The pathogenesis of Helicobacter pylori is significantly influenced by the Cag Pathogenicity Island (cagPAI), a cluster of genes that promote inflammation and modify host cell signaling. Recent research has highlighted notable genetic diversity among H. pylori strains, indicating a complex interaction between host factors and bacterial genetics in disease progression. In Iran, where H. pylori infection rates are notably high, understanding the genetic diversity of these strains is crucial for addressing public health concerns. This study utilized a whole genome sequencing approach to analyze the cagPAI status in H. pylori isolates from Iranian patients in detail.

A total of 30 gastric biopsy samples from patients diagnosed with H. pylori infection were collected and cultured. Isolated H. pylori were subjected to whole genome sequencing to acquire extensive genetic data. For data analysis, a customized alignment tool using Python alongside BLAST+ was developed for sequence alignment. This tool enabled the identification of genes present and absent within cagPAI region of the H. pylori genome. Furthermore, it facilitated the characterization of novel alleles identified in the Iranian H. pylori strains.

The results of this study demonstrate that 14 out of the 30 genomes analyzed (46.7%) completely lacked cagPAI genes. None of the isolates contained an intact cagPAI encompassing all 31 corresponding genes. The cagA gene, a major marker of cagPAI, was detected in 50% of the samples. Notably, the distribution of genes among the strains was non-uniform, suggesting that certain genes were present in a greater number of genomes while others were identified in fewer. Furthermore, 157 novel allelic variations not recorded in reference databases were identified, with the highest diversity observed in the cagA gene, which had nine distinct allelic variants.

In this study, we present a detailed analysis of the genetic variation within the cagPAI of H. pylori isolated from Iranian patients. By identifying novel alleles and investigating their association with clinical outcomes, our findings aim to enhance the understanding of H. pylori pathogenicity in this region. Ultimately, our research seeks to contribute valuable insights that could guide future therapeutic strategies and improve management for gastrointestinal diseases linked to H. pylori infection.