Population structure of Helicobacter pylori and antibiotic resistance-associated variants in a high-risk area of gastric cancer

ABSTRACT The increasing antibiotic resistance of Helicobacter pylori has had a serious impact on gastric cancer prevention. Our study aimed to profile the genomic characteristics and explore variants associated with resistance in H. pylori strains from a high-risk area of gastric cancer in China. We isolated 153 strains from a community-based cohort and assessed their susceptibility to six antibiotics by MIC Test Strip and genomic characteristics by whole-genome sequencing. Phylogenetic analysis identified the strains as an independent cluster within H. pylori East Asian population (hpEastAsia). HefA , an efflux pump gene, showed the highest differentiation in the Linqu strains compared with the other Chinese strains. Bacterial genome-wide association study (GWAS) identified 86 resistance variants covering 44 genes. Novel resistance variants were found in lon and babA for metronidazole, HP1168 for clarithromycin, hcpC for levofloxacin, and sabA for rifamycin. Two newly identified hefA mutations (R229K and A283V) showed significant associations with metronidazole ( P = 0.012) and tetracycline ( P = 0.044) resistance, respectively. HefA mutations and GWAS variants were integrated with the significant literature-reported mutations to optimize the prediction models for metronidazole, levofloxacin, clarithromycin, and tetracycline resistance with area under the receiver operating characteristic curves of 0.82–0.93. Double-antibiotic resistance models were established for clinical applicability. Furthermore, hefA expression may play a potential mediating role in the associations between mutations and resistance. This study identified genetic independence in the representative H. pylori strains from a high-risk area of gastric cancer. Optimized resistance prediction panels, including novel hefA mutations and GWAS variants, may provide preliminary guidance for localized precise treatment and helpful experiences for the similar high-risk populations. IMPORTANCE Helicobacter pylori is a remarkable pathogen due to its virulence in gastric cancer and high genetic plasticity. Linqu County in China, a high-risk area of gastric cancer, faces serious antibiotic resistance issues and necessitates genomic profiling of local H. pylori strains. Phylogenetic analysis revealed the Linqu strains as a relatively independent cluster within the hpEastAsia population. Novel antibiotic resistance-associated hefA mutations and variants from our bacterial genome-wide association study in the Linqu strains were optimized to improve the prediction performances for single antibiotic and double-drug combination resistance compared with traditional literature-reported mutations. This study identified relative genetic independence and high differentiation in the representative H. pylori strains from a population with high risk of gastric cancer and high prevalence of antibiotic resistance. The optimized panels with novel variants improve antibiotic resistance prediction models compared with literature-reported mutations, providing guidance for localized precise treatment and suggesting prevention strategies for similar high-risk populations.