Genomic fingerprinting and genotyping of Helicobacter pylori strains from patients with duodenal ulcer or gastric cancer from different geographic regions

Li Li, David Y. Graham, Oscar Gutierrez, Jong G. Kim, Robert M. Genta, Hala Mt El-Zimaity, Mae F. Go

Research output: Contribution to journalArticle

12 Citations (Scopus)

Abstract

Continuing attempts have been made to classify pathogenic strains within bacterial populations based on DNA fingerprints and to identify virulence factors in H. pylori. We studied 287 H. pylori isolates from patients with duodenal ulcer or gastric cancer from three different geographic regions. DNA fingerprints were generated using REP-PCR and analyzed by cluster analysis. The status of three candidate virulence factors-vacA polymorphism, cagA and iceA,-were examined by PCR amplification. Cluster analysis of the REP-PCR fingerprints showed clustering by geographic region but not by disease presentation, cagA was detected in 91.3% of the isolates. Differences in vacA subtypes were observed among the three geographic regions. There was no association between iceA subtypes and clinical outcome. We conclude that geographic differences among the H. pylori strains exist in single gene allelic variants as well as in the conserved noncoding regions such as REP sequences throughout the entire bacterial genome. We did not detect any association between disease presentation and H. pylori genotypes using either DNA fingerprinting or candidate single gene virulence factors.

Original languageEnglish (US)
Pages (from-to)2512-2518
Number of pages7
JournalDigestive Diseases and Sciences
Volume47
Issue number11
DOIs
StatePublished - Nov 1 2002

Fingerprint

Duodenal Neoplasms
Duodenal Ulcer
Helicobacter pylori
Stomach Neoplasms
DNA Fingerprinting
Virulence Factors
Cluster Analysis
Polymerase Chain Reaction
Bacterial Genomes
Dermatoglyphics
Genes
Genotype
Population

Keywords

  • cagA
  • Duodenal ulcer
  • Gastric cancer
  • Helicobacter pylori
  • iceA
  • REP-PCR
  • vacA

ASJC Scopus subject areas

  • Gastroenterology

Cite this

Genomic fingerprinting and genotyping of Helicobacter pylori strains from patients with duodenal ulcer or gastric cancer from different geographic regions. / Li, Li; Graham, David Y.; Gutierrez, Oscar; Kim, Jong G.; Genta, Robert M.; Mt El-Zimaity, Hala; Go, Mae F.

In: Digestive Diseases and Sciences, Vol. 47, No. 11, 01.11.2002, p. 2512-2518.

Research output: Contribution to journalArticle

Li, Li ; Graham, David Y. ; Gutierrez, Oscar ; Kim, Jong G. ; Genta, Robert M. ; Mt El-Zimaity, Hala ; Go, Mae F. / Genomic fingerprinting and genotyping of Helicobacter pylori strains from patients with duodenal ulcer or gastric cancer from different geographic regions. In: Digestive Diseases and Sciences. 2002 ; Vol. 47, No. 11. pp. 2512-2518.
@article{6832b953265542cd8e3490fce8f94916,
title = "Genomic fingerprinting and genotyping of Helicobacter pylori strains from patients with duodenal ulcer or gastric cancer from different geographic regions",
abstract = "Continuing attempts have been made to classify pathogenic strains within bacterial populations based on DNA fingerprints and to identify virulence factors in H. pylori. We studied 287 H. pylori isolates from patients with duodenal ulcer or gastric cancer from three different geographic regions. DNA fingerprints were generated using REP-PCR and analyzed by cluster analysis. The status of three candidate virulence factors-vacA polymorphism, cagA and iceA,-were examined by PCR amplification. Cluster analysis of the REP-PCR fingerprints showed clustering by geographic region but not by disease presentation, cagA was detected in 91.3{\%} of the isolates. Differences in vacA subtypes were observed among the three geographic regions. There was no association between iceA subtypes and clinical outcome. We conclude that geographic differences among the H. pylori strains exist in single gene allelic variants as well as in the conserved noncoding regions such as REP sequences throughout the entire bacterial genome. We did not detect any association between disease presentation and H. pylori genotypes using either DNA fingerprinting or candidate single gene virulence factors.",
keywords = "cagA, Duodenal ulcer, Gastric cancer, Helicobacter pylori, iceA, REP-PCR, vacA",
author = "Li Li and Graham, {David Y.} and Oscar Gutierrez and Kim, {Jong G.} and Genta, {Robert M.} and {Mt El-Zimaity}, Hala and Go, {Mae F.}",
year = "2002",
month = "11",
day = "1",
doi = "10.1023/A:1020564126960",
language = "English (US)",
volume = "47",
pages = "2512--2518",
journal = "Digestive Diseases and Sciences",
issn = "0163-2116",
publisher = "Springer New York",
number = "11",

}

TY - JOUR

T1 - Genomic fingerprinting and genotyping of Helicobacter pylori strains from patients with duodenal ulcer or gastric cancer from different geographic regions

AU - Li, Li

AU - Graham, David Y.

AU - Gutierrez, Oscar

AU - Kim, Jong G.

AU - Genta, Robert M.

AU - Mt El-Zimaity, Hala

AU - Go, Mae F.

PY - 2002/11/1

Y1 - 2002/11/1

N2 - Continuing attempts have been made to classify pathogenic strains within bacterial populations based on DNA fingerprints and to identify virulence factors in H. pylori. We studied 287 H. pylori isolates from patients with duodenal ulcer or gastric cancer from three different geographic regions. DNA fingerprints were generated using REP-PCR and analyzed by cluster analysis. The status of three candidate virulence factors-vacA polymorphism, cagA and iceA,-were examined by PCR amplification. Cluster analysis of the REP-PCR fingerprints showed clustering by geographic region but not by disease presentation, cagA was detected in 91.3% of the isolates. Differences in vacA subtypes were observed among the three geographic regions. There was no association between iceA subtypes and clinical outcome. We conclude that geographic differences among the H. pylori strains exist in single gene allelic variants as well as in the conserved noncoding regions such as REP sequences throughout the entire bacterial genome. We did not detect any association between disease presentation and H. pylori genotypes using either DNA fingerprinting or candidate single gene virulence factors.

AB - Continuing attempts have been made to classify pathogenic strains within bacterial populations based on DNA fingerprints and to identify virulence factors in H. pylori. We studied 287 H. pylori isolates from patients with duodenal ulcer or gastric cancer from three different geographic regions. DNA fingerprints were generated using REP-PCR and analyzed by cluster analysis. The status of three candidate virulence factors-vacA polymorphism, cagA and iceA,-were examined by PCR amplification. Cluster analysis of the REP-PCR fingerprints showed clustering by geographic region but not by disease presentation, cagA was detected in 91.3% of the isolates. Differences in vacA subtypes were observed among the three geographic regions. There was no association between iceA subtypes and clinical outcome. We conclude that geographic differences among the H. pylori strains exist in single gene allelic variants as well as in the conserved noncoding regions such as REP sequences throughout the entire bacterial genome. We did not detect any association between disease presentation and H. pylori genotypes using either DNA fingerprinting or candidate single gene virulence factors.

KW - cagA

KW - Duodenal ulcer

KW - Gastric cancer

KW - Helicobacter pylori

KW - iceA

KW - REP-PCR

KW - vacA

UR - http://www.scopus.com/inward/record.url?scp=0036845718&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0036845718&partnerID=8YFLogxK

U2 - 10.1023/A:1020564126960

DO - 10.1023/A:1020564126960

M3 - Article

C2 - 12452388

AN - SCOPUS:0036845718

VL - 47

SP - 2512

EP - 2518

JO - Digestive Diseases and Sciences

JF - Digestive Diseases and Sciences

SN - 0163-2116

IS - 11

ER -