The "Cryptic" Escherichia

Abstract

In 2009, five monophyletic Escherichia clades were described and referred to as "cryptic" based on the inability to distinguish them from representative E. coli isolates using diagnostic biochemical reactions. Since this original publication, a number of studies have explored the genomic, transcriptomic, and phenotypic diversity of cryptic clade isolates to better understand their phylogenetic, physiological, and ecological distinctiveness with respect to previously named Escherichia species. This chapter reviews the original discovery of the cryptic clades, discusses available evidence that some are environmentally adapted, and evaluates current support for taxonomic designations of these microorganisms. The importance of these clades to clinical research, epidemiology, population genetics, and microbial speciation is also discussed.

Figure 1

Phylogenetic reconstruction of the known Escherichia isolates based on concatenated nucleotide sequence of 22 houskeeping loci (11,161 bp). This neighbor-joining dendrogram was generated based on the Kimura-2 parameter as implemented in MEGA6 (45) with support for nodes based on 1,000 bootstrap replications. doi:10.1128/ecosalplus.ESP-0002-2015.f1

Figure 2

Phylogenetic reconstruction of clinically relevant cryptic clade I isolates based on 22 housekeeping loci as described in Fig. 1. To date, clade I isolates have been isolated from cases of human disease and found to carry virulence factors that define E. coli pathotypes, including ETEC and STEC. Representative strains referred to in the text are shown. CG, clonal group. doi:10.1128/ecosalplus.ESP-0002-2015.f2

Figure 3

Phylogenetic reconstruction of previously named Salmonella and known Escherichia lineages based on concatenated nucleotide sequences from mdh and recA. This is a time tree as implemented in MEGA6 (45) based on the Kimura-2 parameter. The scale bar displays the relative divergence times of each node. ^aA name has not been proposed for subspecies VII. Representative isolates belonging to subspecies VII share the same biotype as subspecies houtenae (42, 43). doi:10.1128/ecosalplus.ESP-0002-2015.f3

Figure 4

Comparison of ANI and dDDH values (%) for the named Escherichia isolates. Between-genome comparisons mentioned in the text are indicated by colored symbols. Dotted lines represent ANI and dDDH cutoff values for bacterial species. Genome identification numbers can be found in Supplemental Table 1. doi:10.1128/ecosalplus.ESP-0002-2015.f4