New Tool for Phylogenetic Analysis of Helicobacter pylori: An Advanced Study

2021 ◽  
pp. 62-70
Author(s):  
Vladimir Mihajlovich Sorokin ◽  
Ruslan Vjacheslavovich Pisanov ◽  
Aleksej Sergeevich Vodop'janov ◽  
Elena Vadimovna Golubkina
Keyword(s):  
Phylogenetic Analysis ◽  
Helicobacter Pylori ◽  
Advanced Study

scholarly journals Mechanism of Metronidazole Resistance inHelicobacter pylori: Comparison of the rdxA Gene Sequences in 30 Strains

2000 ◽  
Vol 44 (8) ◽  
pp. 2207-2210 ◽  
Author(s):  
Nadia Maggi Solcà ◽  
Marco Valerio Bernasconi ◽  
Jean-Claude Piffaretti
Keyword(s):  
Phylogenetic Analysis ◽  
Helicobacter Pylori ◽  
Amino Acid ◽  
Resistant Strain ◽  
Point Mutations ◽  
Housekeeping Genes ◽  
Amino Acid Substitutions ◽  
Metronidazole Resistance ◽  
Nucleotide Mutation ◽  
Nucleotide Insertion

ABSTRACT The rdxA gene of 30 independently isolatedHelicobacter pylori strains was sequenced. A comparison of the rdxA sequences revealed a higher percentage of amino acid substitutions in the corresponding protein than in other housekeeping genes. Out of 122 point mutations, 41 were missense and 4 were nonsense. A resistant strain with a nucleotide insertion in therdxA sequence was also found. With the exception of the point mutations and the insertion generating a stop signal, no particular nucleotide mutation or amino acid substitution could be associated to metronidazole resistance. Moreover, phylogenetic analysis of the 30 nucleotide sequences did not demonstrate specific clusters associated with the resistance phenotype.

scholarly journals Phylogenetic analysis of Helicobacter pylori cagA gene of Turkish isolates and the association with gastric pathology

Gut Pathogens ◽  
2013 ◽  
Vol 5 (1) ◽  
pp. 33 ◽  
Author(s):  
Barik A Salih ◽  
Bora Bolek ◽  
Mehmet Yildiz ◽  
Soykan Arikan
Keyword(s):  
Phylogenetic Analysis ◽  
Helicobacter Pylori ◽  
Caga Gene ◽  
Gastric Pathology

scholarly journals Molecular Phylogenetic Analysis of 16S rRNA Sequences Identified Two Lineages of Helicobacter pylori Strains Detected from Different Regions in Sudan Suggestive of Differential Evolution

2020 ◽  
Vol 2020 ◽  
pp. 1-12
Author(s):  
Abeer Babiker Idris ◽  
Hadeel Gassim Hassan ◽  
Maryam Atif Salaheldin Ali ◽  
Sulafa Mohamed Eltaher ◽  
Leena Babiker Idris ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Helicobacter Pylori ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Human Migration ◽  
Rrna Gene ◽  
Migration Patterns ◽  
H Pylori ◽  
Rrna Sequences ◽  
16S Rrna Sequences

Background. Helicobacter pylori (H. pylori) is ubiquitous among humans and one of the best-studied examples of an intimate association between bacteria and humans. Phylogeny and Phylogeography of H. pylori strains are known to mirror human migration patterns and reflect significant demographic events in human prehistory. In this study, we analyzed the molecular evolution of H. pylori strains detected from different tribes and regions of Sudan using 16S rRNA gene and the phylogenetic approach. Materials and methods. A total of 75 gastric biopsies were taken from patients who had been referred for endoscopy from different regions of Sudan. The DNA extraction was performed by using the guanidine chloride method. Two sets of primers (universal and specific for H. pylori) were used to amplify the 16S ribosomal gene. Sanger sequencing was applied, and the resulted sequences were matched with the sequences of the National Center for Biotechnology Information (NCBI) nucleotide database. The evolutionary aspects were analyzed using MEGA7 software. Results. Molecular detection of H. pylori has shown that 28 (37.33%) of the patients were positive for H. pylori and no significant differences were found in sociodemographic characteristics, endoscopy series, and H. pylori infection. Nucleotide variations were observed at five nucleotide positions (positions 219, 305, 578, 741, and 763–764), and one insertion mutation (750_InsC_751) was present in sixty-seven percent (7/12) of our strains. These six mutations were detected in regions of the 16S rRNA not closely associated with either tetracycline or tRNA binding sites; 66.67% of them were located in the central domain of 16S rRNA. The phylogenetic analysis of 16S rRNA sequences identified two lineages of H. pylori strains detected from different regions in Sudan. The presence of Sudanese H. pylori strains resembling Hungarian H. pylori strains could reflect the migration of Hungarian people to Sudan or vice versa. Conclusion. This finding emphasizes the significance of studying the phylogeny of H. pylori strains as a discriminatory tool to mirror human migration patterns. In addition, the 16S rRNA gene amplification method was found useful for bacterial identification and phylogeny.

scholarly journals Multiple Chromosomal Loci for the babA Gene in Helicobacter pylori

2006 ◽  
Vol 74 (5) ◽  
pp. 3046-3051 ◽  
Author(s):  
Ewa E. Hennig ◽  
Johnna M. Allen ◽  
Timothy L. Cover
Keyword(s):  
Phylogenetic Analysis ◽  
Helicobacter Pylori ◽  
Membrane Protein ◽  
Protein Expression ◽  
Outer Membrane Protein ◽  
Blood Group Antigen ◽  
Chromosomal Locus ◽  
H Pylori ◽  
Chromosomal Loci ◽  
B Blood Group

ABSTRACT Helicobacter pylori babA encodes an outer membrane protein that binds to fucosylated Lewis b blood group antigen. We analyzed a panel of 35 H. pylori strains and identified three possible chromosomal loci for babA. There was a significant association between the presence of babA and the presence of cagA (P = 0.0001). Phylogenetic analysis of babA alleles revealed two divergent families of signal sequences. Among 17 strains in which an intact in-frame babA allele was identified, 10 expressed a detectable BabA protein. Expression of a BabA protein and the Lewis b-binding phenotype were not dependent on the chromosomal locus of babA. These data indicate that there is marked heterogeneity among H. pylori strains in babA genetic content and BabA expression.

Phylogenetic Analysis of Helicobacter pylori 16S rRNA Gene in Gastric Biopsy from Patients with Dyspepsia

2018 ◽  
Vol 24 (9) ◽  
pp. 6789-6792
Author(s):  
Rike Syahniar ◽  
Mardiastuti ◽  
Ari Fahrial Syam ◽  
Andi Yasmon
Keyword(s):  
Phylogenetic Analysis ◽  
Helicobacter Pylori ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gastric Biopsy ◽  
Rrna Gene

scholarly journals New tool for phylogenetic analysis of Helicobacter pylori

2020 ◽  
Vol 6 (2) ◽  
pp. 060-067
Author(s):  
Sorokin Vladimir Mihajlovich ◽  
Pisanov Ruslan Vjacheslavovich ◽  
Vodop'janov Aleksej Sergeevich ◽  
Golubkina Elena Vadimovna
Keyword(s):  
Phylogenetic Analysis ◽  
Helicobacter Pylori

scholarly journals Phylogenetic analysis of Helicobacter pylori strains circulating in Yakutia by three housekeeping genes atpA, mutY, ppa

2020 ◽  
pp. 105-106
Author(s):  
Т.В. Борисова ◽  
Н.Н. Готовцев ◽  
Н.А. Барашков ◽  
М.В. Пак ◽  
М.П. Алексеева ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Helicobacter Pylori ◽  
Housekeeping Genes

В работе представлен филогенетический анализ штаммов Helicobacter pylori, циркулирующих в Якутии, по данным трех генов домашнего хозяйства atpA, mutY, ppa. The work presents a phylogenetic analysis of Helicobacter pylori strains circulating in Yakutia, according to three housekeeping genes of the atpA, mutY, ppa.

Microevolution between paired antral and paired antrum and corpus Helicobacter pylori isolates recovered from individual patients

2004 ◽  
Vol 53 (7) ◽  
pp. 669-677 ◽  
Author(s):  
Ian M. Carroll ◽  
Niyaz Ahmed ◽  
Sarah M. Beesley ◽  
Aleem A. Khan ◽  
Sheikh Ghousunnissa ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Helicobacter Pylori ◽  
Length Polymorphism ◽  
Fragment Length Polymorphism ◽  
Signal Sequence ◽  
Mixed Infections ◽  
Pcr Fingerprinting ◽  
Sequence Variations ◽  
Rapd Pcr ◽  
Random Amplification

Sequence variations located at the signal sequence and mid-region within the vacA gene, the 3′-end of the cagA gene, the indel motifs at the 3′-end of the cag pathogenicity island and the regions upstream of the vacA and ribA genes were determined by PCR in 19 paired antral or antrum and corpus Helicobacter pylori isolates obtained at the same endoscopic session, and three antral pairs taken sequentially. Random amplification of polymorphic DNA (RAPD)-PCR and fluorescent amplified fragment length polymorphism (FAFLP)-PCR fingerprinting were applied to these paired clinical isolates. The FAFLP-PCR profiles generated were phylogenetically analysed. For the 22 paired isolates there were no differences within pairs at five of the genetic loci studied. However, six pairs of isolates (27 %), of which four were antrum and corpus pairs, showed differences in the numbers of repeats located at the 3′-end of the cagA gene. RAPD-PCR fingerprinting showed that 16 (73 %) pairs, nine of which were antrum and corpus pairs, possessed identical profiles, while six (27 %) displayed distinctly different profiles, indicating mixed infections. Three of the six pairs showing differences at the 3′-end of the cagA gene yielded identical RAPD-PCR fingerprints. FAFLP-PCR fingerprinting and phylogenetic analysis revealed that all 16 pairs that displayed identical RAPD-PCR profiles had highly similar, but not identical, fingerprints, demonstrating that these pairs were ancestrally related but had undergone minor genomic alterations. Two antrum and corpus pairs of isolates, within the latter group, were isolates obtained from two siblings from the same family. This analysis demonstrated that each sibling was colonized by ancestrally related strains that exhibited differences in vacA genotype characteristics.

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