scholarly journals Comparative study between Helicobacter pylori and host human genetics in the Dominican Republic

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Takaaki Ono ◽  
Modesto Cruz ◽  
José A. Jiménez Abreu ◽  
Hiroyuki Nagashima ◽  
Phawinee Subsomwong ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Mitochondrial Dna ◽  
Dominican Republic ◽  
Y Chromosome ◽  
Human Genetics ◽  
African Ancestry ◽  
Human Migration ◽  
High Genetic Diversity ◽  
H Pylori ◽  
Mtdna Haplogroup

Abstract Background Helicobacter pylori, a bacterium that infects the human stomach, has high genetic diversity. Because its evolution is parallel to human, H. pylori is used as a tool to trace human migration. However, there are few studies about the relationship between phylogeography of H. pylori and its host human. Methods We examined both H. pylori DNA and the host mitochondrial DNA and Y-chromosome DNA obtained from a total 119 patients in the Dominican Republic, where human demography consists of various ancestries. DNA extracted from cultured H. pylori were analyzed by multi locus sequence typing. Mitochondrial DNA and Y-chromosome DNA were evaluated by haplogroup analyses. Results H. pylori strains were divided into 2 populations; 68 strains with African group (hpAfrica1) and 51 strains with European group (hpEurope). In Y-chromosomal haplogroup, European origin was dominant, whereas African origin was dominant both in H. pylori and in mtDNA haplogroup. These results supported the hypothesis that mother-to-child infection is predominant in H. pylori infection. The Amerindian type of mtDNA haplogroup was observed in 11.8% of the patients; however, Amerindian type (hspAmerind) of H. pylori was not observed. Although subpopulation type of most hpAfrica1 strains in Central America and South America were hybrid (hspWAfrica/hpEurope), most Dominican Republic hpAfrica1 strains were similar to those of African continent. Conclusions Genetic features of H. pylori, mtDNA, and Y haplogroups reflect the history of colonial migration and slave trade in the Dominican Republic. Discrepancy between H. pylori and the host human genotypes support the hypothesis that adaptability of hspAmerind H. pylori strains are weaker than hpEurope strains. H. pylori strains in the Dominican Republic seem to contain larger proportion of African ancestry compared to other American continent strains.

scholarly journals Virulence genes of Helicobacter pylori in the Dominican Republic

2014 ◽  
Vol 63 (9) ◽  
pp. 1189-1196 ◽  
Author(s):  
Seiji Shiota ◽  
Modesto Cruz ◽  
José A. Jiménez Abreu ◽  
Takahiro Mitsui ◽  
Hideo Terao ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Helicobacter Pylori ◽  
Peptic Ulcer ◽  
Dominican Republic ◽  
Infection Rate ◽  
Rapid Urease Test ◽  
Test Culture ◽  
Urease Test ◽  
The Status ◽  
H Pylori

Although the incidence of gastric cancer in the Dominican Republic is not high, the disease remains a significant health problem. We first conducted a detailed analysis of Helicobacter pylori status in the Dominican Republic. In total, 158 patients (103 females and 55 males; mean age 47.1±16.2 years) were recruited. The status of H. pylori infection was determined based on four tests: rapid urease test, culture test, histological test and immunohistochemistry. The status of cagA and vacA genotypes in H. pylori was examined using PCR and gene sequencing. The overall prevalence of H. pylori infection was 58.9 %. No relationship was found between the H. pylori infection rate and the age range of 17–91 years. Even in the youngest group (patients aged <29 years), the H. pylori infection rate was 62.5 %. Peptic ulcer was found in 23 patients and gastric cancer was found in one patient. The H. pylori infection rate in patients with peptic ulcer was significantly higher than that in patients with gastritis (82.6 versus 54.5 %, P<0.01). The cagA-positive/vacA s1m1 genotype was the most prevalent (43/64, 67.2 %). Compared with H. pylori-negative patients, H. pylori-positive patients showed more severe gastritis. Furthermore, the presence of cagA was related to the presence of more severe gastritis. All CagA-positive strains had Western-type CagA. In conclusion, we found that H. pylori infection is a risk factor for peptic ulcer in the Dominican Republic. Patients with cagA-positive H. pylori could be at higher risk for severe inflammation and atrophy.

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.

Overview of Human Lineage Genetic Marker Studies in Bosnia and Herzegovina: Y chromosome story

2021 ◽  
Vol 3 (1) ◽  
Author(s):  
Aldin Pirić ◽  
Sabahudin Ćordić ◽  
Lejla Smajlović-Skenderagić ◽  
Serkan Dogan ◽  
Damir Marjanović ◽  
...  
Keyword(s):  
Y Chromosome ◽  
Bosnia And Herzegovina ◽  
Human Genetics ◽  
Forensic Genetics ◽  
Human Migration ◽  
Gene Pools ◽  
Maternal Lineage ◽  
Marker Studies ◽  
Lineage Markers ◽  
Different Cultures

Abstract – Modern Bosnia and Herzegovina is a state consisting of multiple ethnicities and regions located in the Western Balkan, with a very complex history. The earliest historical findings show that its area was inhabited since the Paleolithic. From that time, this part of Europe, especially the region of the Modern Bosnia and Herzegovina, could be recognized as the crossroad for the different human migration and the meeting point for different cultures, religions and gene pools. Mitochondrial DNA is being used for maternal lineage testing, while the Y chromosome is being used for paternal lineage testing. Therefore, these markers are being referred to as lineage markers. Lineage markers are often used for parental lineage monitoring in population genetics, human genetics, as well as in forensic genetics. The main intention of this paper is to construct a short overview of the Y chromosome studies performed in Bosnia and Herzegovina within the last two decades.

scholarly journals Human genetics of the Kula Ring: Y-chromosome and mitochondrial DNA variation in the Massim of Papua New Guinea

2014 ◽  
Vol 22 (12) ◽  
pp. 1393-1403 ◽  
Author(s):  
Mannis van Oven ◽  
Silke Brauer ◽  
Ying Choi ◽  
Joe Ensing ◽  
Wulf Schiefenhövel ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Y Chromosome ◽  
Papua New Guinea ◽  
Human Genetics ◽  
New Guinea ◽  
Dna Variation

scholarly journals In VivoSequence Variation in HopZ, a Phase-Variable Outer Membrane Protein of Helicobacter pylori

2012 ◽  
Vol 80 (12) ◽  
pp. 4364-4373 ◽  
Author(s):  
Lynn Kennemann ◽  
Birgit Brenneke ◽  
Sönke Andres ◽  
Lars Engstrand ◽  
Thomas F. Meyer ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Membrane Protein ◽  
Outer Membrane ◽  
Outer Membrane Protein ◽  
Human Migration ◽  
Phase Variable ◽  
Status Change ◽  
Content Type ◽  
H Pylori

ABSTRACTTheHelicobacter pyloriouter membrane protein HopZ is regulated by a phase-variable CT repeat and occurs in two distinct allelic variants. Whole-genome comparisons of isolates from one human volunteer recently provided evidence forin vivoselection for thehopZON status. We explored the frequency of sequence variation inhopZduring acute and chronic human infection and studied the association ofhopZwith the phylogeographic population structure ofH. pylori. hopZON variants were cultured from 24 out of 33 volunteers challenged with thehopZOFF strain BCS 100. Transmission ofH. pyloriwithin families was also frequently associated with a status change ofhopZ. In contrast,hopZsequences obtained from 26 sets of sequential isolates from chronically infected individuals showed no changes of status, suggesting that thehopZstatus selected during early infection is subsequently stable. Mutations leading to amino acid changes in HopZ occurred more frequently in ON than in OFF status isolates during chronic infection, indicating that sequence changes are more likely the result of positive selection in ON isolates than of a loss of negative selection pressure in OFF isolates. Analysis of 63 isolates from chronically infected individuals revealed no significant correlation ofhopZstatus with chronic atrophic gastritis.hopZsequences were obtained from a globally representative collection of 54H. pyloristrains. AllH. pyloripopulations containedhopZ-positive isolates. The data suggest thathopZhas been acquired and split into the two variants before the human migration out of Africa.

scholarly journals Diverse Phenotypes Resulting from Polyphosphate Kinase Gene (ppk1) Inactivation in Different Strains of Helicobacter pylori

2005 ◽  
Vol 187 (22) ◽  
pp. 7687-7695 ◽  
Author(s):  
Shumin Tan ◽  
Cresson D. Fraley ◽  
Maojun Zhang ◽  
Daiva Dailidiene ◽  
Arthur Kornberg ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Brain Heart Infusion ◽  
High Energy ◽  
Soft Agar ◽  
Polyphosphate Kinase ◽  
Initial Growth ◽  
Inorganic Polyphosphate ◽  
Kinase Gene ◽  
High Genetic Diversity ◽  
H Pylori

ABSTRACT Connections among biochemical pathways should help buffer organisms against environmental stress and affect the pace and trajectory of genome evolution. To explore these ideas, we studied consequences of inactivating the gene for polyphosphate kinase 1 (ppk1) in strains of Helicobacter pylori, a genetically diverse gastric pathogen. The PPK1 enzyme catalyzes synthesis of inorganic polyphosphate (poly P), a reservoir of high-energy phosphate bonds with multiple roles. Prior analyses in less-fastidious microbes had implicated poly P in stress resistance, motility, and virulence. In our studies, ppk1 inactivation caused the expected near-complete absence of poly P (>250-fold decrease) but had phenotypic effects that differed markedly among unrelated strains: (i) poor initial growth on standard brain heart infusion agar (five of six strains tested); (ii) weakened colonization of mice (4 of 5 strains); (iii) reduced growth on Ham's F-12 agar, a nutritionally limiting medium (8 of 11 strains); (iv) heightened susceptibility to metronidazole (6 of 17 strains); and (v) decreased motility in soft agar (1 of 13 strains). Complementation tests confirmed that the lack of growth of one Δppk1 strain on F-12 agar and the inability to colonize mice of another were each due to ppk1 inactivation. Thus, the importance of ppk1 to H. pylori differed among strains and the phenotypes monitored. We suggest that quantitative interactions, as seen here, are common among genes that affect metabolic pathways and that H. pylori's high genetic diversity makes it well suited for studies of such interactions, their underlying mechanisms, and their evolutionary consequences.

scholarly journals VARIABILITY OF NEUTROPHIL-ACTIVATING PROTEIN AMONG HELICOBACTER PYLORI STRAINS

2021 ◽  
Vol 80 (1) ◽  
pp. 43-50
Author(s):  
Cecília R.C. Calado
Keyword(s):  
Genetic Diversity ◽  
Helicobacter Pylori ◽  
Immune System ◽  
Virulence Factors ◽  
Immunomodulatory Activity ◽  
Host Immune System ◽  
High Genetic Diversity ◽  
Vacuolating Cytotoxin ◽  
Synonymous Substitutions ◽  
H Pylori

The Helicobacter pylori neutrophil activating protein (NAP) presents relevant inflammatory and immunomodulatory activity and has consequently been explored as a diagnosis and therapeutic target. In the present work, nap gene sequences, retrieved from H. pylori isolated world-wide, were analyzed, a high genetic diversity (with 88% of alleles) being observed in accordance with other virulence factors. The phylogenetic analysis did not reveal the separation of strains per geographical region according to a bacterial panmictic population. When compared to other genes of virulence factors of H. pylori, such as the vacuolating cytotoxin A (vacA), nap presents slightly lower genetic variability, concerning the number of alleles and polymorphic sites, pointing to a possible lower pressure of the host immune system. The nap genetic diversity is associated to a high proportion of synonymous substitutions in relation to non-synonymous substitutions, pointing to equilibrium between the need for antigenic diversity as a mechanism to escape the host immune system and the maintenance of the proteins function. All this information could be put to good use when planning the NAP application as a therapeutic or diagnostic target.

scholarly journals Host-Interactive Genes in Amerindian Helicobacter pylori Diverge from Their Old World Homologs and Mediate Inflammatory Responses

2010 ◽  
Vol 192 (12) ◽  
pp. 3078-3092 ◽  
Author(s):  
S. P. Mane ◽  
M. G. Dominguez-Bello ◽  
M. J. Blaser ◽  
B. W. Sobral ◽  
R. Hontecillas ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Inflammatory Responses ◽  
Pathogenicity Island ◽  
Human Migration ◽  
Human Populations ◽  
Peptic Ulcers ◽  
Ags Cells ◽  
Old World ◽  
Increased Risk ◽  
H Pylori

ABSTRACT Helicobacter pylori is the dominant member of the gastric microbiota and has been associated with an increased risk of gastric cancer and peptic ulcers in adults. H. pylori populations have migrated and diverged with human populations, and health effects vary. Here, we describe the whole genome of the cag-positive strain V225d, cultured from a Venezuelan Piaroa Amerindian subject. To gain insight into the evolution and host adaptation of this bacterium, we undertook comparative H. pylori genomic analyses. A robust multiprotein phylogenetic tree reflects the major human migration out of Africa, across Europe, through Asia, and into the New World, placing Amerindian H. pylori as a particularly close sister group to East Asian H. pylori. In contrast, phylogenetic analysis of the host-interactive genes vacA and cagA shows substantial divergence of Amerindian from Old World forms and indicates new genotypes (e.g., VacA m3) involving these loci. Despite deletions in CagA EPIYA and CRPIA domains, V225d stimulates interleukin-8 secretion and the hummingbird phenotype in AGS cells. However, following a 33-week passage in the mouse stomach, these phenotypes were lost in isolate V225-RE, which had a 15-kb deletion in the cag pathogenicity island that truncated CagA and eliminated some of the type IV secretion system genes. Thus, the unusual V225d cag architecture was fully functional via conserved elements, but the natural deletion of 13 cag pathogenicity island genes and the truncation of CagA impaired the ability to induce inflammation.

scholarly journals Repeated out-of-Africa expansions of Helicobacter pylori driven by replacement of deleterious mutations

2021 ◽  
Author(s):  
Harry Thorpe ◽  
Elise Tourrette ◽  
Koji Yahara ◽  
Filipa Vale ◽  
Siqi Liu ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
African Ancestry ◽  
Deleterious Mutations ◽  
Bacterial Populations ◽  
Synonymous Mutations ◽  
Anatomically Modern Humans ◽  
Population Sizes ◽  
Out Of Africa ◽  
H Pylori

All genomes mutate but the consequences of the resulting deleterious mutational load are poorly understood. Helicobacter pylori lives in the human stomach, has a higher mutation rate than most bacteria and has accompanied anatomically modern humans in migrations including the out-of-Africa expansion more than 50,000 years ago. H. pylori from East Asia have accumulated at least 500 more non-synonymous mutations than African strains, which we propose is due to reduced efficacy of selection during the out-of-Africa bottleneck. H. pylori from Europe and the Middle East trace a substantially higher fraction of ancestry from modern African populations than the humans that carry them, which we find is due to at least three separate admixture events. African ancestry is elevated at positions in the genome where non-synonymous mutations are at high frequency in Asia. We propose that this is due to replacement of deleterious mutations that accumulated during the bottleneck, with the high overall African ancestry proportion due to clonal expansion of strains of African origin. We use simulations to show that a Muller's ratchet like effect can lead to long-term segregation of deleterious mutations within bacterial populations after a bottleneck, despite high rates of homologous recombination, but that population fitness can be restored by migration of small numbers of bacteria from non-bottlenecked populations. Our results demonstrate that population bottlenecks can have long-term genomic and demographic consequences, even in species with enormous population sizes.

The rod-to-coccoid body transformation in cultures of Helicobacter pylori

1990 ◽  
Vol 48 (3) ◽  
pp. 626-627
Author(s):  
A. R. Crooker ◽  
W. G. Kraft ◽  
T. L. Beard ◽  
M. C. Myers
Keyword(s):  
Helicobacter Pylori ◽  
Growth Cycle ◽  
Negative Bacterium ◽  
Body Formation ◽  
Coccoid Form ◽  
Spiral Form ◽  
Prolonged Culture ◽  
H Pylori ◽  
Upper Gastrointestinal

Helicobacter pylori is a microaerophilic, gram-negative bacterium found in the upper gastrointestinal tract of humans. There is strong evidence that H. pylori is important in the etiology of gastritis; the bacterium may also be a major predisposing cause of peptic ulceration. On the gastric mucosa, the organism exists as a spiral form with one to seven sheathed flagella at one (usually) or both poles. Short spirals were seen in the first successful culture of the organism in 1983. In 1984, Marshall and Warren reported a coccoid form in older cultures. Since that time, other workers have observed rod and coccal forms in vitro; coccoid forms predominate in cultures 3-7 days old. We sought to examine the growth cycle of H. pylori in prolonged culture and the mode of coccoid body formation.

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