Genes
The Bordetella MLST scheme uses internal fragments of the following seven house-keeping genes:
| Gene | BB ORF | BPP ORF | BP ORF |
|---|---|---|---|
| adk (Adenylate kinase) | BB2005 | BPP2560 | BP2769 |
| fumC (fumarate hydratase class II) | BB4054 | BPP3619 | BP0248 |
| glyA (serine hydroxymethyltransferase) | BB4348 | BPP3875 | BP2952 |
| tyrB (aromatic amino-acid aminotransferase) | BB2272 | BPP2024 | BP1795 |
| icd (isocitrate dehyrogenase) | BB3924 | BPP3475 | BP2488 |
| pepA (cytosol aminopeptidase) | BB3736 | BPP3285 | BP2421 |
| pgm (phosphoglucomutase) | BB0885 | BPP0800 | BP3141 |
PCR Amplification
The PCR conditions were optimized using HotStar Taq mastermix (Qiagen) and 1M betaine final concentration. The cycling conditions were as follows:
95°C for 15 min
30 cycles of:
95°C for 30 s
54°C for 30 s
72°C for 1 min
Primers
| Primer name | Sequence |
|---|---|
| Adk-F | AGCCGCCTTTCTCACCCAACACT |
| Adk-R | TGGGCCCAGGACGAGTAGT |
| FumC-F | CGTGAACCGGGGCCAGTCGTC |
| FumC-R | GGCCAGCCAGCGCACATCGTT |
| GlyA-F | CAACCAGGGCGTGTACATGGC |
| GlyA-R | CCGCGATGACGTGCATCAG |
| TyrB-F | CGAGACCTACGCTTATTACGAT |
| TyrB-R | TGCCGGCCAGTTCATTTT |
| Icd-F | CTGGTCCACAAGGGCAACAT |
| Icd-R | ACACCTGGGTGGCGCCTTC |
| PepA-F | CGCCCCAGGTTGAAGAAAATCGTC |
| PepA-R | ATCAGGCCCACCACATCCAG |
| Pgm-F | CGCCCATGTCACCAGCACCGA |
| Pgm-R | CGCCGTCTATCGTAACCAG |