Table 1 Oligonucleotides used in this study
Target Gene |  | Nucleotide Sequence (5’- 3’) | Amplicon size (bp) | Annealing Temp (°C) | Reference | |
|---|---|---|---|---|---|---|
1. β-lactam resistance encoding genes | ||||||
1.1. ESBLs encoding genes | ||||||
Class A β-lactamases | ||||||
blaSHV | Fw | ACTATCGCCAGCAGGATC | 356 | 53.5 | 59 | |
Rv | ATCGTCCACCATCCACTG | |||||
blaTEM | Fw | GATCTCAACAGCGGTAAG | 786 | 54 | 59 | |
Rv | CAGTGAGGCACCTATCTC | |||||
blaCTX−M | Fw | ATGTGCAGYACCAGTAARGT | 593 | 50 | 60 | |
Rv | TGGGTRAARTARGTSACCAGA | |||||
blaGES (GES-1 to GES-9 and GES-11) | Fw | AGTCGGCTAGACCGGAAAG | 399 | 60 | 61 | |
Rv | TTTGTCCGTGCTCAGGAT | |||||
blaPER (PER-1 & PER-3) | Fw | GCTCCGATAATGAAAGCGT | 520 | 60 | 61 | |
Rv | TTCGGCTTGACTCGGCTGA | |||||
blaVEB (VEB-1 to VEB-6) | Fw | CATTTCCCGATGCAAAGCGT | 648 | 60 | 61 | |
Rv | CGAAGTTTCTTTGGACTCTG | |||||
Class D β-lactamases | ||||||
blaOXA-1-like(OXA-1, OXA-4 & OXA-30) | Fw | GGCACCAGATTCAACTTTCAAG | 564 | 58 | 61 | |
Rv | GACCCCAAGTTTCCTGTAAGTG | |||||
1.2. AmpC encoding genes (Class C A β-lactamases) | ||||||
blaAmpC | Fw | ACACGAGTTTGCATCGCCTG | 254 | 68 | 62 | |
Rv | CTGAACTTACCGCTAAACAGTGGAAT | |||||
blaCIT−M | Fw | TGGCCAGAACTGACAGGCAAA | 462 | 55 | 62 | |
Rv | TTTCTCCTGAACGTGGCTGGC | |||||
blaFox−1 | Fw | GCAAACCAGCAATACCATCCA | 642 | 60 | 62 | |
Rv | GCTCACCTTGTCATCCAGCTC | |||||
blaACC−1 | Fw | AGCTGTTATCCGTGATTACCTGTCT | 248 | 60 | 62 | |
Rv | AGCGAACCCACTTCAAATAACG | |||||
blaACT−1 | Fw | CATGCTGGATCTGGCAACCT | 343 | 60 | 62 | |
Rv | CTTCAGCGTCCAGCATTCCT | |||||
blaFOX (FOX-1 to FOX-5) | Fw | CTACAGTGCGGGTGGTTT | 162 | 55 | 61 | |
Rv | CTATTTGCGGCCAGGTGA | |||||
blaMOX (MOX1, MOX2, CMY-CMY-8 to CMY 11 and CMY19) | Fw | GCAACAACGACAATCCATCCT | 895 | 60 | 61 | |
Rv | GGGATAGGCGTAACTCTCCCAA | |||||
1.3. Carbapenemases encoding genes | ||||||
Class A (Serine enzymes) | ||||||
blaKPC (KPC-1 to KPC-5) | Fw | CATTCAAGGGCTTTCTTGCTGC | 538 | 55 | 61 | |
Rv | ACGACGGCATAGTCATTTGC | |||||
Class B (MBLs) | ||||||
blaIMP | Fw | CATGGTTTGGTGGTTCTTGT | 448 | 57 | 55 | |
Rv | ATAATTTGGCGGACTTTGGC | |||||
blaVIM−1 | Fw | TGTTATGGAGCAGCAACGATG | 920 | 56 | 63 | |
Rv | AAAGTCCCGCTCCAACGATT | |||||
blaNDM−1 | Fw | GGTTTGGCGATCTGGTTTTC | 621 | 52 | 64 | |
Rv | CGGAATGGCTCATCACGATC | |||||
Class D (Oxacillinases) | ||||||
blaOXA−48−like | Fw | GCTTGATCGCCCTCGATT | 281 | 57 | 61 | |
Rv | GATTTGCTCCGTGGCCGAAA | |||||
2. Quinolones resistance encoding genes | ||||||
qnrA (qnrA1 to qnrA6) | Fw | AGAGGATTTCTCACGCCAGG | 580 | 60 | 65 | |
Rv | TGCCAGGCACAGATCTTGAC | |||||
qnrB (qnrB1 to qnrB6) | Fw | GGMATHGAAATTCGCCACTG | 264 | 60 | 66 | |
Rv | TTTGCYGYYCGCCAGTCGAA | |||||
qnrS (qnrS1 to qnrS2) | Fw | GCAAGTTCATTGAACAGGCT | 428 | 60 | 65 | |
Rv | TCTAAACCGTCGAGTTCGGCG | |||||
qnr C | Fw | GGGTTGTACATTTATTGAATC | 447 | 55 | 67 | |
Rv | TCCACTTTACGAGGTTCT | |||||
qnr D | Fw | CGAGATCAATTTACGGGGAATA | 582 | 55 | 67 | |
Rv | AACAAGCTGAAGCGCCTG | |||||
qepA | Fw | CGTGTTGCTGGAGTTCTTC | 403 | 52 | 68 | |
Rv | CTGCAGGTACTGCGTCATG | |||||
oqxA | Fw | GACAGCGTCGCACAGAATG | 339 | 57 | 69 | |
Rv | GGAGACGAGGTTGGTATGGA | |||||
oqxB | Fw | CGAAGAAAGACCTCCCTACCC | 240 | 57 | 69 | |
Rv | CGCCGCCAATGAGATACA | |||||
aac(6')-Ib-cr | Fw | TTGCGATGCTCTATGAGTGGCTA | 482 | 60 | 70 | |
Rv | CTCGAATGCCTGGCGTGTTT | |||||
3. Integrons and Variable regions | ||||||
Integrons constant regions | ||||||
IntI1 | Fw | GGTCAAGGATCTGGATTTCG | 483 | 58 | 71 | |
Rv | ACATGCGTGTAAATCATCGTC | |||||
IntI2 | Fw | CACGGATATGCGACAAAAAGGT | 788 | 58 | 71 | |
Rv | GTAGCAAACGAGTGACGAAATG | |||||
Variable region of integron I | ||||||
5’CS | Fw | GGCATCCAAGCAGCAAG | Variable | 58 | 71 | |
3’CS | Rv | AAGCAGACTTGACCTGA | ||||
Variable region of integron II | ||||||
attI2 | Fw | GACGGCATGCACGATTTGTA | Variable | 58 | 71 | |
orfX | Rv | GATGCCATCGCAAGTACGAG | ||||
4. Molecular Identification | ||||||
UreC | Fw | GTTATTCGTGATGGTATGGG | 317 | 56.2 | 58 | |
Rv | ATAAAGGTGGTTACGCCAGA | |||||
5. Molecular Typing | ||||||
ERIC-2 typing | 2 | AAGTAAGTGACTGGGGTGAGCG | Variable | 48 | 73 | |