Division of Gastroenterology, University Hospital of Zurich, Zurich 8006, Switzerland.
Institute for Infectious Diseases, University of Bern, Bern 3010, Switzerland.
World J Gastroenterol. 2019 Aug 28;25(32):4629-4660. doi: 10.3748/wjg.v25.i32.4629.
() 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.
幽门螺杆菌感染在人类中非常普遍，可能导致严重的胃肠道病理，包括胃溃疡和十二指肠溃疡、黏膜相关组织淋巴瘤和胃腺癌。近年来，在全球范围内，包括许多欧洲国家在内，都注意到抗生素耐药性的惊人增加，随后经验性根除治疗失败。因此，在实施根除方案之前，快速准确地确定幽门螺杆菌的抗生素敏感性变得越来越重要。传统上，通过培养和表型药敏试验来检测幽门螺杆菌及其抗生素耐药性，但这些方法繁琐，周转时间长。诊断学的最新进展提供了新的工具，如实时聚合酶链反应（PCR）和线探针检测，可直接从临床标本中诊断幽门螺杆菌感染和对某些抗生素的耐药性。此外，高通量全基因组测序技术允许快速分析病原体的基因组，从而识别耐药突变和相关的抗生素耐药性。在本综述的第一部分，我们将概述目前可用于检测幽门螺杆菌及其耐药性的诊断方法及其在幽门螺杆菌管理中的应用。第二部分的综述重点介绍了下一代测序技术在幽门螺杆菌研究中的应用。为此，我们使用了“Helicobacter pylori”、“transcriptomic”、“transcriptome”、“next generation sequencing”和“whole genome sequencing”等术语，对英文原始研究文章进行了文献检索。本综述旨在弥合当前诊断实践（组织学、快速尿素酶试验、幽门螺杆菌培养、PCR 和线探针检测）与新测序技术之间的差距，并探讨其在诊断实验室中的潜在应用，以补充当前推荐的幽门螺杆菌管理指南，并随后改善公共卫生。
