title: Molecular typing of Helicobacter pylori by virulence-gene based multiplex PCR and RT-PCR analysis.
abstract: BACKGROUND
  In recent years, numerous PCR amplification typing methods have been developed for the identification of H. pylori specific virulence genes. To reduce the number of PCR amplifications needed we have previously developed virulence gene based multiplex PCR and RT-PCR assays.
  
  
  OBJECTIVE
  The aim of the present study was to characterise Helicobacter pylori strains by means of virulence-gene based multiplex PCR and reverse-transcription PCR.
  
  
  METHODS
  Helicobacter pylori clinical reference strains HP-HJM 1-25 originally obtained from routine cultures of clinical gastric biopsy specimens from dyspeptic patients were used in the present study.
  
  
  METHODS
  Helicobacter pylori multiplex PCR and RT-PCR assays were carried out using primer pairs targeting the cagA, vacA, ureA, ureI, hspA (hsp60), and sodB genes and their cDNA.
  
  
  RESULTS
  Unexpected multiplex PCR and RT-PCR patterns were observed by ethidium bromide staining of agarose gels and Southern blot hybridisation analysis. DNA sequence analysis revealed a complex pattern of point mutations, deletions and insertions in the sodB, cagA and vacA genes, respectively. Mutations occurring in the PCR and hybridisation primer binding sites might explain some of the discrepancies previously observed in the expression of these genes. Furthermore, the present data show that coexpression of cagA and vacA transcripts of different sizes may take place in the same strain.
  
  
  CONCLUSIONS
  The multiplex PCR and RT-PCR assay described allows rapid characterisation of H. pylori virulence genes at the DNA and RNA (cDNA) levels. However, extensive DNA sequence analysis seems necessary if one wants to reveal details of mutations occurring in the cagA and vacA genes.
authors.affiliation: Molecular Biology Laboratory-LMO, University Hospital, Department of Biomedicine and Surgery, Faculty of Health Sciences, Linköping University, S-58 185 Linköping, Sweden.
authors.forename: Hans-Jürg
authors.initials: HJ
authors.lastname: Monstein
authors.forename: Katarina
authors.initials: K
authors.lastname: Ellnebo-Svedlund
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D015373:Bacterial Typing Techniques; D001483:Base Sequence; D017931:DNA Primers; D004269:DNA, Bacterial / Q000032:analysis; D018076:DNA, Complementary / Q000235:genetics; D005838:Genotype; D016480:Helicobacter pylori / Q000145:classification* / Q000235:genetics / Q000472:pathogenicity*; D006801:Humans; D008969:Molecular Sequence Data; D010641:Phenotype; D016133:Polymerase Chain Reaction; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012680:Sensitivity and Specificity; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D014774:Virulence / Q000235:genetics
chemical_list: D001426:Bacterial Proteins; D017931:DNA Primers; D004269:DNA, Bacterial; D018076:DNA, Complementary