Genomic characterization of clinical Helicobacter pylori strains from Korea: insights into phylogeny, pan-genome structure, and virulence factors

BACKGROUND: Helicobacter pylori (H. pylori) is a globally prevalent gastric pathogen whose genetic diversity and virulence contribute to the varied clinical outcomes. Whole-genome sequencing has revolutionized microbial genomics by allowing high-resolution analyses to obtain insights into the evolution of pathogenic organisms; however, few studies have specifically focused on strains from Korea, where H. pylori infection and gastric cancer are highly prevalent. This study aimed to investigate the phylogenetic characteristics and virulence factor profiles of Korean H. pylori strains using whole-genome sequencing. METHODS: Twelve H. pylori strains from Korean patients with chronic gastritis or early gastric cancer were subjected to whole-genome sequencing. Draft genomes were assembled de novo, and multi-locus sequence typing was conducted to determine the population structure. Pan-genome analysis and virulence factor profiling were also performed. RESULTS: All strains were clustered within the East Asian (hspEAsia) population in the phylogenetic tree. The pan-genome analysis identified 2574 gene clusters, with 1161 core genes (45.1%), 519 shell genes (20.2%), and 894 cloud genes (34.7%). The cytotoxin-associated gene pathogenicity island (cagPAI) was intact in 11/12 strains, and all strains harbored East Asian-type ABD Glu-Pro-Ile-Tyr-Ala (EPIYA) motifs. Notably, cag2 was not detected in all strains and cagY exhibited significant sequence variation. Vacuolating cytotoxin A (vacA) genotyping identified s1c/i1/m1 as the predominant type (66.7%), followed by s1a/i1/m1 (25.0%) and s1c/i1/m2 (8.3%). CONCLUSION: The Korean H. pylori strains demonstrated typical East Asian characteristics, and intact cagPAI and virulent vacA genotypes were highly prevalent, providing essential genomic insights into H. pylori pathogenesis in the Korean populations.