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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\n                      <jats:italic>H. pylori<\/jats:italic>\n                      remained limited.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>\n                      We analyzed whole-genome sequencing data from 1,243\n                      <jats:italic>H. pylori<\/jats:italic>\n                      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\u2013based clustering and chromosome painting. Subpopulations were further characterized by pangenome composition, virulence factor repertoires, genome-wide fixation index (Fst), and predicted antibiotic resistance\u2013associated mutations. E-test minimum inhibitory concentration (MIC) assays were performed to compare phenotypic susceptibility with mutation-based resistance prediction.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      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\n                      <jats:italic>glnA<\/jats:italic>\n                      ,\n                      <jats:italic>frpB4<\/jats:italic>\n                      , and\n                      <jats:italic>HP1501<\/jats:italic>\n                      , highlighted genomic regions contributing disproportionately to population differentiation. Marked heterogeneity in virulence profiles was observed. SubtypeInnerMongolia showed a higher prevalence of\n                      <jats:italic>cagA<\/jats:italic>\n                      -negative or Western-type\n                      <jats:italic>cagA<\/jats:italic>\n                      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\n                      <jats:italic>rpoB<\/jats:italic>\n                      A2414V mutation. E-test validation in the newly collected isolates provided supportive phenotypic evidence for the mutation-based resistance strategy.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>\n                      Chinese\n                      <jats:italic>H. pylori<\/jats:italic>\n                      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.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s40364-026-00932-0","type":"journal-article","created":{"date-parts":[[2026,5,16]],"date-time":"2026-05-16T07:34:21Z","timestamp":1778916861000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Genomic landscape and fine-scale population structure of Helicobacter pylori across China"],"prefix":"10.1186","volume":"14","author":[{"given":"Yi","family":"Dou","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pengfei","family":"Kong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mingzhu","family":"Huang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yonghu","family":"Xu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jingyu","family":"Guo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yong","family":"Xie","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaohua","family":"Jiang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yantao","family":"Duan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gonghong","family":"Wei","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dazhi","family":"Xu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,5,16]]},"reference":[{"issue":"5","key":"932_CR1","doi-asserted-by":"publisher","first-page":"e1002693","DOI":"10.1371\/journal.ppat.1002693","volume":"8","author":"Y Moodley","year":"2012","unstructured":"Moodley Y, Linz B, Bond RP, Nieuwoudt M, Soodyall H, Schlebusch CM, et al. 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