New approaches for genotyping of Helicobacter pylori based on amplification of polymorphisms in intergenic DNA regions and at the insertion site of the cag pathogenicity island |
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Authors: | Stefan Bereswill Ruth Schönenberger Constance Thies Frank Stähler Sonja Strobel Petra Pfefferle Lutz Wille Manfred Kist |
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Institution: | (1) Institute of Medical Microbiology and Hygiene, Department of Microbiology, University Hospital Freiburg, Hermann-Herder-Strasse 11, 79104 Freiburg, Germany e-mail: bereswil@ukl.uni-freiburg.de Tel.: +49-761-2036539; Fax: +49-761-2036562, DE;(2) Department of Public Health Medicine, School of Public Health, University of Bielefeld, PO box 100131, 33501 Bielefeld, Germany, DE |
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Abstract: | The population of the gastric pathogen Helicobacter pylori shows a high degree of genetic diversity. It is well established that heterogeneity at the isolate level is caused by nucleotide
transitions within genes, differences in the gene order, and by genetic instability of single genes as well as of a large
virulence-associated genomic DNA region, the cag pathogenicity island (PAI). Analysis of intergenic regions with specific PCR-assays developed in this study, revealed that
DNA polymorphisms in the noncoding DNA localized in front of the genes ribA and vacA and at the insertion site of the cag PAI contribute to the genetic diversity of H. pylori and are useful for differentiation of individual isolates. Thirteen individual genotypes were identified by PCR analysis
of these polymorphic loci in 487, 241, and 182 clinical H. pylori isolates. Sequence analysis revealed that genetic variability in front of genes ribA and vacA, and in the intergenic region at the PAI insertion site is caused by insertion and deletions of so-far-unknown DNA sequences
as well as by parts of the H. pylori IS elements IS605 and IS606, respectively. The new genotypes identified could be used to differentiate antrum and corpus
isolates from the same patients. Their combination with vacA allele subtypes and with the cagA status allowed to differentiate 140 isolates in 51 subtypes. In 36 cases the corresponding genotype patterns were isolate
specific. In summary, the results confirm that DNA polymorphisms in intergenic regions contribute to the genetic diversity
of H. pylori. Although individual H. pylori genotypes were not associated with peptic ulcer disease, the PCR-based approaches for their detection developed here should
be of use for further investigation of genetic diversity in H. pylori and for epidemiological purposes.
Received: 20 June 2000 |
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Keywords: | Helicobacter pylori Polymerase chain reaction Genetic diversity cag pathogenicity island Genetic instability |
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