Genomics of Helicobacter pylori

Pangenome Analysis of Helicobacter pylori Isolates from Selected Areas of Africa Indicated Diverse Antibiotic Resistance and Virulence Genes

The challenge facing Helicobacter pylori (H. pylori) infection management in some parts of Africa is the evolution of drug-resistant species, the lack of gold standard in diagnostic methods, and the ineffectiveness of current vaccines against the bacteria. It is being established that even though clinical consequences linked to the bacteria vary geographically, there is rather a generic approach to treatment. This situation has remained problematic in the successful fight against the bacteria in parts of Africa. As a result, this study compared the genomes of selected H. pylori isolates from selected areas of Africa and evaluated their virulence and antibiotic drug resistance, those that are highly pathogenic and are associated with specific clinical outcomes and those that are less virulent and rarely associated with clinical outcomes. 146 genomes of H. pylori isolated from selected locations of Africa were sampled, and bioinformatic tools such as Abricate, CARD RGI, MLST, Prokka, Roary, Phandango, Google Sheets, and iTOLS were used to compare the isolates and their antibiotic resistance or susceptibility. Over 20 k virulence and AMR genes were observed. About 95% of the isolates were genetically diverse, 90% of the isolates harbored shell genes, and 50% harbored cloud and core genes. Some isolates did not retain the cagA and vacA genes. Clarithromycin, metronidazole, amoxicillin, and tinidazole were resistant to most AMR genes (vacA, cagA, oip, and bab). Conclusion. This study found both virulence and AMR genes in all H. pylori strains in all the selected geographies around Africa with differing quantities. MLST, Pangenome, and ORF analyses showed disparities among the isolates. This in general could imply diversities in terms of genetics, evolution, and protein production. Therefore, generic administration of antibiotics such as clarithromycin, amoxicillin, and erythromycin as treatment methods in the African subregion could be contributing to the spread of the bacterium's antibiotic resistance.

Helicobacter pylori intragastric colonization and migration: Endoscopic manifestations and potential mechanisms

After being ingested and entering the human stomach, Helicobacter pylori (H. pylori) adopts several effective strategies to adhere to and colonize the gastric mucosa and move to different regions of the stomach to obtain more nutrients and escape from the harsher environments of the stomach, leading to acute infection and chronic gastritis, which is the basis of malignant gastric tumors. The endoscopic manifestations and pathological features of H. pylori infection are diverse and vary with the duration of infection. In this review, we describe the endoscopic manifestations of each stage of H. pylori gastritis and then reveal the potential mechanisms of bacterial intragastric colonization and migration from the perspective of endoscopists to provide direction for future research on the effective therapy and management of H. pylori infection.

Knowledge and Perception of Physicians of Different Specialties in Saudi Arabia Toward Helicobacter pylori

Background

Helicobacter pylori (H. pylori) is a key pathogen causing several gastrointestinal diseases. Fortunately, H. pylori infection is treatable, which can lower its comorbidities. However, data assessing physicians' awareness of H. pylori is lacking in Saudi Arabia.

Objective

To assess the knowledge and awareness of physicians of different specialties who practice in Saudi Arabia about H. pylori infection.

Methods

This is a cross-sectional study conducted between May and September 2022 on physicians across all regions in Saudi Arabia using a validated online questionnaire covering their knowledge and awareness of H. pylori infection. An independent t-test, one-way ANOVA, and Games-Howell as a post hoc test were used to analyze the data. A General Linear Model was also employed to determine significant predictors among the variables reliant on H. pylori awareness.

Results

The results showed that the mean awareness score of 474 physicians was 76.99± 6.9, indicating that participants had sufficient knowledge about H. pylori infection. In general, the internal medicine specialists (28.3%) had better awareness of H. pylori infection than the other specialties. Moreover, the university hospital sector performed the best, scoring 80.68±13.3, and the southern region had the highest-ranked physicians with a score of 81.56 ±13.7 in terms of H. pylori awareness. Furthermore, the general linear model revealed a statistical significance (p<0.05) for the following demographic aspects concerning H. pylori awareness: the physicians' age group of 30-39 years, duration of experience of 11-15 years, the hospital sectors of Nation Guards (NGH) and Security Forces (SFH), and the southern and central regions of practice in Saudi Arabia.

Conclusion

Physicians in Saudi Arabia have relatively sufficient awareness of H. pylori; however, they are highly influenced by age, years of experience, the hospital sector involved, and the region where the physicians practice.

Gut-Testis Axis: Microbiota Prime Metabolome To Increase Sperm Quality in Young Type 2 Diabetes

Young type 2 diabetes (T2D) affects 15% of the population, with a noted increase in cases, and T2D-related male infertility has become a serious issue in recent years. The current study aimed to explore the improvements of alginate oligosaccharide (AOS)-modified gut microbiota on semen quality in T2D. The T2D was established in young mice of 5 weeks of age with a blood glucose level of 21.2 ± 2.2 mmol/L, while blood glucose was 8.7 ± 1.1 mM in control animals. We discovered that fecal microbiota transplantation (FMT) of AOS-improved microbiota (A10-FMT) significantly decreased blood glucose, while FMT of gut microbiota from control animals (Con-FMT) did not. Sperm concentration and motility were decreased in T2D to 10% to 20% of those in the control group, while A10-FMT brought about a recovery of around 5- to 10-fold. A10-FMT significantly increased small intestinal Allobaculum, while it elevated small intestinal and cecal Lactobacillus in some extent, blood butyric acid and derivatives and eicosapentaenoic acid (EPA), and testicular docosahexaenoic acid (DHA), EPA, and testosterone and its derivatives. Furthermore, A10-FMT improved liver functions and systemic antioxidant environments. Most importantly, A10-FMT promoted spermatogenesis through the improvement in the expression of proteins important for spermatogenesis to increase sperm concentration and motility. The underlying mechanisms may be that A10-FMT increased gut-beneficial microbes Lactobacillus and Allobaculum to elevate blood and/or testicular butyric acid, DHA, EPA, and testosterone to promote spermatogenesis and thus to ameliorate sperm concentration and motility. AOS-improved gut microbes could emerge as attractive candidates to treat T2D-diminished semen quality. IMPORTANCE A10-FMT benefits gut microbiota, liver function, and systemic environment via improvement in blood metabolome, consequently to favor the testicular microenvironment to improve spermatogenesis process and to boost T2D-diminished semen quality. We established that AOS-improved gut microbiota may be used to boost T2D-decreased semen quality and metabolic disease-related male subfertility.

Molecular fusion events in carcinogenic organisms: a bioinformatics study for the detection of fused proteins between viruses, bacteria and eukaryotes

Molecular fusion events have a prominent role in the initial steps of carcinogenesis. In this study, a bioinformatics analysis was performed between four organisms that are known to induce cancer development in humans: two viruses, Human Herpesvirus 4, and Human T-cell leukaemia virus, one bacterium, Helicobacter Pylori, and one trematode, Schistosoma mansoni. The annotated proteomes from these organisms were analysed using the SAFE software to identify protein fusion events, which may provide insight into protein function similarities and possible merging events during the course of evolution. Based on the results, five fused proteins with very similar functions were detected, whereas proteins with different functions that might act in the same molecular complex or biochemical pathway were not found. Thus, this study analysed the above four well-known cancer-related organisms with de novo bioinformatics programs and provided useful information on protein fusion events, hopefully leading to deeper understanding of carcinogenenesis.

Helicobacter pylori virulence factors: relationship between genetic variability and phylogeographic origin

Background

Helicobacter pylori is a pathogenic bacteria that colonize the gastrointestinal tract from human stomachs and causes diseases including gastritis, peptic ulcers, gastric lymphoma (MALT), and gastric cancer, with a higher prevalence in developing countries. Its high genetic diversity among strains is caused by a high mutation rate, observing virulence factors (VFs) variations in different geographic lineages. This study aimed to postulate the genetic variability associated with virulence factors present in the Helicobacter pylori strains, to identify the relationship of these genes with their phylogeographic origin.

Methods

The complete genomes of 135 strains available in NCBI, from different population origins, were analyzed using bioinformatics tools, identifying a high rate; as well as reorganization events in 87 virulence factor genes, divided into seven functional groups, to determine changes in position, number of copies, nucleotide identity and size, contrasting them with their geographical lineage and pathogenic phenotype.

Results

Bioinformatics analyses show a high rate of gene annotation errors in VF. Analysis of genetic variability of VFs shown that there is not a direct relationship between the reorganization and geographic lineage. However, regarding the pathogenic phenotype demonstrated in the analysis of many copies, size, and similarity when dividing the strains that possess and not the cag pathogenicity island (cagPAI), having a higher risk of developing gastritis and peptic ulcer was evidenced. Our data has shown that the analysis of the overall genetic variability of all VFs present in each strain of H. pylori is key information in understanding its pathogenic behavior.

Helicobacter pylori infection causes both protective and deleterious effects in human health and disease

Infection with Helicobacter pylori (H. pylori) is necessary but not sufficient for the development of gastric cancer, the third leading cause of cancer death globally. H. pylori infection affects over half of people globally; however, it does not affect populations uniformly. H. pylori infection rates are declining in western industrialized countries but are plateauing in developing and newly industrialized countries where gastric cancer is most prevalent. Despite H. pylori infection being the primary causative agent for gastric cancer, H. pylori infection can also cause other effects, detrimental or beneficial, throughout an individual's life, with the beneficial effects often being seen in childhood and the deleterious effects in adulthood. H. pylori is an ancient bacterium and its likelihood of affecting disease or health is dependent on both human and bacterial genetics that have co-evolved over millennia. In this review, we focus on the impact of infection and its genetic bases in different populations and diseases throughout an individual's lifespan, highlighting the benefits of individualized treatment and argue that universal eradication of H. pylori in its host may cause more harm than good for those infected with H. pylori.

An American lineage of Helicobacter pylori prophages found in Colombia

BACKGROUND

Helicobacter pylori is a human gastric carcinogen that is highly prevalent in Latin American. The prophages of H. pylori show a structured population and contribute to the diversity of this bacterium. However, H. pylori prophages present in American strains have not been described to date. In this study, we identified, characterized, and present the phylogenetic analysis of the prophages present in Colombian H. pylori strains.

METHODS

To characterize Colombian H. pylori strains and their prophages, a Multilocus Sequences Typing (MLST) and a Prophage Sequences Typing (PST), using the integrase and holin genes, were performed. Furthermore, five Colombian H. pylori had their full genome sequenced, and six Colombian H.pylori retrieved from databases, allowing to determine the prophage complete genome and insertion site.

RESULTS

The integrase gene frequency was 12.6% (27/213), while both integrase and holin genes were present in 4.2% (9/213) of the samples analyzed. The PST analysis showed that Colombian prophages belong to different populations, including hpSWEurope, hpNEurope, hpAfrica1, and a new population, named hpColombia. The MLST analysis classified most of the Colombia strains in the hpEurope population.

CONCLUSIONS

The new H. pylori prophage population revealed that Colombian prophages follow a unique evolutionary trajectory, contributing to bacterial diversity. The global H. pylori prophage phylogeny highlighted five phylogenetic groups, one more than previously reported. After the arrival of Europeans, the Colombian H. pylori bacteria and their prophages formed an independent evolutionary line to adapt to the new environment and new human hosts.

Effect of Helicobacter Pylori eradication on patients with ITP: a meta-analysis of studies conducted in the Middle East

Background

Immune thrombocytopenia (ITP) is a bleeding disorder. Helicobacter pylori is a Gram-negative bacterium that is presumed to be associated with ITP and therapeutic response of patients. To evaluate the effect of H. pylori eradication on platelet count of ITP patients, we analyzed the studies conducted on the association between H. pylori infection and response to therapy in ITP patients in Western Asia focusing on the Middle East region.

Methods

A systematic search of databases (PubMed/Medline, ISI Web of Science, Cochrane Central) and Google Scholar search engine results was conducted up until January 2020. The keywords included in the search were Helicobacter pylori and/or H. pylori, ITP and/or immune thrombocytopenia.

Results

Seven studies comprising a total of 228 H. pylori-infected patients (193 with successful eradication) were included in this study. The association between H. pylori eradication and ITP was expressed as odds ratios (OR) and 95% confidence intervals (CI). The findings showed that patients who received eradication treatment for H. pylori infection had significantly higher OR (OR, 8.83; 95% CI, 2.03‒38.35; P=0.004) than those in the non-eradicated group.

Conclusion

Our results indicate a significant therapeutic effect of H. pylori eradication on the platelet count of patients with chronic ITP. Given the inherent limitations of this study, including the small number of patients, further studies with more patients are recommended.

Nutraceuticals as modulators of gut microbiota: Role in therapy

As our knowledge of the various roles of the gut microbiota in the maintenance of homeostasis grows and as we learn how a disrupted microbiota may contribute to disease, therapeutic strategies that target our microbial fellow-travellers become ever more attractive. Most appealing are those interventions that seek to modify or supplement our diet through the addition of nutraceuticals. We now know that our diet, whether in the short or long term, is a major modifier of microbiota composition and function. Of the various nutraceuticals, two categories, prebiotics and probiotics, have received the greatest attention in basic research and product development. While our understanding of the impacts of prebiotics and probiotics on the indigenous microbiota and host biology have been described in great detail in vitro and in animal models, the clinical literature leaves much to be desired. While many claims have been made, few are supported by high quality clinical trials. LINKED ARTICLES: This article is part of a themed section on The Pharmacology of Nutraceuticals. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v177.6/issuetoc.

Helicobacter pylori genotypes among Belarus patients with gastroduodenal disorders and their association with clinical outcome

The aim of this study was to evaluate the prevalence of Helicobacter pylori genotypes (vacA and cagPAI) directly in gastric biopsy specimens in patients with gastric diseases in Belarus. Gastric biopsies were collected from 461 patients with different gastrointestinal disorders: superficial gastritis (287 subjects), atrophy gastritis (59 subjects), erosive gastritis (47 subjects), duodenal ulcer disease (54 subjects), and stomach ulcer (14 subjects). PCR-based genotyping was used to detect s1a, s1b, s2, m1a, m1b, m2, cagM, cagA, and cagT genes. Overall prevalence of vacA s1a allele was 60.5% followed by m2 (47.1%) and m1a (37.5%). The analysis of data showed that genotype s1a/m1a was significantly more prevalent in patients with duodenal ulcer (21.4% vs. 45.1%, OR = 3.0, 95% CI = 1.5-6.1). The cagA gene was found with a high incidence in most patients with inflammatory diseases of stomach and duodenum. There was a significant increase in the frequency of cagT in patients with duodenal ulcer as compared to superficial gastritis. A high cagM prevalence was found in patients with atrophy gastritis and duodenal ulcer disease. All three island genes of pathogenicity of cagPAI are more often detected in patients with duodenal ulcer, which increases the risk of developing duodenal ulcer by 4.5 times.

Analysis of genetic recombination and the pan-genome of a highly recombinogenic bacteriophage species

Bacteriophages are the most prevalent biological entities impacting on the ecosystem and are characterized by their extensive diversity. However, there are two aspects of phages that have remained largely unexplored: genetic flux by recombination between phage populations and characterization of specific phages in terms of the pan-genome. Here, we examined the recombination and pan-genome in Helicobacter pylori prophages at both the genome and gene level. In the genome-level analysis, we applied, for the first time, chromosome painting and fineSTRUCTURE algorithms to a phage species, and showed novel trends in inter-population genetic flux. Notably, hpEastAsia is a phage population that imported a higher proportion of DNA fragments from other phages, whereas the hpSWEurope phages showed weaker signatures of inter-population recombination, suggesting genetic isolation. The gene-level analysis showed that, after parameter tuning of the prokaryote pan-genome analysis program, H. pylori phages have a pan-genome consisting of 75 genes and a soft-core genome of 10 genes, which includes genes involved in the lytic and lysogenic life cycles. Quantitative analysis of recombination events of the soft-core genes showed no substantial variation in the intensity of recombination across the genes, but rather equally frequent recombination among housekeeping genes that were previously reported to be less prone to recombination. The signature of frequent recombination appears to reflect the host–phage evolutionary arms race, either by contributing to escape from bacterial immunity or by protecting the host by producing defective phages.

Relationship between Helicobacter pylori infection and GERD

Gastroesophageal reflux disease (GERD) is due to the chronic exposure of the esophageal mucosa to acid secretion from the stomach. Helicobacter pylori (H.p.) infection, is a risk factor for the development of peptic ulcer, atrophic gastritis and gastric cancer, and causes various effects on gastric function. The relationship between GERD and H.pylori infection is still subject of debate.Background and aim: In literature no clear causal relationship has been established between GERD and H. pylori infection, although some papers support the onset of esophagitis in patients in whom the infection has been cured. Aim of this work is to review the most recent literature data about the relationship between reflux disease and H. pylori infection. Methods: Articles reviewed were found through literature searches on PubMed, Google Scholar using keywords such as gastroesophageal reflux disease, Helicobacter pylori, acid-related disorders, GERD and esophagitis. (www.actabiomedica.it)

Efficacy of Helicobacter pylori eradication regimens in Rwanda: a randomized controlled trial

BACKGROUND

Successful H. pylori treatment requires the knowledge of local antimicrobial resistance. Data on the efficacy of H. pylori eradication regimens available in sub-Saharan Africa are scant, hence the optimal treatment is unknown. Our goals were to determine the efficacy of available regimens in Rwanda as well as evaluate the effect of treatment on health-related quality of life (HRQoL) in patients undergoing esophagogastroduodenoscopy.

METHODS

This is a randomized controlled trial conducted from November 2015 to October 2016 at a tertiary hospital in Rwanda. Enrollees were 299 patients (35% male, age 42 ± 16 years (mean ± SD)) who had a positive modified rapid urease test on endoscopic biopsies. After a fecal antigen test (FAT) and HRQoL assessment by the Short Form Nepean Dyspepsia Index (SF-NDI) questionnaire, patients were randomized 1:1:1:1 to either a triple therapy combining omeprazole, amoxicillin and one of clarithromycin/ciprofloxacin/metronidazole or a quadruple therapy combining omeprazole, amoxicillin, ciprofloxacin and doxycycline. All therapies were given for a duration of 10 days. The outcome measures were the persistence of positive FAT (treatment failure) 4 to 6 weeks after treatment and change in HRQoL scores.

RESULTS

The treatment success rate was 80% in the total population and 78% in patients with a history of prior triple therapy. Significant improvement in HRQoL in the total group (HRQoL mean scores before and after treatment respectively: 76 ± 11 and 32 ± 11, p < 0.001) and the group with functional dyspepsia (HRQoL mean scores before and after treatment respectively: 73 ± 11 and 30 ± 9, P < 0.001) was observed across all treatment groups. Using clarithromycin based triple therapy (standard of care) as a reference, the group treated with metronidazole had worse HRQoL (p = 0.012) and had a trend towards worse treatment outcome (p = 0.086) compared to the ciprofloxacin based combination therapies.

CONCLUSION

Clarithromycin and ciprofloxacin based combination therapies are effective and safe to use alternatively for H. pylori eradication and improve HRQoL. Among the regimens studied, metronidazole based triple therapy is likely to be clinically inferior.

TRIAL REGISTRATION

The clinical trial was retrospectively registered ( PACTR201804003257400 ) with the Pan African Clinical Trial Registry database, on April 6th, 2018 in South Africa.