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

作     者：Daniel Pohl Peter M Keller Valentine Bordier Karoline Wagner 

作者机构：Division of GastroenterologyUniversity Hospital of ZurichZurich 8006Switzerland Institute for Infectious DiseasesUniversity of BernBern 3010Switzerland Institute of Medical MicrobiologyUniversity of ZurichZurich 8006Switzerland 

出 版 物：《World Journal of Gastroenterology》 (世界胃肠病学杂志（英文版）)

年 卷 期：2019年第25卷第32期

页      面：4629-4660页

核心收录：

学科分类：10[医学] 

主　　题：Helicobacter pylori Advances in diagnostics Next generation sequencing Whole genome sequencing Clinical management 

摘      要：Helicobacter 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 *** recent years,an alarming increase in antimicrobial resistance and subsequently failing empiric *** eradication therapies have been noted worldwide,also in many European ***,rapid and accurate determination of ***’s antibiotic susceptibility prior to the administration of eradication regimens becomes ever more ***,detection of *** and its antimicrobial resistance is done by culture and phenotypic drug susceptibility testing that are cumbersome with a long *** 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 ***,high-throughput whole genome sequencing technologies allow the rapid analysis of the pathogen’s genome,thereby allowing identification of resistance mutations and associated antibiotic *** 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 *** *** second part of the review focusses on the use of next generation sequencing technology in *** *** this end,we conducted a literature search for original research articles in English using the terms“Helicobacter,“transcriptomic,“transcriptome,“next generation sequencingand“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