Genes
The Helicobacter MLST scheme uses internal fragments of the following seven house-keeping genes:
atpA, efp, mutY, ppa, trpC, ureI, yphC
Primers
The primer pairs we use for the PCR amplification of internal fragments of these genes are:
| Number | Name | Gene | Sequence |
|---|---|---|---|
| O_1369 | HptrpC1_for | trpC | CAAGCTCCTAGAAGTCTCTG |
| O_1370 | HptrpC6_for | trpC | TAGAATGCAAAAAAGCATCGCCCTC |
| O_1371 | HptrpC5_rev | trpC | CCCAGCTAGCATGAAAGG |
| O_1372 | HptrpC7_rev | trpC | TAAGCCCGCACACTTTATTTTCGCC |
| O_1379 | yphCF1_for | yphC | CACTATTACCACGCCTATTTTTTTGAC |
| O_1382 | yphCR5_rev | yphC | TTTCTARGCTTTCTAAAATATC |
| O_1493 | HPvacA-4 | vacA | ATACGCTCCCACGTATTGC |
| O_1514 | OLHPVacA-3(+) | vacA | ACAACCGTGATCATTCCAGC |
| O_1958 | vacA_for2 | vacA | CTGCTGTAGGAACGGTCTC |
| O_1959 | vacA_rev2 | vacA | GCGTGGCGCCATCATAAAGAG |
| O_1960 | yphC_for2 | yphC | CACGCCTATTTTTTTGACTAAAAAC |
| O_1961 | yphC_rev2 | yphC | GCGTTTAAGAGCGARCTTTTGC |
| O_1962 | yphC_for3 | yphC | GCTTTAAATAACTATAATATTGTAATC |
| O_1963 | yphC_rev3 | yphC | CATTYACCCTCCCAATGATGC |
| O_1964 | atpA_for2 | atpA | GGACTAGCGTTAAACGCACG |
| O_1965 | atpA_rev2 | atpA | CTTGAAACCGACAAGCCCAC |
| O_1966 | atpA_for3 | atpA | GTTCCTGTTGGCGATGCGGT |
| O_1967 | atpA_rev3 | atpA | CCTGAATAAAACAAATCCGTTTC |
| O_1979 | mutY_for2 | mutY | GTGGTTGTAGYTGGAAACTTTACAC |
| O_1980 | mutY_rev2 | mutY | CAACGCCCAAGTAACGCTCTTC |
| O_1981 | mutY_for3 | mutY | GGAATTTAAAGGGCATTAACGCC |
| O_1982 | mutY_rev3 | mutY | CTTAAGCGTGTGTYTTTCTAGG |
| O_2044 | efp_for1 | efp | GGCAATTTGGATGAGCGAGCTC |
| O_2045 | efp_rev1 | efp | CTTCACCTTTTCAAGATACTC |
| O_2046 | efp_for2 | efp | GGGCTTGAAAATTGAATTGGGCGG |
| O_2047 | efp_rev2 | efp | GTATTGACTTTAATGATCTCACCC |
| O_2201 | ppa_for1 | ppa | GGAGTGAGCCATGACGCTGA |
| O_2204 | ppa_rev2 | ppa | GCTTTTATSGCTTTYTCTAAAAC |
| O_2356 | ureIfor | ureI | AGGTTATTCGTAAGGTGCG |
| O_2357 | atpAinternal-for | atpA internal | GCTATTGGGCAAAAAGAATC |
| O_2358 | atpAinternal-rev | atpA internal | ACGACGCTGTATTCCATCGC |
| O_3151 | ureI-rev2 | ureI | GTTTAAATCCCTTAGATTGCC |
| O_3152 | ureI-rev3 | ureI | GAAATCCAAGGGGTTTAAATC |
| O_3225 | yphC-for3 | yphC | GACCCTTATTTAAGCTTTAAATAAC |
| O_3226 | yphC-rev3 | yphC | CCCAATGATGCCTACTTGAAT |
| O_3237 | ppa-for4 | ppa | CAATGAATTTAGACCAATTAGAAGT |
| O_3238 | ppa-for5 | ppa | GGAGATTGCAATGAATTTAGA |
| O_3239 | ppa-for6 | ppa | TTCAAAGGAGATTGCAATGAATT |
| O_3240 | ppa-rev4 | ppa | GGGTTAARATCGTTAAATTGTAG |
| O_3241 | ppa-rev5 | ppa | GTGGGGTTAARATCGTTAAATTG |
| O_3242 | ureI-for4 | ureI | CTTTATGATTRGCTCAAGCAAC |
| O_3243 | ureI-for5 | ureI | GCTCAAGCAACAAARGTTATTCG |
Primer combinations
| Amplification | Sequencing | |||
|---|---|---|---|---|
| Gene fragment | for | rev | for | rev |
| atpA | O_1964 | O_1965 | O_1964 | O_1965 |
| internal atpA | O_2357 | O_2358 | ||
| efp | O_2044 | O_2045 | O_2044 | O_2045 |
| mutY | O_1979 | O_1982 | O_1979 | O_1982 |
| ppa | O_3238 | O_3241 | O_3238 | O_3241 |
| trpC | O_1370 | O_1372 | O_1370 | O_1372 |
| ureI | O_2356 | O_3151 | O_2356 | O_3151 |
| yphC | O_1960 | O_1963 | O_1960 | O_1963 |
| vacA | O_1514 | O_1493 | O_1514 | O_1493 |