Changes in gastric microbiota associated with Helicobacter pylori eradication therapy in a patient with gastritis

Objective. To evaluate dynamic changes in the gastric microbiota against the background of Helicobacter pylori eradication therapy in a patient with gastritis using the method of high-throughput sequencing based on the analysis of variable regions of the 16s rRNA gene.

Materials and methods. The patient (male, 57 years old) with chronic associated Helicobacter pylori (H. pylori) moderately severe and moderately active gastritis of the antrum and body of the stomach without atrophy and metaplasia. There is no primary resistance of H. pylori to clarithromycin according to polymerase chain reaction results.

Next generation sequencing method based on the analysis of variable regions of the 16S rRNA gene was used to study the gastric microbiota. H. pylori eradication was performed according to the following scheme: amoxicillin, clarithromycin, omeprazole. The study included gastric mucosa (GM) biopsy samples obtained from unchanged tissue (N) and pathologically altered tissue (P) at different stages of treatment during 12 months. Taxonomic identification of reads was performed using the DRAGEN Metagenomics software package (Kraken2 algorithm).

Results. Negative dynamics of alpha-diversity of gastric microbiome (by 5.8 times) was noted in the patient without treatment when assessing the unchanged tissue of the stomach. When antibiotic therapy was used, an increase in alpha-diversity of the gastric microbiota by more than eight times was noted.

Conclusion. Analysis of the data of taxonomic diversity of gastric microbiota in morphologically different samples of the gastric microbiota at different stages of therapy indicates positive changes in the dynamic composition of the gastric microbiota in the course of treatment, which is confirmed by a decrease in the relative representation of H. pylori. When using therapy based only on proton pump inhibitors, the number of H. pylori is not significantly reduced. The dynamics of alpha-diversity of gastric microbiota is related to the morphological state of the tissue, and without the use of therapy has a significant and rather rapid tendency to a significant decrease (2-fold in less than two months). It is possible to achieve reduction of H. pylori to minimal amounts using standard first-line eradication therapy based on clarithromycin, but complete eradication does not occur.

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