Genomic fingerprinting and genotyping of Helicobacter pylori strains from patients with duodenal ulcer or gastric cancer from different geographic regions
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...
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| Veröffentlicht in: | Digestive diseases and sciences 2002-11, Vol.47 (11), p.2512-2518 |
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| creator | Li, Li Graham, David Y Gutierrez, Oscar Kim, Jong G Genta, Robert M El-Zimaity, Hala M T Go, Mae F |
| description | 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. |
| doi_str_mv | 10.1023/A:1020564126960 |
| format | Article |
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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.</description><identifier>ISSN: 0163-2116</identifier><identifier>EISSN: 1573-2568</identifier><identifier>DOI: 10.1023/A:1020564126960</identifier><identifier>PMID: 12452388</identifier><identifier>CODEN: DDSCDJ</identifier><language>eng</language><publisher>United States: Springer Nature B.V</publisher><subject>Antigens, Bacterial ; Bacterial Proteins - genetics ; Demography ; DNA Fingerprinting ; DNA, Bacterial - genetics ; Duodenal Ulcer - microbiology ; Genotype ; Helicobacter Infections - epidemiology ; Helicobacter Infections - microbiology ; Helicobacter pylori - genetics ; Helicobacter pylori - pathogenicity ; Humans ; Polymerase Chain Reaction - methods ; Repetitive Sequences, Nucleic Acid ; Stomach Neoplasms - microbiology ; Virulence</subject><ispartof>Digestive diseases and sciences, 2002-11, Vol.47 (11), p.2512-2518</ispartof><rights>Copyright Kluwer Academic Publishers Nov 2002</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c280t-ed8212bc2b4c3423dfce82c46d76b431a0cd181ed3fdb6865b65af45d4bf6ce23</citedby></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,776,780,27901,27902</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/12452388$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Li, Li</creatorcontrib><creatorcontrib>Graham, David Y</creatorcontrib><creatorcontrib>Gutierrez, Oscar</creatorcontrib><creatorcontrib>Kim, Jong G</creatorcontrib><creatorcontrib>Genta, Robert M</creatorcontrib><creatorcontrib>El-Zimaity, Hala M T</creatorcontrib><creatorcontrib>Go, Mae F</creatorcontrib><title>Genomic fingerprinting and genotyping of Helicobacter pylori strains from patients with duodenal ulcer or gastric cancer from different geographic regions</title><title>Digestive diseases and sciences</title><addtitle>Dig Dis Sci</addtitle><description>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.</description><subject>Antigens, Bacterial</subject><subject>Bacterial Proteins - genetics</subject><subject>Demography</subject><subject>DNA Fingerprinting</subject><subject>DNA, Bacterial - genetics</subject><subject>Duodenal Ulcer - microbiology</subject><subject>Genotype</subject><subject>Helicobacter Infections - epidemiology</subject><subject>Helicobacter Infections - microbiology</subject><subject>Helicobacter pylori - genetics</subject><subject>Helicobacter pylori - pathogenicity</subject><subject>Humans</subject><subject>Polymerase Chain Reaction - methods</subject><subject>Repetitive Sequences, Nucleic Acid</subject><subject>Stomach Neoplasms - microbiology</subject><subject>Virulence</subject><issn>0163-2116</issn><issn>1573-2568</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2002</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><recordid>eNpdkD1PHDEQhi0UBBegThdZKegu-Gu9vnQnFO6QkNJAvfLa48Vo197YXkX3V_Jr8RHSUM3X885oXoS-UPKdEsZvtj9qII0UlMmNJCdoRZuWr1kj1Se0IlTWnFJ5jj7n_EII2bRUnqFzykTDuFIr9HcHIU7eYOfDAGlOPpSaYR0sHuqoHOZjGR3ew-hN7LUpkPB8GGPyOJekfcjYpTjhWRcPoWT8x5dnbJdoIegRL6OpgpjwoCteLxkdjp03jfXOQaqqeiwOSc_PFUgw-BjyJTp1esxw9R4v0NPdz8fb_frh1-7-dvuwNkyRsgarGGW9Yb0wXDBunQHFjJC2lb3gVBNjqaJgubO9VLLpZaOdaKzonTTA-AW6_rd3TvH3Arl0k88GxlEHiEvuWtYyUk2s4LcP4EtcUv0xd4wKzilTR-jrO7T0E9iuOjrpdOj-W85fATqRh0g</recordid><startdate>200211</startdate><enddate>200211</enddate><creator>Li, Li</creator><creator>Graham, David Y</creator><creator>Gutierrez, Oscar</creator><creator>Kim, Jong G</creator><creator>Genta, Robert M</creator><creator>El-Zimaity, Hala M T</creator><creator>Go, Mae F</creator><general>Springer Nature B.V</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>3V.</scope><scope>7RV</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BENPR</scope><scope>CCPQU</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>K9-</scope><scope>K9.</scope><scope>KB0</scope><scope>M0R</scope><scope>M0S</scope><scope>M1P</scope><scope>NAPCQ</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>7X8</scope></search><sort><creationdate>200211</creationdate><title>Genomic fingerprinting and genotyping of Helicobacter pylori strains from patients with duodenal ulcer or gastric cancer from different geographic regions</title><author>Li, Li ; Graham, David Y ; Gutierrez, Oscar ; Kim, Jong G ; Genta, Robert M ; El-Zimaity, Hala M T ; Go, Mae F</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c280t-ed8212bc2b4c3423dfce82c46d76b431a0cd181ed3fdb6865b65af45d4bf6ce23</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2002</creationdate><topic>Antigens, Bacterial</topic><topic>Bacterial Proteins - genetics</topic><topic>Demography</topic><topic>DNA Fingerprinting</topic><topic>DNA, Bacterial - genetics</topic><topic>Duodenal Ulcer - microbiology</topic><topic>Genotype</topic><topic>Helicobacter Infections - epidemiology</topic><topic>Helicobacter Infections - microbiology</topic><topic>Helicobacter pylori - genetics</topic><topic>Helicobacter pylori - pathogenicity</topic><topic>Humans</topic><topic>Polymerase Chain Reaction - methods</topic><topic>Repetitive Sequences, Nucleic Acid</topic><topic>Stomach Neoplasms - microbiology</topic><topic>Virulence</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Li, Li</creatorcontrib><creatorcontrib>Graham, David Y</creatorcontrib><creatorcontrib>Gutierrez, Oscar</creatorcontrib><creatorcontrib>Kim, Jong G</creatorcontrib><creatorcontrib>Genta, Robert M</creatorcontrib><creatorcontrib>El-Zimaity, Hala M T</creatorcontrib><creatorcontrib>Go, Mae F</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>ProQuest Central (Corporate)</collection><collection>Nursing & Allied Health Database</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>ProQuest Central</collection><collection>ProQuest One Community College</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>Consumer Health Database (Alumni Edition)</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Nursing & Allied Health Database (Alumni Edition)</collection><collection>Consumer Health Database</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Nursing & Allied Health Premium</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>MEDLINE - Academic</collection><jtitle>Digestive diseases and sciences</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Li, Li</au><au>Graham, David Y</au><au>Gutierrez, Oscar</au><au>Kim, Jong G</au><au>Genta, Robert M</au><au>El-Zimaity, Hala M T</au><au>Go, Mae F</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Genomic fingerprinting and genotyping of Helicobacter pylori strains from patients with duodenal ulcer or gastric cancer from different geographic regions</atitle><jtitle>Digestive diseases and sciences</jtitle><addtitle>Dig Dis Sci</addtitle><date>2002-11</date><risdate>2002</risdate><volume>47</volume><issue>11</issue><spage>2512</spage><epage>2518</epage><pages>2512-2518</pages><issn>0163-2116</issn><eissn>1573-2568</eissn><coden>DDSCDJ</coden><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. 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| subjects | Antigens, Bacterial Bacterial Proteins - genetics Demography DNA Fingerprinting DNA, Bacterial - genetics Duodenal Ulcer - microbiology Genotype Helicobacter Infections - epidemiology Helicobacter Infections - microbiology Helicobacter pylori - genetics Helicobacter pylori - pathogenicity Humans Polymerase Chain Reaction - methods Repetitive Sequences, Nucleic Acid Stomach Neoplasms - microbiology Virulence |
| title | Genomic fingerprinting and genotyping of Helicobacter pylori strains from patients with duodenal ulcer or gastric cancer from different geographic regions |
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