ArticleGigaScience2026
Within-host diversity and phased variant analysis reveal structures and recombination of Helicobacter pylori subpopulations in stomach.
Article in GigaScience, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
1 citing paper in PubMed.
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Authors and funding
10 authors.
Funding
Abstract
backgroundHelicobacter pylori (H. pylori) has a highly plastic genome and can generate substantial within-host diversity during chronic gastric colonization. However, the delineation of its within-host subpopulations, particularly regarding the emergence and spread of antibiotic resistance-conferring mutations, remains poorly understood.
resultsIn this study, we enrolled 25 chronic gastritis patients from southern China, collecting multiple isolates from distinct gastric regions. Among them, 14 patients exhibited heterogeneity in antibiotic susceptibility across isolates (heteroresistant), while the remaining 11 showed consistent profiles (homoresistant). Using ultra-deep short- and long-read sequencing, we showed that co-existing H. pylori subpopulations were prevalent in these patients, particularly within the same anatomical niche. Two patients presented mixed infections involving different strains as subpopulations, while others exhibited microevolution from a common ancestor. We reconstructed the subpopulation structures and found that isolates from heteroresistant patients had greater within-host diversity compared to those from homoresistant patients. Notably, subpopulations in the antrum demonstrated higher diversity than those in the gastric corpus and incisura angularis. Through a custom-developed phasing bioinformatics workflow, we resolved subpopulation-level genomic regions and directly observed extensive homologous recombination among them. Importantly, we traced the distribution of levofloxacin- and clarithromycin-associated resistance mutations across subpopulations, which was mainly mediated by recombination.
conclusionsTo our knowledge, this study provides the first detailed depiction of H. pylori subpopulation distribution within the human stomach, illustrating how recombination drives within-host diversification and contributes to the spread of antibiotic resistance mutations.
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