Improvement of Multiple-Locus VNTR Analysis Typing Scheme for Helicobacter pylori

Сорокин, В. М.; Pisanov, R. V.; Vodop'janov, Aleksej Sergeevich

doi:10.9734/ajbgmb/2018/v1i430045

Cited by 2 publications

(1 citation statement)

References 13 publications

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“…Therefore, H. pylori is a species without a significant clonal structure [2,3]. The real genetic diversity of H. pylori was confirmed by various methodological approaches [3][4][5][6][7][8].…”

Section: Introductionmentioning

confidence: 99%

New tool for phylogenetic analysis of Helicobacter pylori

Сорокин¹,

Vjacheslavovich²,

Sergeevich³

et al. 2020

World J. Adv. Res. Rev.

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The aim of this study was to detect canonical insertion/deletion (INDEL) markers in the genome of Helicobacter pylori and offer INDEL-typing method for differentiation of H. pylori strains. For comparative analysis of the genomes of H. pylori presented in the GenBank database, a local database of nucleotide sequences of 69 H. pylori strains was created. For detecting all INDEL markers with a preset size of 6-20 bp a pairwise comparison of more than 1500 open reading frames (ORF) in the genomes of local database strains was performed. Ten loci containing INDEL markers were founded. The five most variable loci were tested in silico with 21 strains with known geographical origin from the most common populations of hpEurope, hspWAfrica, and hspEAsia. Fifteen individual genotypes with a high diversity index (DI=0.95) were identified. For cluster analysis, the minimal spanning tree (MST) method was used, which demonstrated a clear distribution of clusters according to the geographical origin of the strains tested. INDEL-typing of 21 regional strains from the Astrakhan region was performed in vitro. It was shown that an extensive majority of them belong to the population hpEurope. The findings in this study indicate that the proposed INDEL-typing method almost perfectly reflects the geographical distribution of H. pylori strains determined by the multilocus sequence typing (MLST) method, despite the fact that the primary object of research is completely different genes. Further research is needed to determine the geographical origin of H. pylori strains in Russia.

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Section: Introductionmentioning

confidence: 99%

New tool for phylogenetic analysis of Helicobacter pylori

Сорокин¹,

Vjacheslavovich²,

Sergeevich³

et al. 2020

World J. Adv. Res. Rev.

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Geographical diversity of Helicobacter pylori strains circulating in the European Part of the Russian Federation

Сорокин

Сварваль

Водопьянов

et al. 2021

Russian Journal of Infection and Immunity

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The aim of the study was to identify INDEL markers and study geographical origin of regional H. pylori strains circulating in the European part of the Russian Federation. The study included 56 strains of H. pylori isolated in three regions of the Russian Federation: Saint Petersburg, Astrakhan and Rostov Regions. Genomic DNA was isolated using a set of Probe NA (DNA Technology, Russia), according to the manufacturer’s instructions. Detection of INDEL markers hp5605, hp6405, hp340, hp1390, hp3660 was performed using PCR. Clustering of the identified INDEL genotypes and building a phylogenetic tree were performed using the BioNumerics 7.6 and GrapeTree software packages. 21 strains from the GenBank database with known geographical origin were used as reference strains. In 20 strains from Saint Petersburg, 13 individual genotypes were identified, while 17 strains belong to the European cluster (hpEurope), 2 strains belong to the hspEAsia cluster and one strain belongs to the hspWAfrica cluster. The most common genotype identified in the European cluster includes six strains from Saint Petersburg and two strains from the GenBank database. For further differentiation of these strains, the VNTR typing method was used, which allowed identifying eight individual genotypes in eight strains. Fifty-six studied russian strains are represented by thirty individual genotypes, which reflects the high heterogeneity of strains circulating in the European part of the Russian Federation. The most frequent genotype is represented by two hpEurope strains, one strain from the Astrakhan region, as well as 5 and 6 strains from the Rostov Region and Saint Petersburg, respectively. The vast majority of Russian strains (52/56) belong to the hpEurope population, while two strains from Saint Petersburg are included in the hspEAsia population, and one strain from Saint Petersburg and the Astrakhan Region is included in the hspWAfrica population. Total, 77 H. pylori strains are represented by 37 individual genotypes with a high diversity index (DI = 0.95), which allows us to consider the proposed INDEL typing method as an independent method for genotyping H. pylori strains. Taking into consideration the complexity of the problem of accurately determining the geographical origin of H. pylori strains, the proposed simple and convenient method of INDEL typing of H. pylori strains, based on an available PCR method becomes very relevant and allows us to conduct an adequate primary analysis of the geographical origin of Russian H. pylori strains.

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Improvement of Multiple-Locus VNTR Analysis Typing Scheme for Helicobacter pylori

Cited by 2 publications

References 13 publications

New tool for phylogenetic analysis of Helicobacter pylori

New tool for phylogenetic analysis of Helicobacter pylori

Geographical diversity of Helicobacter pylori strains circulating in the European Part of the Russian Federation

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