TABLE 2.
Primers used in this study
| Primera | Sequence (5′-3′) | Target regionb | PCR
|
Reference | |
|---|---|---|---|---|---|
| No.c | Size (bp) | ||||
| U9-L1 (+) | TACTACAAGCAGATAACGCC | 2771-3679 | St1 | 909 | 13 |
| P1-R1 (−) | TAGAAACGACAAAGCGCGTG | 13 | |||
| P134-L2 (+) | TGACCCAATTCCAAAGCCAC | 16784-17839 | St4 | 1,490 | 13 |
| P134-R1 (−) | GTGTTTGGGCAAGATCCCAG | 13 | |||
| StGP21 (+) | ATAACGGCAGGTTCCGGTTC | 20173-21108 | St5 | 936 | 13 |
| StGP6 (−) | CGATGAAGCGCACAAATTTG | 13 | |||
| StGP24 (+) | TCAAGATTCCTATCTGCAGG | 24363-25201 | St6 | 838 | 13 |
| StGP28 (−) | AGAGTTACTAGACCAAGCGC | 13 | |||
| LJ-R1 (−) | AGTTCTAAAGGTTCGTAGTCG | int | 1 | 500 | 3 |
| PmLJ1 (+) | ACACCTACAACAAGGCTATC | thdF of P. mirabilis | 1 | 500 | This study |
| 23 | 348 | ||||
| 104RJ (+) | CTGACGAGCTGAAGCGAATTG | S044 | 2 | 476 | 3 |
| PmRJ1 (−) | GATGCACACTGAGTTGATAG | hipB of P. mirabilis | 2 | 476 | This study |
| 23 | 348 | ||||
| 5′-CS (+) | GGCATCCAAGCAGCAAGC | 5′-CS region | 3 | Variabled | 10 |
| 3′-CS (−) | AAGCAGACTTGACCTGAT | 3′-CS region | 3 | Variabled | 10 |
| tetG-1s (+) | GCTCGGTGGTATCTCTGCTC | tet(G) | 4 | 468 | 15 |
| tetG-2s (−) | AGCAACAGAATCGGGAACAC | tet(G) | 4 | 468 | 15 |
| StCm-L (+) | CACGTTGAGCCTCTATATGG | floR | 5 | 888 | 2 |
| StCm-R (−) | ATGCAGAAGTAGAACGCGAC | floR | 5 | 888 | 2 |
| F4 (+) | TTCCTCACCTTCATCCTACC | floR | 6 | 599 | 6 |
| F6 (−) | TTGGAACAGACGGCATGG | tetR | 6 | 599 | 6 |
| MDR-13 (+) | TCCCGATTCTGTTGCTGCTTG | tet(G) | 7 | 1,078 | This study |
| MDR-B3 (−) | AAGCATGGCTGCTGACAAC | orf1 | 7 | 1,078 | This study |
| floR-R1 (−) | TCAACGTGAGTTGGATCATAG | floR | 8 | 1,430 | This study |
| MDR-5 (+) | TAGGTATGGGGCTCATAATTG | qacEΔ1 | 8 | 1,430 | This study |
| 104-D4 (+) | ATGCCTAGCATTCACCTTCC | sulI | 9 | 1,183e | This study |
| DB-B4 (−) | ATCACATCACCCTGGAAATGG | IS6100 | 9 | 1,183e | This study |
| 21 | 2,954e | ||||
| 22 | 2,642e | ||||
| DB-T1 (+) | TGCCACGCTCAATACCGAC | IS6100 | 10 | 930 | 2 |
| DB-B6 (−) | CTGTGCCTTCTTGCGAGC | S044 | 10 | 930 | This study |
| StGP-23 (+) | CCTTGGTACGTTCGCTAATC | res | 11 | 1,417 | This study |
| 16 | 1,848 | ||||
| 20 | 2,262 | ||||
| int-R (−) | GCCTTGCTGTTCTTCTACGG | intI1 | 11 | 1,417 | This study |
| AadA2-L (+) | TGTTGGTTACTGTGGCCG | aadA2 | 12 | 538 | 15 |
| AadA2-R2 (−) | TGCTTAGCTTCAAGTAAGACG | aadA2 | 12 | 538 | 3 |
| 15 | 1,316, 2,360f | ||||
| MDR-20 (+) | TAGTTCAAAGTTTCAGCAAG | blaPSE-1 | 13 | 765 | This study |
| 17 | 1,751, 2,608g | ||||
| PSE-R2 (−) | ACAATCGCATCATTTCGCTC | blaPSE-1 | 13 | 765 | 3 |
| PSE-R3 (−) | CTGAAACTTTGAACTACTTGC | blaPSE-1 | 14 | 935 | This study |
| MDR-19 (−) | AACCGGATCAGAAATCCATGC | groEL/int | 14 | 935 | This study |
| 19 | 1,254 | ||||
| MDR-1 (+) | TGATCGAAATCCAGATCCTG | intI1 | 15 | 1,316, 2,360f | This study |
| AadA2-R3 (−) | GGTTCGAAATTTCGATGGTC | aadA2 | 16 | 1,848 | This study |
| QS-2 (−) | TGAGTGCATAACCACCAGCC | sul1 | 17 | 1,751, 2,608g | 3 |
| dfrA1-F (+) | CGAAGAATGGAGTTATCGG | dfrA1 | 18 | 919 | 11 |
| orfC-R (−) | TCTCGAATCAAGCAGGAACC | orfC | 18 | 919 | 11 |
| dfrA1-R (−) | TTAGAGGCGAAGTCTTGG | dfrA1 | 19 | 1,254 | 11 |
| 20 | 2,262 | ||||
| orfC-F (+) | CATTACGAAGCGAA GCACC | orfC | 21 | 2,954e | 11 |
| PSE-D1 (+) | AGAGCGAAATGATGCGATTG | blaPSE-1 | 22 | 2,642e | This study |
| Ag5 (−) | ACAAACGACAAGCCACGT | orf513 | Negh | 750 | This study |
| Ag6 (+) | TATCGTCTATCGTACACTCTC | orf513 | Negh | 750 | This study |
b
Coordinates are from SGI1 (accession no. AF261825), and genes are as shown in Fig. 2.
c
PCR numbers as shown in Fig. 2.
d
Size varies depending on number of cassettes in this region.
e
Size would be ∼2.9 kb larger if this region contained common region 1 (CR1) and dfrA10 as found in some SGI1 variants (2, 14).
f
Size was 1,316 bp in SGI1 but 2,360 bp in P. mirabilis C04014.
g
Size was 1,751 bp in SGI1 but 2,608 bp in P. mirabilis C04014.
h
PCR with Ag5/Ag6 primers was negative for all strains tested but would be expected to give a product of 750 bp if CR1 was present.