Primers and probes.

Table 3 indicates primers and probes designed for the 16S rRNA RT-qPCR, the primers described by Fyfe et al., and a re-designed hydrolysis probe used for the amplification, detection, and quantification of IS2404[9].aTF, forward primer; TR, reverse primer; TP2, hydrolysis probe (TibMolBiol, Berlin, Germany).b16S rRNA, gene for the ribosomal 16S RNA detected as 16S cDNA; IS2404, insertion sequence 2404.cNucleotide positions are provided for the first (IS2404) or single (16S rRNA) copy of the respective amplicon in M. ulcerans Agy99 (GenBank accession no. CP000325.1) as determined by BLASTN analysis within GenBank (NCBI) [13].dbp, base pairs.e6 FAM, 6-Carboxyfluorescein fluorescent dye; BBQ, BlackBerry Quencher.fPrimers T13 (forward) and T39 (reverse) were used for the amplification of a 935-bp region of the M. ulcerans 16S rRNA gene, encompassing the region amplified by qPCR primers MU16S TF and MU16S TR, to generate single copy replicates. Furthermore, these primers were used for sequencing of the M. ulcerans 16S rRNA gene (Table 1).