Table 1 Characteristics of 26 Peruvian H. pylori isolates obtained from Amerindians and distribution, presence/absence and or rearrangement of various gene loci in their genomes; 0 – region not amplified, 1 – region present.
Strains | Diagnostic PCR | Phylogenetic placement | oip A status | cagA genotype | cag-PAI spanning PCR | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Â | cagA | GlmM | FAFLP/MLST | babB | oipA | No. of CT | Frame | gene | EPIYA motif | cagAP1 | cagAP2 | cagA1 | cagA2 | cagE | cagT | LEC1 | LEC2 |
A) Native Peruvian Strains | |||||||||||||||||
SJM184 | 1 | 1 | hp Europe | Modern | Eastern | 5 | Out | 1 | EPIYA A, B, C | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
SJM80 | 1 | 1 | hp Europe | Modern | Western | 6 | Out | 1 | EPIYA A, B, C | 1 | 1 | 0 | 1 | 1 | 1 | 1 | 1 |
SJM83 | 1 | 1 | hsp Amerind | Amerind | Western | 6 | Out | 1 | EPIYA A, B, C | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
SJM92 | 1 | 1 | hsp Amerind | Amerind | Eastern | 3 | In | 1 | EPIYA A, B, C | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
SJM93 | 1 | 1 | hp Europe | Modern | Western | 6 | In | 1 | EPIYA A, B, C | 1 | 1 | 0 | 1 | 1 | 1 | 1 | 0 |
SJM10 | 1 | 1 | hsp Amerind | Amerind | Western | 6 | In | 1 | EPIYA A, B, C | 1 | 1 | 0 | 1 | 1 | 1 | 1 | 1 |
SJM12 | 1 | 1 | hsp Amerind | Amerind | Eastern | 4 | In | 1 | EPIYA A, B, C | 1 | 1 | 0 | 1 | 1 | 1 | 1 | 1 |
SJM148 | 1 | 1 | hp Europe | Modern | Western | 6 | In | 1 | EPIYA A, B, C | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
SJM14 | 1 | 1 | hp Europe | Modern | Western | 7 | Out | 1 | EPIYA A, B, C | 1 | 1 | 0 | 1 | 1 | 1 | 1 | 1 |
SJM179 | 1 | 1 | hp Europe | Modern | Western | 6 | In | 1 | EPIYA A, B, C | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
SJM180 | 1 | 1 | hp Europe | Modern | Western | 6 | In | 1 | EPIYA A, B, C | 1 | 1 | 0 | 1 | 1 | 1 | 1 | 1 |
SJM189 | 1 | 1 | hp Europe | Modern | Western | 6 | In | 1 | EPIYA A, B, C | 1 | 0 | 1 | 1 | 1 | 1 | 1 | 1 |
SJM18 | 1 | 1 | hp Europe | Modern | Eastern | 4 | In | 1 | EPIYA A, B, C | 1 | 1 | 0 | 1 | 1 | 1 | 1 | 1 |
SJM19 | 1 | 1 | hp Europe | Modern | Eastern | 4 | Out | 1 | EPIYA A, B, C, C | 1 | 0 | 1 | 1 | 1 | 1 | 1 | 1 |
SJM1 | 0 | 1 | hp Europe | Modern | Western | 6 | In | 1 | EPIYA A, B, C | 0 | 0 | 0 | 1 | 1 | 1 | 1 | 1 |
SJM20 | 1 | 1 | hp Europe | Modern | Western | 6 | In | 1 | EPIYA A, B, C | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
SJM21 | 1 | 1 | hp Europe | Modern | Western | 6 | In | 1 | EPIYA A, B, C | 1 | 1 | 0 | 1 | 1 | 1 | 1 | 1 |
SJM23 | 1 | 1 | hsp Amerind | Amerind | Western | 6 | In | 1 | EPIYA A, B, C | 1 | 1 | 0 | 1 | 1 | 1 | 1 | 1 |
SJM37 | 1 | 1 | hp Europe | Modern | Western | 6 | In | 1 | EPIYA A, B, C | 1 | 1 | 1 | 1 | 1 | 0 | 1 | 1 |
SJM38 | 1 | 1 | hp Europe | Modern | Western | 6 | In | 1 | EPIYA A, B, C | 1 | 0 | 1 | 1 | 1 | 0 | 1 | 1 |
SJM41 | 1 | 1 | hp Europe/WAfrica | Modern | Eastern | 2 | Out | 1 | EPIYA A, B, C | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
SJM45 | 1 | 1 | hp Europe | Modern | Western | 8 | In | 1 | EPIYA A, B, C, C | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
SJM50 | 1 | 1 | hp Europe | Modern | Eastern | 5 | Out | 1 | EPIYA A, B, C, C | 1 | 1 | 1 | 1 | 0 | 1 | 1 | 1 |
SJM53 | 0 | 1 | hp Europe | Modern | Western | 6 | In | 1 | EPIYA A, B, C | 0 | 0 | 1 | 1 | 1 | 1 | 1 | 1 |
SJM63 | 1 | 1 | hp Europe | Modern | Western | 6 | Out | 1 | EPIYA A, B, C | 1 | 1 | 0 | 1 | 1 | 1 | 1 | 1 |
SJM69 | 1 | 1 | hp Europe | Modern | Western | 6 | In | 1 | EPIYA A, B, C | 1 | 1 | 0 | 1 | 1 | 1 | 1 | 1 |
B) Other Strains | |||||||||||||||||
Spain (HUPB76) | 1 | 1 | hp Europe | Modern | Western | 9 | In | 1 | EPIYA A, B, C, C | 1 | 0 | 1 | 1 | 1 | 0 | 1 | 1 |
Japan (HU178) | 1 | 1 | hp East Asia | East Asia | Eastern | 4 | In | 1 | EPIYA A, B, D | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
Africa (10) | 1 | 1 | hp S Africa | Modern | Western | 6 | In | 1 | EPIYA A, B, C | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
India (MS8) | 1 | 1 | hp Europe | Modern | Western | 6 | In | 1 | EPIYA A, B, C | 1 | 1 | 1 | 1 | 1 | 1 | 0 | 0 |