TABLE 1.

Primers used for amplification and sequencing and fluorogenic probes used for real-time PCR

Gene targetGenBank no.Forward and reverse primersaFluorogenic probeInternal primera
PositionbSequencePositionbSequencePositionbSequence
lasRD308134 (F)5′-GCCTTGGTTGACGGTTTTCTTG-3′4735′-GCGTAGTCCTTGAGCATCCA-3′
713 (R)5′-GTAATAAGACCCAAATTAACGGC-3′4545′-TGGATGCTCAAGGACTACGC-3′
2715′-TCCATCTACCAGACGCGAAAG-3′
532 (F)5′-ACCAGCTGGGAGAAGGAAG-3′5725′-CCGATGGCGCACCAC-3′
595 (R)5′-CCGATATCTCCCAACTGGTCTTG-3′
lasBcM19472363 (F)5′-TCGTTGCGATCATGGGTGT-3′
842 (R)5′-CGGGAATCAGGTAGGAGACG-3′
588 (F)5′-GCGAAGCCATCACCGAAGT-3′6465′-CCATTTCGTCGCCAACA-3′
713 (R)5′-CCTGCTCGGCGGATACC-3′
588 (F)5′-CGAGGCCATCACCGAAGT-3′6465′-CCATTTCGTCGCCAACA-3′
713 (R)5′-ACCTGCTCGGCGGAGAC-3′
aprAcX645585042 (F)5′-TTGCATTGAAAGGTCGTAGCGATG-3′5270
5813 (R)5′-GTGCGAGTGGTCAGGTTGGC-3′53735′-GGTGACGTCCGACCAGGAT-3′
5495 (F)5′-GGCAATCCTGGTACCTGATCAA-3′55265′-CAGCGCCAACGTCAA-3′
5554 (R)5′-AGGGTCTGGCGTCCGTAGTT-3′
5495 (F)5′-GCCAGTCCTGGTACCTGATCAA-3′55265′-CAGCGCCAACGTCAA-3′
5554 (R)5′-AGCGTCTGGCGTCCGTAGTT-3′
5495 (F)5′-GGCAATCCTGGTACCTGATCAA-3′55265′-CAGCGCCAACGTCAA-3′
5554 (R)5′-AGCGTCTGGCGCCCGTAGTT-3′
Small-subunit rDNAX06684485 (F)5′-CAACAGAATAAGCACCGGCTAA-3′5255′-CGCGGCTGCTGGCACGAA-3′
547 (R)5′-ACGCTTGCACCCTTCGTATTA-3′
  • a For each gene target, two primers, forward (F) and reverse (R), were used for amplification and sequencing, while the internal primer was used only for sequencing.

  • b The numbers indicate the position in the gene sequence, as published in GenBank (see the accession numbers in the GenBank column), corresponding to the nucleotide at the 5′ end of each forward, reverse, and internal primer and of each fluorogenic probe.

  • c For the lasB and aprA genes, different primers were chosen according to the strain to be amplified by real-time PCR.