TABLE 1.
Primers used in PCR and DNA sequencing
| Target and primera | No.b | Sequence (5′-3′) | Reference |
|---|---|---|---|
| qnr genes | |||
| qnrA or -C (screening) | |||
| qnr-F | TCAGCAAGAGGATTTCTCA | This study | |
| qnr-R | GGCAGCACTATTACTCCCA | ||
| qnrS (screening) | |||
| qnrS-F | ACGACATTCGTCAACTGCAA | 6 | |
| qnrS-R | TAAATTGGCACCCTGTAGGC | ||
| qnrB (screening) | |||
| qnrB-F | 1 | CCGACCTGAGCGGCACTGA | This study |
| qnrB-R | 2 | CGCTCCATGAGCAACGATGCCT | |
| qnrB10 (complete gene)c | |||
| qnrB-Met-F | ATGTTGTCATTACTGTATA | This study | |
| qnrB-STOP-R | CTAACCAATCACAGCGATG | ||
| Complex class 1 integrons | |||
| intI1 | |||
| Inti1-R | 3 | TTCGAATGTCGTAACCGC | 11 |
| Inti1-F | CGAGGCATAGACTGTAC | ||
| Sulpro3 (F) | 4 | GCCTGACGATGCGTGGA | 8 |
| vr-1 | |||
| 5′CS (F) | 5 | GGCATCCAAGCAGCAAG | 8 |
| 3′CS (R) | 6 | AAGCAGACTTGACCTGA | |
| orf513 (3′-CS junction), orf513-R5′ | 7 | CGTAACCGTTTGTTTGAGTG | This study |
| orf513 (screening) | |||
| orf513-F | ATGGTTTCATGCGGGTT | 2 | |
| orf513-R | CTGAGGGTGTGAGCGAG | 11 | |
| vr-2 | |||
| orf513-F3′ | 8 | GTTCGATCCATCACAGAG | This study |
| sul1-R | 9 | TTTGAAGGTTCGACAGC | 1 |
| orf5, orf5 lower (R) | TGTCGACGTGGGTGAAT | This study | |
| orf6, In21-R | 10 | CGGTCGGACTGCAAGTGA | This study |
| Resistance cassettes and other genes of the integrons characterized in this study | |||
| aadA1 | |||
| aadA1-F | TTGCTGGCCGTACATTTG | This study | |
| aadA1-R | TCATTGCGCTGCCATTC | ||
| aac(6′)-Ib (any variant) and aac(6′)-IId | |||
| aacF7334 | 11 | CATCACAAAGTACAGCATCGTGACCAACAG | This study |
| aacR7907 | 12 | TTAGGCAACACTGCGTGTTCGCTCGAATGC | |
| aac6IB (R) | TGTGACGGAATCGTTGC | 8 | |
| aacA4R (F) | AAACACGCCAGGCATTC | 1 | |
| blaOXA-30 | |||
| oxaIII-F | CATTATTTGAAGGAACTGAAG | This study | |
| oxaIII-R | CACCAGTTTTCCCATACAGT | ||
| catB3 | |||
| catout3′-1 (F) | 13 | TTTCTGCTCTATCGGGAG | This study |
| arr3out5′-1 (R) | TTGTTAGACGGCAAACTC | ||
| arr-3, sapC-sapB | 14 | GACTTGCTAACCACAGGG | This study |
| arr-3, arr3-F | |||
| sapC1-R | GAATGTGATTCAGTATCG | This study | |
| sapB4-F | AACCCGTCGGCACAGGCCCG | ||
| arr-3, sapA | |||
| sapA-F | 15 | CAGTGGGTTCGTCTATTGC | This study |
| sapA-R | CGTTACTGTCCGTCGCC | ||
| arr-3, sapA-qnrB10 Junction | |||
| sapA3-R | GCAGCAGCCTGACCACTC | This study | |
| qnrB-F3′ | CTTGGCATCGCTGTGATTG |
a
Only relevant primers (F, forward; R, reverse) are shown. Other sequence-based primers used in primer walking were excluded for brevity.
b
Numbers correspond to primer locations in the PCR chart shown in Fig. 1A.
c
Primers used for cloning qnrB10 in the pCR2.1 vector.