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Gut Pathogens
Published in: Gut Pathogens 1/2022

01-12-2022 | Levofloxacin | Research

Antimicrobial resistance patterns and genetic elements associated with the antibiotic resistance of Helicobacter pylori strains from Shanghai

Authors: Yixin Liu, Su Wang, Feng Yang, Wenjing Chi, Li Ding, Tao Liu, Feng Zhu, Danian Ji, Jun Zhou, Yi Fang, Jinghao Zhang, Ping Xiang, Yanmei Zhang, Hu Zhao

Published in: Gut Pathogens | Issue 1/2022

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Abstract

Background

Shanghai, in east China, has one of the world’s highest burdens of Helicobacter pylori infection. While multidrug regimens can effectively eradicate H. pylori, the increasing prevalence of antibiotic resistance (AR) in H. pylori has been recognized by the WHO as ‘high priority’ for urgent need of new therapies. Moreover, the genetic characteristics of H. pylori AR in Shanghai is under-reported. The purpose of this study was to determine the resistance prevalence, re-substantiate resistance-conferring mutations, and investigate novel genetic elements associated with H. pylori AR.

Results

We performed whole genome sequencing and antimicrobial susceptibility testing of 112 H. pylori strains isolated from gastric biopsy specimens from Shanghai patients with different gastric diseases. No strains were resistant to amoxicillin. Levofloxacin, metronidazole and clarithromycin resistance was observed in 39 (34.8%), 73 (65.2%) and 18 (16.1%) strains, respectively. There was no association between gastroscopy diagnosis and resistance phenotypes. We reported the presence or absence of several subsystem protein coding genes including hopE, hofF, spaB, cagY and pflA, and a combination of CRISPRs, which were potentially correlated with resistance phenotypes. The H. pylori strains were also annotated for 80 genome-wide AR genes (ARGs). A genome-wide ARG analysis was performed for the three antibiotics by correlating the phenotypes with the genetic variants, which identified the well-known intrinsic mutations conferring resistance to levofloxacin (N87T/I and/or D91G/Y mutations in gyrA), metronidazole (I38V mutation in fdxB), and clarithromycin (A2143G and/or A2142G mutations in 23S rRNA), and added 174 novel variations, including 23 non-synonymous SNPs and 48 frameshift Indels that were significantly enriched in either the antibiotic-resistant or antibiotic-susceptible bacterial populations. The variant-level linkage disequilibrium analysis highlighted variations in a protease Lon with strong co-occurring correlation with a series of resistance-associated variants.

Conclusion

Our study revealed multidrug antibiotic resistance in H. pylori strains from Shanghai, which was characterized by high metronidazole and moderate levofloxacin resistance, and identified specific genomic characteristics in relation to H. pylori AR. Continued surveillance of H. pylori AR in Shanghai is warranted in order to establish appropriate eradication treatment regimens for this population.
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Metadata
Title
Antimicrobial resistance patterns and genetic elements associated with the antibiotic resistance of Helicobacter pylori strains from Shanghai
Authors
Yixin Liu
Su Wang
Feng Yang
Wenjing Chi
Li Ding
Tao Liu
Feng Zhu
Danian Ji
Jun Zhou
Yi Fang
Jinghao Zhang
Ping Xiang
Yanmei Zhang
Hu Zhao
Publication date
01-12-2022
Publisher
BioMed Central
Published in
Gut Pathogens / Issue 1/2022
Electronic ISSN: 1757-4749
DOI
https://doi.org/10.1186/s13099-022-00488-y

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