Review of current diagnostic methods and advances inHelicobacter pyloridiagnostics in the era of next generation sequencing

Abstract

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.

Comparison of endoscopic and pathological findings of the upper gastrointestinal tract in transplant candidate patients undergoing hemodialysis or peritoneal dialysis treatment: a review of literature

“…Gastric and duedonal ulcers were seen in the normal population between 11 and 20% [ 43 ]. A study found that HP infection was an independent protective factor for gastric erosion, but it was not associated with other mucosal lesions [ 26 ].…”

Types of 23S Ribosomal RNA Point Mutations and Therapeutic Outcomes for Helicobacter pylori

“…11 When the standard triple regimen is considered as a first-line therapy, in areas of high resistance to clarithromycin, either a culture-based susceptibility test or a molecular test (poly-merase chain reaction, PCR) is recommended, to detect clarithromycin resistance. [11][12][13][14][15] Nevertheless, standard triple therapy continues to be used as a first-line therapy for H. pylori in Korea and Japan, without antibiotic resistance testing. 7,16,17 Recently, a dual-priming oligonucleotide (DPO)-based multiplex PCR assay was made commercially available, to detect genetic mutations.…”

Genomic Analysis of Antimicrobial Resistance Genotype-to-Phenotype Agreement in Helicobacter pylori

“…To address these challenges of variable resistance rates, as well as other logistical challenges involved in AST of H. pylori isolates, culture-independent techniques have been implemented. Several PCR-based commercial kits are commonly used to identify genotypic resistance from clinical samples [ 11 ], usually by targeting three to seven point mutations in the 23S rRNA (A2142C, A2142G, and A2143G) and gyrA (N87K, D91G, D91N, D91Y) genes that are generally considered to correlate with resistance [ 11 , 12 ]. However, these tests are limited due to imperfect correlations between these mutations and resistance [ 13 , 14 , 15 , 16 ], the numerous other mutations associated with resistance [ 17 ], and the possibility of co-infection with other organisms like Epstein-Barr Virus [ 18 ].…”