Development of an allele-specific PCR for Escherichia coli B2 sub-typing, a rapid and easy to perform substitute of multilocus sequence typing

•An assay to type B2 E. coli strains at the sequence type complex level is described.•The method is simple and based on the principle of allele-specific PCR.•It allows an assignation of E. coli B2 bacteremia strains in 95% of the cases.

We developed and validated an allele-specific PCR method for detecting the nine main Escherichia coli phylogroup B2 lineages involved in extra-intestinal infections, which could be used as a substitute for multilocus sequence typing in studies for which the greater resolution at the sequence type level is not needed.