A whole genome sequencing approach for unraveling the genetic basis of antibiotic resistance in Iranian Helicobacter pylori isolates

Introduction: Antimicrobial resistance (AMR) among Helicobacter pylori strains is the major cause oferadication failure [۱]. Based on studies conducted in Iran, the level of resistance has reached analarming level and most Iranian H. pylori isolates reported as multi-drug resistant [۲]. However theunderlying cause of this high resistance is not clear. In this study, whole genome sequencing was usedto analyze ۳۱ randomly selected Iranian H. pylori strains to trace genomebased resistance.۳۱ H. pylori strains were isolated from Iranian patients with gastric disorders and subjected to DNAextraction. Whole genome sequencing was performed by the Illumina platform. After assembly andmapping of raw data, all isolates were analyzed by ResFinder, Comprehensive Antimicrobial ResistanceDatabase (CARD) and ABRicate tools which are widely used for analyzing whole genome sequencingdata to identify genes that confer resistance to various antibiotics [۲].ResFinder found some unidentified point mutations along with AMR to tetracycline, doxycycline andminocycline in only ۱/۳۱ isolates. ABRicate analysis showed AMR to tetracycline in only ۲/۳۱ isolates,one of them was the same as founded isolate by ResFinder. Although CARD showed some strict-hitAMR with a low percentage identity of matching region, no perfect-hit AMR was found in examinedisolates.Despite a high prevalence of antibiotic resistance in Iran which detected by laboratory susceptibilitytesting, bioinformatics tools revealed limited genetic resistance in only ۲/۳۰ of recruited isolates. Thisdiscrepancy between phenotypic and whole genome-based results in Iranian H. pylori strains indicatesthe need for further investigations.

کلیدواژه ها:

Helicobacter pylori ، WGS ، Antibiotic resistance