Basic Info

Using ClermonTyping for Rapid Systematic Phylotyping of Escherichia Genus Strains

More Details

The genus Escherichia is composed of Escherichia albertii, E. fergusonii, five cryptic Escherichia clades and E. coli sensu stricto, with the E. coli species can be divided into seven main phylogroups termed A, B1, B2, C, D, E and F. When rooted on E. fergusonii, the most closely related sister species of E. coli, phylogroups B2, F and D appear as the most basal. Phylogroup E then emerges, followed by phylogroups C, B1 and A, which are the most recently diverged phylogroups. Notably, the phylogenetic history of the species is linked to the lifestyle of the strains. The most anciently diverged phylogroups B2, F and D encompass the majority of extra-intestinal pathogenic strains, while the strains causing severe intestinal pathologies such as haemolytic and uremic syndrome and dysentery belong to the most recently diverged phylogroups. In general, phylogroup G strains are uncommon. Phylogroup G strains belong to a group intermediate between the F and B2 phylogroups.

What's New

ClermonTyping is a phylogrouping tool specifically designed for E. coli and its closely related species. By simulating the outcomes of a quadruplex PCR method, it divides E. coli into eight subgroups.  As whole genome sequences become increasingly accessible, ClermonTyper can now assign a given strain sequence to E. albertii, E. fergusonii, Escherichia clades I–V, E. coli sensu stricto, as well as to the seven main E. coli phylogroups. Based on the concept of in vitro PCR assays, ClermonTyping retains the ease of use and speed that were hallmarks of the in vitro assays during their development. This in silico approach demonstrates a 99.4% concordance with in vitro PCR assays and a 98.8% concordance with the Mash genome-clustering tool. The few discrepancies observed are primarily due to errors arising from horizontal gene transfers or SNPs in the primers.

Additional Information

Related links:

https://github.com/A-BN/ClermonTyping

Literature

Beghain J, Bridier-Nahmias A, Le Nagard H, Denamur E, Clermont O. ClermonTyping: an easy-to-use and accurate in silico method for Escherichia genus strain phylotyping. Microb Genom. 2018;4(7):e000192. doi:10.1099/mgen.0.000192

Clermont O, Dixit OVA, Vangchhia B, et al. Characterization and rapid identification of phylogroup G in Escherichia coli, a lineage with high virulence and antibiotic resistance potential. Environ Microbiol. 2019;21(8):3107-3117. doi:10.1111/1462-2920.14713