Genomic DNA fingerprinting of clinical isolates of Helicobacter pylori by REP-PCR and restriction fragment end-labelling

Abstract

Genetic diversity of 32 Helicobacter pylori strains isolated from patients with gastritis, gastric or duodenal ulcer, carcinoma, or lymphoma was determined by repetitive sequence element polymerase chain reaction (REP-PCR), and by the new typing method restriction fragment end-labelling (RFEL). Furthermore, these two methods were used to investigate a possible correlation between clinical symptoms and the genetic background of Helicobacter pylori. Both REP-PCR and RFEL revealed 31 different patterns for the 32 strains tested, but the pair of isolates with identical REP-PCR patterns was not the same as the pair of isolates with identical RFEL patterns. Computer-assisted analysis of the DNA fingerprints was used to determine similarity coefficients. This analysis revealed no clustering of disease-specific strains by any of the two methods.

Clustering of South African Helicobacter pylori Isolates from Peptic Ulcer Disease Patients Is Demonstrated by Repetitive Extragenic Palindromic-PCR Fingerprinting

“…REP-PCR typing has generated stable, reproducible DNA fingerprints that have been successfully used to discriminate H. pylori strains associated with PUD in a U.S. study (7), but this was not confirmed in a European study (16). The results from the present study suggest that REP fingerprints may be useful for defining disease-associated strains in a recent bacterial population derived from mixed population groups (European, Southeast Asian, and African).…”

“…The REP-and RAPD-PCR fingerprints of the H. pylori strains were analyzed with GelCompar software, Windows version 4.1 (Applied Math, Kortrijk, Belgium) (16). Both REP-and RAPD-PCR patterns were normalized using the 0.1-kbp molecular size standard.…”

“…The similarity coefficient indicates the relatedness of the strains and was calculated using band positions (coefficient of Jaccard) per the GelCompar program. Briefly, for each couple of tracks, the coefficient of Jaccard [S J ]divides the number of corresponding bands by the total number of bands in both tracks using the formula S J ϭ nAB/[(nA ϩ nB) Ϫ nAB], where nAB is the number of bands common for A and B, nA is the total number of bands in A, and nB is the total number of bands in B (16). A similarity coefficient of Ͼ70% was considered significant for analysis in this study.…”

“…Despite this high level of recombination, comparisons between strains based both on sequence analysis and on multilocus enzyme electrophoresis have shown that clonal population structure is not entirely destroyed (1, 9). It has been hypothesized that different clonal groupings may be associated with disease, but two studies using repetitive extragenic palindromic (REP)-PCR have reached different conclusions (7,16).In contrast to genome-based strategies such as REP-PCR, studies examining the association between specific virulence marker genes and disease have shown consistent associations. Virulence markers associated with disease include the presence of the gene cagA and the cag pathogenicity island (PAI), the s1/m1 and s1/m2 types of the vacuolating cytotoxin gene, vacA, and type 1 of the epithelial contact-induced gene, iceA.…”

“…Despite this high level of recombination, comparisons between strains based both on sequence analysis and on multilocus enzyme electrophoresis have shown that clonal population structure is not entirely destroyed (1, 9). It has been hypothesized that different clonal groupings may be associated with disease, but two studies using repetitive extragenic palindromic (REP)-PCR have reached different conclusions (7,16).…”