Escherichia coli molecular phylogeny using the incongruence length difference test

Abstract

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.

The type 1 pili regulator gene fimX and pathogenicity island PAI-X as molecular markers of uropathogenic Escherichia coli

“…While specific pathotypes of E. coli are difficult to define given a high degree of genomic heterogeneity, certain genetic features can distinguish pathogenic strains from commensal strains (Groisman & Ochman, 1994). Phylogenetic analyses have shown that E. coli strains fall into four main phylogenetic groups (A, B1, B2 and D) (Herzer et al, 1990;Lecointre et al, 1998). Virulent extraintestinal pathogenic E. coli (ExPEC) belong mainly to group B2 and, to a lesser extent, to group D and encompass the UPEC strains as well (Boyd & Hartl, 1998;Picard et al, 1999).…”

Vertical Transmission of Biosynthetic Plasmids in Aphid Endosymbionts ( Buchnera )

“…fluidity in most bacterial species, where plasmids mobilize ecologically important features such as pathogenic and symbiotic capacities (69) and antibiotic resistance (4, 37) and contribute to the mosaic-like genome structure of some bacterial genomes (26,32,34,41). For example, in Escherichia coli, the close free-living relative of Buchnera, incongruence among genealogies of chromosomal and plasmid-encoded genes indicates several recombination and horizontal transfer events (35).…”

CARACTERIZAÇÃO FILOGENÉTICA MOLECULAR E RESISTÊNCIA ANTIMICROBIANA DE Escherichia coli ISOLADAS DE CAPRINOS NEONATOS COM DIARREIA

“…Nas análises filogenéticas, temse verificado que cepas podem ser classificadas em quatro grupos principais conhecidos para esta espécie bacteriana, sendo: A, B1, B2 e D (5) . As cepas virulentas geralmente classificam-se no grupo B2, porém algumas são classificadas no grupo D. Por outro lado, as cepas comensais pertencem aos grupos A e B1 (6)(7)(8) . Cepas extraintestinais patogênicas e comensais de E. coli diferem de acordo com os fatores de virulência, expressos por genes geralmente agrupados em ilhas de patogenicidade, proporcionando um mecanismo de transferência horizontal coordenada desses genes de virulência (9) .…”