title: Genotyping of the Helicobacter pylori cagA Gene Isolated From Gastric Biopsies in Shiraz, Southern Iran: A PCR-RFLP and Sequence Analysis Approach.
abstract: BACKGROUND
  Cytotoxin-associated gene A (cagA) is an important virulence factor in the pathogenesis of Helicobacter pylori.
  
  
  OBJECTIVE
  The aim of this study was to genotype the H. pylori cagA gene isolated from antral biopsies of patients with stomach symptoms, using a PCR-restriction fragment length polymorphism (PCR-RFLP) analysis.
  
  
  METHODS
  A total of 161 gastric biopsies were collected from patients with stomach symptoms. After isolation of H. pylori from the biopsy culture, the cagA gene was assessed using PCR. The PCR products were then digested by the HinfI restriction endonuclease enzyme. A sample of each genotype was also subjected to direct sequencing for further analysis.
  
  
  RESULTS
  From 161 antral biopsies, 61 (37.9%) were positive for H. pylori in culture. Overall, 24 cagA-positives were detected in the isolates. RFLP indicated three different genotypes (I, II, and III) of cagA with a frequency of 62.5%, 25%, and 12.5% among the isolates, respectively. Genotypes I and II of cagA were predominant in patients who had gastritis. However, genotype III was found in three patients with duodenitis and duodenal ulcers. Alignment of the nucleotide sequences of the three isolated genotypes, with H. pylori 26695 as a reference strain, revealed 12 inserted nucleotides in genotype III. When the sequence of genotype III was aligned with 15 additional H. pylori strains available in GenBank, the same inserted nucleotides were detected in six of them.
  
  
  CONCLUSIONS
  Using the PCR-RFLP method, three distinctive H. pylori cagA genotypes were detected in antral biopsies. Genotype I, which was predominant among the isolates, was significantly associated with gastritis. However, the data showed that cagA genotype III may play a role in duodenitis and duodenal ulcers in patients infected with H. pylori.
authors.affiliation: Department of Pathobiology, School of Veterinary Medicine, Shiraz University, Shiraz, IR Iran.
authors.forename: Afsaneh
authors.initials: A
authors.lastname: Moaddeb
authors.affiliation: Gastroentrohepatology Research Center, Shiraz University of Medical Sciences, Shiraz, IR Iran.
authors.forename: Mohammad Reza
authors.initials: MR
authors.lastname: Fattahi
authors.affiliation: Department of Pathobiology, School of Veterinary Medicine, Shiraz University, Shiraz, IR Iran.
authors.forename: Roya
authors.initials: R
authors.lastname: Firouzi
authors.affiliation: Department of Pathobiology, School of Veterinary Medicine, Shiraz University, Shiraz, IR Iran.
authors.forename: Abdollah
authors.initials: A
authors.lastname: Derakhshandeh
authors.affiliation: Clinical Microbiology Research Center, Shiraz University of Medical Sciences, Shiraz, IR Iran.
authors.forename: Shohreh
authors.initials: S
authors.lastname: Farshad
keywords: Polymerase Chain Reaction; Restriction Fragment Length Polymorphism