E. coli typing methods within a phylogenetic framework and the correspondence among schemes
Numerous tools allowing the rapid and universal identification of the clones/clonal complexes/phylogroups of Escherichia coli have been developed. The ability to identify clones/clonal complexes/phylogroups is crucial, as a strain’s ecological niche, lifestyle, and propensity to cause disease varies with its phylogenetic origins. However, these typing tools have to be understood and interpreted according to the genetic population structure of the species and a phylogenetic framework. There are currently three multi-locus sequence typing (MLST) schemes for E. coli, as well as several PCR based assays for determining a strain’s phylogroup or clonal complex. I will discuss the benefits and well as the shortcomings of the various approaches and give the correspondence between the PCR based assays and the three MSLT schemes. Although whole-genome sequencing will replace classical MLST and most alternative PCR-based methods, the ST nomenclature of the MLST scheme hosted at the University of Warwick will largely persist.