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)

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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

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PCR conditions

PCR amplification is performed at an annealing temperature of 55°C for all genes.

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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

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Allele templates

Please refer to allele 1 from the sequence download page