Helicobacter pylori genotypes, virulence and antibiotic resistance patterns among outpatients with gastric diseases in representative urban-rural areas of Yunnan, China

Abstract Background The epidemiological and molecular characteristics of Helicobacter pylori ( H. pylori ) across different gastric lesion stages remain unclear. This study aimed to analyse H. pylori positivity, phylogenetic lineages, virulence genotypes, and antibiotic resistance-associated mutation profiles among patients with gastric diseases in representative urban and rural areas of Yunnan. Results H . pylori infection status was determined by qPCR. Seven housekeeping gene loci were amplified and sequenced for multilocus sequence typing (MLST), sequence type assignment, and phylogenetic analysis. Virulence genotypes and antibiotic resistance-associated mutations were identified by PCR amplification and Sanger sequencing. The H. pylori positivity rate was 29.0%, with a higher rate in urban areas than in rural areas (33.8% vs. 22.7%), and positivity increased across the Correa cascade spectrum ( P < 0.05). A total of 140 novel STs were identified, and 96.5% of successfully typed isolates belonged to the hpEastAsia lineage. cagA genotyping showed that the 39-bp deletion and ABD combination were more common in urban areas, whereas the 18-bp deletion and AABD combination were enriched in rural areas. In addition, cagA pre-EPIYA deletion types were significantly associated with advanced gastric mucosal lesions ( P < 0.05). vacA genotyping showed that, compared with the m2 genotype, the m1b genotype was more strongly associated with urban areas ( P < 0.01). Among antibiotic resistance-associated mutations, those associated with levofloxacin and clarithromycin were the most common, with detection rates of 37.6% and 36.9%, respectively; 20.1% of samples carried mutations associated with resistance to two antibiotic classes. Conclusions In summary, these findings provide useful evidence for molecular epidemiological surveillance, risk assessment of advanced gastric lesions, and region-specific optimization of H. pylori eradication strategies.