Table 10 Primers for screening for genetic elements and resistance genes and for analysis for physical linkages among such elements and selected resistance genes
Target Gene/region | Primer name | 5'-3' sequence | Annealing Temperature | Expected product size (bp) | Gene accession Number |
|---|---|---|---|---|---|
Integrons | |||||
intI1 | INT-1 F | GTTCGGTCAAGGTTCTG | 50 | 923 | U12338 |
INT-1R | GCCAACTTTCAGCACATG | ||||
intI2 | INT-2 F | ATGTCTAACAGTCCATTTT | 50 | 450 | AJ001816.1 |
INT-2R | AAATCTTTAACCCGCAAAC | ||||
intI3 | INT3-F | GCAGGGTGTGGACGAATACG | 57 | 760 | AY219651 |
INT3-R | ACAGACCGAGAAGGCTTATG | ||||
3'-CS | qacED1 | ATCGCAATAGTTGGCGAAGT | 56 | 800 | X15370 |
sul1-B | GCAAGGCGGAAACCCGCGCC | X12869 | |||
integron class 1 VCR | In-F | GGCATACAAGCAGCAAGC | 52 | Variable | U12338 |
In-B | AAGCAGACTTGACCTGAT | ||||
integron 2 VCR | hep74 | CGGGATCCCGGACGGCATGCACGATTTGTA | 55 | Variable | EU780012 |
hep51 | GATGCCATCGCAAGTACGAG | AJ002782 | |||
IS elements | |||||
ISEcp1 | ISEcp1-F | GTT GCT CTG TGG ATA ACT TG | 55 | 180 | AJ242809 |
ISEcp1-R | CCT AAA TTC CAC GTG TGT | ||||
ISCR1 | ISCR1-F | CGC CCA CTC AAA CAA ACG | 55 | 469 | L06418 |
ISCR1-R | GAG GCT TTG GTG TAA CCG | ||||
IS26 | IS26-F | GCGGTAAATCGTGGAGTGAT | 55 | 704 | NC 007941.1 |
IS26-R | ATTCGGCAAGTTTTTGCTGT | ||||
Tn21 and Tn7 | |||||
tnpM of Tn21 | TnpM-F | TCAACCTGACGGCGGCGA | 55 | 348 | AF071413 |
TnpM-R | GGAGGTGGTAGCCGAGG | ||||
tnpR of Tn21 | TnpR-F | GTC AGC AGC TTC GAC CAG AA | 62 | 500 | NC 002134.1 |
TnpR-R | GAG GTA CTG GTA GAG GGT TT | ||||
tnpA of Tn21 | TnpA21-F | TGC GCT CCG GCG ACA TCT GG | 62 | 1200 | NC 002134.1 |
TnpA21-R | TCA GCC CGG CAT GCA CGC G | ||||
tnpA of Tn7 | TnA7-F | CCCAGCAATAAAAGAGCTCATTGAGCAAGC | 55 | 738 | FJ914220.1 |
TnA7-R | TATCTAGAAACAGAGTGTCTTG | ||||
(fluoro)quinolone resistance genes | |||||
qnrA | qnrA-F | TTCAGCAAGAGGATTTCTCA | 55 | 627 | AY070235 |
qnrA-R | GGCAGCACTATTACTCCCAA | ||||
qnrB | qnrB-F | CCTGAGCGGCACTGAATTTAT | 60 | 408 | DQ351241 |
qnrB-R | GTTTGCTGCTCGCCAGTCGA | ||||
qnrS | qnrS-F | CAATCATACATATCGGCACC | 60 | 641 | AB187515 |
qnrS-R | TCAGGATAAACAACAATACCC | ||||
aac(6′)-Ib-cr | aac(6′)-Ib-cr-F | TTGCGATGCTCTATGAGTGGCTA | 55 | 482 | AAL93141.1 |
aac(6′)-Ib-cr-R | CTCGAATGCCTGGCGTGTTT | ||||
aac(6′)-Ib-cr (sequencing) | CGTCACTCCATACATTGCAA | ||||
bla genes | |||||
blaTEM | TEM-F | ATGAGTATTCAACAT TTC CG | 55 | 840 | EF125012 |
TEM-R | CCAATGCTTAATCAG TGA GG | ||||
blaSHV | SHV-F | TTCGCCTGTGTATTATCTCCCTG | 50 | 854 | AF148850 |
SHV-R | TTAGCGTTGCCAGTGYTCG | ||||
blaCTX-M | CTX-M-F | ATGTGCAGYACCAGTAARGTKATGGC | 60 | 593 | Y10278 |
CTX-m-R | TGGGTRAARTARGTSACCAGAAYCAGCGG | ||||
blaCMY | CMY-F | ATGATGAAAAAATCGTTATGC | 55 | 1200 | U77414 |
CMY-R | TTGCAGCTTTTCAAGAATGCGC | ||||
blaOXA-1 | OXA-1 F | ATGAAAAACACAATACATATCAACTTCGC | 62 | 820 | JO2967 |
OXA-1R | GTGTGTTTAGAATGGTGATCGCATT | ||||
blaOXA-2 | OXA-2 F | ACGATAGTTGTGGCAGACGAAC | 62 | 602 | AF300985 |
OXA-2R | ATYCTGTTTGGCGTATCRATATTC | ||||