Antibiotic Resistance Landscape and Genomic Characterization of Helicobacter pylori in Western Inner Mongolia, China

Abstract Background Helicobacter pylori (H. pylori) infection is associated with chronic gastritis, peptic ulcer, gastric cancer, and has been classified as a Group I carcinogen by the World Health Organization. With approximately 4.4 billion people infected globally, the increasing antibiotic resistance has become the leading cause of declining eradication rates, posing a major public health challenge. However, current treatment strategies in Western Inner Mongolia remain largely empirical due to the lack of region-specific resistance data. Objective To investigate the antibiotic resistance profiles of H. pylori in Western Inner Mongolia and characterize the genomic features of multidrug-resistant strains through whole-genome sequencing (WGS), thereby providing evidence for regionally adapted treatment strategies. Methods A total of 232 adult patients with H. pylori infection were enrolled from January 2020 to December 2022. Resistance-associated mutations in six antibiotics (clarithromycin, levofloxacin, amoxicillin, furazolidone, tetracycline, and metronidazole) were detected by PCR and Sanger sequencing. Among them, 69 isolates were successfully cultured for phenotypic antimicrobial susceptibility testing using the disk diffusion method. Furthermore, 20 phenotypically multidrug-resistant isolates were selected for WGS to analyze phylogenetic lineages, virulence factors, and gene ontology (GO) enrichment. CYP2C19 genotyping was also performed to evaluate proton pump inhibitor metabolism phenotypes. Results Among the 232 patients, the highest resistance gene mutation rate was observed for metronidazole (90.52%), followed by furazolidone (79.31%) and clarithromycin (78.02%), while amoxicillin showed the lowest rate (25.86%). The mutation rates of clarithromycin and levofloxacin increased significantly with age (P < 0.05). Among the 69 cultured isolates, phenotypic resistance rates were 94.20% for metronidazole, 73.91% for clarithromycin, and 39.13% for levofloxacin, with no phenotypic resistance detected for amoxicillin, furazolidone, or tetracycline. The most common dual-resistance pattern was clarithromycin-metronidazole (72.46%). Excellent concordance between genotype and phenotype was observed for clarithromycin (κ= 0.797) and levofloxacin (κ= 0.869). CYP2C19 genotyping revealed that fast metabolizers (49.57%) were the most predominant phenotype, followed by intermediate (43.53%) and slow metabolizers (6.90%). WGS of 20 multidrug-resistant isolates revealed that 65% of strains clustered within the East Asia lineage. A total of 88 H. pylori-associated virulence genes were detected, with only one isolate lacking vacA and cagA. GO enrichment analysis identified chemotaxis, glutamine metabolism, and metal ion binding as key biological processes in multidrug-resistant strains. Conclusion This study demonstrates a high burden of antibiotic resistance in H. pylori isolates from Western Inner Mongolia, particularly to metronidazole, clarithromycin, and levofloxacin. The strong genotype-phenotype concordance for clarithromycin and levofloxacin supports the use of genetic testing as an alternative to culture-based susceptibility testing. The predominance of CYP2C19 fast metabolizers suggests that optimized PPI dosing or P-CAB agents may improve eradication success. Genomic analysis reveals that multi-drug-resistant strains predominantly belong to the East Asian lineage and harbor conserved virulence factors and specific metabolic pathways. These findings provide a scientific basis for individualized therapy and regional resistance surveillance.