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

( ) 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...

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Bibliographic Details
Published in:World journal of gastroenterology : WJG 2019-08, Vol.25 (32), p.4629-4660
Main Authors: Pohl, Daniel, Keller, Peter M, Bordier, Valentine, Wagner, Karoline
Format: Article
Language:English
Subjects:
Anti-Bacterial Agents - pharmacology
Anti-Bacterial Agents - therapeutic use
DNA, Bacterial - genetics
DNA, Bacterial - isolation & purification
Drug Resistance, Bacterial - genetics
Genome, Bacterial - genetics
Helicobacter Infections - diagnosis
Helicobacter Infections - drug therapy
Helicobacter Infections - microbiology
Helicobacter pylori - drug effects
Helicobacter pylori - isolation & purification
Helicobacter pylori - physiology
High-Throughput Nucleotide Sequencing
Humans
Microbial Sensitivity Tests
Molecular Typing - methods
Real-Time Polymerase Chain Reaction
Review
Whole Genome Sequencing
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Summary:( ) 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 eradication therapies have been noted worldwide, also in many European countries. Therefore, rapid and accurate determination of 's antibiotic susceptibility prior to the administration of eradication regimens becomes ever more important. Traditionally, detection of 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 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 and its drug resistance and their implementation in management. The second part of the review focusses on the use of next generation sequencing technology in research. To this end, we conducted a literature search for original research articles in English using the terms " ", "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, 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 management guidelines and subsequently improve public health.
ISSN:1007-9327
2219-2840
DOI:10.3748/wjg.v25.i32.4629