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High genetic diversity and rapid microevolution are a peculiarity of genomes Helicobacter pylori,... more High genetic diversity and rapid microevolution are a peculiarity of genomes Helicobacter pylori, a phenomenon that is proposed to play a functional role in persistence and colonisation of diverse human populations. Isolates of H. pylori can be classified phylogeographically. To characterise diverse strains of this pathogen in different human populations, we compare MLVA genotypes of 48 H. pylori strains isolated from different regions in the South of Russia. Cluster analysis identified 48 individual MLVA types (MTs) and revealed the possible belonging the greatest part of the strains to hpEurope, and two strains to hpEastAsia population, when compared to the 4 publically available genomes. MLVA typing is a faster and more standardized method for studying the genetic relatedness and is available for every standard PCR laboratory. The proposed method may be successfully used in molecular epidemiology and possibly for population identification of H. pylori. A similar study was conducted in Russia and Europe for the first time.

The aim of this study was to detect canonical insertion/deletion (INDEL) markers in the genome of... more 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.

Сравнительный анализ генотипов штаммов Helicobacter pylori в Ростовской и Астраханской областях. Медицинский вестник Юга Рос-сии, 2018

Цель: изучить инфицированность бактериями Нelicobacter pylori взрослого и детского населения Рост... more Цель: изучить инфицированность бактериями Нelicobacter pylori взрослого и детского населения Ростовской и Астраханской области, определить частоту встречаемости факторов патогенности H. pylori у разных возрастных групп населения. Материалы и методы: обследованы 118 взрослых и 112 детей. Наличие ДНК H. pylori и факторов пато-генности CagA и VacA в биопсийном материале слизистой оболочки антрального отдела желудка определяли мето-дом полимеразной цепной реакции. Результаты: для детской популяции характерен значимо меньший процент H. pylori-позитивных пациентов, Превалирующим генотипом H.pylori в детской популяции является авирулентный ге-нотип Vac s2m2 (60 %) (χ2: p <0,005). Для взрослого населения Ростовской области генотип CagA+VacA s1VacA m1 является маркером язвенной болезни. Заключение: проведенные исследования позволили установить различия в инфицированности населения бактериями H. pylori и частоте распространения вирулентных генотипов в зависимости от региона, возраста и тяжести патологии. Ключевые слова: H. pylori, факторы патогенности, хронический гастрит, язвенная болезнь, взрослые, дети. Objective: to study the infection of the adult and children's population of the Rostov and Astrakhan regions by the bacteria Helicobacter pylori, to determine the frequency of H. pylori pathogenicity factors in diff erent age groups of the population. Materials and methods: 118 adults and 112 children were examined. Th e presence of H. pylori DNA and the pathogenicity factors of CagA and VacA in the biopsy material of the mucous membrane of the antrum of the stomach was determined by PCR. Results: a signifi cantly smaller percentage of H. pylori-positive patients is characteristic of the child population. Th e prevalent H. pylori genotype in the infant population is the avirulent genotype Vac s2m2 (60%) (χ2: p <0.005). Genotype CagA + VacAs1 VacAm1 is a marker of peptic ulcer for adult population of the Rostov region. Conclusion: Th e conducted studies allowed to establish diff erences in infection of the population with H. pylori bacteria and the frequency of the distribution of virulent genotypes depending on the region, age and severity of the pathology.

Improvement of Multiple-Locus VNTR Analysis Typing Scheme for Helicobacter pylori, 2019

Aims: To improve a multiple-locus variable-number tandem-repeat (VNTR) analysis (MLVA) assay for ... more Aims: To improve a multiple-locus variable-number tandem-repeat (VNTR) analysis (MLVA) assay for Helicobacter pylori typing. Materials and Methods: Polymorphic VNTRs were searched by Gene Expert. The distribution and polymorphism of each VNTR locus were analyzed in 18 H. pylori genomes from the NCBI genome database by BLAST and were compared with a collection of 15 clinical H. pylori strains. The MLVA assay was compared with MLST-typing for discriminating H. pylori isolates. Results: Twelve VNTR loci were identified by bioinformatic screening of H. pylori genomes, and five of them were highly polymorphic. Therefore, an MLVA assay composed of five VNTR loci was developed with greatest discriminatory power. Conclusion: MLVA typing is a faster and more standardized method for studying the genetic relatedness of H. pylori isolates. At preliminary stage it is sufficient to use only 3 VNTR loci for the differentiation of H. pylori strains. Original Research Article Sorokin et al.; AJBGMB, 1(4): 1-7, 2018; Article no.AJBGMB.46609 2

New tool for phylogenetic analysis of Helicobacter pylori, 2020

The aim of this study was to detect canonical insertion/deletion (INDEL) markers in the genome of... more 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.

Abstract: High genetic diversity and rapid microevolution are a peculiarity of genomes Helicobac... more Abstract: High genetic diversity and rapid microevolution are a peculiarity of genomes Helicobacter pylori, a phenomenon
that is proposed to play a functional role in persistence and colonisation of diverse human populations. Isolates of H. pylorican
be classified phylogeographically. To characterise diverse strains of this pathogen in different human populations, we compare
MLVA genotypes of 48 H. pyloristrains isolated from different regions in the South of Russia. Cluster analysis identified 48
individual MLVA types (MTs) and revealed the possible belonging the greatest part of the strains to hpEurope, and two strains to
hpEastAsia population, when compared to the 4 publically available genomes. The proposed method may be successfully used in
molecular epidemiology and possibly for population identification of H. pylori. A similar study was conducted in Russia and
Europe for the first time.

High genetic diversity and rapid microevolution are a peculiarity of genomes Helicobacter pylori,... more High genetic diversity and rapid microevolution are a peculiarity of genomes Helicobacter pylori, a phenomenon that is proposed to play a functional role in persistence and colonisation of diverse human populations. Isolates of H. pylori can be classified phylogeographically. To characterise diverse strains of this pathogen in different human populations, we compare MLVA genotypes of 48 H. pylori strains isolated from different regions in the South of Russia. Cluster analysis identified 48 individual MLVA types (MTs) and revealed the possible belonging the greatest part of the strains to hpEurope, and two strains to hpEastAsia population, when compared to the 4 publically available genomes. MLVA typing is a faster and more standardized method for studying the genetic relatedness and is available for every standard PCR laboratory. The proposed method may be successfully used in molecular epidemiology and possibly for population identification of H. pylori. A similar study was conducted in Russia and Europe for the first time.

The aim of this study was to detect canonical insertion/deletion (INDEL) markers in the genome of... more 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.

Сравнительный анализ генотипов штаммов Helicobacter pylori в Ростовской и Астраханской областях. Медицинский вестник Юга Рос-сии, 2018

Цель: изучить инфицированность бактериями Нelicobacter pylori взрослого и детского населения Рост... more Цель: изучить инфицированность бактериями Нelicobacter pylori взрослого и детского населения Ростовской и Астраханской области, определить частоту встречаемости факторов патогенности H. pylori у разных возрастных групп населения. Материалы и методы: обследованы 118 взрослых и 112 детей. Наличие ДНК H. pylori и факторов пато-генности CagA и VacA в биопсийном материале слизистой оболочки антрального отдела желудка определяли мето-дом полимеразной цепной реакции. Результаты: для детской популяции характерен значимо меньший процент H. pylori-позитивных пациентов, Превалирующим генотипом H.pylori в детской популяции является авирулентный ге-нотип Vac s2m2 (60 %) (χ2: p <0,005). Для взрослого населения Ростовской области генотип CagA+VacA s1VacA m1 является маркером язвенной болезни. Заключение: проведенные исследования позволили установить различия в инфицированности населения бактериями H. pylori и частоте распространения вирулентных генотипов в зависимости от региона, возраста и тяжести патологии. Ключевые слова: H. pylori, факторы патогенности, хронический гастрит, язвенная болезнь, взрослые, дети. Objective: to study the infection of the adult and children's population of the Rostov and Astrakhan regions by the bacteria Helicobacter pylori, to determine the frequency of H. pylori pathogenicity factors in diff erent age groups of the population. Materials and methods: 118 adults and 112 children were examined. Th e presence of H. pylori DNA and the pathogenicity factors of CagA and VacA in the biopsy material of the mucous membrane of the antrum of the stomach was determined by PCR. Results: a signifi cantly smaller percentage of H. pylori-positive patients is characteristic of the child population. Th e prevalent H. pylori genotype in the infant population is the avirulent genotype Vac s2m2 (60%) (χ2: p <0.005). Genotype CagA + VacAs1 VacAm1 is a marker of peptic ulcer for adult population of the Rostov region. Conclusion: Th e conducted studies allowed to establish diff erences in infection of the population with H. pylori bacteria and the frequency of the distribution of virulent genotypes depending on the region, age and severity of the pathology.

Improvement of Multiple-Locus VNTR Analysis Typing Scheme for Helicobacter pylori, 2019

Aims: To improve a multiple-locus variable-number tandem-repeat (VNTR) analysis (MLVA) assay for ... more Aims: To improve a multiple-locus variable-number tandem-repeat (VNTR) analysis (MLVA) assay for Helicobacter pylori typing. Materials and Methods: Polymorphic VNTRs were searched by Gene Expert. The distribution and polymorphism of each VNTR locus were analyzed in 18 H. pylori genomes from the NCBI genome database by BLAST and were compared with a collection of 15 clinical H. pylori strains. The MLVA assay was compared with MLST-typing for discriminating H. pylori isolates. Results: Twelve VNTR loci were identified by bioinformatic screening of H. pylori genomes, and five of them were highly polymorphic. Therefore, an MLVA assay composed of five VNTR loci was developed with greatest discriminatory power. Conclusion: MLVA typing is a faster and more standardized method for studying the genetic relatedness of H. pylori isolates. At preliminary stage it is sufficient to use only 3 VNTR loci for the differentiation of H. pylori strains. Original Research Article Sorokin et al.; AJBGMB, 1(4): 1-7, 2018; Article no.AJBGMB.46609 2

New tool for phylogenetic analysis of Helicobacter pylori, 2020

The aim of this study was to detect canonical insertion/deletion (INDEL) markers in the genome of... more 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.

Abstract: High genetic diversity and rapid microevolution are a peculiarity of genomes Helicobac... more Abstract: High genetic diversity and rapid microevolution are a peculiarity of genomes Helicobacter pylori, a phenomenon
that is proposed to play a functional role in persistence and colonisation of diverse human populations. Isolates of H. pylorican
be classified phylogeographically. To characterise diverse strains of this pathogen in different human populations, we compare
MLVA genotypes of 48 H. pyloristrains isolated from different regions in the South of Russia. Cluster analysis identified 48
individual MLVA types (MTs) and revealed the possible belonging the greatest part of the strains to hpEurope, and two strains to
hpEastAsia population, when compared to the 4 publically available genomes. The proposed method may be successfully used in
molecular epidemiology and possibly for population identification of H. pylori. A similar study was conducted in Russia and
Europe for the first time.