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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)

GeneDirectionPrimer Sequence
dinBF:dinBoFGTTTTCCCAGTCACGACGTTGTATGAGAGGTGAGCAATGCGTA
R:dinB2oRTTGTGAGCGGATAACAATTTCCGTAGCCCCATCGCTTCCAG
icdAF:icd2oFGTTTTCCCAGTCACGACGTTGTAATTCGCTTCCCGGAACATTG
R:icdoRTTGTGAGCGGATAACAATTTCATGATCGCGTCACCAAAYTC
pabBF:pabB2oFGTTTTCCCAGTCACGACGTTGTAAATCCAATATGACCCGCGAG
R:pabBoRTTGTGAGCGGATAACAATTTCGGTTCCAGTTCGTCGATAAT
polBF:polB2oFGTTTTCCCAGTCACGACGTTGTAGGCGGCTATGTGATGGATTC
R:polBoRTTGTGAGCGGATAACAATTTCGGTTGGCATCAGAAAACGGC
putBF:putP2oFGTTTTCCCAGTCACGACGTTGTACTGTTTAACCCGTGGATTGC
R:putPoRTTGTGAGCGGATAACAATTTCGCATCGGCCTCGGCAAAGCG
trpAF:trpAoFGTTTTCCCAGTCACGACGTTGTAGCTACGAATCTCTGTTTGCC
R:trpAoRTTGTGAGCGGATAACAATTTCGCTTTCATCGGTTGTACAAA
trpBF:trpB2oFGTTTTCCCAGTCACGACGTTGTACACTATATGCTGGGCACCGC
R:trpBoRTTGTGAGCGGATAACAATTTCCCTCGTGCTTTCAAAATATC
uidAF:uidAoFGTTTTCCCAGTCACGACGTTGTACATTACGGCAAAGTGTGGGTCAAT
R:uidAoRTTGTGAGCGGATAACAATTTCCCATCAGCACGTTATCGAATCCTT

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

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