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 empiricH. pylori eradication therapies have been noted worldwide, also in many European countries. Therefore, rapid and accurate determination ofH. pylori's antibiotic susceptibility prior to the administration of eradication regimens becomes ever more important. Traditionally, detection ofH.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 diagnoseH. 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 ofH. pylori and its drug resistance and their implementation inH. pylori management. The second part of the review focusses on the use of next generation sequencing technology inH. 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 recommendedH. pylori management guidelines and subsequently improve public health.

Conflict-of-interest statement: None of the authors have any potential conflicts of interest to declare.