| Literature DB >> 35284346 |
Jina Vazirzadeh1, Vajihe Karbasizadeh1, Jamal Falahi2, Sharareh Moghim1, Tahmineh Narimani1, Rahmatollah Rafiei3.
Abstract
Background: Helicobacter pylori (H. pylori), a spiral-shaped bacterium colonizing the human stomach, is generally acquired in childhood. This pathogen is highly diverse and can be used as genetic markers for predict the history of human migrations. This study aimed to determine the genetic diversity of H. pylori isolates from patients with dyspepsia by the multi-locus sequence typing (MLST) and update data on the prevalence of H. pylori among Iranian dyspeptic patients. Materials andEntities:
Keywords: Helicobacter pylori; multilocus sequence typing; prevalence
Year: 2022 PMID: 35284346 PMCID: PMC8906086 DOI: 10.4103/abr.abr_25_21
Source DB: PubMed Journal: Adv Biomed Res ISSN: 2277-9175
Characteristics of strains for phylogenetic analysis used in this study
| Patient ID | Age (years) | Gender | Area | Pathology | |
|---|---|---|---|---|---|
| 2633 | 42 | Male | Esfahan | CG | + |
| 2634 | 68 | Male | Esfahan | CAG | + |
| 2635 | 70 | Female | Shahreza | CG | + |
| 2636 | 48 | Female | Esfahan | CG | − |
| 2637 | 32 | Male | Esfahan | EG | + |
| 2638 | 76 | Male | Esfahan | CAG | + |
| 2639 | 56 | Female | Flavarjan | EG | + |
| 2640 | 40 | Female | Esfahan | CG | − |
| 2641 | 53 | Male | Najaf Abad | EG | − |
| 2642 | 44 | Female | Khomeinishahr | CG | + |
| 2643 | 28 | Male | Shahreza | CAG | + |
| 2644 | 65 | Male | Zarrinshahr | EG | − |
| 2645 | 59 | Female | Mobarakeh | CAG | + |
| 2646 | 75 | Female | Esfahan | CAG | + |
| 2647 | 66 | Male | Khomeinishahr | CG | + |
| 2648 | 50 | Female | Esfahan | EG | − |
| 2649 | 38 | Male | Flavarjan | CAG | + |
| 2650 | 61 | Female | Esfahan | CAG | + |
| 2651 | 77 | Male | Shahreza | CG | + |
| 2652 | 36 | Female | Esfahan | EG | + |
CG: Chronic gastritis, CAG: Chronic active gastritis, EG: Erosive gastritis, PAI: Pathogenicity island
Primers used for the amplification of Helicobacter pylori genes
| Target gene | Primers (5’- 3’) | Annealing temperature (°C) | Size of PCR products (bp) |
|---|---|---|---|
|
| TGG GAC TGA TGG CGT GAG GG | 50 | 820 |
|
| AAG GGC GTT TTT AGA TTT TT | ||
|
| AATACACCAACGCCTCCAAG | 55 | 400 |
|
| TTGTTGGCGCTTGCTCTC |
PCR: Polymerase chain reaction
Primer sequences used for polymerase chain reaction amplification and sequencing of the seven housekeeping genes for Helicobacter pylori and expected product sizes for each reaction
| Target gene | Primers (5’- 3’) | Annealing temperature (°C) | Size of PCR products (bp) |
|---|---|---|---|
|
| F: TAGAATGCAAAAAAGCATCGCCCTC | 58 | 633 |
|
| F: CACTATTACCACGCCTATTTTTTTGAC | 56 | 734 |
|
| F: GGACTAGCGTTAAACGCACG | 56 | 841 |
|
| F: GTGGTTGTAGYTGGAAACTTTACAC | 58 | 676 |
|
| F: GGCAATTTGGATGAGCGAGCTC | 56 | 559 |
|
| F: GGAGTGAGCCATGACGCTGA | 53 | 706 |
|
| F: AGGTTATTCGTAAGGTGCG | 52 | 686 |
*http://pubmlst.org/Helicobacter. PCR: Polymerase chain reaction
Figure 1The frequency of grading the severity of inflammation of the samples studied, according to the Sydney System
The allelic profile for the isolates included in the study*
| Number | ID | Isolate | Allele | ST | ||||||
|---|---|---|---|---|---|---|---|---|---|---|
|
| ||||||||||
|
|
|
|
|
|
|
| ||||
| 1 | 2633 | ISF1 |
| 1861 | 1672 |
|
|
|
| 3482 |
| 2 | 2634 | ISF2 |
|
|
|
|
| 118 |
| 3483 |
| 3 | 2635 | ISF3 |
|
|
|
|
| 44 |
| 3484 |
| 4 | 2636 | ISF4 |
|
|
|
|
| 44 |
| 3484 |
| 5 | 2637 | ISF5 |
|
| 1714 |
|
|
|
| 3485 |
| 6 | 2638 | ISF6 |
|
|
|
|
|
|
| 3486 |
| 7 | 2639 | ISF7 |
|
|
|
|
|
|
| 3487 |
| 8 | 2640 | ISF8 |
|
|
|
|
|
|
| 3488 |
| 9 | 2641 | ISF9 |
| 71 | 2801 |
|
| 1660 | 1705 | 3489 |
| 10 | 2642 | ISF10 |
| 71 | 2801 |
|
| 1660 | 1705 | 3489 |
| 11 | 2643 | ISF11 | 1692 |
|
|
|
|
|
| 3490 |
| 12 | 2644 | ISF12 |
| 2506 | 1990 |
|
|
|
| 3491 |
| 13 | 2645 | ISF13 |
| 2506 | 1990 |
|
|
|
| 3491 |
| 14 | 2646 | ISF14 |
| 2506 | 1990 |
|
|
|
| 3491 |
| 15 | 2647 | ISF15 |
| 866 |
|
|
| 2140 |
| 3492 |
| 16 | 2648 | ISF16 |
| 866 |
|
|
| 2140 |
| 3492 |
| 17 | 2649 | ISF17 |
|
|
|
|
|
|
| 3493 |
| 18 | 2650 | ISF18 |
|
|
| 2577 | 2864 | 1774 |
| 3494 |
| 19 | 2651 | ISF19 |
|
|
| 1367 | 1434 | 1698 |
| 3495 |
| 20 | 2652 | ISF20 |
|
|
| 1367 | 1434 | 1698 |
| 3495 |
*The numbers correspond to the identification of the alleles in the H. pylori public MLST database and the numbers in bold represent the alleles that were first described in this study. H. pylori: Helicobacter pylori, MLST: Multi-locus sequence typing
Figure 2Analysis of MLST 20 Isolated Iranian Helicobacter pylori. Phylogenetic tree using neighbor-joining-tree algorithm in software Viewer 8 CLC Sequence been plotted
Figure 3Phylogenetic analysis of 20 isolated Iranian Helicobacter pylori isolates with 25 isolates from neighboring Asian countries using data from 7 housekeeping genes in the iTol software
Figure 4Global analysis of 20 Iranian isolates with103 strains from other countries using 7 housekeeping genes in the iTol Software based on population structure of isolates (H. pylori strains of Isfahan are red)