Molecular characterization of Helicobacter pylori clinical isolates from Eastern Saudi Arabia

Objectives: To describe the frequency of cytotoxin-associated gene A (CagA) and vacuolating cytotoxin A (VacA) virulence genes and clarithromycin resistance-associated mutations among Helicobacter pylori (H. pylori) clinical isolates from Eastern Saudi Arabia. Methods: A cross-sectional study was carried out between July 2020 and June 2021 in a tertiary hospital in AL-Khobar, Saudi Arabia. A total of 34 H. pylori isolates were obtained from gastric biopsies of patients with dyspepsia. The existence of the virulence genes was studied by polymerase chain reaction and the gene fragment of the 23s ribosomal subunit (23s rRNA) gene was sequenced. Results: All isolates harbored the CagA gene. Approximately 97.1% (33/34) isolates were positive using the VacA M primer and 91.2% (31/34) isolates were positive using the VacA S primer. The most frequent allelic combination was S2/M2/cag (60%), followed by S1/M2/cag (26.7%), S1/M1/cag (10%), and S2/M1/cag (3.3%). Approximately 6.5% isolates harbored the A2142G mutation and 29% isolates harbored the A2143G mutation. One isolate contained the mutation T2182C. The phylogenetic analysis showed that 58% isolates clustered with the regional and global isolates while the remaining 42% isolates seemed to be specifically circulating in Saudi Arabia. Most of the patients (73.5%) had already underwent a previous H. pylori eradication therapy. Conclusion: We showed that there is a regional variation in the frequency of the virulence genes among H. pylori isolates. Additionally, we showed the frequency of 23s rRNA mutations related to clarithromycin resistance in Saudi Arabia.