Table 1 Primers used in this study for H. pylori genotyping.
Primer | Sequence (5'-3') | Size of amplified fragment | Annealing temperature °C | Position in genome of reference (H. pylori 26695)* |
|---|---|---|---|---|
16S rRNA | ||||
HPGF-16S | CAATCAGCGTCAGTAATGTTC | 516 | 55 | 1208359-1208379 |
HPGR-16S | CTAAGAGATCAGCCTATGTCC | 1208855-1208875 | ||
cag PAI genes | ||||
cag1-F | TTCATTAGGTCTCATTGGAGCAGG | 230 | 62 | 547429-547452 |
cag1-R | TTGGCTTCAGTTGGTTCGTTG | 547639-547659 | ||
cag1-F | TTCATTAGGTCTCATTGGAGCAGG | 430 | 66 | 547429-547452 |
cag1-2-R | CCCTTACAGCCGCCTTTATTTAC | 547837-547859 | ||
cag5-F | CGCCACTCTTATCTTCTTCACCTC | 645 | 66 | 551152-551175 |
cag5-R | GGGGATTTTATCGCTTACGCAG | 551776-551797 | ||
cag7-F | AAGCGTGTCATAATGGGTGTGC | 986 | 66 | 554726-554747 |
cag7-R | AGAAAAGGCTGTTGCGGATTG | 555692-555712 | ||
cag9-F | ATGTCCCCCCAACAAATCGC | 627 | 62 | 562353-562372 |
cag9-R | CCATTAGCCACAAGTTTAGCCG | 562959-562980 | ||
cagT-F | GTTCACCATTCTAAAAAGATTACGC | 555 | 66 | 565331-565355 |
cagT-R | GATTTCGCAAGTATTCATTCTCTC | 565863-565886 | ||
cagS-F | CAATGGTTTTTAGATTAGCG | 342 | 54 | 566203-566222 |
cagS-R | AAGGGAGCGTTAGATAAGG | 566527-566545 | ||
cagS-Q-F | TCTAACGCTCCCTTGTTTGTATGC | 687 | 66 | 566532-566555 |
cagS-Q-R | TTGGTTGGTAATGGTTTTGGTAGC | 567196-567219 | ||
cagQ-F | CCAAAACCATTACCAACCAAAGC | 292 | 66 | 567200-567222 |
cagQ-R | CCGAACAAGCAAGAACTTACACAAC | 567468-567492 | ||
cagM-F | GGTTGCGTTTGGAGTTTTGTCG | 485 | 66 | 568752-568773 |
cagM-R | TGAGCCTTATCTTTAGTGGTAGCGG | 569213-569237 | ||
cagI-F | TGTTCTTCCCAAAGGTCGGC | 510 | 62 | 571644-571663 |
cagI-R | CTTCTGACAACGCTCAATACATCG | 572131-572154 | ||
cagE-F | AGTGATGCTTTGAGTCGCAAGTC | 923 | 64 | 575506-575528 |
cagE-R | TGGGGCAATAGTGTGATGACG | 576409-576429 | ||
cagA-F | GCCTAATTTAAATAATCTCGCTATCAC | 744 | 55 | 581555-581581 |
cagA-R | ATTGAGATTGTCAACTTTATCCG | 582277-582299 | ||
IS605-F | TTTGATAAAAACGGATGTGTGG | 1,016 | 55 | 13986-14007 (AC000108)# |
IS605-R | TGTTTTTGCAATAAGGGGAT | 14983-15002 | ||
TnpB-cagS-F | CGTTCTTAAGCCCATGTCTAAACC | 1,597 | 56 | 14038-14061 (AC000108)# |
TnpB-cagS-R | TCTAACGCTCCCTTGTTTGTATGC | 15612-15635 |