Molecular characteristics and clinical relevance of Cytotoxin-associated genes A and E of Helicobacter pylori from patients with gastric diseases

Background: Helicobacter pylori colonizes about a half of the world’s population. It possesses several genes that associated with virulence, among which are cytotoxin‑associated antigen (CagA) and cytotoxin‑associated gene E (CagE) genes within the cag pathogenicity island. These genes encode for proteins involved in the pathogenicity of the bacteria. Objective: This study aimed to investigate the prevalence of CagA and CagE genes among H. pylori isolates from patients with different gastric pathologies and for phylogenetic analysis of the isolated bacteria according to gene sequence. Materials and Methods: A total of 104 gastric biopsies were collected for patients suffering from different gastric pathologies. DNA was extracted from these biopsies, and a conventional polymerase chain reaction (PCR) was performed to amplify the gene fragments corresponding CagA and CagE genes using specific primers. PCR product of selected samples of positive for CagE was undergone direct sequencing. The result of sequences was aligned with reference sequences in National Center for Biotechnology Information (NCBI), and the phylogenetic tree was constructed. Results: Out of 104 isolates of H. pylori, 89/104 (85.58%) were found to have either CagA, CagE, or both genes. The frequencies of CagA, CagE, and coexistence of both genes were 71.15%, 46.15%, and 31.73%, respectively. The phylogenetic tree revealed two main clades, one of which involved isolates 6 and 9 as separated isolates and another clade involved all other isolates. The isolate 4 clustered with AY153111.1 and AP014523.1, the isolate 3 clustered with AY153124.1, the isolate 5 clustered with LC339073.1 and LC339017.1, the isolates 7 and 11 clustered with EU090726.1, the isolate 2 clustered with AB191082.1, the isolate 10 clustered very close to LC339004.1 and less close to LS483488.1, while the isolate 1 clustered with AP017334.1. Conclusion: CagA and CagE genes are highly prevalence among H. pylori isolate from gastric pathologies from Iraqi patients.