Helicobacter pylori (HP) is a bacterium that colonizes the human stomach and can establish a
long-term infection of the gastric mucosa. Persistent Hp
infection often induces
gastritis and is associated with the development of
peptic ulcer disease,
atrophic gastritis, and gastric
adenocarcinoma. Virulent HP isolates harbor the cag (
cytotoxin-associated genes) pathogenicity island (cagPAI), a 40 kb stretch of
DNA that encodes components of a
type IV secretion system (T4SS). This T4SS forms a pilus for the injection of
virulence factors into host target cells, such as the CagA
oncoprotein. We analyzed the genetic variability in cagA and other selected genes of the HP cagPAI (cagC, cagE, cagL, cagT, cagV and cag Gamma) using
DNA extracted from frozen gastric biopsies or from clinical isolates. Study subjects were 95 cagA+ patients that were histologically diagnosed with chronic
gastritis or
gastric cancer in Venezuela and Mexico, areas with high prevalence of Hp
infection. Sequencing reactions were carried out by both Sanger and next-generation pyrosequencing (454 Roche) methods. We found a total of 381 variants with unambiguous calls observed in at least 10% of the originally tested samples and reference strains. We compared the frequencies of these genetic variants between
gastric cancer and chronic
gastritis cases. Twenty-six SNPs (11 non-synonymous and 14 synonymous) showed statistically significant differences (P<0.05), and two SNPs, in position 1039 and 1041 of cagE, showed a highly significant association with
cancer (p-value = 2.07×10⁻⁶), and the variant
codon was located in the VirB3 homology domain of Agrobacterium. The results of this study may provide preliminary information to target
antibiotic treatment to high-risk individuals, if effects of these variants are confirmed in further investigations.