Cryptic lineages of the genus Escherichia - PubMed (original) (raw)

Cryptic lineages of the genus Escherichia

Seth T Walk et al. Appl Environ Microbiol. 2009 Oct.

Abstract

Extended multilocus sequence typing (MLST) analysis of atypical Escherichia isolates was used to identify five novel phylogenetic clades (CI to CV) among isolates from environmental, human, and animal sources. Analysis of individual housekeeping loci showed that E. coli and its sister clade, CI, remain largely indistinguishable and represent nascent evolutionary lineages. Conversely, clades of similar age (CIII and CIV) were found to be phylogenetically distinct. When all Escherichia lineages (named and unnamed) were evaluated, we found evidence that Escherichia fergusonii has evolved at an accelerated rate compared to E. coli, CI, CIII, CIV, and CV, suggesting that this species is younger than estimated by the molecular clock method. Although the five novel clades were phylogenetically distinct, we were unable to identify a discriminating biochemical marker for all but one of them (CIII) with traditional phenotypic profiling. CIII had a statistically different phenotype from E. coli that resulted from the loss of sucrose and sorbitol fermentation and lysine utilization. The lack of phenotypic distinction has likely hindered the ability to differentiate these clades from typical E. coli, and so their ecological significance and importance for applied and clinical microbiology are yet to be determined. However, our sampling suggests that CIII, CIV, and CV represent environmentally adapted Escherichia lineages that may be more abundant outside the host gastrointestinal tract.

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Figures

FIG. 1.

FIG. 1.

The phylogenetic relationship of novel Escherichia lineages. (A) Position of MLST housekeeping genes relative to the E. coli K-12 MG1655 genome. (B) Split network of isolates showing the phylogenetic position of the five novel clades relative to previously named Escherichia species. (C) UPGMA dendrogram based on the proportion of nucleotide polymorphism differences (_p_-distance).

FIG. 2.

FIG. 2.

Principal coordinates analysis of all pairwise (strain by strain) chi-square test statistics for Tajima's test of relative evolutionary rates. The analysis ordered isolates into two groups, suggesting that there are two distinct evolutionary rates among the phylogenetic groups of Escherichia species in this study. ECI to ECV, Escherichia clades I to V.

FIG. 3.

FIG. 3.

Relationship between genetic distance (proportion of nucleotide polymorphisms) and the presence of 27 E. coli pan-genome genes among Escherichia phylogenetic groups. No clear association was found between genetic distance and the percentage of shared loci.

FIG. 4.

FIG. 4.

NMDS of biochemical profiles for named Escherichia species (green and black circles) and novel Escherichia clades (gray, red, blue, and yellow circles) relative to 692 E. coli isolates (unfilled circles). Only the isolates that represent the 50 most positive and negative positions for each axis are shown. The number of isolates from each clade is given in parentheses. Isolates of the novel clades are highly similar to E. coli (CI to CIV) or completely indistinguishable (CV).

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