The high prevalence of Helicobacter pylori and the variety of gastroduodenal diseases caused by this pathogen necessitate the use of only accurate methods both for the primary diagnosis and for monitoring the eradication effectiveness. There is a broad spectrum of diagnostic methods available for detecting H. pylori. All methods can be classified as invasive or non-invasive. The need for upper endoscopy, different clinical circumstances, sensitivity and specificity, and accessibility defines the method chosen. This article reviews the advantages and disadvantages of the current options and novel developments in diagnostic tests for H. pylori detection. The progress in endoscopic modalities has made it possible not only to diagnose precancerous lesions and early gastric cancer but also to predict H. pylori infection in real time. The contribution of novel endoscopic evaluation technologies in the diagnosis of H. pylori such as visual endoscopy using blue laser imaging (BLI), linked color imaging (LCI), and magnifying endoscopy is discussed. Recent studies have demonstrated the capability of artificial intelligence to predict H. pylori status based on endoscopic images. Non-invasive diagnostic tests such as the urea breathing test and stool antigen test are recommended for primary diagnosis of H. pylori infection. Serology can be used for initial screening and epidemiological studies. The histology showed its value in detecting H. pylori and provided more information about the degree of gastric mucosa inflammation and precancerous lesions. Molecular methods are mainly used in detecting antibiotic resistance of H. pylori. Cultures from gastric biopsies are the gold standard and recommended for antibiotic susceptibility tests.

Background Escherichia coli (E. coli) has been increasingly implicated in the pathogenesis of Crohn’s disease (CD). The phylogeny of E. coli isolated from Crohn’s disease patients (CDEC) was controversial, and while genotyping results suggested heterogeneity, the sequenced strains of E. coli from CD patients were closely related.ResultsWe performed the shotgun genome sequencing of 28 E. coli isolates from ten CD patients and compared genomes from these isolates with already published genomes of CD strains and other pathogenic and non-pathogenic strains. CDEC was shown to belong to A, B1, B2 and D phylogenetic groups. The plasmid and several operons from the reference CD-associated E. coli strain LF82 were demonstrated to be more often present in CDEC genomes belonging to different phylogenetic groups than in genomes of commensal strains. The operons include carbon-source induced invasion GimA island, prophage I, iron uptake operons I and II, capsular assembly pathogenetic island IV and propanediol and galactitol utilization operons.ConclusionsOur findings suggest that CDEC are phylogenetically diverse. However, some strains isolated from independent sources possess highly similar chromosome or plasmids. Though no CD-specific genes or functional domains were present in all CD-associated strains, some genes and operons are more often found in the genomes of CDEC than in commensal E. coli. They are principally linked to gut colonization and utilization of propanediol and other sugar alcohols.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3917-x) contains supplementary material, which is available to authorized users.

Background: There has been a negative trend in the effectiveness of classic eradication therapy regimens for Helicobacter pylori (H. pylori), which has largely been determined from the emergence and spread of antibiotic resistance. Several studies have shown that adding rebamipide to eradication regimens leads to an increase in the effectiveness of treatment. Aim: To evaluate the efficacy and safety of including rebamipide in the eradication regimens for H. pylori infection. Methods: The literature search was conducted in the MEDLINE/PubMed, EMBASE, Cochrane Central Register, Korean Medical Citation Index, and Russian Science Citation Index databases. All identified randomized controlled trials comparing rebamipide supplementation with non-rebamipide-containing eradication regimens for the treatment of H. pylori infection were included in the final analysis. Results: We identified 11 randomized controlled trials (RCTs) involving 1227 patients (631 in groups with rebamipide and 596 in groups without rebamipide). The meta-analysis showed that the addition of rebamipide to eradication regimens significantly increased the effectiveness of treatment (odds ratio (OR) 1.753, 95% confidence interval (CI) 1.312–2.333, p < 0.001). The subgroup analysis demonstrated that rebamipide significantly increased the effectiveness of eradication when added to a dual therapy regimen (OR 1.766, 95% CI: 1.167–2.495, p = 0.006); however, no significant improvement in effectiveness was observed when it was added to the triple therapy regimen (OR 1.638, 95% CI 0.833–3.219, p = 0.152). Conclusion: This meta-analysis demonstrated that the addition of rebamipide to H. pylori eradication regimens significantly increases the effectiveness of treatment.

A steady decline in the effectiveness of standard eradication therapy (ET) regimens for Helicobacter pylori infection necessitates a search for ways of their optimization, by enhancing the efficiency of treatment protocols and by improving their safety and tolerability. The review systematizes the data available in the literature on main accessible methods for optimizing ET regimens. Among the optimization methods that can considerably enhance the efficiency of ET regimens, one may identify their addition of a bismuth agent (by 10—20%), the use of rebamipide (by 11.9%), adjuvant therapy with probiotics (by 8.1—13%), or double-dose proton pump inhibitors (by 8%). Only adjuvant therapy with probiotics results in a significant decrease in the incidence of side effects from ET. In posteradication period, rebamipide should be used to potentiate gastric mucosal repair and to regress inflammatory processes.

BackgroundCrohn’s disease is associated with gut dysbiosis. Independent studies have shown an increase in the abundance of certain bacterial species, particularly Escherichia coli with the adherent-invasive pathotype, in the gut. The role of these species in this disease needs to be elucidated.MethodsWe performed a metagenomic study investigating the gut microbiota of patients with Crohn’s disease. A metagenomic reconstruction of the consensus genome content of the species was used to assess the genetic variability.ResultsThe abnormal shifts in the microbial community structures in Crohn’s disease were heterogeneous among the patients. The metagenomic data suggested the existence of multiple E. coli strains within individual patients. We discovered that the genetic diversity of the species was high and that only a few samples manifested similarity to the adherent-invasive varieties. The other species demonstrated genetic diversity comparable to that observed in the healthy subjects. Our results were supported by a comparison of the sequenced genomes of isolates from the same microbiota samples and a meta-analysis of published gut metagenomes.ConclusionsThe genomic diversity of Crohn’s disease-associated E. coli within and among the patients paves the way towards an understanding of the microbial mechanisms underlying the onset and progression of the Crohn’s disease and the development of new strategies for the prevention and treatment of this disease.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5306-5) contains supplementary material, which is available to authorized users.

It is appropriate to prescribe a sequential ET regimen as more effective and safe for patients with concomitant CHC during therapy for H. pylori infection-associated diseases. LF increases the risk of adverse events during ET.

In current clinical practice, there is no optimal empirical therapy for Helicobacter pylori (H. pylori) infection and there is a progressive decrease in the efficiency of classical eradication therapy (ET) regimens. The variability in the efficiency of ET in a specific patient is largely due to the heterogeneous molecular genetic mechanisms underlying the resistance of the microorganism to the components of the treatment regimens. The basis of the mechanisms for antibiotic resistance in H. pylori is mainly the point mutations in some genes, which determine alterations in the mechanisms of action of drugs, such as clarithromycin (domain V of 23S rRNA), metronidazole (rdxA, frxA), amoxicillin (pbp1A), tetracycline (16S rRNA), and levofloxacin (gyrA). The predictors of resistance to ET are also the CagA-negative status of the microorganism and the presence of the vacA s2 allele. There are a number of host genetic determinants (the CYP2C19 genotype (*1/*1, *1/*17, *17/*17) and the MDR1 3435 T/T genotype (in an Asian population)) that reduce the efficiency of ET, by altering the pharmacokinetics of proton pump inhibitors. In addition, the IL-1β-511 C/C polymorphism that affects gastric acid secretion is a predictor of the inefficiency of ET.

Chronic pancreatitis (CP) is an inflammatory disease of the pancreas, accompanied by damage to the functioning parenchyma and ducts to develop irreversible structural changes (fibrosis, calcification) and irreparable loss of the endocrine and exocrine functions of this organ. Maldigestion is a typical outcome of CP of any etiology with a long-term history. Fat malabsorption is considered as a basis for malnutrition in patients with CP. The severity of malnutrition in patients with CP correlates with three major pathogenetic factors: primary nutrient deficiency, pancreatic maldigestion and secondary malabsorption syndrome (nutrient loss), hypermetabolism that is caused by an inflammatory process in the pancreas and that determines the severity of the disease. Malnutrition in patients with CP is not just a complication of this disease, but has an important impact on its course. Patients with severe malnutrition are noted to have the significantly lower activity of pancreatic enzymes in the duodenal contents, feces, and blood, which is correlated with the smaller blood amount of total protein and albumin.