Primers and probes used in this study.

1The nucleotide numbering refers to the numbering from the Tohama I genome [19]. Segment accession numbers: BX640414 (prn), BX640422 (ptxP, ptxA, ptxB), BX640416 (fimD and bvgS) and BX640414 (tcfA).
2The “colder”primer forming only two hydrogen bonds at the specific base has a one base extension at its 5´-end to compensate the reduced Tm.
A, Primers prnAF (top) and prnAR (bottom) [14] were used for prn sequencing. B,C-1, ARMS-qPCR primers for the determination of the ptxA, ptxB, fimD, bvgS and tcfA alleles (B) as well as for the discrimination between the ptxP1-like and ptxP3 alleles (C-1). For each gene, the forward primer is shown on top, then the reverse primer corresponding to the Tohama I sequence and the reverse primer corresponding to the alternative allele, with the base at the SNP site underlined, and finally the labelled hydrolysis probe. Lower case letters, artificial base replacement with both sequences at the SNP site; FAM, 6-carboxyfluorescein; TET, 4,5,6,7-tetrachlorofluorescein; BHQ1, Black Hole Quencher-1; Cy5, red sulfoindocyanine dye. C-2, oligonucleotides for the fimD non-discriminatory control assay.