TABLE 1.
PCR and sequencing primers used in the study
| Target | Primer use (direction)h | Primer identifier | Sequence (5′ to 3′) | Reference |
|---|---|---|---|---|
| porA | PCR (fwd) | 210 | ATGCGAAAAAAACTTACCGCCCTC | 7 |
| PCR (rev) | 211 | AATGAAGGCAAGCCGTCAAAAACA | 7 | |
| porA (VR1) | Seq (fwd) | P3 | CAAAGCCGGCGTGGAAG | 32 |
| Seq (rev) | 103L | AACGGATACGTCTTGCTC | 35 | |
| porA (VR2) | Seq (fwd) | 8U | TCCGTACGCTACGATTCTCC | 35 |
| Seq (rev) | 122L | GGCGAGATTCAAGCCGCC | 35 | |
| fhbp | PCR/Seq (fwd) | gna1870F | TGACCTGCCTCATTGATGC | 14 |
| PCR/Seq (rev) | gna1870R | CGGTAAATTATCGTGTTCGGACGGC | 14 | |
| PCR/Seq (rev) | gna1870v3Ra | CGTGCCGTCGTGTCCTAG | 16 | |
| Seq (fwd) | gna1870S2 | CAAATCGAAGTGGACGGGCAG | 14 | |
| Seq (fwd) | gna1870S3 | TGTTCGATTTTGCCGTTTCCCTG | 14 | |
| gna2132 | PCR/Seq (fwd) | gna2132F | GGCGTTCAGACGGCATATTTTTACA | 14 |
| PCR/Seq (rev) | gna2132R | GGTTTATCAACTGATGCGGACTTGA | 14 | |
| Seq (fwd) | gna2132S2 | GCGGACACGCTGTCAAAACC | 14 | |
| Seq (fwd) | gna2132S4 | GGCGTTCTGCACGGTCGAGG | 14 | |
| Seq (fwd) | gna2132S5 | ATGGGTACGCAAAAATTCAA | 14 | |
| Seq (rev) | gna2132S7 | AATGCAGTACTTCGCCGTTGT | 14 | |
| Seq (rev) | gna2132S8 | CCTCGACCGTGCAGAACGCC | 14 | |
| Seq (rev) | gna2132S9 | CCGCACCGCCATTGCCTGTA | 14 | |
| Seq (fwd) | gna2132s3new | AGAAAATACAGGCAATGGCGGTGC | NAi | |
| Seq (fwd) | gna2132s3s4b | ACGGAAT(G/A)CAGGG(G/T)GACGATCC | NA | |
| Seq (rev) | gna2132s8s9b | GGATCGTC(A/C)CCCTG(C/T)ATTCCGT | NA | |
| nadA | PCR/Seq (fwd) | nadAFc,d,e,f | GTGGACGTACTCGACTACGAAGG | 6 |
| PCR/Seq (rev) | nadARc,d,e,f | CGAGGCGATTGTCAAACCGTTC | 6 | |
| PCR/Seq (fwd) | nadAintFc,d,e,f,g | TATGTAAACAAACTTGGTGGGG | 16 | |
| PCR/Seq (rev) | nadAintRc,d,e,f,g | GAAATAGAAAAGTTAACAACCAAGTT | 16 | |
| Seq (fwd) | nadAS1c,d | TATGTAAACAAACTTGGTGGGG | 6 | |
| Seq (fwd) | nadAS2c | GAAATAGAAAAGTTAACAACCAAGTT | 6 | |
| Seq (fwd) | nadAS3c,d,e | GACATCAAAGCTGATATCGCTAC | 6 | |
| Seq (rev) | nadAS4c,d,e,f | TTTCGAGGTGGCGCGTTCGGG | 6 | |
| Seq (rev) | nadAS5c | GTAGCGATATCAGCTTTGATGTC | 6 | |
| Seq (rev) | nadAS6c | CTTGGTTGTTAACTTTTCTATTTC | 6 | |
| Seq (fwd) | NadA4fd,e,f | TCAACGGATTCACAGTCGGAGACA | NA | |
| Seq (rev) | NadA4rd,e,f | CCAATCCATTGGCAGTAGTGTTCAG | NA | |
| Seq (fwd) | 328-Ff | GCCATCCTTGCCTCCTTCTG | NA | |
| Seq (rev) | 328-Re | TTTACCGATAGCAGTCTCGT | NA | |
| Seq (fwd) | E030-Af | GTCGTGGCTCAACACGACC | NA | |
| Seq (rev) | E030C-Re | CCGGACACTTCATCCAGTTTG | NA |
a
Alternative primer for PCR failures due to deletion in gna1870R primer binding site.
b
Bridges chromatograms for primers gna2132S3 and gna2132S4 or primers gna2132S8 and gna2132S9 (where required).
c
Use for nadA-1, nadA-2, and nadA-3.
d
Use for nadA-4.
e
Use for nadA-5.
f
Use for nadA-4/nadA-5-related variant.
g
Internally directed PCR primers; provides additional confirmation of the genome-wide absence of nadA.
h
Seq, sequencing; for, forward; rev, reverse.
i
NA, not applicable.