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Long term effects of H.pylori eradication on Gastro intestinal tract microbiome and development of screening system for detection of extended-spectrum beta-lactamase coding genes within feces samples

 

 

Project Title:Long term effects of H.pylori eradication on Gastro intestinal tract microbiome and development of screening system for detection of extended-spectrum beta-lactamase coding genes within feces samples.

Funding: European Regional Development Fund (ERDF), Measure 1.1.1.1 “Industry-Driven Research”

Project Nr.: 1.1.1.1/16/A/272

Period: 1st March 2017 – 29 st February 2020

Project costs: 648 648, 00 EUR

Principle Investigator: Dr. biol. D. Fridmanis

Collaboration:

 

The current international guidelines are encouraging “search-and-treat” strategy for H.pylori to prevent gastric cancer. The highest yield of this approach is expected in countries with high incidence of gastric cancer and high prevalence of H.pylori infection. In Latvia this would require antibiotic treatment to 79% of population. The potential adverse events caused by such therapies to microbiome are insufficiently studied; the expert opinion is generally limited to the consideration that single-time antibiotic treatment would be a minor intervention upon microbiome. However, limited data suggests, that even one-week treatment with macrolides is increasing the resistance of macrolide-resistant S.pneumoniae in pharynx; this difference was statistically significant within a period of 180 days.

The aim of this Project is, within the scope of industrial research, to evaluate the long term effects of H.pylori eradication on GIT microbiome, asses its effects on abundance and prevalence of extended-spectrum b-lactamases coding genes and develop cost effective ESBL screening test prototype. The results acquired through the implementation of this Project shall provide us with enhanced understanding on long term effects of antimicrobial agents on GIT microbiome and development of antibiotic resistance. They shall also contribute to development of National eradication treatment strategy

Summary of results

from 1 march to 31 may

Project scientific management

During initial stages of the project the application was submitted to the Riga Eastern Clinical University Hospital’s support fund’s Medical and Biomedical ethics committee for evaluation of project “Long term effects of H.pylori eradication on Gastro intestinal tract microbiome and development of screening system for detection of extended-spectrum beta-lactamase coding genes within feces samples”. Following the receipt of the application the committee provided positive response, thus allowing us to proceed with the implementation of the project.

Acquisition of samples

Acquisition of initial sample set – within the scope of this activity using various types of sample containers 20 fecal samples were collected from five healthy subjects. Since the purpose of this sample set is to evaluate the applicability of standardized fecal occult blood test containers for microbiome studies, following the acquisition they were subjected to various temperature regimes to simulate different environmental condition that could occur before the samples reach the laboratory. During the following project stages these samples shall be used for DNA extraction using extraction method that is developed within the scope of “Development of experimental procedures” activity.

Genetic analysis

During the first stages of this activity detailed analysis of available literature was carried out, with the goal to identify and develop the most suitable primers for amplification of V3 region of 16S rRNA gene. Following their development and acquisition, DNA samples that were acquired during “Development of experimental procedures” activity were used to identify the most suitable conditions for the amplification of the region of interest, which was followed sequencing of acquired products using IonTorrent PGM sequencing system. Next stages of the project shall involve sequencing of 16S rRNA V3 for all other samples thus identifying the most suitable DNA extraction method.

Development of experimental procedures

During the initial stages of this activity in-depth literature analysis and compilation of both project partners knowledge was carried out to identify the most effective sample acquisition and storage method. As the result of these actions the sample acquisition methodology was developed that in a form of detailed instruction shall be issued to all enrolled patients. In parallel development of effective gastrointestinal tract microbiome DNA extraction method was also carried out. During this latest action fresh – in-house acquired samples were used to evaluate the DNA extraction efficiency for various extraction reagent and material kits. During the next project stages within the scope of “Genetic analysis” activity all acquired DNA samples shall be analyzed through 16S rRNA V3 sequencing and as the result we shall identify the most suitable DNA extraction method.

 

Information published: 31.05.2017.



Mājas lapas izstrādi finansēja ERAF 2.1.1.2. aktivitātes projekts Nr. 2010/0196/2DP/2.1.1.2.0/10/APIA/VIAA/004 "Latvijas biomedicīnas pētījumu integrācija Eiropas zinātnes telpā".