Application of next-generation sequencing to characterize novel mutations in clarithromycin-susceptible Helicobacter pylori strains with A2143G of 23S rRNA gene

Abstract

BackgroundClarithromycin (CLR) resistance has become a predominant factor for treatment failure of Helicobacter pylori eradication. Although the molecular mechanism of CLR resistance has been clearly understood in H. pylori, it is lack of evidence of other genes involved in drug resistance. Furthermore, the molecular mechanism of phenotype susceptible to CLR while genotype of 23S rRNA is mutant with A2143G is unclear. Here, we characterized the mutations of CLR-resistant and -susceptible H. pylori strains to explore bacterial resistance.MethodsIn the present study, the whole genomes of twelve clinical isolated H. pylori strains were sequenced, including two CLR-susceptible strains with mutation of A2143G. Single nucleotide variants (SNVs) were extracted and analyzed from multidrug efflux transporter genes.ResultsWe did not find mutations associated with known CLR-resistant sites except for controversial T2182C outside of A2143G in the 23S rRNA gene. Although total SNVs of multidrug efflux transporter gene and the SNVs of HP0605 were significant differences (P ≤ 0.05) between phenotype resistant and susceptible strains. There is no significant difference in SNVs of RND or MFS (HP1181) family. However, the number of mutations in the RND family was significantly higher in the mutant strain (A2143G) than in the wild type. In addition, three special variations from two membrane proteins of mtrC and hefD were identified in both CLR-susceptible strains with A2143G.ConclusionsNext-generation sequencing is a practical strategy for analyzing genomic variation associated with antibiotic resistance in H. pylori. The variations of membrane proteins of the RND family may be able to participate in the regulation of clinical isolated H. pylori susceptibility profiles.

<p>Mutations in the Antibiotic Target Genes Related to Clarithromycin, Metronidazole and Levofloxacin Resistance in <em>Helicobacter pylori</em> Strains from Children in China</p>

“…A study in adults from the same district in Zhejiang Province showed that all of phenotype-resistant strains (n=6) presented mutation A to G at position 2143 of the 23S rRNA, while 2 mutant-type of 23S rRNA gene at position 2143 (A>G) was also detected in sic phenotype-susceptible strains. 22 Another study in adults from the same area showed that 90.4% gene mutations of the 23S rRNA were the A2143G mutation. 23 H. pylori strains were found to carry A2143G, A2142G, A2147G and A2146G mutations that can lead to clarithromycin-resistance in Africa, Asia, South America, Europe and North America.…”

Molecular Assessment of Resistance to Clarithromycin in Helicobacter pylori Strains Isolated from Patients with Dyspepsia by Fluorescent In Situ Hybridization in the Center of Iran

“…Quek et al revealed that A2143G and T2182C genotypes were detected not only in resistant isolates but also in clarithromycin-susceptible strains [31]. Chen et al isolated two clarithromycinsusceptible H. pylori strain with mutation A2143G of the 23S rRNA gene [15].…”

“…H. pylori was identified based on colony morphology (small and translucent colonies) and typical appearance on Gram stain as a gull wing-shape bacteria and also by positive reactions for oxidase, catalase, and strong urease activity. After subculturing on Columbia agar, all of them were stored in brain heart infusion broth with 30% glycerol and 7% FCS at −70°C [15,16].…”

Helicobacter pylori biofilm cells are metabolically distinct, express flagella, and antibiotic tolerant

“…Several of these already stand out as interesting proteins. HPG27_715 encodes for a multi drug and toxic compound extrusion (MATE)type multidrug efflux pump (Chen, Ye et al 2018). Inactivation of gene HPG27_715 significantly decreased biofilm formation.…”