Genomic insights into virulence, biofilm formation, and antimicrobial resistance of multidrug-resistant Helicobacter pylori strains of novel sequence types isolated from Vietnamese patients with gastric diseases

Helicobacter pylori (H. pylori) is a clinically important pathogen associated with gastric diseases. Here, we characterized the genome of multidrug-resistant H. pylori strains of novel sequence types, which were recovered from Vietnamese patients with gastritis or a stomach ulcer. Phenotypic-antibiotic susceptibility testing was performed against amoxicillin, clarithromycin, metronidazol, tetracycline, and levofloxacin using an E-test. The whole genome sequence of three H. pylori strains was de novo assembled, followed by in silico analysis of multilocus sequence typing (MLST), core-genome based phylogeny, genetic determinants associated with virulence, biofilm formation, and antibiotic-resistance. The genome sequence of H. pylori strains exhibited a high similarity with the average nucleotide identity (ANI) values of 98.5% to 99.2%, carried 5 to 7 pathogenicity islands, and 3 to 6 mobilomes. The MLST profile of strains revealed novel sequence types ST4511, ST4512, and ST4513. Core-genome based phylogeny exhibited that the three H. pylori strains belong to the Asian genotype. These strains possessed 128 to 131 virulence genes, including toxin-encoding genes cagA and vacA. Double amoxicillin-resistant mutations on pbp1 and pbp2, or a mutation on pbp3, triple clarithromycin-resistant mutations on 23S rRNA gene and a levofloxacin-resistant mutation on gyrA were detected in antibiotic-resistant strains. Mutations on rdxA were detected in both metronidazole-resistant and -sensitive strains, whereas frxA mutations were detected in only one metronidazole-sensitive strain. Finally, a rifamycin-resistant mutation in rpoB was also detected. This study provides insights into the genome of multidrug-resistant H. pylori strains of a novel sequence type circulating in Vietnam for future investigations of its pathobiology and spread through human populations.