title: Clustering of South African Helicobacter pylori isolates from peptic ulcer disease patients is demonstrated by repetitive extragenic palindromic-PCR fingerprinting.
abstract: The present report assesses the association between clonal groupings, disease, and the virulence fingerprint of 76 South African Helicobacter pylori cagA(+) strains isolated from 57 Cape-colored subjects. Two methods, repetitive extragenic palindromic (REP)-PCR and random amplified polymorphic DNA (RAPD)-PCR, were used to generate DNA fingerprints, and computer-assisted analysis was used to derive clusters. The two PCR techniques were only partially complementary (48%). REP-PCR fingerprints identified a distinct pathological cluster consisting of strains from 63% of the patients and was strongly associated with both disease (P < 0.00001) and the vacuolating cytotoxin A (vacA) signal sequence type (P < 0.003). RAPD-PCR fingerprinting was not associated with disease and was less strongly associated with vacA (P < 0.05) than REP-PCR was. Hierarchical analysis indicated that isolates from patients with peptic ulcer disease tended to cluster differently than isolates from patients with gastritis alone or gastric adenocarcinoma. These relationships are consistent with a loosely clonal population structure associated with disease for H. pylori in the Cape-colored population in South Africa.
authors.affiliation: GI Clinic and Department of Medicine, University of Cape Town & Groote Schuur Hospital, Cape Town, South Africa.
authors.forename: M
authors.initials: M
authors.lastname: Kidd
authors.forename: J C
authors.initials: JC
authors.lastname: Atherton
authors.forename: A J
authors.initials: AJ
authors.lastname: Lastovica
authors.forename: J A
authors.initials: JA
authors.lastname: Louw
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D002648:Child; D016000:Cluster Analysis; D016172:DNA Fingerprinting / Q000379:methods; D016481:Helicobacter Infections / Q000382:microbiology*; D016480:Helicobacter pylori / Q000145:classification* / Q000235:genetics* / Q000472:pathogenicity; D006801:Humans; D008875:Middle Aged; D010437:Peptic Ulcer / Q000382:microbiology*; D016133:Polymerase Chain Reaction / Q000379:methods; D019105:Random Amplified Polymorphic DNA Technique; D013019:South Africa; D014774:Virulence