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Genes
The Escherichia coli MLST scheme uses internal fragments of the following eight 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)
PCR amplification
dinB: F : dinBoF GTTTTCCCAGTCACGACGTTGTATGAGAGGTGAGCAATGCGTA
dinB: R : dinB2oR TTGTGAGCGGATAACAATTTCCGTAGCCCCATCGCTTCCAG
icdA : F : icd2oF GTTTTCCCAGTCACGACGTTGTAATTCGCTTCCCGGAACATTG
icdA : R : icdoR TTGTGAGCGGATAACAATTTCATGATCGCGTCACCAAAYTC
pabB : F : pabB2oF GTTTTCCCAGTCACGACGTTGTAAATCCAATATGACCCGCGAG
pabB: R : pabBoR TTGTGAGCGGATAACAATTTCGGTTCCAGTTCGTCGATAAT
polB : F : polB2oF GTTTTCCCAGTCACGACGTTGTAGGCGGCTATGTGATGGATTC
polB : R : polBoR TTGTGAGCGGATAACAATTTCGGTTGGCATCAGAAAACGGC
putP : F : putP2oF GTTTTCCCAGTCACGACGTTGTACTGTTTAACCCGTGGATTGC
putP : R : putPoR TTGTGAGCGGATAACAATTTCGCATCGGCCTCGGCAAAGCG
trpA : F : trpAoF GTTTTCCCAGTCACGACGTTGTAGCTACGAATCTCTGTTTGCC
trpA : R : trpAoR TTGTGAGCGGATAACAATTTCGCTTTCATCGGTTGTACAAA
trpB: F : trpB2oF GTTTTCCCAGTCACGACGTTGTACACTATATGCTGGGCACCGC
trpB: R : trpBoR TTGTGAGCGGATAACAATTTCCCTCGTGCTTTCAAAATATC
uidA : F : uidAoF GTTTTCCCAGTCACGACGTTGTACATTACGGCAAAGTGTGGGTCAAT
uidA : R : uidAoR TTGTGAGCGGATAACAATTTCCCATCAGCACGTTATCGAATCCTT
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
dinB (450 bp)
CCTGCCCTGCGCGATATCCCTATTGCTATTGGCGGCAGCCGCGAACGTCGGGGGGTGATCAGCACCGCCAATTATC CCGCGCGTAAATTTGGCGTACGTAGCGCTATGCCGACAGGGATGGCGCTCAAATTTTGCCCACATCTCACGCTGCT TCCAGGGCGCTTTGACGCCTACAAAGAAGCCTCAAATCATATCCGCGAAATTTTCTCGCGCTATACCTCGCGCATT GAACCGTTATCACTGGATGAAGCCTATCTCGACGTCACCGATAGTGTGCATTGCCACGGTTCTGCGACCCTCATCG CCCAGGAAATCCGCCAGACAATCTTCAACGAGCTGCAACTGACGGCGTCTGCGGGCGTTGCGCCGGTAAAGTTTCT CGCTAAAATCGCTTCCGACATGAATAAACCCAACGGTCAGTTTGTGATTACTCCGGCAGAAGTTCCGGCA
icdA (516 bp)
ATCGAATACGCAATTGCTAACGATCGTGACTCTGTGACCCTGGTGCACAAAGGCAACATCATGAAGTTCACCGAAG GCGCGTTTAAAGACTGGGGCTACCAGCTGGCGCGTGAAGAGTTTGGCGGTGAACTGATCGACGGCGGCCCGTGGCT GAAAGTTAAAAACCCGAATACCGGCAAAGAGATCGTCATTAAAGATGTGATTGCTGATGCATTCCTGCAACAGATC CTGCTGCGTCCGGCTGAATATGATGTTATCGCCTGTATGAACCTGAACGGTGACTACATTTCTGACGCTCTGGCTG CACAGGTCGGCGGTATCGGTATCGCCCCAGGCGCAAACATCGGTGACGAATGCGCCCTGTTTGAAGCCACCCACGG TACTGCGCCGAAATATGCCGGTCAGGACAAAGTAAACCCAGGCTCTATTATTCTCTCCGCTGAGATGATGTTACGC CATATGGGCTGGACTGAAGCCGCAGACCTGATTGTTAAAGGTATGGAAGGCGCAATCAAC
pabB (468 bp)
GGTGATTGCTATCAGGTGAATCTCGCCCAGCGTTTTCATACGACCTATTCTGGCGATGAATGGCAGGCATTCCTTC AGCTTAATCAGGCCAACCGCGCGCCGTTTAGCGCTTTTTTACGTCTTGAACAGGGTGCGATTTTAAGCCTTTCGCC AGAGCGGTTTATCCTTTGTGATAATAGTGAAATCCAGACCCGCCCGATTAAAGGCACGCTACCACGCCTGCCCGAT CCTCAGGAAGATAGCAAACAAGCAGAAAAACTGGCGAACTCAGCGAAAGATCGTGCCGAAAATCTGATGATTGTCG ATTTAATGCGTAATGATATCGGTCGTGTTGCCGTAGCCGGTTCGGTAAAAGTACCAGAGCTGTTCGTGGTCGAACC CTTCCCTGCCGTGCATCATCTGGTCAGCACCATAACGGCGCGGCTACCAGAACAGTTACACACCAGCGATCTGCTG CGCGCAGCTTTT
polB (450 bp)
TCGATCATCCGCACCTTTCTGATTGATCCCGTCGGGCTGGTGGAAGGCATGGCGCAGCCTGATCCAGAGCACAGCA CCGAAGGTTTTCTCGATGCCTGGTTCTCGCGGGAGAAACATTGCCTGCCGGAGATTGTGACTAACATCTGGCACGG GCGCGATGAAGCCAAACGTCAGGGTAATAAGCCGCTTTCGCAGGCGCTGAAGATCATTATGAATGCCTTTTATGGC GTGCTTGGCACCACCGCCTGCCGCTTCTTCGATCCGCGCCTGGCGTCGTCGATCACCATGCGTGGTCATCAGATCA TGCGGCAAACCAAAGCGTTGATTGAAGCGCAGGGCTACGACGTGATCTACGGCGATACCGACTCAACGTTTGTCTG GTTGAAAGGCGCACATTCGGAAGAAGAAGCGGCGAAAATTGGTCGTGCACTGGTGCAGCACGTTAACGCC
putP (456 bp)
CTGTCGGCGATTCTGGCGGCGGTAATGTCAACGTTAAGTTGCCAGCTGCTGGTATGTTCCAGTGCGATTACCGAAG ATTTATACAAAGCGTTTCTGCGTAAACAGGCCAGCCAGAAAGAGCTGGTGTGGGTAGGGCGAGTGATGGTGCTGGT GGTGGCGCTGGTGGCGATTGCGCTGGCGGCAAACCCGGAAAACCGCGTGCTGGGCTTAGTGAGCTACGCGTGGGCA GGCTTTGGCGCAGCGTTTGGTCCGGTGGTGCTGTTCTCGGTGATGTGGTCACGCATGACGCGCAACGGTGCGCTGG CGGGGATGATCATCGGTGCGCTGACGGTTATCGTCTGGAAACAGTTCGGCTGGCTGGGTCTGTACGAAATTATTCC GGGCTTTATCTTCGGCAGTATCGGGATTGTAGTGTTTAGTTTGCTGGGTAAAGCGCCGTCAGCGGCGATGCAAAAA
trpA (561 bp)
GGTATCCCCTTCTCCGACCCACTGGCGGATGGCCCGACGATTCAAAACGCCACTCTGCGCGCCTTTGCGGCAGGTG TGACTCCGGCACAATGTTTTGAAATGCTGGCACTGATTCGCCAGAAACACCCGACCATTCCCATTGGCCTGTTGAT GTATGCCAATCTGGTGTTTAACAAAGGCATTGATGAGTTTTATGCCCAGTGCGAAAAAGTCGGCGTCGATTCGGTG CTGGTTGCCGATGTGCCAGTTGAAGAGTCCGCGCCCTTCCGCCAGGCCGCGTTGCGTCATAATGTCGCACCTATCT TCATCTGCCCGCCAAATGCCGATGACGACCTGCTGCGCCAGATAGCCTCTTACGGTCGTGGTTACACCTATTTGCT GTCACGAGCAGGCGTGACCGGCGCAGAAAACCGCGCCGCGTTACCCCTCAATCATCTGGTTGCGAAGCTGAAAGAG TACAACGCTGCACCTCCATTGCAGGGATTTGGTATTTCCGCCCCGGATCAGGTAAAAGCAGCGATTGATGCAGGAG CTGCGGGCGCGATTTCTGGTTCGGCCATT
trpB (594 bp)
GCAGCTGGCCCACATCCTTATCCGACCATTGTCCGTGAGTTCCAGCGGATGATTGGCGAAGAAACCAAAGCACAGA TTCTGGAAAGAGAAGGTCGCCTGCCGGATGCGGTTATCGCTTGTGTTGGCGGCGGTTCAAATGCCATCGGCATGTT TGCTGATTTTATCAACGAAACCGACGTCGGCCTGATTGGTGTCGAACCAGGCGGTCACGGTATCGAAACTGGCGAG CACGGCGCACCGTTAAAACACGGTCGCGTGGGCATCTATTTCGGTATGAAAGCGCCGATGATGCAAACCGAAGACG GACAGATTGAAGAATCTTACTCCATCTCCGCCGGACTGGATTTCCCGTCTGTCGGCCCACAACACGCGTATCTTAA CAGCACTGGACGCGCTGATTACGTGTCAATTACCGATGATGAAGCACTGGAAGCCTTCAAAACGCTGTGCCTGCAC GAAGGGATCATCCCGGCGCTGGAGTCCTCCCACGCCCTGGCCCATGCGCTGAAAATGATGCGCGAAAACCCGGAAA AAGAGCAGCTACTGGTGGTTAACCTTTCCGGTCGCGGCGATAAAGACATCTTCACCGTTCCA
uidA (600 bp)
ATGGAGCATCAGGGCGGCTATACGCCATTTGAAGCCGATGTCACGCCGTATGTTATTGCCGGGAAAAGTGTACGTA TCACCGTTTGTGTGAACAATGAACTGAACTGGCAGACTATCCCGCCGGGAATGGTGATTACCGATGAAAACGGCAA GAAAAAGCAGTCTTACTTCCATGATTTCTTTAACTATGCCGGGATCCATCGCAGCGTAATGCTCTACACCACGCCG AACACCTGGGTGGACGATATCACCGTGGTGACGCATGTCGCGCAAGACTGTAACCACGCGTCTGTTGACTGGCAGG TGGTGGCCAATGGTGATGTCAGCGTTGAACTGCGTGATGCGGATCAACAGGTGGTTGCAACTGGACAAGGCACCAG CGGGACTTTGCAAGTGGTGAATCCGCACCTCTGGCAACCGGGTGAAGGTTATCTCTATGAACTGTGCGTCACAGCC AAAAGCCAGACAGAGTGTGATATCTACCCGCTGCGCGTCGGCATCCGGTCAGTGGCAGTGAAGGGCGAGCAGTTCC TGATTAACCACAAACCGTTCTATTTTACTGGCTTTGGTCGTCATGAAGATGCGGATTTGCGTGGCAAA
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