Genomic insights into antibiotic resistance, virulence traits and phylogenetic lineages of 141 clinical Helicobacter pylori isolates from Eastern China

Objective To characterize antibiotic resistance, virulence genotypes and phylogenetic lineages of Helicobacter pylori ( H. pylori ) isolates from Eastern China and identify resistance/virulence-associated genetic variants. Methods Whole-genome sequencing (WGS) and phenotypic antimicrobial susceptibility testing (AST) for 6 antibiotics were performed on 141 H. pylori isolates from Hangzhou, China. Genetic analysis (resistance mutations, virulence genotyping, phylogenetic tree) and the assessment of antibiotic resistance related phenotype-genotype concordance were conducted. Results Metronidazole resistance was highest (85.1%), followed by levofloxacin (57.4%), clarithromycin (53.9%) and amoxicillin (21.3%); tetracycline and furazolidone resistance was low at 2.8% and 0.7%, respectively. Key resistance mutations included 23S rRNA A2143G (clarithromycin, 92.91% phenotype-genotype concordance), gyrA N87K (levofloxacin, 89.13% concordance) and pbp1A 1785_1786insAGC (amoxicillin, 83.69% concordance). Dominant virulence genotypes: cagA ABD (86.26%), vacA s1-type (100%, 58.02% s1m2, 41.22% s1m1), htrA 171S (61.07%). 95.4% of strains clustered in hpEastAsia lineage; 3.8% in hpEurope, 0.76% in hpAsia2. Conclusion H. pylori isolate in Eastern China show high resistance to common antibiotics and dominant high-virulence genotypes. WGS identifies key resistance markers, aiding targeted H. pylori treatment.