Table 1 The primers used in this study
Target gene description | Primer | Sequence 5’→3’ | Amplicon size (bp) | Annealing Temperature | References | |
|---|---|---|---|---|---|---|
K.pneumoniae | 16s-rRNA-F 16s-rRNA-R | 5-ATTTGAAGAGGTTGCAAACGAT-3 5-TTCACTCTGAAGTTTTCTTGTGTTC-3 | 130 | 54 | [15] | |
β-Lactamase ESBL+ | TEM-F TEM-R | 5-AAAGATGCTGAAGATCA-3 5-TTTGGTATGGCTTCATTC-3 | 425 | 44 | [18] | |
SHV-F SHV-R | 5-GCGAAAGCCAGCTGTCGGGC-3 5-GATTGGCGGCGCTGTTATCGC-3 | 304 | 62 | [18] | ||
CTX-M1-F CTX-M1-R | 5-AAGACTGGGTGTGGCATTGA-3 5-AGGCTGGGTGAAGTAAGTGA-3 | 670 | 52 | [18] | ||
CTX-M2-F CTX-M2-R | 5-CGACGCTACCCCTGCTATT-3 5-CCAGCGTCAGATTTTTCAGG-3 | 552 | 60 | [18] | ||
CTX-M8-F CTX-M8-R | 5-CGCTTTGCCATGTGCAGCACC-3 5-GCTCAGTACGATCGAGCC-3 | 307 | 55 | [18] | ||
CTX-M15-F CTX-M15-R | 5-CACACGTGGAATTTAGGGACT-3 5-GCCGTCTAAGGCGATAAACA-3 | 955 | 55 | [18] | ||
β-Lactamase AmpC+ | CMY-2-F CMY-2-R | 5′-GCACTTAGCCACCTATACGGCAG-3′ 5′-GCTTTTCAAGAATGCGCCAGG-3′ | 758 | 58 | [18] | |
Fox-F Fox-R | 5-AACATGGGGTATCAGGGAGATG-3 5-CAAAGCGCGTAACCGGATTGG-3 | 190 | 64 | [18] | ||
Mox-F Mox-R | 5-GCTGCTCAAGGAGCACAGGAT-3 5-CACATTGACATAGGTGTGGTGC-3 | 520 | 64 | [18] | ||
DHA-F DHA-R | 5-AACTTTCACAGGTGTGCTGGGT-3 5-CCGTACGCATACTGGCTTTGC-3 | 405 | 64 | [18] | ||
ACC-F ACC-R | 5-AACAGCCTCAGCAGCCGGTTA-3 5-TTCGCCGCAATCATCCCTAGC-3 | 346 | 64 | [18] | ||
CIT-F CIT-R | 5-TGGCCAGAACTGACAGGCAAA-3 5-TTTCTCCTGAACGTGGCTGGC-3 | 462 | 64 | [18] | ||
Carbapenemase | Ambler class A blactamases | KPC-F KPC-R | 5-CGTCTAGTTCTGCTGTCTTG-3 5-CTTGTCATCCTTGTTAGGCG-3 | 798 | 52 | [16] |
GES-F GES-R | 5-ATGCGCTTCATTCACGCAC-3 5-CTATTTGTCCGTGCTCAGG-3 | 846 | 52 | [17] | ||
Ambler class B metallo- β -lactamases (MBLs) | NDM-F NDM-R | 5-GGTTTGGCGATCTGGTTTTC-3 5-CGGAATGGCTCATCACGATC-3 | 621 | 52 | [16] | |
VIM-F VIM-R | 5-GATGGTGTTTGGTCGCATA-3 5-CGAATGCGCAGCACCAG-3 | 390 | 52 | [16] | ||
SIM-F SIM-R | 5-TACAAGGGATTCGGCATCG-3 5-TAATGGCCTGTTCCCATGTG-3 | 570 | 52 | [16] | ||
GIM-F GIM-R | 5-TCGACACACCTTGGTCTGAA-3 5-AACTTCTGGGTACGCAAACG-3 | 477 | 52 | [16] | ||
SPM-F SPM-R | 5-AAAATCTGGGTACGCAAACG-3 5-ACATTATCCGCTGGAACAGG-3 | 271 | 52 | [16] | ||
IMP-F IMP-R | 5-GGAATAGAGTGGCTTAAYTCTC-3 5-GGTTTAAYAAAACAACCACC-3 | 232 | 52 | [16] | ||
Ambler class D b-lactamases | Oxa-48-F Oxa-48-R | 5-GCGTGGTTAAGGATGAACAC-3 5-CATCAAGTTCAACCCAACCG-3 | 438 | 52 | [16] | |
Fluoroquinolone | gyrA-F gyrA-R | 5-AAATCTGCCCGTGTCGTTGGT-3 5-GCCATACCTACGGCGATACC-3 | 344 | 55 | [19] | |
parC-F parC-R | 5-CTGAATGCCAGCGCCAAATT-3 5-GCGAACGATTTCGGATCGTC-3 | 168 | 55 | [19] | ||
qnrS-F qnrS-R | 5-TGGAAACCTACAATCATACATATCG-3 5-TTAGTCAGGATAAACAACAATACCC-3 | 656 | 60 | [19] | ||
qnrA-F qnrA-R | 5-GATAAAGTTTTTCAGCAAGAGG-3 5-ATCCAGATCGGCAAAGGTTA-3 | 593 | 60 | [19] | ||
qnrB-F qnrB-R | 5-GTTGGCGAAAAAATTGACAGAA-3 5-ACTCCGAATTGGTCAGATCG-3 | 264 | 53 | [19] | ||
Tetracycline | tetA-F tetA-R | 5-GTGAAACCCAACATACCCC-3 5-GAAGGCAAGCAGGATGTAG-3 | 888 | 55 | [20] | |
tetB-F tetB-R | 5-CCTTATCATGCCAGTCTTGC-3 5-ACTGCCGTTTTTTCGCC-3 | 774 | 55 | [20] | ||
Integrase1 | Int1-F Int1-R | 5-CAGTGGACATAAGCCTGTTC-3 5-CCCGAGGCATAGACTGTA-3 | 160 | 55 | [21] | |
Integrase2 | Int2-F Int2-R | 5-TTGCGAGTATCCATAACCTG-3 5-TTACCTGCACTGGATTAAGC-3 | 288 | 55 | [21] | |
Integrase3 | Int3-F Int3-R | 5-GCCTCCGGCAGCGACTTTCAG-3 5-ACGGATCTGCCAAACCTGACT-3 | 979 | 59 | [21] | |
Sulfonamide resistance | Sul1-F Sul1-R | 5-TCACCGAGGACTCCTTCTTC-3 5-CAGTCCGCCTCAGCAATATC-3 | 331 | 65 | [18] | |
Sul2-F Sul2-R | 5-CCTGTTTCGTCCGACACAGA-3 5-GAAGCGCAGCCGCAATTCAT-3 | 435 | 58 | [18] | ||
Quaternary ammonium compounds | qac-F qac-R | 5-GCCCTACACAAATTGGGAGA-3 5-CTGCGGTACCACTGCCACAA-3 | 370 | 55 | [22] | |