Helicobacter Pylori Strains Research Articles

Ancestral European Origins and Population Structure of Helicobacter pylori Strains from an Iranian Population

Ancestral European Origins and Population Structure of Helicobacter pylori Strains from an Iranian Population

Polyacrylamide Gel Electrophoresis of Proteins Method versus Enzyme-Linked Immunosorbent Assay and Immunochromatography with Monoclonal Antibodies in Pediatric Infection with Helicobacter Pylori

The current methods for the diagnosis of Helicobacter pylori infection in children include invasive (direct) methods, that enable the detection of the bacteria or the bacterial urease in gastric biopsies, or noninvasive (indirect) methods, which consist of researching specific antibodies, antigens and urease in other different samples (serum, saliva, urine, stool, exhaled air). The urease functions in H. pylori infection is to neutralize gastric acid by producing NH3 through the hydrolysis of urea. Monochloramine, a NH3-derived compounds has cytotoxic effects on host cells. The Western Blot method refers to the extraction of a a sodium dodecyl sulphate from a Helicobacter pylori strain followed by a separation of the solubilised protein using discontinous polyacrylamide gel electrophoresis according to molecular mass and transfer of the separated proteins to nitrocellulose. The ELISA (enzyme-linked immunosorbent assay) technique refers to the detection of Anti-Helicobacter pylori antibodies type Ig G. We also used an immunochromatographic system with the lateral leakage test strip based on the principle of the sandwich technique with monoclonal antibodies. As a result, more than two types of reactions can be detected on a single assay device by the combination of colloidal gold �labelled antibodies and complementary oligonucleotide-labelled immobilized at different places on a nitrocellulose membrane. Our study aims to assess the performances of the Western Blot method for determining anti-Helicobacter pylori Ig A and Ig G antibodies in correlation with clinical data and other available diagnosis methods. For validation purposes, the results were compared to those obtained using the enzyme-linked immunosorbent assay technique, gastric biopsy and immunochromatography.

High Primary Antibiotic Resistance of Helicobacter pylori Strains Isolated from Pediatric and Adult Patients in Poland during 2016-2018.

Monitoring the antibiotic resistance of H. pylori is an important step in the effective treatment of this bacterium, thus the aim of the present study was to assess the prevalence of antimicrobial resistance of H. pylori strains isolated from pediatric and adult patients with primary infections in 2016–2018. Antral biopsies from 334 treatment-naïve patients (126 children and 208 adults) were obtained. A total of 71 clinical H. pylori strains (22 from children and 49 from adults) were isolated and examined for amoxicillin (AMX), clarithromycin (CLR), metronidazole (MTZ), tetracycline (TET), and levofloxacin (LEV) susceptibility. The activity of the antibiotics was measured by E-tests. Strains were considered as resistant to antibiotics with minimum inhibitory concentrations (MICs) equal to ≥0.125 μg/mL (AMX), ≥0.5 μg/mL (CLR), ≥8 μg/mL (MTZ), and ≥1 μg/mL (TET and LEV). The highest prevalence of antibiotic resistance in H. pylori strains was observed for CLR and MTZ, at frequencies of 54.5% and 31.8% vs. 30.6% and 46.9% for children and adults, respectively. A much lower frequency of isolation of resistant strains was demonstrated for LEV and TET, this being 9.1% and 4.5% vs. 18.4% and 4.1% for pediatric and adult patients, respectively. The presence of AMX-resistant strains was not observed. The H. pylori strains isolated from Polish patients with primary infections showed a high level of antibiotic resistance to CLR and MTZ (>30%).

Genome Sequences of Three Colombian Helicobacter pylori Strains Isolated from Tolimense Patients.

We present the complete genome sequences of three Helicobacter pylori strains isolated from patients who resided in Tolima Department, Colombia, diagnosed with chronic gastritis. The genomes present an average length of 1.6 Mbp and 1,546 genes and correspond to different H. pylori subpopulations.

Variations in cag pathogenicity island genes of Helicobacter pylori from Latin American groups may influence neoplastic progression to gastric cancer

Helicobacter pylori (HP) colonizes the human stomach and induces acute gastritis, peptic ulcer disease, atrophic gastritis, and gastric adenocarcinoma. Increased virulence in HP isolates derives from harboring the cag (cytotoxin-associated genes) pathogenicity island (cagPAI). We analyzed the microvariants in cagPAI genes with the hypothesis that they may play an important role in determining HP virulence. We tested DNAs from cagA positive patients HP isolates; a total of 74 patients with chronic gastritis (CG, N = 37), intestinal metaplasia (IM, N = 21) or gastric cancer (GC, N = 16) from Mexico and Colombia. We selected 520 non-synonymous variants with at least 7.5% frequency in the original sequence outputs or with a minimum of 5 isolates with minor allele. After adjustment for multiple comparisons, no variants were statistically significantly associated with IM or GC. However, 19 non-synonymous showed conventional P-values < 0.05 comparing the frequency of the alleles between the isolates from subjects with gastritis and isolates from subjects with IM or GC; 12 of these showed a significant correlation with the severity of the disease. The present study revealed that several cagPAI genes from Latin American Western HP strains contains a number of non-synonymous variants in relatively high frequencies which could influence on the clinical outcome. However, none of the associations remained statistically significant after adjustment for multiple comparison.

Antibacterial activity of ethoxzolamide against Helicobacter pylori strains SS1 and 26695

With the rise of bacterial resistance to conventional antibiotics, re-purposing of Food and Drug Administration (FDA) approved drugs currently used to treat non-bacteria related diseases as new leads for antibacterial drug discovery has become an attractive alternative. Ethoxzolamide (EZA), an FDA-approved diuretic acting as a human carbonic anhydrase inhibitor, is known to kill the gastric pathogenic bacterium Helicobacter pylori in vitro via an, as yet, unknown mechanism. To date, EZA activity and resistance have been investigated for only one H. pylori strain, P12. We have now performed a susceptibility and resistance study with H. pylori strains SS1 and 26695. Mutants resistant to EZA were isolated, characterized and their genomes sequenced. Resistance-conferring mutations were confirmed by backcrossing the mutations into the parent strain. As with P12, resistance to EZA in strains SS1 and 26695 does not develop easily, since the rate of spontaneous resistance acquisition was less than 10−8. Acquisition of resistance was associated with mutations in 3 genes in strain SS1, and in 6 different genes in strain 26695, indicating that EZA targets multiple systems. All resistant isolates had mutations affecting cell wall synthesis and control of gene expression. EZA’s potential for treating duodenal ulcers has already been demonstrated. Our findings suggest that EZA may be developed into a novel anti-H. pylori drug.

The Helicobacter pylori Cag Type IV Secretion System.

Colonization of the human stomach with Helicobacter pylori strains containing the cag pathogenicity island is a risk factor for development of gastric cancer. The cag pathogenicity island contains genes encoding a secreted effector protein (CagA) and components of a type IV secretion system (Cag T4SS). The molecular architecture of the H. pylori Cag T4SS is substantially more complex than that of prototype T4SSs in other bacterial species. In this review, we discuss recent discoveries pertaining to the structure and function of the Cag T4SS and its role in gastric cancer pathogenesis.

Acid formation in gastroenterological patients with colonization of the stomach with virulent and non-virulent strains of helicobacter

Objective. To prove that increased acid production in patients with gastric ulcer and duodenal ulcer is associated with the impact of the virulent strains of Helicobacter pylori but due not to the persistence of non-virulent strains.Materials and methods. Patients with active gastroduodenal ulcer and patients with active chronic pancreatitis accompanied by the gastritis were compared in the respect of the level of pH in the antrum and corpus gastricum, as well as Helicobacter pylori virulence according to the presence cagA gene, especially in combination with vacA allele s1 / m1 (if any of the strains were found in gastric biopsy specimen).Results. In patients with gastric ulcer the average values of pH were significantly lower, both in the antrum and corpus gastricum, than in patients with chronic pancreatitis accompanied by gastritis. Helicobacter pylori strains were found only in half of the patients, either in the gastric ulcer group or in the group of chronic pancreatitis accompanied by the gastritis. Significant difference was revealed after virulent genes identification: virulent strains prevailed in patients with gastric ulcer and in contrast to the prevalence of non-virulent strains in patients with chronic pancreatitis accompanied by the gastritis (Mann-Whitney test, p = 0.001). Since there is no available data that Helicobacter has an affinity for a highly acidic medium in comparison with moderately acidic medium, it is concluded that just primary colonization of the stomach with virulent strains results in hyperacidity (as the consequence of cytotoxicity) and that persistence of non-virulent strains hardly effects hyperacidity.

Association between polymorphisms in HLA-A, HLA-B, HLA-DR, and DQ genes from gastric cancer and duodenal ulcer patients and cagL among cagA-positive Helicobacter pylori strains: The first study in a Turkish population

Colonization of the human gastric mucosa by H. pylori may cause peptic and duodenal ulcers (DUs), gastric lymphomas, and gastric cancers. The cagL gene is a component of cag T4SS and is involved in cagA translocation into host. An association between the risk of gastric cancer and the type of HLA class II (DR and/or DQ) was suggested in different populations. The aim of this study was to investigate, the clinical association of the cagL gene with host HLA alleles in H. pylori strains that were isolated from patients with gastric cancer, DU, and non-ulcer dyspepsia (NUD) and to determine the HLA allele that confers susceptibility or resistance for the risk of gastric cancer and DU development in Turkish patients.A total of 94 patients (44 gastric cancer and 50 DU patients; 58 male, 36 female; mean age, 49.6 years), and 86 individuals (50 NUD patients and 36 persons with normal gastrointestinal system [NGIS]; 30 male, 56 female; mean age, 47.3 years) were included as the patient and the control groups, respectively. CagA and cagL were determined by PCR method. DNA from peripheral blood samples was obtained by EZ-DNA extraction kit. For HLA SSO typing, LIFECODES SSO Typing kits (HLA-A, HLA-B HLA-C, HLA-DRB1 and HLA-DQA1/B1 kits) were used.The CagL/CagA positivity distribution in the groups were as follows: 42 (95.4%) gastric cancer, 46 (92%) DU and, 34 (68%) NUD and no NGIS cases. The HLA-DQA1*01 (OR: 3.82) allele was significantly different, suggesting that these individuals with H. pylori strains harbouring the CagL/CagA positivity are susceptible to the risk of gastric cancer and DU, and the HLA-DQA1*05 (OR, 0.318) allele was suggested as a protective allele for the risk of gastric cancer and DU using univariate analyses. HLA-DQA1*01 (OR, 2.21), HLA-DQB1*06 (OR, 2.67), sex (male, OR, 2.27), and CagL/CagA/(<2) EPIYA C repeats (OR, 5.72) were detected independent risk factors that increased the risk of gastric cancer and DU using multivariate analyses. However, the HLA-DRB1*04 (OR, 0.28) allele was shown to be a protective allele, which decreased the risk of gastric cancer and DU.Gastric pathologies result from an interaction between bacterial virulence factors, host epigenetic and environmental factors, and H. pylori strain heterogeneity, such as genotypic variation among strains and variations in H. pylori populations within an individual host.

Helicobacter pylori Antibiotic resistance patterns among Egyptian children and predictors of resistance

Abstract Background Most individuals are infected by Helicobacter pylori during early childhood; in developing countries, 50% of children are infected by the age of 5 years. Successful eradication is important to prevent the development of antibiotic resistance, as well as to reduce the number of treatments and procedures. Among children receiving the standard triple therapy regimen, eradication rates are declining. Thus, national/ regional antibiotic resistance data could be used to guide treatment regimens for H pylori infection Aim of the work to evaluate the antibiotic resistance patterns of Helicobacter pylori strains among pediatric patients and the predictors of this resistance. Patients and Methods Cross sectional, carried out on 30 pediatric patients who presented to gastroenterology unit Ain Shams University for endoscopic evaluation of their upper GI symptoms including hematemesis, vomiting and abdominal pain. Five gastric biopsies were taken, two from the corpus for histopathology and culture, and 3 from the antrum, where one of them was sent for histopathology, and the second one for rapid urease test, and the third one was sent for culture and sensitivity. Results Results of culture and sensitivity has shown that resistance to amoxicillin was 20%, to clarithromycin was 50%, metronidazole resistance was 86.7%, tetracycline resistance showed to be 13.3%, finally levofloxacin resistance was 6.7%. Excess intake of fat was associated with resistance to amoxicillin and clarithromycin. While, duodenal ulcer and duodenal nodularity were associated with resistance to tetracycline and levofloxacin respectively. Conclusion The eradication regimen in Egypt should be revised according to our national antibiotic resistance data. Further studies are needed to assess predictors of resistance to antibiotics.

Novel and potent inhibitors for dihydropteroate synthase of Helicobacter pylori

An endless drug-resistant strains of Helicobacter pylori and multitudinous drug reactions are obstacles in the treatment of H. pylori infections, thereby ambitious novel proof-of-concept for inhibitor design was practiced in advancement of medication. Dihydropteroate synthase (DHPS) is an alluring target that plays a great role in folate synthesis pathway essential for amino acids biosynthesis was selected for designing novel drugs to prevent infections caused by pathogenic H. pylori. In the present study, a reliable tertiary structure of DHPS in complex with inhibitor 6MB was constructed by Modeler 9v19. DrugBank compounds of DHPS, published inhibitors, and co-crystal ligand (6MB) were docked against DHPS. The best docked compounds were screened against 28.5 million compounds resulted 1186 structural analogs. Virtual screening workflow and quantum polarized ligand dockings of these compounds against DHPS resulted three leads that showed better XP Gscores, ADME properties, and binding-free energies compared to 6MB, DrugBank compounds, and published inhibitors. The proposed leads were also validated by receiver operative characteristic (ROC) curve metrics in the presence of thousand decoys and the best docked existing compounds against DHPS. Long-range molecular dynamics (MD) simulations for 100 ns were executed after post-docking evaluations. Trajectory analysis showed the lead–DHPS docking complex’s inter-molecular interactions were stable throughout the entire runtime of MD simulations than 6MB–DHPS complex and Eliglustat–DHPS complex. The study outcomes showed good competitive binding propensity and active-tunneling of leads over the existing inhibitors, thereby these leads could be ideal inhibitors against DHPS to target H. pylori.

Evaluation of Antibiotic Resistance of Helicobacter pylori Strains Isolated in Bari, Southern Italy, in 2017-2018 by Phenotypic and Genotyping Methods.

Objective: Helicobacter pylori antibiotic resistance is a constantly evolving process and local surveillance is warranted to guide clinicians in the choice of therapy. Materials and Methods: Antibiotic susceptibility testing was performed by E-test on 92 H. pylori strains, and resistance to clarithromycin and levofloxacin was also evaluated using a commercially available genotyping method. Results: In naïve patients the resistance to clarithromycin, levofloxacin, and metronidazole was 37.7%, 26.2%, and 16.4%, respectively, significantly lower than the percentage found in treated patients. Concomitant resistance to ≥2 antibiotics was also observed in naïve patients. The A2143G mutation of the 23S-rRNA gene was the most frequently detected, also in naïve patients. The highest minimum inhibitory concentration (MIC)50 value (256 mg/L) was associated with A2142 mutations in all the patients carrying them. For levofloxacin resistance a mutation in codon 87 was detected in 63.9% and in codon 91 in 36.1% of the H. pylori strains, without significant differences in the patients groups. A mutation in codon 87 was associated with the highest MIC50 value (32 mg/L). Conclusions: In our area, a high prevalence of H. pylori primary resistance was detected; these rates were higher in patients who had experienced failure of several courses of therapy. A better knowledge of the local epidemiology of resistance, and the genotypes responsible, will improve the H. pylori eradication rates.

An Experimental Bacteriostasis of the Banxiaxiexin Decoction and 7 Kinds of Single Taste Traditional Chinese Medicine on Helicobacter Pylori Resistant Strains in Vitro

Objectives: To research experimental bacteriostasis on the Banxiaxiexin decoction and 7 kinds of single taste Traditional Chinese Medicine (TCM) for Helicobacter pylori resistant strains in vitro. Methods: Collecting specimens of gastric mucosa in patients with upper gastrointestinal disease, separated and identified 8 strains of Hp resistant strains, the E-test methods of metronidazole and clarithromycin, drug resistance status of amoxicillin, selected eight strains of clinical drug resistance strains; Using liquid dilution method to determine the Banxiaxiexin decoction and 7 kinds of single Chinese medicine clinical drug-resistant strains of 8 strains of antibacterial effect in vitro. Results: Banxiaxiexin decoction MIC is 0.31 mg/ml, MIC of Radix scutellariae is 0.09 mg/ml, Rhizoma coptidis MIC 0. 16 mg/ml, Glycyrrhizin realness MIC 0. 31 mg/ml, Ginseng MIC 0. 75 mg/ml, there are four of seven kinds of single taste Traditional Chinese Medicine of TCM has bacteriostatic action, the order of antibacterial strength: Scutellaria baicalensis&gt;Coptis chinesis&gt;Glycyrrhizin realness &gt;Ginseng, three kinds of Pinellia, Jujube and dry Zingibe in vitro for H. P ylori no inhibition, the method of MIC with liquid dilution in this decoction were determined, the decoction of resistant isolates average MIC isolates was 0.20±0.09mg/ml, the results showed that this decoction have stronger antibacterial effect on eight kinds of drug resistant strains in vitro. Banxiaxiexin decoction and 4kinds of single taste TCM have stronger antibacterial effect on drug resistant strains in vitro. Conclusion: Banxiaxiexin decoction and 4 kinds of single TCM have strong bacteriostatic effect on the bacteria resistance of Helicobacter pylori strains in vitro, therefore, we suggest that this decoction could be used as an effective method in the treatment of resistant HP associated gastritis.

Antibiotic resistance and clonal relatedness of Helicobacter pylori strains isolated from stomach biopsy specimens in northeast of Iran.

Resistant Helicobacter pylori to commonly used antimicrobial agents are associated with severe upper gastrointestinal disorders. To provide an epidemiological picture of Hpylori and characterize the resistance pattern and genetic variation of clinical isolates, stomach biopsies from patients with functional dyspepsia were evaluated in northeast of Iran. In this study, 80 patients were recruited. Finally, fifty Hpylori strains were isolated from antrum and corpus biopsies by culturing on Columbia agar. All strains were identified by standard laboratory procedures. Susceptibility testing of antibiotics was performed using minimum inhibitory concentration test. Allele-specific primer (ASP)-PCR of 23S rRNA which associated with clarithromycin resistance was done among resistant strains. Moreover, cagA gene and polymorphism in vacA were detected. Random amplified polymorphic DNA polymerase chain reaction (RAPD-PCR) was applied to investigate the genetic variations among all strains. Antibiotic resistance pattern of Hpylori strains was as follows: 68% (34/50) to metronidazole, 50% (25/50) to rifampicin, 30% (15/50) to amoxicillin, 28% (14/50) to levofloxacin, 22% (11/50) to clarithromycin, and 16% (8/50) to tetracycline. Multidrug-resistant strains were observed in 19 strains (38%). ASP-PCR of 23S rRNA showed four strains had A2143G mutation, six strains had A2142G mutation, and one strain had a Wt+A2143G mutation. Amplification of virulence-associated genes revealed that cagA was present in 27 isolates (54%) and vacA in 36 isolates (72%). The most common genotype of Hpylori was vacA s1am2 (40%) followed by vacA s2m2 (14%), vacA s1am1 (12%), vacA s1bm1 (4%), and vacA s1bm2 (2%). DNA fingerprinting pattern indicated a high heterogeneity among isolated strains. An alarming level of resistance to metronidazole and rifampicin and high heterogeneity among Hpylori isolates highlighted the importance of continued monitoring of antimicrobial susceptibility and epidemiological surveillance of this pathogen.

Mutations in the Antibiotic Target Genes Related to Clarithromycin, Metronidazole and Levofloxacin Resistance in Helicobacter pylori Strains from Children in China.

PurposeThis study aimed to characterize common mutations of antibiotic-resistant gene of clarithromycin, metronidazole and levofloxacin in Helicobacter pylori (H. pylori) and determine their association with antibiotic resistance of H. pylori for providing a strategy for eradication therapy of H. pylori infection in children.Patients and MethodsThe antibiotic resistance to clarithromycin, metronidazole and levofloxacin for H. pylori strains isolated from children was determined by E-test. The mutation of domain V of 23S rRNA, rdxA and frxA genes, gyrA and gyrB genes was performed by PCR-based sequencing of DNA fragments.ResultsOut of the 79 H. pylori strains examined, 66 (83.5%) were resistant to at least one of the tested antibiotics and 13 (16.5%) were fully sensitive. A total of 29 (36.7%) strains were resistant to clarithromycin. Analysis of the 23S rRNA gene showed that most mutations occurred at the A2143G and T2182C sites, showing a frequency of 82.8% (24/29) and 89.7% (26/29) respectively. In the 11 sensitive strains to clarithromycin, the frequency of A2143G mutation was only 45.5%, which was significantly lower than that in resistant strains (P<0.05). There were 54 strains (68.4%) resistant to metronidazole, with most mutations occurring at G47A and T184G in the rdxA gene. T184G mutation was recognized in metronidazole-sensitive strains, but no G47A mutation was identified. Twelve strains (15.2%) were resistant to levofloxacin. Position 91 mutation of the gyrA gene occurred only in resistant strains, whereas position 87 mutations were detected in both sensitive and resistant strains to levofloxacin.ConclusionIn H. pylori resistant strains isolated from children in China, most mutations occurred at A2143G of the 23S rRNA gene for clarithromycin; G47A mutation of rdxA gene for metronidazole; and at 91 mutation of gyrA gene for levofloxacin. It is suggested that susceptibility testing together with screening the mutation of antimicrobial-resistant gene prior to treatment is important for the eradication of H. pylori in children.

An Experimental Bacteriostasis of the Banxiaxiexin Decoction and 7 Kinds of Single Taste Traditional Chinese Medicine on Helicobacter Pylori Resistant Strains in Vitro

Objectives: To research experimental bacteriostasis on the Banxiaxiexin decoction and 7 kinds of single taste Traditional Chinese Medicine (TCM) for Helicobacter pylori resistant strains in vitro. Methods: Collecting specimens of gastric mucosa in patients with upper gastrointestinal disease, separated and identified 8 strains of Hp resistant strains, the E-test methods of metronidazole and clarithromycin, drug resistance status of amoxicillin, selected eight strains of clinical drug resistance strains; Using liquid dilution method to determine the Banxiaxiexin decoction and 7 kinds of single Chinese medicine clinical drug-resistant strains of 8 strains of antibacterial effect in vitro. Results: Banxiaxiexin decoction MIC is 0.31 mg/ml, MIC of Radix scutellariae is 0.09 mg/ml, Rhizoma coptidis MIC 0. 16 mg/ml, Glycyrrhizin realness MIC 0. 31 mg/ml, Ginseng MIC 0. 75 mg/ml, there are four of seven kinds of single taste Traditional Chinese Medicine of TCM has bacteriostatic action, the order of antibacterial strength: Scutellaria baicalensis>Coptis chinesis>Glycyrrhizin realness >Ginseng, three kinds of Pinellia, Jujube and dry Zingibe in vitro for H. P ylori no inhibition, the method of MIC with liquid dilution in this decoction were determined, the decoction of resistant isolates average MIC isolates was 0.20±0.09mg/ml, the results showed that this decoction have stronger antibacterial effect on eight kinds of drug resistant strains in vitro. Banxiaxiexin decoction and 4kinds of single taste TCM have stronger antibacterial effect on drug resistant strains in vitro. Conclusion: Banxiaxiexin decoction and 4 kinds of single TCM have strong bacteriostatic effect on the bacteria resistance of Helicobacter pylori strains in vitro, therefore, we suggest that this decoction could be used as an effective method in the treatment of resistant HP associated gastritis.

INDEL-типирование – новый метод дифференциации штаммов Helicobacter pylori

For the first time INDEL-typing method of Helicobacter pylori strains is offered. Analysis of the nucleotide sequences of 69 strains from the local database was carried out. Ten INDEL-markers were identified, five of which, with the highest variability, served as the basis for the differentiation scheme. INDEL-typing of twenty one strains of H. pylori of different geographical origin was carried out. Аnd fifteen individual genotypes with a high diversity index were identified (DI = 0.95). For cluster analysis, the MST (minimal spanning tree) method was used, which demonstrated a clear distribution of clusters according to the geographical origin of the strains studied. In addition to the proposed method of typing, if necessary, the MLVAtyping method can be used. Keywords: Helicobacter pylori, PCR, INDEL, MST dendrogram, MLVA, geographical origin

Analysis and Comparison of the Phylogenetic Diversity Within Helicobacter pylori Isolates from Iranian and Global Populations by Multi-Locus Sequence Typing

Background: Helicobacter pylori is a spiral-shaped bacterium that chronically resides in the human gastric epithelium. Helicobacter pylori strains are genetically diverse organisms encoding informative genotypic polymorphisms that can reflect both ancestral and human migrations history. Objectives: In this study we aimed to investigate the phylogenetic diversity of Iranian H. pylori isolates by using multi-locus sequence typing (MLST). Methods: A total of 37 H. pylori isolates cultured from biopsy specimens from patients who referred to endoscopy unit at Taleghani Hospital in Tehran during 2015 to 2016 were included in this study. The MLST was performed for all the isolates using seven housekeeping genes, including atpA, efp, mutY, ppa, trpC, ureI and yphC . Phylogenetic analysis was performed using sequence datasets of our H. pylori strains intermingled with MLST datasets of neighboring countries and global populations. Results: Our results showed that approximately 38% (14/37) of the Iranian H. pylori strains were identical in at least three gene loci, with the ureI gene (48.6%, 18/37) found as the most identical allele. Additionally, the phylogenetic analyses showed that Iranian strains fall into distinct clusters, and were intermingled mostly amongst the hpEurope isolates, including isolates from Turkey, Palestine, Israel, Lebanon, Egypt, Greece, Germany, Netherlands, Spain, UK, Finland, and Italy. The present study revealed that Iranian H. pylori strains are drastically diverse, and are originally comparable to the ancestry of the hpEurope populations. Conclusions: In conclusion, although similarity of the Iranian H. pylori strains is shown in few gene loci comparable to those mostly find in the hpEurope population, diversity at nucleotide sequences and STs is common among them.

Rearrangement analysis of multiple bacterial genomes

BackgroundGenomes are subjected to rearrangements that change the orientation and ordering of genes during evolution. The most common rearrangements that occur in uni-chromosomal genomes are inversions (or reversals) to adapt to the changing environment. Since genome rearrangements are rarer than point mutations, gene order with sequence data can facilitate more robust phylogenetic reconstruction. Helicobacter pylori is a good model because of its unique evolution in niche environment.ResultsWe have developed a method to identify genome rearrangements by comparing almost-conserved genes among closely related strains. Orthologous gene clusters, rather than the gene sequences, are used to align the gene order so that comparison of large number of genomes becomes easier. Comparison of 72 Helicobacter pylori strains revealed shared as well as strain-specific reversals, some of which were found in different geographical locations.ConclusionDegree of genome rearrangements increases with time. Therefore, gene orders can be used to study the evolutionary relationship among species and strains. Multiple genome comparison helps to identify the strain-specific as well as shared reversals. Identification of the time course of rearrangements can provide insights into evolutionary events.

A variety of Helicobacter pylori strains colonize the stomach of non-bleeding Egyptian patients with upper gastrointestinal disorders

BackgroundChronic infection with Helicobacter pylori is associated with protean manifestations, which vary from no symptoms to multiple gastric diseases. Other H. pylori infections could provide protection against reflux esophagitis, and lower esophageal cancer. The current study aims to scan H. pylori strains that colonize the stomach of Egyptian patients with upper gastrointestinal disorders and its association with the endoscopic outcomes. Identification of H. pylori strains was done by PCR amplification of the 16s rRNA gene from gastric biopsies, proved to be positive for H. pylori by both Giemsa stain and histopathology. PCR products were purified, sequenced, and aligned to GenBank.ResultsBLAST results of H. pylori 16s rRNA gene sequences showed identity between Egyptian H. pylori isolates and four H. pylori strain subpopulations: hspSAfrica, hspEAsia, hpEurope, hspWAfrica. The frequency of H. pylori isolates that showed identity to hspEAsia subpopulation was significantly higher in Ulcerative lesions. H. pylori isolates from ulcerative and neoplasm specimens illustrate base substitutions in 16s rRNA gene variable 9 region compared to the consensus sequence of H. pylori 43504 16s rRNA.ConclusionDifferent H. pylori strains may be associated with differences in the clinical manifestations and could be used as a prognostic marker to predict the outcome of the H. pylori-associated diseases.