthy Adult
Oshima, K., Toh, H., Ogura, Y., Sasamoto, H., Morita, H., Park, S.-H., Ooka, T., Iyoda, S., Taylor, T. D., Hayashi, T., et al. (2008) · DNA Research · doi:10.1093/dnares/dsn026 · Cited by 97
The Life of Commensal Escherichia coli in the Mammalian Intestine
Conway, T., Krogfelt, K. A., & Cohen, P. S. (2004) · EcoSal Plus · doi:10.1128/ecosalplus.8.3.1.2 · Cited by 96
Distribution of multilocus genotypes ofEscherichia coliwithin and between host families
Caugant, D. A., Levin, B. R., & Selander, R. K. (1984) · Journal of Hygiene · doi:10.1017/s0022172400064597 · Cited by 93
Efficiency of Various Intestinal Bacteria in Assuming Normal Functions of Enteric Flora After Association with Germ-Free Mice
Syed, S. A., Abrams, G. D., & Freter, R. R. (1970) · Infection and Immunity · doi:10.1128/iai.2.4.376-386.1970 · Cited by 93
O, K, and H Antigens Predict Virulence Factors, Carboxylesterase B Pattern, Antimicrobial Resistance, and Host Compromise among Escherichia coli Strains Causing Urosepsis
Johnson, J. R., Ørskov, I., Orskov, F., Goullet, P., Picard, B., Moseley, S. L., Roberts, P. L., & Stamm, W. E. (1994) · The Journal of Infectious Diseases · doi:10.1093/infdis/169.1.119 · Cited by 92
Self-citation
Association of carboxylesterase B electrophoretic pattern with presence and expression of urovirulence factor determinants and antimicrobial resistance among strains of Escherichia coli that cause urosepsis
Johnson, J. R., Goullet, P., Picard, B., Moseley, S. L., Roberts, P. L., & Stamm, W. E. (1991) · Infection and Immunity · doi:10.1128/iai.59.7.2311-2315.1991 · Cited by 91
Self-citation
Recombination and Population Structure in Escherichia coli
Milkman, R. (1997) · Genetics · doi:10.1093/genetics/146.3.745 · Cited by 88
Laboratory strains of Escherichia coli : model citizens or deceitful delinquents growing old disgracefully?
Hobman, J. L., Penn, C. W., & Pallen, M. J. (2007) · Molecular Microbiology · doi:10.1111/j.1365-2958.2007.05710.x · Cited by 85
Phylogenetic relationships among clonal groups of extraintestinal pathogenic Escherichia coli as assessed by multi-locus sequence analysis
Johnson, J. R., Owens, K., Clabots, C., Weissman, S. J., & Cannon, S. B. (2006) · Microbes and Infection · doi:10.1016/j.micinf.2006.02.007 · Cited by 84
Molecular evolution of the Escherichia coli chromosome. IV. Sequence comparisons.
Milkman, R., & Bridges, M. M. (1993) · Genetics · doi:10.1093/genetics/133.3.455 · Cited by 83
The diversity of alleles at the hsd locus in natural populations of Escherichia coli.
Barcus, V. A., Titheradge, A. J. B., & Murray, N. E. (1995) · Genetics · doi:10.1093/genetics/140.4.1187 · Cited by 80
Transduction, restriction and recombination patterns in Escherichia coli.
McKane, M., & Milkman, R. (1995) · Genetics · doi:10.1093/genetics/139.1.35 · Cited by 78
Structure and urovirulence characteristics of the fecal Escherichia coli population among healthy women
Moreno, E., Johnson, J. R., Pérez, T., Prats, G., Kuskowski, M. A., & Andreu, A. (2008) · Microbes and Infection · doi:10.1016/j.micinf.2008.12.002 · Cited by 76
Effects of Intrapartum Penicillin Prophylaxis on Intestinal Bacterial Colonization in Infants
Jauréguy, F., Carton, M., Panel, P., Foucaud, P., Butel, M., & Doucet‐Populaire, F. (2004) · Journal of Clinical Microbiology · doi:10.1128/jcm.42.11.5184-5188.2004 · Cited by 72
Diversity analysis of commensal porcine Escherichia coli – associations between genotypes and habitat in the porcine gastrointestinal tract
Dixit, S. M., Gordon, D. M., Wu, X., Chapman, T. A., Kailasapathy, K., & Chin, J. J.-C. (2004) · Microbiology · doi:10.1099/mic.0.26733-0 · Cited by 64
Caenorhabditis elegans as a simple model to study phenotypic and genetic virulence determinants of extraintestinal pathogenic Escherichia coli
Diard, M., Baeriswyl, S., Clermont, O., Gouriou, S., Picard, B., Taddéi, F., Denamur, É., & Matić, I. (2006) · Microbes and Infection · doi:10.1016/j.micinf.2006.11.009 · Cited by 63
Self-citation
Characteristics of human intestinal Escherichia coli with changing environments
Skurnik, D., Bonnet, D., Bernède‐Bauduin, C., Michel, R., Guette, C., Becker, J., Balaire, C., Chau, F., Mohler, J., Jarlier, V., et al. (2008) · Environmental Microbiology · doi:10.1111/j.1462-2920.2008.01636.x · Cited by 61
Self-citation
Decreasing the effects of horizontal gene transfer on bacterial phylogeny: the Escherichia coli case study
Escobar‐Páramo, P., Sabbagh, A., Darlu, P., Pradillon, O., Vaury, C., Denamur, É., & Lecointre, G. (2003) · Molecular Phylogenetics and Evolution · doi:10.1016/s1055-7903(03)00181-7 · Cited by 60
Inhibition of Escherichia coli precursor‐16S rRNA processing by mouse intestinal contents
Licht, T. R., Tolker‐Nielsen, T., Holmstrøm, K., Krogfelt, K. A., & Molin, S. (1999) · Environmental Microbiology · doi:10.1046/j.1462-2920.1999.00001.x · Cited by 59
Estimation of Growth Rates of Escherichia coli BJ4 in Streptomycin-Treated and Previously Germfree Mice by In Situ rRNA Hybridization
Rang, C. U., Licht, T. R., Midtvedt, T., Conway, P. L., Chao, L., Krogfelt, K. A., Cohen, P. S., & Molin, S. (1999) · Clinical and Diagnostic Laboratory Immunology · doi:10.1128/cdli.6.3.434-436.1999 · Cited by 59
ExPEC‐typical virulence‐associated genes correlate with successful colonization by intestinal E. coli in a small piglet group
Schierack, P., Walk, N., Ewers, C., Wilking, H., Steinrück, H., Filter, M., & Wieler, L. H. (2008) · Environmental Microbiology · doi:10.1111/j.1462-2920.2008.01595.x · Cited by 52
Phylogenetic background, virulence gene profiles, and genomic diversity in commensal Escherichia coli isolated from ten mammal species living in one zoo
Baldy-Chudzik, K., Mackiewicz, P., & Stosik, M. P. (2008) · Veterinary Microbiology · doi:10.1016/j.vetmic.2008.02.019 · Cited by 49
Comparative Esterase Electrophoretic Polymorphism of Escherichia coli Isolates Obtained from Animal and Human Sources
Goullet, P., & Picard, B. (1986) · Microbiology · doi:10.1099/00221287-132-7-1843 · Cited by 47
Self-citation
Molecular Evolution of the Escherichia coli Chromosome. V. Recombination Patterns Among Strains of Diverse Origin
Milkman, R., Raleigh, E. A., McKane, M., Cryderman, D. E., Bilodeau, P. S., & McWeeny, K. (1999) · Genetics · doi:10.1093/genetics/153.2.539 · Cited by 45
Multiple acquisitions of CTX-M plasmids in the rare D2 genotype of Escherichia coli provide evidence for convergent evolution
Deschamps, C., Clermont, O., Hipeaux, M. C., Arlet, G., Denamur, É., & Branger, C. (2009) · Microbiology · doi:10.1099/mic.0.023234-0 · Cited by 45
[The fecal flora in man. I. Composition of the fecal flora of various age groups].
MITSUOKA, T., & Hayakawa, K. (1973) · PubMed · Cited by 43
Molecular population genetics of Escherichia coli: DNA sequence diversity at the celC, crr, and gutB loci of natural isolates.
Hall, B. G., & Sharp, P. M. (1992) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040751 · Cited by 41
BIOTYPING CONFIRMS A NEARLY CLONAL POPULATION STRUCTURE INESCHERICHIA COLI
Miller, R. D., & Hartl, D. L. (1986) · Evolution · doi:10.1111/j.1558-5646.1986.tb05712.x · Cited by 41
Order and Disorder during Escherichia coli Divergence
Hendrickson, H. L. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000335 · Cited by 32
Implantation and in vivo Antagonistic Effects of Antibiotic-Susceptible Escherichia Coli Strains Administered to Premature Newborns
Lari, A. R., Gold, F., Borderon, J. C., Laugier, J., & Lafont, J. P. (2009) · Biology of the Neonate · doi:10.1159/000243235 · Cited by 27
Phylogenetic group B2 Escherichia coli strains from the bowel microbiota of Pakistani infants carry few virulence genes and lack the capacity for long-term persistence
Nowrouzian, F. L., Östblom, A., Wold, A. E., & Adlerberth, I. (2009) · Clinical Microbiology and Infection · doi:10.1111/j.1469-0691.2009.02706.x · Cited by 24
aes, the gene encoding the esterase B in Escherichia coli, is a powerful phylogenetic marker of the species
Lescat, M., Hoede, C., Clermont, O., Garry, L., Darlu, P., Tufféry, P., Denamur, É., & Picard, B. (2009) · BMC Microbiology · doi:10.1186/1471-2180-9-273 · Cited by 13
Self-citation

The Clermont Escherichia coli phylo‐typing method revisited: improvement of specificity and detection of new phylo‐groups
Clermont, O., Christenson, J. K., Denamur, E., & Gordon, D. M. (2013) · Environmental Microbiology Reports · doi:10.1111/1758-2229.12019 · Cited by 1,698
Genomic variation landscape of the human gut microbiome
Schloissnig, S., Arumugam, M., Sunagawa, S., Mitreva, M., Tap, J., Zhu, A., Waller, A., Mende, D. R., Kultima, J. R., Martin, J., et al. (2013) · Nature · doi:10.1038/nature11711 · Cited by 907
Environmental Escherichia coli : ecology and public health implications-a review
Jang, J., Hur, H.-G., Sadowsky, M. J., Byappanahalli, M. N., Yan, T., & Ishii, S. (2017) · Journal of Applied Microbiology · doi:10.1111/jam.13468 · Cited by 849
Mechanisms and consequences of intestinal dysbiosis
Weiss, G. A., & Hennet, T. (2017) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-017-2509-x · Cited by 775
Integrons: Past, Present, and Future
Gillings, M. R. (2014) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00056-13 · Cited by 743

See all 1,533

Authors: Tenaillon, O., Skurnik, D., Picard, B., & Denamur, E.
Venue: Nature Reviews Microbiology
Publisher: Springer Science and Business Media LLC
Published: 2010-03
Volume: 8
Issue: 3
Pages: 207-217
ISSN: 1740-1526 (ISSN-L)
1740-1534
DOI: 10.1038/nrmicro2298
OpenAlex: W1980310800
Cited by: 1,533
References: 128
FWCI: 3.43
Type: journal article
Language: en
Open access: closed

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The population genetics of commensal Escherichia coli

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