Molecular Biology and Evolution, Vol 15, 1685-1695, Copyright © 1998 by Society for Molecular Biology and Evolution
G Lecointre, L Rachdi, P Darlu and E Denamur
Molecular phylogeny of the species Escherichia coli using the E. coli
reference (ECOR) collection strains has been hampered by (1) the absence of
rooting in the commonly used phenogram obtained from multilocus enzyme
electrophoresis (MLEE) data and (2) the existence of recombination events
between strains that scramble phylogenetic trees reconstructed from the
nucleotide sequences of genes. We attempted to determine the phylogeny for
E. coli based on the ECOR strain data by extracting from GenBank the
nucleotide sequences of 11 chromosomal structural and 2 plasmid genes for
which the Salmonella enterica homologous gene sequences were available. For
each of the 13 DNA data sets studied, incongruence with a nonnucleotide
whole-genome data set including MLEE, random amplified polymorphic DNA, and
rrn restriction fragment length polymorphism data was measured using the
incongruence length difference (ILD) test of Farris et al. As previously
reported, the incongruence observed between the gnd and plasmid gene data
and the whole-genome data was multiple, indicating numerous horizontal
transfer and/or recombination events. In five cases, the incongruence
detected by the ILD test was punctual, and the donor group was identified.
Congruence was not rejected for the remaining data sets. The strains
responsible for incongruences with the whole-genome data set were removed,
leading to a "prior-agreement" approach, i.e., the determination of a
phylogeny for E. coli based on several genes, excluding (1) the genes with
multiple incongruences with the whole genome data, (2) the strains
responsible for punctual incongruences, and (3) the genes incongruent with
each other. The obtained phylogeny shows that the most basal group of E.
coli strains is the B2 group rather than the A group, as generally thought.
The D group then emerges as the sister group of the rest. Finally, the A
and B1 groups are sister groups. Interestingly, the most primitive taxon
within E. coli in terms of branching pattern, i.e., the B2 group, includes
highly virulent extraintestinal strains with derived characters
(extraintestinal virulence determinants) occurring on its own branch.
ORIGINAL ARTICLE
Escherichia coli molecular phylogeny using the incongruence length difference test
Service de Systematique Moleculaire, Museum National d'Histoire Naturelle, Paris, France.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  G. Rouquet, G. Porcheron, C. Barra, M. Reperant, N. K. Chanteloup, C. Schouler, and P. Gilot A Metabolic Operon in Extraintestinal Pathogenic Escherichia coli Promotes Fitness under Stressful Conditions and Invasion of Eukaryotic Cells J. Bacteriol., July 1, 2009; 191(13): 4427 - 4440. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Iguchi, N. R. Thomson, Y. Ogura, D. Saunders, T. Ooka, I. R. Henderson, D. Harris, M. Asadulghani, K. Kurokawa, P. Dean, et al. Complete Genome Sequence and Comparative Genome Analysis of Enteropathogenic Escherichia coli O127:H6 Strain E2348/69 J. Bacteriol., January 1, 2009; 191(1): 347 - 354. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S.-T. Kim and M. J. Donoghue Incongruence between cpDNA and nrITS trees indicates extensive hybridization within Eupersicaria (Polygonaceae) Am. J. Botany, September 1, 2008; 95(9): 1122 - 1135. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. Le Gall, O. Clermont, S. Gouriou, B. Picard, X. Nassif, E. Denamur, and O. Tenaillon Extraintestinal Virulence Is a Coincidental By-Product of Commensalism in B2 Phylogenetic Group Escherichia coli Strains Mol. Biol. Evol., November 1, 2007; 24(11): 2373 - 2384. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Becq, M. C. Gutierrez, V. Rosas-Magallanes, J. Rauzier, B. Gicquel, O. Neyrolles, and P. Deschavanne Contribution of Horizontally Acquired Genomic Islands to the Evolution of the Tubercle Bacilli Mol. Biol. Evol., August 1, 2007; 24(8): 1861 - 1871. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 P. Germon, D. Roche, S. Melo, S. Mignon-Grasteau, U. Dobrindt, J. Hacker, C. Schouler, and M. Moulin-Schouleur tDNA locus polymorphism and ecto-chromosomal DNA insertion hot-spots are related to the phylogenetic group of Escherichia coli strains Microbiology, March 1, 2007; 153(3): 826 - 837. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. Restieri, G. Garriss, M.-C. Locas, and C. M. Dozois Autotransporter-Encoding Sequences Are Phylogenetically Distributed among Escherichia coli Clinical Isolates and Reference Strains Appl. Envir. Microbiol., March 1, 2007; 73(5): 1553 - 1562. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J.-M. Hu, H.-C. Fu, C.-H. Lin, H.-J. Su, and H.-H. Yeh Reassortment and Concerted Evolution in Banana Bunchy Top Virus Genomes J. Virol., February 15, 2007; 81(4): 1746 - 1761. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. M. Turner, R. R. Chaudhuri, Z.-D. Jiang, H. DuPont, C. Gyles, C. W. Penn, M. J. Pallen, and I. R. Henderson Phylogenetic Comparisons Reveal Multiple Acquisitions of the Toxin Genes by Enterotoxigenic Escherichia coli Strains of Different Evolutionary Lineages J. Clin. Microbiol., December 1, 2006; 44(12): 4528 - 4536. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. H. Lymberopoulos, S. Houle, F. Daigle, S. Leveille, A. Bree, M. Moulin-Schouleur, J. R. Johnson, and C. M. Dozois Characterization of Stg Fimbriae from an Avian Pathogenic Escherichia coli O78:K80 Strain and Assessment of Their Contribution to Colonization of the Chicken Respiratory Tract. J. Bacteriol., September 1, 2006; 188(18): 6449 - 6459. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. L. Nouen, G. Rivallan, D. Toquin, P. Darlu, Y. Morin, V. Beven, C. de Boisseson, C. Cazaban, S. Comte, Y. Gardin, et al. Very virulent infectious bursal disease virus: reduced pathogenicity in a rare natural segment-B-reassorted isolate J. Gen. Virol., January 1, 2006; 87(1): 209 - 216. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 P. J. Planet and I. N. Sarkar mILD: a tool for constructing and analyzing matrices of pairwise phylogenetic character incongruence tests Bioinformatics, December 15, 2005; 21(24): 4423 - 4424. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. P. Girardeau, A. Dalmasso, Y. Bertin, C. Ducrot, S. Bord, V. Livrelli, C. Vernozy-Rozand, and C. Martin Association of Virulence Genotype with Phylogenetic Background in Comparison to Different Seropathotypes of Shiga Toxin-Producing Escherichia coli Isolates J. Clin. Microbiol., December 1, 2005; 43(12): 6098 - 6107. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. Hommais, S. Pereira, C. Acquaviva, P. Escobar-Paramo, and E. Denamur Single-Nucleotide Polymorphism Phylotyping of Escherichia coli Appl. Envir. Microbiol., August 1, 2005; 71(8): 4784 - 4792. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. Li, E. W. Brown, C. D'Agostino, J. E. LeClerc, and T. A. Cebula Structure and distribution of the phosphoprotein phosphatase genes, prpA and prpB, among Shigella subgroups Microbiology, August 1, 2005; 151(8): 2671 - 2683. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. Le Gall, P. Darlu, P. Escobar-Paramo, B. Picard, and E. Denamur Selection-driven transcriptome polymorphism in Escherichia coli/Shigella species Genome Res., February 1, 2005; 15(2): 260 - 268. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. Dufraigne, B. Fertil, S. Lespinats, A. Giron, and P. Deschavanne Detection and characterization of horizontal transfers in prokaryotes using genomic signature Nucleic Acids Res., January 13, 2005; 33(1): e6 - e6. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Taoka, Y. Yamauchi, T. Shinkawa, H. Kaji, W. Motohashi, H. Nakayama, N. Takahashi, and T. Isobe Only a Small Subset of the Horizontally Transferred Chromosomal Genes in Escherichia coli Are Translated into Proteins Mol. Cell. Proteomics, August 1, 2004; 3(8): 780 - 787. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C.-P. Ren, R. R. Chaudhuri, A. Fivian, C. M. Bailey, M. Antonio, W. M. Barnes, and M. J. Pallen The ETT2 Gene Cluster, Encoding a Second Type III Secretion System from Escherichia coli, Is Present in the Majority of Strains but Has Undergone Widespread Mutational Attrition J. Bacteriol., June 1, 2004; 186(11): 3547 - 3560. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Escobar-Paramo, O. Clermont, A.-B. Blanc-Potard, H. Bui, C. Le Bouguenec, and E. Denamur A Specific Genetic Background Is Required for Acquisition and Expression of Virulence Factors in Escherichia coli Mol. Biol. Evol., June 1, 2004; 21(6): 1085 - 1094. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. Diamant, Y. Palti, R. Gur-Arie, H. Cohen, E. M. Hallerman, and Y. Kashi Phylogeny and Strain Typing of Escherichia coli, Inferred from Variation at Mononucleotide Repeat Loci Appl. Envir. Microbiol., April 1, 2004; 70(4): 2464 - 2473. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
O. Clermont, S. Bonacorsi, and E. Bingen Characterization of an Anonymous Molecular Marker Strongly Linked to Escherichia coli Strains Causing Neonatal Meningitis J. Clin. Microbiol., April 1, 2004; 42(4): 1770 - 1772. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. R. Johnson, A. C. Murray, A. Gajewski, M. Sullivan, P. Snippes, M. A. Kuskowski, and K. E. Smith Isolation and Molecular Characterization of Nalidixic Acid-Resistant Extraintestinal Pathogenic Escherichia coli from Retail Chicken Products Antimicrob. Agents Chemother., July 1, 2003; 47(7): 2161 - 2168. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Schubert, B. Picard, S. Gouriou, J. Heesemann, and E. Denamur Yersinia High-Pathogenicity Island Contributes to Virulence in Escherichia coli Causing Extraintestinal Infections Infect. Immun., September 1, 2002; 70(9): 5335 - 5337. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Mereghetti, P. Lanotte, V. Savoye-Marczuk, N. Marquet-Van Der Mee, A. Audurier, and R. Quentin Combined Ribotyping and Random Multiprimer DNA Analysis To Probe the Population Structure of Listeria monocytogenes Appl. Envir. Microbiol., June 1, 2002; 68(6): 2849 - 2857. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. R. Johnson, A. L. Stell, T. T. O'Bryan, M. Kuskowski, B. Nowicki, C. Johnson, J. N. Maslow, A. Kaul, J. Kavle, and G. Prats Global Molecular Epidemiology of the O15:K52:H1 Extraintestinal Pathogenic Escherichia coli Clonal Group: Evidence of Distribution beyond Europe J. Clin. Microbiol., June 1, 2002; 40(6): 1913 - 1923. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Darlu and G. Lecointre When Does the Incongruence Length Difference Test Fail? Mol. Biol. Evol., April 1, 2002; 19(4): 432 - 437. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
O. Clermont, C. Cordevant, S. Bonacorsi, A. Marecat, M. Lange, and E. Bingen Automated Ribotyping Provides Rapid Phylogenetic Subgroup Affiliation of Clinical Extraintestinal Pathogenic Escherichia coli Strains J. Clin. Microbiol., December 1, 2001; 39(12): 4549 - 4553. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. R. Johnson, T. T. O'Bryan, M. Kuskowski, and J. N. Maslow Ongoing Horizontal and Vertical Transmission of Virulence Genes and papA Alleles among Escherichia coli Blood Isolates from Patients with Diverse-Source Bacteremia Infect. Immun., September 1, 2001; 69(9): 5363 - 5374. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Duriez, O. Clermont, S. Bonacorsi, E. Bingen, A. Chaventre, J. Elion, B. Picard, and E. Denamur Commensal Escherichia coli isolates are phylogenetically distributed among geographically distinct human populations Microbiology, June 1, 2001; 147(6): 1671 - 1676. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. W. Brown, J. E. LeClerc, B. Li, W. L. Payne, and T. A. Cebula Phylogenetic Evidence for Horizontal Transfer of mutS Alleles among Naturally Occurring Escherichia coli Strains J. Bacteriol., March 1, 2001; 183(5): 1631 - 1644. [Abstract] [Full Text]
|
|
|
|
|
|
J. J. Wernegreen and N. A. Moran Vertical Transmission of Biosynthetic Plasmids in Aphid Endosymbionts (Buchnera) J. Bacteriol., January 15, 2001; 183(2): 785 - 790. [Abstract] [Full Text]
|
|
|
|
|
|
J. R. Johnson, V. Souza, M. Rocha, A. Valera, and L. E. Eguiarte Genetic Diversity within E. coli Appl. Envir. Microbiol., November 1, 2000; 66(11): 5104 - 5105. [Full Text]
|
|
|
|
|
|
O. Clermont, S. Bonacorsi, and E. Bingen Rapid and Simple Determination of the Escherichia coli Phylogenetic Group Appl. Envir. Microbiol., October 1, 2000; 66(10): 4555 - 4558. [Abstract] [Full Text]
|
|
|
|
|
|
D. Mazel, B. Dychinco, V. A. Webb, and J. Davies Antibiotic Resistance in the ECOR Collection: Integrons and Identification of a Novel aad Gene Antimicrob. Agents Chemother., June 1, 2000; 44(6): 1568 - 1574. [Abstract] [Full Text]
|
|
|
|
|
|
J. R. Johnson, T. A. Russo, P. I. Tarr, U. Carlino, S. S. Bilge, J. C. Vary Jr., and A. L. Stell Molecular Epidemiological and Phylogenetic Associations of Two Novel Putative Virulence Genes, iha and iroNE. coli, among Escherichia coli Isolates from Patients with Urosepsis Infect. Immun., May 1, 2000; 68(5): 3040 - 3047. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. R. Johnson and T. T. O'Bryan Improved Repetitive-Element PCR Fingerprinting for Resolving Pathogenic and Nonpathogenic Phylogenetic Groups within Escherichia coli Clin. Vaccine Immunol., March 1, 2000; 7(2): 265 - 273. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. R. Johnson, M. Kuskowski;, E. Denamur, J. Elion, and B. Picard Clonal Origin, Virulence Factors, and Virulence Infect. Immun., January 1, 2000; 68(1): 424 - 425. [Full Text] [PDF]
|
|
|
|
|
|
V. Souza, M. Rocha, A. Valera, and L. E. Eguiarte Genetic Structure of Natural Populations of Escherichia coli in Wild Hosts on Different Continents Appl. Envir. Microbiol., August 1, 1999; 65(8): 3373 - 3385. [Abstract] [Full Text]
|
|
|
|
|
|
B. Picard, J. S. Garcia, S. Gouriou, P. Duriez, N. Brahimi, E. Bingen, J. Elion, and E. Denamur The Link between Phylogeny and Virulence in Escherichia coli Extraintestinal Infection Infect. Immun., February 1, 1999; 67(2): 546 - 553. [Abstract] [Full Text] [PDF]
|
|