Caroli syndrome: a clinical case with detailed histopathological analysis

© 2018, Japanese Society of Gastroenterology. Herein we present a clinical case of the Caroli syndrome caused by the compound heterozygous mutation in the PKHD1 gene. Histopathological assessment of liver detected biliary cirrhosis, numerous dilated bile ducts of various sizes, hyperplastic cholangiocytes containing a large amount of acid mucopolysaccharides, decreased ß-tubulin expression and increased proliferation of cholangiocytes. A significant proportion of hepatic tissue was composed of giant cysts lined with a single layer of cholangiocytes, containing pus and bile in its lumen and surrounded by granulation tissue. An accumulation of neutrophils in the lumen of the bile ducts was observed, as well as an infiltration of the ducts and cysts surrounding connective tissue by CD4+ and to a lesser extent CD8+ lymphocytes. This may be caused by the expression of HLA-DR by cholangiocytes. Atrophy and desquamation of the epithelium of collecting tubules with the formation of microcysts were detected in the kidneys without a clinically significant loss of renal function. Morphopathogenetic mechanisms of the Caroli syndrome can be targets for a potential pathogenetic therapy and prevention of its manifestations and complications

Gut Microbiome Shotgun Sequencing in Assessment of Microbial Community Changes Associated with H. pylori Eradication Therapy

© 2016, Springer Science+Business Media New York.Disturbance of intestinal microbiota content and functions often results in different pathological conditions. Pharmacotherapy including antibiotics use is one of the factors leading to dysbiosis. To evaluate the influence of antibiotics use on intestinal microbiota metagenomic profiles of stool, samples of 74 patients before and after Helicobacter pylori—eradication therapy—were analyzed. Evaluation of taxonomic diversity changes based on Shannon index and Bray-Curtis metrics allows to range patients according to mild, moderate, and severe risk of disturbance of intestinal microbiota pathological conditions

Antibiotic Susceptibility Assessment of Helicobacter pylori Isolates by Disk-Diffusion Method

© 2018, Springer Science+Business Media, LLC, part of Springer Nature. Helicobacter pylori (H. pylori) infection is tightly associated with gastrointestinal disorders such as chronic gastritis, peptic ulcer, gastric MALToma, and gastric cancer. Decreased antibiotic susceptibility in H. pylori is a worldwide problem. Our objective was to determine in vitro antimicrobial susceptibility of H. pylori isolates obtained from gastric mucosa biopsies of children with H. pylori-associated gastroduodenal diseases using disk-diffusion method. A total 76 biopsy specimens were studied; antibiotic susceptibility was assessed in case of 30 children in whom H. pylori was revealed by bacteriology. The maximum resistance of H. pylori isolates was revealed to clarithromycin with nine resistant isolates (30.0%). The rate of resistance to metronidazole, amoxicillin, furazolidone, tetracycline, and levofloxacin was 23.3, 33.3, 16.7, 25.0, and 16.7%, respectively. Multidrug resistance was detected in 20.0% of H. pylori strains. The high prevalence of resistance to antibiotics used in eradication therapy is becoming a problem which needs eradication therapy regimen use based on regional H. pylori resistance rates

Data on gut metagenomes of the patients with Helicobacter pylori infection before and after the antibiotic therapy

© 2017Antibiotic therapy can lead to the disruption of gut microbiota community with possible negative outcomes for human health. One of the diseases for which the treatment scheme commonly included antibiotic intake is Helicobacter pylori infection. The changes in taxonomic and functional composition of microbiota in patients can be assessed using “shotgun” metagenomic sequencing. Ten stool samples were collected from 4 patients with Helicobacter pylori infection before and directly after the H. pylori eradication course. Additionally, for two of the subjects, the samples were collected 1 month after the end of the treatment. The samples were subject to “shotgun” (whole-genome) metagenomic sequencing using Illumina HiSeq platform. The reads are deposited in the ENA (project ID: PRJEB18265)

Competitive ability of <i>Escherichia coli</i> strains in the intestinal microbiota of patients with Crohn's disease and healthy volunteers: physiological, biochemical and genetic characteristics

Introduction. Crohn's disease (CD) is a chronic inflammation of various parts of the gastrointestinal tract with an increased proportion of Escherichia coli. However, the role of E. coli in disease remains unclear. This study aims to evaluate the competitive abilities of E. coli strains from CD patients and healthy volunteers, and to identify the biochemical and genetic determinants underlying these features. Materials and methods. The antagonistic activity was assessed by co-cultivation of 11 clinical E. coli strains inhibiting the growth of the K-12, with Enterobacter cloacae, Klebsiella pneumonia and Salmonella enterica. To elucidate the mechanism of antagonistic activity, the evaluation of biochemical properties and a comparative genomic analysis were used. Results and discussion. Genes of bacteriocin production systems were identified in genomes of 11 strains from CD patients and healthy volunteers active against the E. coli K-12 strain. Three strains from healthy individuals demonstrated activity against several Enterobacteriaceae bacteria. The strains biochemical properties were typical of representatives of E. coli. Strains 1_34_12, active against E. cloacae, and 1_45_11, inhibiting all tested enterobacteria, are phylogenetically related to the laboratory strain K-12. Strain 1_39_1, active against K. pneumonia and S. enterica, is phylogenetically close to the Nissle1917, contains the genes for colibactin biosynthesis and a variant of the fimH gene that increases the adhesive ability of bacteria. Conclusion. The identified E. coli strains are able to displace Enterobacteriaceae bacteria and can be used to study the bacteria-bacteria and host-bacteria interactions, to understand their role in gut homeostasis and intestinal inflammation

Serum cytokine signature that discriminates Helicobacter pylori positive and negative juvenile gastroduodenitis

© 2016 Khaiboullina, Abdulkhakov, Khalikova, Safina, Martynova, Davidyuk, Khuzin, Faizullina, Lombardi, Cherepnev and Rizvanov.Gastroduodenitis caused by H. pylori, often acquired in early childhood, is found in about 50% of the adult population. Although H. pylori infections can remain asymptomatic, its virulence factors usually trigger epithelial vacuolization and degeneration, loss of microvilli, disintegration of cytoplasm, and leukocyte accumulation. It is believed that leukocyte infiltration is driven by cytokines produced locally in infected tissue. However, so far little is known about changes in serum cytokines in juvenile patients infected with H. pylori. Serum cytokine profiles were analyzed in 62 juvenile patients diagnosed with gastroduodenitis using the Bio-Plex multiplex assay. H. pylori infection was confirmed in 32 patients, while 30 patients were H. pylori-free. Cytokines CXCL5 and CXCL6, potent neutrophil chemoattractants, were upregulated in all patients diagnosed with gastroduodenitis. Serum levels of IL8, a prototype neutrophil attractant, remained unchanged in subjects with gastroduodenitis relative to controls. Therefore, our data suggest that CXCL5 and CXCL6 play a role in directing neutrophil trafficking into inflamed gastroduodenal tissue. In addition, the CCL25/GM-CSF ratio differed significantly between H. pylori-positive and -negative juveniles. Further, study is needed to evaluate the role of CCL25 and GM-CSF in the pathogenesis of the different etiologies of gastroduodenitis

Human gut microbiota community structures in urban and rural populations in Russia

The microbial community of the human gut has a crucial role in sustaining host homeostasis. High-throughput DNA sequencing has delineated the structural and functional configurations of gut metagenomes in world populations. The microbiota of the Russian population is of particular interest to researchers, because Russia encompasses a uniquely wide range of environmental conditions and ethnogeographical cohorts. Here we conduct a shotgun metagenomic analysis of gut microbiota samples from 96 healthy Russian adult subjects, which reveals novel microbial community structures. The communities from several rural regions display similarities within each region and are dominated by the bacterial taxa associated with the healthy gut. Functional analysis shows that the metabolic pathways exhibiting differential abundance in the novel types are primarily associated with the trade-off between the Bacteroidetes and Firmicutes phyla. The specific signatures of the Russian gut microbiota are likely linked to the host diet, cultural habits and socioeconomic status. © 2013 Macmillan Publishers Limited. All rights reserved

European registry on the management of helicobacter pylori infection (HP-EUREG protocol): The first results of Russian centers

Aim: To assess the clinical practice of diagnosis and treatment in patients with Helicobacter pylori infection and to compare this practice with the international guidelines in the European Registry on the management of Helicobacter pylori infection, Hp-EuReg protocol), a multicenter prospective observational study initiated by the European Helicobacter and Microbiota Study Group. Materials and methods: The data of 813 patients infected with H. pylori and entered in the Hp-EuReg register by the Russian centers in 2013-2015 were analyzed. Results: The most common methods for the primary diagnosis of H. pylori infection are histology (40.3%), rapid urease test (35.7%), and serology (17.2%). The duration of H. pylori eradication therapy was 7, 10, and 14 days in 18.0, 49.3, and 25.1%, respectively. To monitor the effectiveness of treatment, the investigators used a histological examination (34%), a urea breath test (27.3%), H. pylori stool antigen (22.8%), and a rapid urease test (16.3%). A serological test was carried out in 2.5% of the cases. No monitoring was done in 13.5% of the patients. The average eradication efficiency was 82.6%. If the therapy was ineffective, 80% of physicians did not intend to prescribe a new cycle of treatment. Conclusion: Significant differences were found between clinical practice and the current guidelines