Genetic Determinants and Prediction of Antibiotic Resistance Phenotypes in Helicobacter pylori.

Lauener, Francis N; Imkamp, Frank; Lehours, Philippe; Buissonnière, Alice; Benejat, Lucie; Zbinden, Reinhard; Keller, Peter M.; Wagner, Karoline (2019). Genetic Determinants and Prediction of Antibiotic Resistance Phenotypes in Helicobacter pylori. Journal of clinical medicine, 8(1) MDPI 10.3390/jcm8010053

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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.

Item Type:

Journal Article (Original Article)

Division/Institute:

04 Faculty of Medicine > Service Sector > Institute for Infectious Diseases > Clinical Microbiology
04 Faculty of Medicine > Service Sector > Institute for Infectious Diseases > General Bacteriology
04 Faculty of Medicine > Service Sector > Institute for Infectious Diseases > Mycobacteriology

UniBE Contributor:

Keller, Peter Michael

ISSN:

2077-0383

Publisher:

MDPI

Language:

English

Submitter:

Siegfried Hektor Hapfelmeier-Balmer

Date Deposited:

31 Jan 2020 08:46

Last Modified:

31 Jan 2020 08:46

Publisher DOI:

10.3390/jcm8010053

PubMed ID:

30621024

Uncontrolled Keywords:

Helicobacter pylori antibiotic resistance prediction laboratory automation phenotypic drug susceptibility testing whole genome sequencing

BORIS DOI:

10.7892/boris.138173

URI:

https://boris.unibe.ch/id/eprint/138173

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