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Escherichia coli molecular phylogeny using the incongruence length difference test
G Lecointre1, L Rachdi, P Darlu
1Service de Systématique Moléculaire, Muséum National d'Histoire Naturelle, Paris, France.
Molecular Biology and Evolution
|December 29, 1998
Summary
Phylogenetic analysis of Escherichia coli strains reveals the B2 group as the most basal, challenging previous assumptions. This group harbors virulent extraintestinal strains, suggesting early evolution of virulence factors.
Area of Science:
- Microbiology
- Evolutionary Biology
- Bioinformatics
Background:
- Phylogenetic reconstruction of Escherichia coli has been complicated by recombination events and lack of rooting in existing data.
- Multilocus enzyme electrophoresis (MLEE) data, while useful, often lacks clear rooting for E. coli phylogeny.
Purpose of the Study:
- To establish a robust molecular phylogeny for Escherichia coli using the ECOR collection.
- To resolve phylogenetic ambiguities caused by recombination and horizontal gene transfer.
Main Methods:
- Utilized nucleotide sequences of 13 genes (11 chromosomal, 2 plasmid) from E. coli ECOR strains and homologous sequences from Salmonella enterica.
- Employed the incongruence length difference (ILD) test to assess congruence between individual gene phylogenies and a whole-genome data set.
- Implemented a 'prior-agreement' approach, excluding incongruent genes and strains to refine phylogenetic analysis.
Main Results:
- Identified significant incongruence between certain gene phylogenies (gnd, plasmid genes) and whole-genome data, indicating horizontal transfer/recombination.
- The refined phylogeny places the B2 group as the most basal lineage of E. coli, contrary to the previously accepted A group.
- The B2 group, identified as the most basal, contains highly virulent extraintestinal strains possessing specific virulence determinants.
Conclusions:
- The study provides a revised phylogeny for Escherichia coli, establishing the B2 group as the earliest diverging lineage.
- The basal position of the B2 group, which includes extraintestinal pathogenic strains, suggests an early evolutionary origin of virulence in E. coli.