Antibiotic Resistance and Genetic Determinants of Helicobacter pylori in Oman: Insights from Phenotypic and Whole-Genome Analysis.

Helicobacter pylori antibiotic resistance data in Oman are limited yet crucial for effective treatment selection. The genetic diversity within H. pylori influences its pathogenicity and clinical outcomes. This study evaluates resistance patterns and genetic determinants to guide treatment strategies. This study assessed antibiotic susceptibility in 15 H. pylori isolates (from 169 clinical samples) from naïve and treatment-failed patients. Resistance to clarithromycin (CLA), amoxicillin (AMX), metronidazole (MTZ), tetracycline, rifampicin (RIF), and levofloxacin (LEV) was tested alongside genetic analysis of virulence and resistance-associated mutations by whole-genome sequencing (WGS). Among the 15 resistant isolates, 20% were resistant to one antibiotic, 33.3% to two, 20% to three, and 26.6% to four antibiotics. MTZ resistance was universal among single-drug resistant isolates (100%). AMX-MTZ dual resistance was present in 60%, while triple resistance (CLA-AMX-MTZ) was present in 66.7%. Quadruple resistance (CLA-AMX-MTZ-RIF) was present in 75%. WGS revealed 23S rRNA mutations in 33.3% of CLA-resistant strains and pbp-1 mutations in 66.6% of AMX-resistant strains. MTZ resistance was linked to rdxA/frxA mutations, while RIF and LEV resistance correlated with rpoB (65.7%) and gyrA (20%) mutations, respectively. The genotype-phenotype agreement was insignificant (p = 1). High mutation heterogeneity, virulence factors, and environmental influences contribute to resistance. Further studies on host-pathogen interactions are needed to understand resistance mechanisms.