Integrated virulence–resistance profiling of Helicobacter pylori reveals context-dependent pathogenic signatures in gastric cancer

Background Helicobacter pylori contributes to gastric carcinogenesis through diverse virulence mechanisms, transcriptional plasticity, and rising antimicrobial resistance. However, how these features integrate into coordinated bacterial states within the tumor microenvironment remains unclear. This study integrates virulence, expression, and antimicrobial signatures to define potentially meaningful H. pylori profiles. Methods We analyzed 159 histologically confirmed, H. pylori -positive gastric cancer tissues. Virulence gene presence, expression, and antimicrobial resistance–associated mutations were quantified using polymerase chain reaction–based assays. Twenty-one molecular features were standardized and integrated using unsupervised k -means and TwoStep clustering. Associations with clinicopathological characteristics were evaluated using false-discovery-rate-adjusted statistical tests. Results Two dominant H. pylori molecular states were identified: a virulence-competent Colonizer profile (127/158, 80.4%) enriched for cagA / vacA gene carriage and expression ( q < 0.001), and a putative Resistant Inflammatory profile (31/158, 19.6%) characterized by elevated iceA expression ( q = 0.002) and clarithromycin resistance mutations ( q = 0.022), with reduced cagA / vacA ( q < 0.001). Histological detectability of H. pylori differed markedly between profiles (91.3% vs 45.2%, p < 0.001). Univariate differences were observed in tumor differentiation ( p = 0.047) and anatomical distribution ( p = 0.042), while multivariable associations were directional but non-significant. Four-cluster modelling identified additional sub-phenotypes. Conclusions Integrated profiling suggests that H. pylori adopts distinct molecular states in gastric cancer associated with specific clinicopathological features. These findings support systems-level microbial characterization as a hypothesis-generating framework for exploring whether microbial molecular states may contribute to future risk stratification and eradication strategies in AMR-endemic regions, pending functional and external validation.