Primers used for MLST of Escherichia coli
Genes
The Escherichia coli MLST scheme uses internal fragments of the following housekeeping genes:
dinB (DNA polymerase)
icdA (isocitrate dehydrogenase)
pabB (p-aminobenzoate synthase)
polB (polymerase PolII)
putP (proline permease)
trpA (tryptophan synthase subunit A)
trpB (tryptophan synthase subunit B)
uidA (beta-glucuronidase)
Primers for PCR amplification (Note: all primers include universal 3' tails used for sequencing)
| Gene | Direction | Primer Sequence |
|---|---|---|
| dinB | F:dinBoF | GTTTTCCCAGTCACGACGTTGTATGAGAGGTGAGCAATGCGTA |
| R:dinB2oR | TTGTGAGCGGATAACAATTTCCGTAGCCCCATCGCTTCCAG | |
| icdA | F:icd2oF | GTTTTCCCAGTCACGACGTTGTAATTCGCTTCCCGGAACATTG |
| R:icdoR | TTGTGAGCGGATAACAATTTCATGATCGCGTCACCAAAYTC | |
| pabB | F:pabB2oF | GTTTTCCCAGTCACGACGTTGTAAATCCAATATGACCCGCGAG |
| R:pabBoR | TTGTGAGCGGATAACAATTTCGGTTCCAGTTCGTCGATAAT | |
| polB | F:polB2oF | GTTTTCCCAGTCACGACGTTGTAGGCGGCTATGTGATGGATTC |
| R:polBoR | TTGTGAGCGGATAACAATTTCGGTTGGCATCAGAAAACGGC | |
| putB | F:putP2oF | GTTTTCCCAGTCACGACGTTGTACTGTTTAACCCGTGGATTGC |
| R:putPoR | TTGTGAGCGGATAACAATTTCGCATCGGCCTCGGCAAAGCG | |
| trpA | F:trpAoF | GTTTTCCCAGTCACGACGTTGTAGCTACGAATCTCTGTTTGCC |
| R:trpAoR | TTGTGAGCGGATAACAATTTCGCTTTCATCGGTTGTACAAA | |
| trpB | F:trpB2oF | GTTTTCCCAGTCACGACGTTGTACACTATATGCTGGGCACCGC |
| R:trpBoR | TTGTGAGCGGATAACAATTTCCCTCGTGCTTTCAAAATATC | |
| uidA | F:uidAoF | GTTTTCCCAGTCACGACGTTGTACATTACGGCAAAGTGTGGGTCAAT |
| R:uidAoR | TTGTGAGCGGATAACAATTTCCCATCAGCACGTTATCGAATCCTT |
PCR conditions
PCR amplification is performed at an annealing temperature of 55°C for all genes.
Sequencing
We use the same primers for sequencing all genes:
oF : GTT TTC CCA GTC ACG ACG TTG TA
oR: TTG TGA GCG GAT AAC AAT TTC
Allele templates
Please refer to allele 1 from the sequence download page