Table 2. Primer and probe sequences for qPCR.
| Gene | Primer/Probe name | Sequence | Start/end | Concentration (nM) | Reference |
|---|---|---|---|---|---|
| porA | porA_fwd_1 | GCC GGC GTT GAT TAT GAT TT | 1126–1145 | 600 | Present study |
| porA_rev_1 | AGT TGC CGA TGC CGG TAT T | 1210–1192 | 600 | ||
| porA_Pb_1 FAM (MGB) | CTT CCG CCA TCG TGT C | 1157–1172 | 200 | ||
| sodC | Nm sodC FWd 351 | GCA CAC TTA GGT GAT TTA CCT GCA T | 446–470 | 600 | Dolan, T, 2011 |
| Nm sodC Rev 478 | CCA CCC GTG TGG ATC ATA ATA GA | 551–573 | 600 | ||
| sodC Pb387 NED (MGB) | CAT GAT GGC ACA GCA A | 482–497 | 100 | Present study | |
| galE/cnl/tex | cnl_fwd_2 | GAA TTG CAT AGG TTA TCC AAA ATC AC | 110–85 | 900 | Present study |
| cnl_fwd_2b | GAG TTG CAC AGA TTA TCC AGA ATC AC | 110–85 | 900 | ||
| cnl_rev_4 | TTT GCC CGA TAC AAT CTG AAA G | 85–106 | 900 | ||
| cnl_Pb_2 VIC (MGB) | ATA AAA CCG GTG CCG CC | 38–22 | 250 | ||
| csw/synG | F857 | TAT TTA TGG AAG GCA TGG TGT ATG | 935–958 | 600 | Wang, X, 2011 |
| R964 | TTG CCA TTC CAG AAA TAT CAC C | 1063–1042 | 600 | ||
| Pb907i FAM (BHQ) | AAA TAT GGA GCG AAT GAT TAC AGT AAC TAT AAT GAA | 985–1020 | 200 | ||
| csaB/sacB | F2531 | AAA ATT CAA TGG GTA TAT CAC GAA GA | 934–959 | 900 | Mothershed, EA, 2004 |
| R2624 | ATA TGG TGC AAG CTG GTT TCA ATA G | 1025–1001 | 900 | ||
| Pb2591i HEX (BHQ) | CTA AAA GTA GGA AGG GCA CTT TGT GGC ATA AT | 992–961 | 250 | ||
| csxB/xcbB | F173 | TGT CCC CAA CCG TTT ATT GG | 429–448 | 900 | Mothershed, EA, 2004 |
| R237 | TGC TGC TAT CAT AGC CGC C | 493–475 | 900 | ||
| Pb196 CY5 (BHQ) | TGT TTG CCC ACA TGA ATG GCG G | 452–473 | 250 | ||
| csb/synD | F737 | GCT ACC CCA TTT CAG ATG ATT TGT | 737–760 | 900 | Wang, X, 2011 |
| R882 | ACC AGC CGA GGG TTT ATT TCT AC | 905–883 | 900 | ||
| Pb839i CY5 (BHQ) | AAG AGA TGG GYA ACA ACT ATG TAA TGT CTT TAT TT | 839–873 | 250 | ||
| csc/synE | F478 | CCC TGA GTA TGC GAA AAA AAT T | 591–612 | 600 | Mothershed, EA, 2004 |
| R551 | TGC TAA TCC CGC CTG AAT G | 664–646 | 600 | ||
| Pb495i FAM (BHQ) | TTT CAA TGC TAA TGA ATA CCA CCG TTT TTT TGC | 612–644 | 200 | ||
| csy/synF | F787 | TCC GAG CAG GAA ATT TAT GAG AAT AC | 865–890 | 900 | Wang, X, 2011 |
| R929 | TTG CTA AAA TCA TTC GCT CCA TAT | 1010–987 | 900 | ||
| Pb1099i HEX (BHQ) | TAT GGT GTA CGA TAT CCC TAT CCT TGC CTA TAA T | 948–981 | 250 | ||
| cseE/cap29eF | cseE-2_Fwd1 | GAGGCTGGCAATGACCAATT | 470–488 | 600 | Present study |
| cseE-2_Rev1 | CCCAGCATATCGACAACCAA | 548–529 | 600 | ||
| cseE-2_Pb1 FAM (MGB) | ATCTTATGTGAACGTGGCGC | 490–509 | 200 | ||
| cszC/capZD | cszC-1_Fwd1 | CAG GCC GAA GAG CGT TAT CA | 895–914 | 900 | Present study |
| cszC-1_Rev1 | CGC CAT TCA GGG CGA TT | 950–934 | 900 | ||
| cszC-1_Pb1 NED (MGB) | ACA GCT CTG GCC TTA G | 916–931 | 250 | ||
| cshC | cshC-1_Fwd1 | AAG CCC GTT CCA AGA TCA TG | 1491–1510 | 600 | Present study |
| cshC-1_Rev1 | GCG GTT TGG AGA AAT AAT ATG TGT T | 1563–1539 | 600 | ||
| cshC-1_Pb1 VIC (MGB) | AAT GTC AGC CGT AAC TT | 1513–1529 | 200 |
Sequences, positions and concentrations of primers and probes used in the 4 multiplexes, MGB: Minor Groove Binding/ BHQ: Black Whole Quencher, are two different types of Quencher. The probes obtained from CDC had a BHQ while the ones designed for this study the MGB quencher. In bold are base pairs that showed a mismatch with at least one of the alleles present in pubMLST, but not with the majority of them.