Phenotypic and Molecular Antimicrobial Susceptibility of Helicobacter pylori

Abstract

Failure to eradicate Helicobacter pylori infection is often a result of antimicrobial resistance, which for clarithromycin is typically mediated by specific point mutations in the 23S rRNA gene. The purpose of this study was to define current patterns of antimicrobial susceptibility in H. pylori isolates derived primarily from the United States and to survey them for the presence of point mutations in the 23S rRNA gene and assess the ability of these mutations to predict phenotypic clarithromycin susceptibility. Antimicrobial susceptibility testing was performed using agar dilution on 413 H. pylori isolates submitted to Mayo Medical Laboratories for susceptibility testing. For a subset of these isolates, a 150-bp segment of the 23S rRNA gene was sequenced. A total of 1,970 MICs were reported over the 4-year study period. The rate of clarithromycin resistance was high (70.4%), and elevated MICs were frequently observed for metronidazole (82.4% of isolates had an MIC of Ͼ8 g/ml) and ciprofloxacin (53.5% of isolates had an MIC of Ͼ1 g/ml). A total of 111 archived H. pylori isolates underwent 23S rRNA gene sequencing; we found 95% concordance between genotypes and phenotypes (P ϭ 0.9802). Resistance to clarithromycin was most commonly due to an A2143G mutation (82%), followed by A2142G (14%) and A2142C (4%) mutations. Clinical H. pylori isolates derived primarily from the United States demonstrated a high rate of clarithromycin resistance and elevated metronidazole and ciprofloxacin MICs. The relative distribution of point mutations at positions 2143 and 2142 in the 23S rRNA gene in clarithromycin-resistant H. pylori was similar to that reported from other parts of the world; these mutations predict phenotypic resistance to clarithromycin.

Helicobacter pylori Mutations Detected by Next-Generation Sequencing in Formalin-Fixed, Paraffin-Embedded Gastric Biopsy Specimens Are Associated with Treatment Failure

“…Previous studies have shown a correlation between the presence of H. pylori mutations and in vitro antibiotic resistance (3), and the present study demonstrates that mutation screening directly from biopsy specimens can predict treatment failure. The NGS assay described in this study can be performed with FFPE specimens, which are routinely obtained as part of standard of care.…”

“…The primers were designed to target the DNA regions that have been associated with antibiotic resistance. Clarithromycin resistance is due to single point mutations in the peptidyl transferase region of domain V of 23S rRNA (3). Tetracycline resistance is due to mutation in the binding site of tetracycline in 16S rRNA (14).…”

“…For determining variations in 23S rRNA and gyrA genes, all reads were aligned to the corresponding gene from the reference genome (NC_000915) followed by the identification of variants as described above for 16S. There is limited published data describing the clinical significance of a majority of variants for gyrA and 23S, and so only variants with a clear link to antibiotic resistance were considered clinically significant mutations (3,8,(25)(26)(27)(28)(29)(30)(31)(32)(33)(34)(35).…”

“…H elicobacter pylori infects close to one-half of the global population and is the main cause of peptic ulcer disease and a trigger for gastric cancer (1,2). The current recommended empirical treatment for H. pylori eradication includes two or three antibiotics (typically clarithromycin and either amoxicillin or metronidazole) and one antisecretory drug for 14 days, with the eradication goal being higher than 80% (3)(4)(5). However, H. pylori acquires antibiotic resistance by mutation, which has dramatically increased over the past decades (6)(7)(8).…”

“…However, H. pylori acquires antibiotic resistance by mutation, which has dramatically increased over the past decades (6)(7)(8). The rate of clarithromycin resistance in the United States has increased from 10% to 24% in the 1990s to 24% to 70% in recent years (1,3,9). Increasing rates of resistance have also been reported in Europe and Asia (1,2,6,10).…”