Genomic landscape and fine-scale population structure of Helicobacter pylori across China

Background East Asian Helicobacter pylori ( H. pylori ) strains are commonly classified as a single hspEAsia lineage characterized by elevated virulence. However, gastric cancer incidence varies markedly across China, suggesting that clinically relevant bacterial heterogeneity may exist within this framework. A systematic assessment of fine-scale population structure and its functional correlates in Chinese H. pylori remained limited. Methods We analyzed whole-genome sequencing data from 1,243 H. pylori isolates collected from 20 provinces and regions across China, including 50 newly sequenced clinical strains from Shanghai. Fine-scale population structure was resolved using coancestry–based clustering and chromosome painting. Subpopulations were further characterized by pangenome composition, virulence factor repertoires, genome-wide fixation index (Fst), and predicted antibiotic resistance–associated mutations. E-test minimum inhibitory concentration (MIC) assays were performed to compare phenotypic susceptibility with mutation-based resistance prediction. Results Six geographically structured subpopulations were identified within Chinese hspEAsia. SubtypeCentral represented a widely distributed mainland lineage, whereas subpopulations from Inner Mongolia and Taiwan showed the greatest genetic divergence. Chromosome painting revealed strong within-lineage ancestry cohesion in SubtypeTaiwan, contrasted by extensive admixture in Inner Mongolia and Yunnan. Recurrent high-Fst loci across subpopulations, including glnA , frpB4 , and HP1501 , highlighted genomic regions contributing disproportionately to population differentiation. Marked heterogeneity in virulence profiles was observed. SubtypeInnerMongolia showed a higher prevalence of cagA -negative or Western-type cagA variants and a reduced overall repertoire of virulence genes. Predicted antibiotic resistance patterns were also strongly subtype dependent. Notably, SubtypeTaiwan exhibited an exceptionally high rifampicin resistance rate driven almost exclusively by a single rpoB A2414V mutation. E-test validation in the newly collected isolates provided supportive phenotypic evidence for the mutation-based resistance strategy. Conclusions Chinese H. pylori hspEAsia strains comprise multiple regionally structured subpopulations with distinct evolutionary histories, gene content, virulence profiles, and predicted resistance determinants. This fine-scale genomic classification provides a biological basis for understanding regional disparities in gastric cancer risk and genotypic resistance, and supports the need for subtype-aware surveillance and region-specific clinical management strategies in China.