Table 3.
Oligonucleotides used for the detection of antibiotic resistance genes.
| Primer | Antibiotic | Sequence (5′ → 3′) | GenBank | Amplicon size [bp] | Annealing | References |
|---|---|---|---|---|---|---|
| Acc. No. | temperature | |||||
| [◦C] | ||||||
| aac6-aph2a fw | gentamicin | GCCAGAACATGAATTACACGAG | NC_005024 | 610 | 56 | Schiwon et al., 2013 |
| aac6-aph2a rev | CTGTTGTTGCATTTAGTCTTTCC | |||||
| aadD_pSK41 fw | kanamycin | TGTCGTTCTGTCCACTCCTG | AF051917 | 525 | 62 | Schiwon et al., 2013 |
| aadD_pSK41 rev | ATGAATGGACAACCGGTGAG | |||||
| ampC fw | ampicillin | GTGACCAGATACTGGCCACA | AJ005633 | 821 | 55 | Schiwon et al., 2013 |
| ampC rev | TTACTGTAGCGCCTCGAGGA | |||||
| aph(2)-Ib fw | gentamicin | AGGATGCCCTTGCATATGATGAAGCGACGT | AF207840 | 449 | 56 | Schiwon et al., 2013 |
| aph(2)-Ib rev | ATCAGCATAAGGCGCCGGAAGTAGCAGAAA | |||||
| aph(2)-Ic fw | gentamicin | AGCATACAATCCGTCGAGTCGCTTGGTGAG | U51479 | 641 | 56 | Schiwon et al., 2013 |
| aph(2)-Ic rev | CTGGCGCTGCAACTTGCTGAGTTCATGAAT | |||||
| aph(2)-Id fw | gentamicin | GTGGTTTTTACAGGAATGCCATC | AF016483 | 134 | 56 | Schiwon et al., 2013 |
| aph(2)-Id rev | CCCTCTTCATACCAATCCATATAACC | |||||
| aph3-III fw | kanamycin | CCGCTGCGTAAAAGATAC | X92945 | 592 | 56 | Schiwon et al., 2013 |
| aph3-III rev | GTCATACCACTTGTCCGC | |||||
| blaSHV-5 fw | ß-lactams | TGTTAGCCACCCTGCCGCT | 825 | 60 | Schiwon et al., 2013 | |
| blaSHV-5 rev | GTTGCCAGTGCTCGATCAG | |||||
| blaZ fw | ß-lactams | TTAAAGTCTTAC CGAAAGCAG | AB245468 | 777 | 60 | Sidhu et al., 2002 |
| blaZ rev | TAAGAGATTTGC CTATGCTT | |||||
| ermA fw | erythromycin | ACGATATTCACGGTTTACCCACTTA | WP_001072201 | 584 | 58 | Khan et al., 1999 |
| ermA rev | AACCAGAAAAACCCTAAAGACACG | |||||
| ermB fw | erythromycin | GCATTTAACGACGAAACTGGCT | U00453 | 572 | 56 | Schiwon et al., 2013 |
| ermB rev | GACAATACTTGCTCATAAGTAATGGT | |||||
| ermC fw | erythromycin | CGTAACTGCCATTGAAATAGACC | V01278 | 519 | 58 | Schiwon et al., 2013 |
| ermC rev | TCCTGCATGTTTTAAGGAATTG | |||||
| ermD fw | erythromycin | CGGGCAAATATTAGCATAGACG | M29832 | 463 | 56 | Schiwon et al., 2013 |
| ermD rev | ATTCTGACCATTGCCGAGTC | |||||
| ermG fw | erythromycin | TGCAGGGAAAGGTCATTTTAC | M15332 | 483 | 56 | Schiwon et al., 2013 |
| ermG rev | AACCCATTTCATTACAAAAGTTTC | |||||
| mecA fw | methicillin | TAATAGTTGTAGTTGTCGGGTTTG | X52593 | 707 | 60 | Schiwon et al., 2013 |
| mecA rev | TAACCTAATAGATGTGAAGTCGCT | |||||
| qnrB (B1, B7) fw | fluoroquinolone | AGCGGCACTGAATTTAT | 497 | 56 | Broszat, 2014 | |
| qnrB (B1, B7) rev | GTTTGCTGCTCGCCAGTC | |||||
| qnrS1 fw | fluoroquinolone | GGAAACCTACAATCATACATA | 600 | 56 | Broszat, 2014 | |
| qnrS1 rev | GTCAGGATAAACAATACC | |||||
| sul1 fw | sulfamethoxazole | CACCGGAAACATCGCTGCA | 158 | 60 | Broszat, 2014 | |
| sul1 rev | AAGTTCCGCCGCAAGGCT | |||||
| sul2 fw | sulfamethoxazole | CTCCGATGGAGGCCGGTAT | 190 | 60 | Broszat, 2014 | |
| sul2 rev | GGGAATGCCATCTGCCTTGA | |||||
| tetK_pT181 fw | tetracycline | TTTGAGCTGTCTTGGTTCATTG | CP000045 | 539 | 55 | Schiwon et al., 2013 |
| tetK_pT181 rev | AGCCCACCAGAAAACAAACC | |||||
| tetL | tetracycline | CATTTGGTCTTATTGGATCG | AY081910 | 475 | 55 | Schiwon et al., 2013 |
| tetL | ATTACACTTCCGATTTCGG | |||||
| tetM fw | tetracycline | GAACTCGAACAAGAGGAAAGC | M85225 | 729 | 55 | Schiwon et al., 2013 |
| tetM rev | ATGGAAGCCCAGAAAGGAT | |||||
| tetO fw | tetracycline | GGATGGCATACAGGCACAGA | M18896 | 737 | 55 | Schiwon et al., 2013 |
| tetO rev | GTTTGGATCATAGGGAGAGGAT | |||||
| tetS fw | tetracycline | TGGTCAACGGCTTGTCTATG | X92946 | 546 | 55 | Schiwon et al., 2013 |
| tetS rev | AGCCCAGAAAGGATTTGGAG |
Reference strain for bla-SHV-5, K. pneumoniae DSM13661; sul1, E. coli Hm06-20; sul2, E. coli PS84.