ArticleBiomarker research2026
Genomic landscape and fine-scale population structure of Helicobacter pylori across China.
Article in Biomarker research, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
backgroundEast 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.
methodsWe 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.
resultsSix 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.
conclusionsChinese 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.
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