Table 1.
Primers used for PCR and qPCR
| Gene target | Primers | Reference | Temperature and step |
|---|---|---|---|
| cagA | 5’-GTTAARAATRGTGTRAAYGG -3’ 5’-TTTAGCTTCTGATACCGC-3’ |
19 | 94°C 30s, 56°C 30s, 72°C 1min. |
| Empty-site | 5’-CTCTTTTTGTGCCTTTGATTGAA-3’ 5’-CCAAATACATTTTGGCTAAATAAAC-3’ |
21 | 94°C 30s, 54°C 45s, 72°C 1min. |
| hspA | 5’GCTATCTGAAAATTTGATTTCTTTTGC-3’ 5’-TGCGCTATAGTTGTGTCGC-3’ |
23 | 94°C 30s, 52°C 30s, 72°C 2min. |
| Intergenic region |
5'-GTGGCGCGTTTCTTGCAATACC-3' 5'-AACTCGCTCAAAAACTCGGC-3' |
24 | 94°C 30s, 57°C 30s, 72°C 1min. |
| 23S rRNA | 5’-CTCCATAAGAGCCAAAGCCC-3’ 5’-CCACAGCGATGTGGTCTC-3’ |
25 | 94°C 60s, 60°C 45s, 72°C 1min. |
| VacA status | |||
| vacA s-region | 5’-TGAGTTGTTTGATATTGAC-3’ 5’-CAATCTGTCCAATCAAGCGAG-3’ |
22 | 94°C 30s, 50°C 45s, 72°C 45s. |
| vacA m-region | 5’-CTGCTTGAATGCGCCAAAC-3’ 5’-ATGGAAATACAACAAACACAC-3’ |
This study | 94°C 30s, 52°C 30s, 72°C 2min. |
| qPCR | |||
| Hp 16S rRNA | 5’ –AGAGACTAAGCYCTCCAACAAC-3 5’ –AATACTCATTGCGAAGGCGA-3’ |
This study | |
| HP probe 5’ -CATTACTGACGCTGATTGYGC | This study | ||
|
Eubacteria 16s rRNA |
5’ –CAGCAGCCGCGGTRATA-3 5’ –CGYCAATTGBGBAADATTCC-3’ |
26 | |
| Eubacteria probe 5’ –TACGGGAGGCAGCAGT- 3’ |
26 |