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

Summary There is extensive genetic substructure within the species E scherichia coli . In 2000 a simple triplex PCR method was described by C lermont and colleagues that enables an E . coli isolate to be assigned to one of the phylo‐groups A , B 1, B 2 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 , B 1, B 2, C , D , E , F ) belong to E . coli sensu stricto , whereas the eighth is the E scherichia 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 E scherichia 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 .