Clustering of South African Helicobacter pylori isolates from peptic ulcerdisease patients is demonstrated by repetitive extragenic palindromic-PCR fingerprinting

The present report assesses the association between clonal groupings, disea se, and the virulence fingerprint of 76 South African Helicobacter pylori c agA(+) strains isolated from 57 Cape-colored subjects. Two methods, repetit ive extragenic palindromic (REP)-PCR and random amplified polymorphic DNA ( RAPD)-PCR, were used to generate DNA fingerprints, and computer-assisted an alysis was used to derive clusters. The two PCR techniques were only partia lly complementary (48%). RE P-PCR fingerprints identified a distinct pathol ogical cluster consisting of strains from 63% of the patients and was stron gly associated with both disease (P < 0.00001) and the vacuolating cytotoxi n A (vacA) signal sequence type (P < 0.003). RAPD-PCR fingerprinting was no t associated with disease and was less strongly associated with vacA (P < 0 .05) than REP-PCR was. Hierarchical analysis indicated that isolates from p atients with peptic ulcer disease tended to cluster differently than isolat es from patients with gastritis alone or gastric adenocarcinoma. These rela tionships are consistent with a loosely clonal population structure associa ted,vith disease for H. pylori in the Cape-colored population in South Afri ca.