Genetic Determinants and Prediction of Antibiotic Resistance Phenotypes in Helicobacter pylori
Open Access
- 7 January 2019
- journal article
- research article
- Published by MDPI AG in Journal of Clinical Medicine
- Vol. 8 (1), 53
- https://doi.org/10.3390/jcm8010053
Abstract
Helicobacter pylori is a major human pathogen. Diagnosis of H. pylori infection and determination of its antibiotic susceptibility still mainly rely on culture and phenotypic drug susceptibility testing (DST) that is time-consuming and laborious. Whole genome sequencing (WGS) has recently emerged in medical microbiology as a diagnostic tool for reliable drug resistance prediction in bacterial pathogens. The aim of this study was to compare phenotypic DST results with the predictions based on the presence of genetic determinants identified in the H. pylori genome using WGS. Phenotypic resistance to clarithromycin, metronidazole, tetracycline, levofloxacin, and rifampicin was determined in 140 clinical H. pylori isolates by E-Test®, and the occurrence of certain single nucleotide polymorphisms (SNPs) in target genes was determined by WGS. Overall, there was a high congruence of >99% between phenotypic DST results for clarithromycin, levofloxacin, and rifampicin and SNPs identified in the 23S rRNA, gyrA, and rpoB gene. However, it was not possible to infer a resistance phenotype for metronidazole based on the occurrence of distinct SNPs in frxA and rdxA. All 140 H. pylori isolates analysed in this study were susceptible to tetracycline, which was in accordance with the absence of double or triple nucleotide substitutions in the 16S rRNA gene.Keywords
This publication has 62 references indexed in Scilit:
- Standardisation of disk diffusion results for antibiotic susceptibility testing using the sirscan automated zone readerBMC Microbiology, 2013
- Fluoroquinolone Resistance in Helicobacter pylori: Role of Mutations at Position 87 and 91 of GyrA on the Level of Resistance and Identification of a Resistance Conferring Mutation in GyrBHelicobacter, 2012
- A Method for Metagenomics of Helicobacter pylori from Archived Formalin-Fixed Gastric Biopsies Permitting Longitudinal Studies of Carcinogenic RiskPLOS ONE, 2011
- Perceiving a Stranger's Voice as Being One's Own: A ‘Rubber Voice’ Illusion?PLOS ONE, 2011
- Mechanisms ofHelicobacter pyloriantibiotic resistance: An updated appraisalWorld Journal of Gastrointestinal Pathophysiology, 2011
- Evaluation of a New Test, GenoType HelicoDR, for Molecular Detection of Antibiotic Resistance in Helicobacter pyloriJournal of Clinical Microbiology, 2009
- Novel Mutation in 23S rRNA That Confers Low-Level Resistance to Clarithromycin in Helicobacter pyloriAntimicrobial Agents and Chemotherapy, 2008
- Effect of eradication of Helicobacter pylori on incidence of metachronous gastric carcinoma after endoscopic resection of early gastric cancer: an open-label, randomised controlled trialThe Lancet, 2008
- A Coefficient of Agreement for Nominal ScalesEducational and Psychological Measurement, 1960