High prevalence of antibiotic resistance in Helicobacter pylori isolates from Iran: importance of functional and mutational analysis of resistance genes and virulence genotyping

The high prevalence of antibiotic resistance in Helicobacter pylori has become a great challenge in Iran. The genetic mutations that contribute to the resistance have yet to be precisely identified. This study aimed to investigate the prevalence of antibiotic resistance and virulence markers in Iranian H. pylori isolates and to analyze if there is any association between resistance and genotype. Antibiotic susceptibility patterns of 33 H. pylori isolates were investigated against metronidazole, clarithromycin, amoxicillin, rifampicin, ciprofloxacin, levofloxacin and tetracycline by the agar dilution method. The frxA, rdxA, gyrA, gyrB and 23S rRNA genes of the isolates were sequenced. The virulence genotypes were also determined using PCR. Metronidazole resistance was present in 81.8% of the isolates, followed by clarithromycin (36.4%), ciprofloxacin (36.4%), amoxicillin (30.3%), rifampicin (30.3%), levofloxacin (27.3%) and tetracycline (6.1%). Most of the metronidazole-resistant isolates carried frameshift mutations in both frxA and rdxA genes, and premature termination was occurred in positions Q5Stop and Q50Stop, respectively. Amino acid substitutions M191I, G208E, and V199A were predominantly found in gyrA gene of fluoroquinolone-resistant isolates. A2143G and C2195T mutations of 23S rRNA were found in four isolates. Interestingly, significant associations were demonstrated between intact cagPAI and resistance to rifampicin (P = 0.027), and between susceptibility to amoxicillin and cagPAI intactness (P = 0.016). The prevalence of H. pylori antibiotic resistance is high in our region, particularly that of metronidazole, clarithromycin, ciprofloxacin and multidrug resistance. Occurrence of mutations in resistance genes were involved in the development of resistance, especially in less virulent isolates.