Table 2. PCR primer and probe sequences.
| Primers | Gene target | Sequence (5’ 3’) | Ann. temp(°C) | Amplicon size (bp) | GenBank access. no. a | Reference |
|---|---|---|---|---|---|---|
| FP_TETA_2 | tet(A) | TTGGCATTCTGCATTCACTC | 60 | 125 (840–974) | X00006 | This study |
| RP_TETA_2 | GAAGGCAAGCAGGATGTAGC | 60 | ||||
| PR_TETA_2 | GATCACCGGCCCTGTAGCCG | |||||
| FP_TETB_Aminov b | tet(B) | TTACGTGAATTTATTGCTTCGG | 60 | 206 (913–1119) | EF646764 | [28] and this study |
| RP_TETB_Aminov | ATACAGCATCCAAAGCGCAC | 60 | ||||
| PR_TETB_Aminov_own | CGCCGACCAAATCGGTCAGA | |||||
| FP_TETC_6 | tet(C) | GCCAGTCACTATGGCGTGCT | 60 | 120 (124–244) | EU751613 | This study |
| RP_TETC_6 | CAAGTAGCGAAGCGAGCAGG | 60 | ||||
| PR_TETC_6 | ACTGTCCGACCGCTTTGGCC | |||||
| FP_TETM_7 | tet(M) | CAACGAGGACGGATAATACGC | 60 | 191 (119–311) | X92947 | This study |
| RP_TETM_7 | CCATCTTTTGCAGAAATCAGTAGA | 60 | ||||
| PR_TETM_7 | GGTGAACATCATAGACACGCCAGGA | |||||
| FP_TETO_Böck | tet(O) | AAGAAAACAGGAGATTCCAAAACG | 60 | 75 (607–682) | AY660531 | [29] |
| RP_TETO_Böck | CGAGTCCCCAGATTGTTTTTAGC | 60 | ||||
| PR_TETO_Böck | ACGTTATTTCCCGTTATCACGGAAGCG | |||||
| FP_TETW_Smith | tet(W) | GCAGAGCGTGGTTCAGTCT | 60 | 66 (411–476) | AJ222769 | [30] |
| RP_TETW_Smith | GACACCGTCTGCTTGATGATAAT | 60 | ||||
| PR_TETW_Smith | TTCGGGATAAGCTCTCCGCCGA | |||||
| FP_SUL1_2 | sulI | ACGAGATTGTGCGGTTCTTC | 60 | 159 (440–598) | EU056266 | This study |
| RP_SUL1_2 | CCGACTTCAGCTTTTGAAGG | 60 | ||||
| PR_SUL1_2 | ACCGGCTCATCCTCGATCCG | |||||
| FP_SUL2_3 | sulII | GATATTCGCGGTTTTCCAGA | 60 | 141 (313–453) | AY360321 | This study |
| RP_SUL2_3 | CGCAATGTGATCCATGATGT | 60 | ||||
| PR_SUL2_3 | AAGACGGGCAGGCAGATCGG | |||||
| FP_ERMB_Böck | ermB | GGATTCTACAAGCGTACCTTGGA | 60 | 86 (390–476) | AB563188 | [29] |
| RP_ERMB_Böck b | TGGCAGCTTAAGCAATTGCT | 60 | ||||
| PR_ERMB_Böck | CACTAGGGTTGCTCTTGCACACTCAAGTC | |||||
| FP_ERMF_KNAPP | ermF | TCGTTTTACGGGTCAGCACTT | 60 | 182 (24–205) | M14730;M17124;M17808;M62487 | [11] and this study |
| RP_ERMF_KNAPP | CAACCAAAGCTGTGTCGTTT | 60 | ||||
| PR_ERMF_OWN | ATATTGGGGCAGGCAAGGGGTT | |||||
| FP_vanA_Böck | vanA | CTGTGAGGTCGGTTGTGCG | 60 | 64 (614–705) | AF516335 | [29] |
| RP_vanA_Böck | TTTGGTCCACCTCGCCA | 60 | ||||
| PR_vanA_Böck | CAACTAACGCGGCACTGTTTCCCAAT | |||||
| FW3_SHV_lahey | bla SHV family | GCTGGAGCGAAAGATCCACT | 60 | 247 (258–504) | All available at http://www.lahey.org/Studies/ | [31] and this study |
| RV5_SHV_lahey | CGCCTCATTCAGTTCCGTTT | 60 | ||||
| Pr_SHV_Lahey2 | AYGTCACCCGCCTTGACCGC | |||||
| FW3_CMY-2_Lahey | bla CMY-2 | AGACGTTTAACGGCGTGTTG | 60 | 127 (260–387) | All available at http://www.lahey.org/Studies/ | [31] and this study |
| RV4_CMY-2_Lahey | TAAGTGCAGCAGGCGGATAC | 60 | ||||
| PR_CMY-2_Lahey | TATCGCCCGCGGCGAAAT | |||||
| FW_CTX-M-1 | bla CTX-M-1group | ATGTGCAGYACCAGTAARGTKATGGC | 58 | 335 | X92506 | [32] |
| RV_CTX-M-1 | ATCACKCGGRTCGCCXGGRAT | 58 | ||||
| PR_CTX-M-1 | CCCGACAGCTGGGAGACGAAACGT | |||||
| FW_SMI_114 | 16S rDNA | CGCGAAGAACCTTACC | 60 | 126 (916–1041) | NA | The Public Health Agency of Sweden |
| R_SMI_115 | ACTTAACCCAACATTTCAC | 60 | ||||
| PR_SMI_116 | CACGAGCTGACGACAGCC |
Forward primer = FP; Reverse primer = RP; Probe = PR, gene targets, annealing temperatures (Ann. temp.), amplicon lengths in base pairs (bp), and GenBank sequence accession number (GenBank access. no.).
a GenBank accession numbers for previously published primers and/or probes. For primers and probes designed in this study, a GenBank accession number representative of those included in the sequence alignments is given.
b Primer modified to fit assay in the present study.