title: Guide to the various phylogenetic classification schemes for Escherichia coli and the correspondence among schemes.
abstract: Numerous tools allowing the rapid and universal identification of the clones/clonal complexes/phylogroups of Escherichia coli have been developed, as it is a commensal of the vertebrate gut, a major pathogen in veterinary and human medicine, and a bacterial indicator of faecal contamination. The ability to identify clones/clonal complexes/phylogroups is crucial, as a strain's ecological niche, lifestyle and propensity to cause disease vary with its phylogenetic origins. 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. In this work, we present data that will enable investigators to determine the correspondence between the PCR-based assays and the three MLST schemes, and provide the means for assigning a sequence type (ST) to a phylogroup when no other data on the strain phylogroup membership are available. Such information will help the scientific community to accurately identify the E. coli clones reported in various publications. 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.
authors.affiliation: Université Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, F-75018 Paris, France.|INSERM, IAME, UMR 1137, F-75018 Paris, France.
authors.forename: Olivier
authors.initials: O
authors.lastname: Clermont
authors.affiliation: Division of Evolution, Ecology & Genetics, Research School of Biology, Australian National University, Canberra, ACT 0200 Australia.
authors.forename: David
authors.initials: D
authors.lastname: Gordon
authors.affiliation: Université Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, F-75018 Paris, France.|INSERM, IAME, UMR 1137, F-75018 Paris, France.
authors.forename: Erick
authors.initials: E
authors.lastname: Denamur
mesh_terms: D004926:Escherichia coli / Q000145:classification* / Q000235:genetics*; D029968:Escherichia coli Proteins / Q000235:genetics; D055106:Genome-Wide Association Study; D058885:Multilocus Sequence Typing; D010802:Phylogeny; D016133:Polymerase Chain Reaction
chemical_list: D029968:Escherichia coli Proteins