Characterization and genetic diversity of Helicobacter pylori type IV secretion system components, CagI and CagN and its association with clinical outcomes among Iranian patients

Abstract

Background A number of cagPAI genes in H. pylori genome was proposed to be the most probably evolved under a diversifying selection and evolutionary pressure. Among them, CagI and CagN are described as a part of the two different-operon of cagPAI that are involved in the T4SS, but the definite association of these factors with clinical manifestations is unclear. Methods A total of 70 H. pylori isolates were obtained from different gastroduodenal pateints. All isolates were examined for the presence of primary H. pylori virulence genes by PCR analysis. Direct DNA sequence analysis was performed for the cagI and cagN genes. The results were compared with reference strain. Results The cagI, cagN, cagA, cagL, vacA s1m1, vacA s1m2, vacA s2m2, babA2, sabA and dupA genotypes were detected in 80%, 91.4%, 84%, 91.4%, 32.8%, 42.8%, 24.4%, 97.1%, 84.3%, and 84.3% of the total isolates, respectively. The most variable codon usage in cagI was observed at residues 20 to 25, 55 to 60, 94, 181 to 199, 213 to 221, 241 to 268, and 319 to 320, while the most variable codon usage in CagN hypervariable motif (CagNHM) was observed at residues 53 to 63. This CagNHM region is postulated to contain GDEEITEEEKK sequence in the P12 reference strain. Sequencing data analysis of cagN revealed a conserved hypothetical hexapeptide repeat (EAKDEN/K) in residues of 278–283 among six H. pylori isolates, which needs further studies to evaluate its putative function. Conclusion The present study demonstrated a high prevalence of cagI and cagN genes among Iranian H. pylori isolates with gastroduodenal diseases. Furthermore, no significant correlation between cagI and cagN variants and clinical outcomes was observed. However, all patients had high prevalence of cagPAI genes including cagI, cagN, cagA and cagL that indicates more potential role of these genes in disease outcome.