The Clermont Escherichia coli phylo-typing method revisited: improvement of specificity and detection of new phylo-groups

Environ Microbiol Rep. 2013 Feb;5(1):58-65. doi: 10.1111/1758-2229.12019. Epub 2012 Dec 24.


There is extensive genetic substructure within the species Escherichia coli. In 2000 a simple triplex PCR method was described by Clermont and colleagues that enables an E. coli isolate to be assigned to one of the phylo-groups A, B1, B2 or D. The growing body of multi-locus sequence data and genome data for E. coli has refined our understanding of E. coli's phylo-group structure and eight phylo-groups are now recognized: seven (A, B1, B2, C, D, E, F) belong to E. coli sensu stricto, whereas the eighth is the Escherichia cryptic clade I. Here a new PCR-based method is developed that enables an E. coli isolate to be assigned to one of the eight phylo-groups and which allows isolates that are members of the other cryptic clades (II to V) of Escherichia to be identified. The development of the method is described and the method is validated. Over 95% of E. coli isolates can be correctly assigned to a phylo-group. Two collections of human faecal isolates were screened using the new phylo-group assignment method demonstrating that about 13% of E. coli isolates belong to the newly described phylo-groups C, E, F and clade I.

MeSH terms

  • Bacterial Typing Techniques / methods*
  • DNA, Bacterial / genetics
  • Escherichia coli / classification*
  • Escherichia coli / genetics
  • Escherichia coli / isolation & purification
  • Escherichia coli Proteins / genetics
  • Feces / microbiology
  • Humans
  • Phylogeny*
  • Polymerase Chain Reaction
  • Reproducibility of Results
  • Sensitivity and Specificity
  • Sequence Analysis, DNA


  • DNA, Bacterial
  • Escherichia coli Proteins