{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,2]],"date-time":"2026-02-02T19:50:51Z","timestamp":1770061851436,"version":"3.49.0"},"reference-count":36,"publisher":"American Society for Microbiology","issue":"12","license":[{"start":{"date-parts":[[2012,12,1]],"date-time":"2012-12-01T00:00:00Z","timestamp":1354320000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["J Clin Microbiol"],"published-print":{"date-parts":[[2012,12]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n          <jats:p>\n            The present report describes a novel method for genotyping the virulence-associated\n            <jats:italic>vacA<\/jats:italic>\n            intermediate (i) region of\n            <jats:named-content content-type=\"genus-species\">Helicobacter pylori<\/jats:named-content>\n            in archive material.\n            <jats:italic>vacA<\/jats:italic>\n            i-region genotypes as determined by the novel method were completely concordant with those of sequence analysis and with those of functional vacuolation activity. The method was further validated directly in gastric biopsy specimens of 386\n            <jats:named-content content-type=\"genus-species\">H. pylori<\/jats:named-content>\n            -positive cases, and effective characterization of the\n            <jats:italic>vacA<\/jats:italic>\n            i region was obtained in 191 of 192 (99.5%) frozen and in 186 of 194 (95.9%) formalin-fixed paraffin-embedded gastric biopsy specimens, respectively. The genotyping method was next used to address the relationship between the\n            <jats:italic>vacA<\/jats:italic>\n            genotypes and the\n            <jats:italic>cagA<\/jats:italic>\n            status. The\n            <jats:italic>vacA<\/jats:italic>\n            i1 genotype was associated with\n            <jats:italic>vacA<\/jats:italic>\n            s1 (where s indicates signal region),\n            <jats:italic>vacA<\/jats:italic>\n            m1 (where m indicates middle region), and\n            <jats:italic>cagA<\/jats:italic>\n            -positive genotypes (\n            <jats:italic>P<\/jats:italic>\n            &lt; 0.0001), while the\n            <jats:italic>vacA<\/jats:italic>\n            i2 genotype was closely related with\n            <jats:italic>vacA<\/jats:italic>\n            s2,\n            <jats:italic>vacA<\/jats:italic>\n            m2, and\n            <jats:italic>cagA<\/jats:italic>\n            -negative genotypes (\n            <jats:italic>P<\/jats:italic>\n            &lt; 0.0001). The relationship between\n            <jats:italic>H. pylori vacA<\/jats:italic>\n            i-region genotypes and gastric disease development was subsequently evaluated in the Portuguese population. Patients infected with\n            <jats:italic>vacA<\/jats:italic>\n            i1 strains showed an increased risk for gastric atrophy and for gastric carcinoma, with odds ratios of 8.0 (95% confidence interval [CI], 2.3 to 27) and of 22 (95% CI, 7.9 to 63), respectively. Taken together, the results show that this novel\n            <jats:italic>H. pylori vacA<\/jats:italic>\n            i-region genotyping method can be applied directly to archive material, providing a fast evaluation of strain virulence determinants without the need of culture. The results further emphasize that the characterization of the\n            <jats:italic>vacA<\/jats:italic>\n            i region may be useful to identify patients at higher risk of gastric carcinoma development.\n          <\/jats:p>","DOI":"10.1128\/jcm.02087-12","type":"journal-article","created":{"date-parts":[[2012,10,4]],"date-time":"2012-10-04T05:36:11Z","timestamp":1349328971000},"page":"3983-3989","update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":40,"title":["A Novel Method for Genotyping the\n            <i>Helicobacter pylori vacA<\/i>\n            Intermediate Region Directly in Gastric Biopsy Specimens"],"prefix":"10.1128","volume":"50","author":[{"given":"Rui M.","family":"Ferreira","sequence":"first","affiliation":[{"name":"IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal"},{"name":"Medical Faculty of the University of Porto, Porto, Portugal"}]},{"given":"Jose C.","family":"Machado","sequence":"additional","affiliation":[{"name":"IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal"},{"name":"Medical Faculty of the University of Porto, Porto, Portugal"}]},{"given":"Darren","family":"Letley","sequence":"additional","affiliation":[{"name":"NIHR Biomedical Research Unit, Nottingham Digestive Diseases Centre, University of Nottingham, Nottingham, United Kingdom"}]},{"given":"John C.","family":"Atherton","sequence":"additional","affiliation":[{"name":"NIHR Biomedical Research Unit, Nottingham Digestive Diseases Centre, University of Nottingham, Nottingham, United Kingdom"}]},{"given":"Maria L.","family":"Pardo","sequence":"additional","affiliation":[{"name":"Department of Pathology, Complejo Hospitalario de Soria, Soria, Spain"}]},{"given":"Carlos A.","family":"Gonzalez","sequence":"additional","affiliation":[{"name":"Unit of Nutrition, Environment and Cancer, Catalan Institute of Oncology, Barcelona, Spain"}]},{"given":"Fatima","family":"Carneiro","sequence":"additional","affiliation":[{"name":"IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal"},{"name":"Medical Faculty of the University of Porto, Porto, Portugal"},{"name":"Department of Pathology, Centro Hospitalar de Sao Jo\u00e3o, Porto, Portugal"}]},{"given":"Ceu","family":"Figueiredo","sequence":"additional","affiliation":[{"name":"IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal"},{"name":"Medical Faculty of the University of Porto, Porto, Portugal"}]}],"member":"235","reference":[{"key":"e_1_3_2_2_2","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.pathol.1.110304.100125"},{"key":"e_1_3_2_3_2","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.270.30.17771"},{"key":"e_1_3_2_4_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1523-5378.2010.00759.x"},{"key":"e_1_3_2_5_2","doi-asserted-by":"publisher","DOI":"10.1053\/j.gastro.2008.03.041"},{"key":"e_1_3_2_6_2","doi-asserted-by":"publisher","DOI":"10.1172\/JCI20925"},{"key":"e_1_3_2_7_2","doi-asserted-by":"publisher","DOI":"10.1128\/jcm.28.3.495-503.1990"},{"key":"e_1_3_2_8_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.93.25.14648"},{"key":"e_1_3_2_9_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.01815-09"},{"key":"e_1_3_2_10_2","first-page":"6735","article-title":"Human gastric carcinogenesis: a multistep and multifactorial process\u2014First American Cancer Society Award Lecture on Cancer Epidemiology and Prevention","volume":"52","author":"Correa P","year":"1992","unstructured":"CorreaP. 1992. 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