Trends in Helicobacter pylori resistance to clarithromycin: from phenotypic to genomic approaches

Abstract

For a long time Helicobacter pylori infections have been treated using the macrolide antibiotic, clarithromycin. Clarithromycin resistance is increasing worldwide and is the most common cause of H. pylori treatment failure. Here we review the mechanisms of antibiotic resistance to clarithromycin, detailing the individual and combinations of point mutations found in the 23S rRNA gene associated with resistance. Additionally, we consider the methods used to detect clarithromycin resistance, emphasizing the use of high-throughput next-generation sequencing methods, which were applied to 17 newly sequenced pairs of H. pylori strains isolated from the antrum and corpus of a recent colonized paediatric population. This set of isolates was composed of six pairs of resistant strains whose phenotype was associated with two point mutations found in the 23S rRNA gene: A2142C and A2143G. Other point mutations were found simultaneously in the same gene, but, according to our results, it is unlikely that they contribute to resistance. Further, among susceptible isolates, genomic variations compatible with mutations previously associated with clarithromycin resistance were detected. Exposure to clarithromycin may select low-frequency variants, resulting in a progressive increase in the resistance rate due to selection pressure.

Keywords: 23S ribosomal RNA subunit; Helicobacter pylori; clarithromycin; next-generation sequencing; point mutations; resistance.

Fig. 1.

Two-dimensional chemical structure of erythromycin A (a) and CLA (b). CLA is the 6-O-methyl ether oferythromycin A. Structures from PubChem (accessed August 2019) [67].

Fig. 2.

Secondary structure model of the peptidyl transferase centre in the domain V (green) and domain VI (blue) of the H. pylori 23S rRNA. The indicated point mutation positions correspond to single mutations (not requiring combination with other mutations) conferring low-level to high-level CLA resistance. Mutations 2141 (G2141A), 2144 (A2144T), 2182 (T2182C), 2190 (T2190C), 2195 (C2195T), 2244 (T2244C), 2694 (C2694A) and 2711 (T2711C) are indicated by black circles and the most prevalent mutations 2142 (A2142G) and 2143 (A2143G) are indicated by red circles. Image available at (and modified from) http://www.rna.icmb.utexas.edu (accessed July 2019) [68]). The circled nucleotides indicate the positions of mutations that confer CLA resistance in H. pylori (details and references are given in Table 2).