title: Detection and typing of the virulence determinants cagA and vacA of Helicobacter pylori directly from biopsy DNA: are in vitro strains representative of in vivo strains?
abstract: BACKGROUND
  The relationship of Helicobacter pylori genotypes to gastrointestinal disease has relied on cultured isolates. This assumes that cultured strains are representative of in vivo strains.
  
  
  OBJECTIVE
  To detect and type the cagA status and the vacA genotypes directly from biopsy DNA without the need for culture, and to further define the relationship between H. pylori genotypes and gastroduodenal pathology.
  
  
  METHODS
  Fifty-two Caucasian patients undergoing routine endoscopy for dyspepsia had additional biopsies taken from four gastric sites and one duodenal site for biopsy DNA preparation. An antral sample was taken for biopsy culture. All recruited patients were H. pylori-positive on rapid urease test for Campylobacter-like organisms (CLO test) and/or histology. By polymerase chain reaction (PCR), the cagA status and the vacA s and m types were detected directly from biopsy DNA.
  
  
  RESULTS
  H. pylori isolates were cultured from 28/52 patients in whom infection was detected by PCR. Two isolate types differed from biopsy types. Fifty of the 52 patients, strains were typable from all four gastric sites and in 51/52 the same strain predominated throughout. The cancer strains were all cagA-positive/vacA s1 type. There was a correlation between cagA positivity and vacA s1 (41/43). There was no difference between the cagA-positive/vacA s1 strains and the presence or absence of ulcers. There were only 5/52 vacA s2 m2 and four were in the non-ulcer dyspeptic group.
  
  
  CONCLUSIONS
  cagA status and the vacA genotyping was successful with tissue samples taken directly from gastric and duodenal biopsies. Discrepancies between isolate and biopsy strain types stress the need for caution when interpreting in vitro strain types and suggest that direct PCR of biopsies is the preferred typing technique. The cagA status and the s1 vacA allele are unreliable as single markers in determining the risk of developing peptic ulcer disease.
authors.affiliation: Department of Gastroenterology, Leicester Royal Infirmary, UK.
authors.forename: M C
authors.initials: MC
authors.lastname: Gunn
authors.forename: J C
authors.initials: JC
authors.lastname: Stephens
authors.forename: J D
authors.initials: JD
authors.lastname: Stewart
authors.forename: B J
authors.initials: BJ
authors.lastname: Rathbone
mesh_terms: D000942:Antigens, Bacterial; D001426:Bacterial Proteins / Q000302:isolation & purification*; D001427:Bacterial Toxins / Q000302:isolation & purification*; D001706:Biopsy; D004269:DNA, Bacterial / Q000032:analysis*; D004381:Duodenal Ulcer / Q000382:microbiology* / Q000473:pathology; D005838:Genotype; D016481:Helicobacter Infections / Q000382:microbiology* / Q000473:pathology; D016480:Helicobacter pylori / Q000737:chemistry / Q000472:pathogenicity; D006801:Humans; D016133:Polymerase Chain Reaction; D013274:Stomach Neoplasms / Q000382:microbiology / Q000473:pathology; D013276:Stomach Ulcer / Q000382:microbiology* / Q000473:pathology; D014774:Virulence
chemical_list: D000942:Antigens, Bacterial; D001426:Bacterial Proteins; D001427:Bacterial Toxins; D004269:DNA, Bacterial; C074689:VacA protein, Helicobacter pylori; C080866:cagA protein, Helicobacter pylori