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Review of current diagnostic methods and advances in Helicobacter pylori diagnostics in the era of next generation sequencing

Helicobacter pylori (H. pylori) infection is highly prevalent in the human population and may lead to severe gastrointestinal pathology including gastric and duodenal ulcers, mucosa associated tissue lymphoma and gastric adenocarcinoma. In recent years, an alarming increase in antimicrobial resistan...

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Autores principales: Pohl, Daniel, Keller, Peter M, Bordier, Valentine, Wagner, Karoline
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Baishideng Publishing Group Inc 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6718044/
https://www.ncbi.nlm.nih.gov/pubmed/31528091
http://dx.doi.org/10.3748/wjg.v25.i32.4629
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author Pohl, Daniel
Keller, Peter M
Bordier, Valentine
Wagner, Karoline
author_facet Pohl, Daniel
Keller, Peter M
Bordier, Valentine
Wagner, Karoline
author_sort Pohl, Daniel
collection PubMed
description Helicobacter pylori (H. pylori) infection is highly prevalent in the human population and may lead to severe gastrointestinal pathology including gastric and duodenal ulcers, mucosa associated tissue lymphoma and gastric adenocarcinoma. In recent years, an alarming increase in antimicrobial resistance and subsequently failing empiric H. pylori eradication therapies have been noted worldwide, also in many European countries. Therefore, rapid and accurate determination of H. pylori’s antibiotic susceptibility prior to the administration of eradication regimens becomes ever more important. Traditionally, detection of H.pylori and its antimicrobial resistance is done by culture and phenotypic drug susceptibility testing that are cumbersome with a long turn-around-time. Recent advances in diagnostics provide new tools, like real-time polymerase chain reaction (PCR) and line probe assays, to diagnose H. pylori infection and antimicrobial resistance to certain antibiotics, directly from clinical specimens. Moreover, high-throughput whole genome sequencing technologies allow the rapid analysis of the pathogen’s genome, thereby allowing identification of resistance mutations and associated antibiotic resistance. In the first part of this review, we will give an overview on currently available diagnostic methods for detection of H. pylori and its drug resistance and their implementation in H. pylori management. The second part of the review focusses on the use of next generation sequencing technology in H. pylori research. To this end, we conducted a literature search for original research articles in English using the terms “Helicobacter”, “transcriptomic”, “transcriptome”, “next generation sequencing” and “whole genome sequencing”. This review is aimed to bridge the gap between current diagnostic practice (histology, rapid urease test, H. pylori culture, PCR and line probe assays) and new sequencing technologies and their potential implementation in diagnostic laboratory settings in order to complement the currently recommended H. pylori management guidelines and subsequently improve public health.
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spelling pubmed-67180442019-09-16 Review of current diagnostic methods and advances in Helicobacter pylori diagnostics in the era of next generation sequencing Pohl, Daniel Keller, Peter M Bordier, Valentine Wagner, Karoline World J Gastroenterol Review Helicobacter pylori (H. pylori) infection is highly prevalent in the human population and may lead to severe gastrointestinal pathology including gastric and duodenal ulcers, mucosa associated tissue lymphoma and gastric adenocarcinoma. In recent years, an alarming increase in antimicrobial resistance and subsequently failing empiric H. pylori eradication therapies have been noted worldwide, also in many European countries. Therefore, rapid and accurate determination of H. pylori’s antibiotic susceptibility prior to the administration of eradication regimens becomes ever more important. Traditionally, detection of H.pylori and its antimicrobial resistance is done by culture and phenotypic drug susceptibility testing that are cumbersome with a long turn-around-time. Recent advances in diagnostics provide new tools, like real-time polymerase chain reaction (PCR) and line probe assays, to diagnose H. pylori infection and antimicrobial resistance to certain antibiotics, directly from clinical specimens. Moreover, high-throughput whole genome sequencing technologies allow the rapid analysis of the pathogen’s genome, thereby allowing identification of resistance mutations and associated antibiotic resistance. In the first part of this review, we will give an overview on currently available diagnostic methods for detection of H. pylori and its drug resistance and their implementation in H. pylori management. The second part of the review focusses on the use of next generation sequencing technology in H. pylori research. To this end, we conducted a literature search for original research articles in English using the terms “Helicobacter”, “transcriptomic”, “transcriptome”, “next generation sequencing” and “whole genome sequencing”. This review is aimed to bridge the gap between current diagnostic practice (histology, rapid urease test, H. pylori culture, PCR and line probe assays) and new sequencing technologies and their potential implementation in diagnostic laboratory settings in order to complement the currently recommended H. pylori management guidelines and subsequently improve public health. Baishideng Publishing Group Inc 2019-08-28 2019-08-28 /pmc/articles/PMC6718044/ /pubmed/31528091 http://dx.doi.org/10.3748/wjg.v25.i32.4629 Text en ©The Author(s) 2019. Published by Baishideng Publishing Group Inc. All rights reserved. http://creativecommons.org/licenses/by-nc/4.0/ This article is an open-access article which was selected by an in-house editor and fully peer-reviewed by external reviewers. It is distributed in accordance with the Creative Commons Attribution Non Commercial (CC BY-NC 4.0) license, which permits others to distribute, remix, adapt, build upon this work non-commercially, and license their derivative works on different terms, provided the original work is properly cited and the use is non-commercial.
spellingShingle Review
Pohl, Daniel
Keller, Peter M
Bordier, Valentine
Wagner, Karoline
Review of current diagnostic methods and advances in Helicobacter pylori diagnostics in the era of next generation sequencing
title Review of current diagnostic methods and advances in Helicobacter pylori diagnostics in the era of next generation sequencing
title_full Review of current diagnostic methods and advances in Helicobacter pylori diagnostics in the era of next generation sequencing
title_fullStr Review of current diagnostic methods and advances in Helicobacter pylori diagnostics in the era of next generation sequencing
title_full_unstemmed Review of current diagnostic methods and advances in Helicobacter pylori diagnostics in the era of next generation sequencing
title_short Review of current diagnostic methods and advances in Helicobacter pylori diagnostics in the era of next generation sequencing
title_sort review of current diagnostic methods and advances in helicobacter pylori diagnostics in the era of next generation sequencing
topic Review
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6718044/
https://www.ncbi.nlm.nih.gov/pubmed/31528091
http://dx.doi.org/10.3748/wjg.v25.i32.4629
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