Dataset Information

Shifts in the Human Gut Microbiota Structure Caused by Quadruple Helicobacter pylori Eradication Therapy.

ABSTRACT: The human gut microbiome plays an important role both in health and disease. Use of antibiotics can alter gut microbiota composition, which can lead to various deleterious events. Here we report a whole genome sequencing metagenomic/genomic study of the intestinal microbiota changes caused by Helicobacter pylori (HP) eradication therapy. Using approaches for metagenomic data analysis we revealed a statistically significant decrease in alpha-diversity and relative abundance of Bifidobacterium adolescentis due to HP eradication therapy, while the relative abundance of Enterococcus faecium increased. We have detected changes in general metagenome resistome profiles as well: after HP eradication therapy, the ermB, CFX group, and tetQ genes were overrepresented, while tetO and tetW genes were underrepresented. We have confirmed these results with genome-resolved metagenomic approaches. MAG (metagenome-assembled genomes) abundance profiles have changed dramatically after HP eradication therapy. Focusing on ermB gene conferring resistance to macrolides, which were included in the HP eradication therapy scheme, we have shown a connection between antibiotic resistance genes (ARGs) and some overrepresented MAGs. Moreover, some E. faecium strains isolated from stool samples obtained after HP eradication have manifested greater antibiotic resistance in vitro in comparison to other isolates, as well as the higher number of ARGs conferring resistance to macrolides and tetracyclines.

SUBMITTER: Olekhnovich EI

PROVIDER: S-EPMC6718723 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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Shifts in the Human Gut Microbiota Structure Caused by Quadruple Helicobacter pylori Eradication Therapy.

Olekhnovich Evgenii I EI Manolov Alexander I AI Samoilov Andrey E AE Prianichnikov Nikita A NA Malakhova Maja V MV Tyakht Alexander V AV Pavlenko Alexander V AV Babenko Vlad V VV Larin Andrey K AK Kovarsky Boris A BA Starikova Elizaveta V EV Glushchenko Oksana E OE Safina Dilyara D DD Markelova Maria I MI Boulygina Eugenia A EA Khusnutdinova Dilyara R DR Malanin Sergey Y SY Abdulkhakov Sayar R SR Abdulkhakov Rustam A RA Grigoryeva Tatiana V TV Kostryukova Elena S ES Govorun Vadim M VM Ilina Elena N EN

Frontiers in microbiology 20190827

The human gut microbiome plays an important role both in health and disease. Use of antibiotics can alter gut microbiota composition, which can lead to various deleterious events. Here we report a whole genome sequencing metagenomic/genomic study of the intestinal microbiota changes caused by Helicobacter pylori (HP) eradication therapy. Using approaches for metagenomic data analysis we revealed a statistically significant decrease in alpha-diversity and relative abundance of Bifidobac ...[more]

PMID: 31507546

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Project description:BACKGROUND Considering the importance of Helicobacter pylori (H. pylori) eradication, this clinical trial was designed to prospectively evaluate the efficacy of levofloxacin-based, sequential therapy in comparison with quadruple therapy for eradicating H. pylori. METHODS Overall 156 patients with dyspepsia and H. pylori infection were included in this study and were randomly allocated to either 10-day sequential therapy group (group A) to receive pantoprazole (40 mg twice daily), amoxicillin (1 gr twice daily), levofloxacin (500 mg twice daily), and tinidazole (500 mg twice daily) (PALT) or 14-day quadruple therapy group (group B) to receive pantoprazole, clarithromycin, bismuth subcitrate, and amoxicillin (PABC). At the end of the study the eradication rate in each group was assessed by urea breath test (UBT). RESULTS Age range of the participants was 18-65 years (average 36.9 years) and 50% of them (78 patients) were men. 78 patients were allocated to group A and 78 patients to groupe B. After antibiotic therapy, all the patients received acid suppression therapy with Proton Pump Inhibitor (PPI) for 4 weeks and then the eradication rate was confirmed by UBT (Heli FAN plus 13C, Germany). Before performing UBT, all the participants were requested to halt consumption of PPI for at least 1 week. During the treatment there was not any major complication but in group A (sequential therapy), two patients complained of minor complications including musculoskeletal pain. None of the patients in group B had any complaint or side effect. The rate of H. pylori eradication in group A was 78.2% (61 patients) while this rate in group B was 83.3% (65 patients) with no significant difference between the two groups (p = 0.42). In subgroup analysis, the rate of eradication among men in group A and B were 76.9% and 89.7%, respectively (p = 0.22) while the eradication rate among women were 79.4% and 76.9%, respectively (p = 1.00). CONCLUSION It seems that levofloxacin base sequential therapy does not have any advantage in comparison with quadruple regimen and until finding any more effective short course therapy for H. Pylori eradication; we encourage quadruple regimen to be used as the first line therapy.

Project description:Antibiotics resistance in Helicobacter pylori (H. pylori) is the major factor for eradication failure. Molecular tests including fluorescence in situ hybridization, PCR-restriction fragment length polymorphism, and dual priming oligonucleotide-PCR (DPO-PCR) play critical roles in the detection of antibiotic susceptibility; however, limited knowledge is known about application of multiple genetic analysis system (MGAS) in the area of H. pylori identification and antibiotics resistance detection.The aim of this study is to determine the antibiotics resistance using different molecular tests and evaluate the treatment outcomes of E-test-based genotypic resistance.A total of 297 patients with dyspepsia complaint were recruited for gastroscopies. Ninety patients with H. pylori culture positive were randomly divided into 2 groups (test group and control group). E-test, general PCR, and MGAS assay were performed in test group. Patients in control group were treated with empirical therapy (rabeprazole + bismuth potassium citrate + amoxicillin [AMX] + clarithromycin [CLR]), whereas patients in test group received quadruple therapy based on E-test results twice daily for 14 consecutive days. The eradication effect of H. pylori was confirmed by C-urea breath test after at least 4 weeks when treatment was finished.Rapid urease test showed 46.5% (128/297) patients with H. pylori infection, whereas 30.3% (90/297) patients were H. pylori culture positive. E-test showed that H. pylori primary resistance rate to CLR, AMX, metronidazole, tetracycline, and levofloxacin (LVX) was 40.0% (18/45), 4.4% (2/45), 53.3% (24/45), 0% (0/45), and 55.6% (25/45), respectively. In addition, there are many multidrug resistant (MDR) phenotypes, and the MDR strains have higher minimum inhibitory concentration than their single-drug resistant counterparts. Considering E-test as the reference test, the sensitivities of general PCR and MGAS in detecting CLR resistance were 83.3% (15/18) and 94.4% (17/18), whereas in detecting LVX resistance were 100% (25/25) and 83.3% (15/18), respectively. Finally, the eradication rate in test group was significantly higher than that in control group as demonstrated by intention-to-treat analysis and per-protocol analysis.MGAS is a promising assay for H. pylori identification and antibiotic susceptibility testing. Phenotypic resistance-guided quadruple therapy showed a high efficacy in treating patients with H. pylori infection.

Dataset Information

Shifts in the Human Gut Microbiota Structure Caused by Quadruple Helicobacter pylori Eradication Therapy.

Publications

Shifts in the Human Gut Microbiota Structure Caused by Quadruple <i>Helicobacter pylori</i> Eradication Therapy.

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