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In this study, Vietnamese patient <jats:italic>H. pylori<\/jats:italic> samples (46 duodenal ulcer (DU), 51 non-cardia gastric cancer (NCGC), 39 chronic gastritis (CG)) were fully sequenced using next-generation sequencing and assembled into contigs. <jats:italic>tfs3, tfs4,<\/jats:italic> and cagPAI genes were compared with the public database. Most (94%) <jats:italic>H. pylori<\/jats:italic> strains possessed a complete cagPAI, which was the greatest risk factor for clinical outcomes, while the prevalences of <jats:italic>tfs3<\/jats:italic> and <jats:italic>tfs4<\/jats:italic> were 45% and 77%, respectively. Complete <jats:italic>tfs3<\/jats:italic> and <jats:italic>tfs4<\/jats:italic> were found in 18.3% and 17.6% of strains, respectively. The prevalence of <jats:italic>H. pylori<\/jats:italic> strains with complete <jats:italic>tfs3<\/jats:italic> ICE in DU patients was significantly higher than that in NCGC patients (30.4% vs 11.7%, <jats:italic>P<\/jats:italic>\u2009&lt;\u20090.05). In addition, the prevalence of strains with complete <jats:italic>tfs3<\/jats:italic> ICE and cagPAI was significantly higher in DU patients than that in NCGC (28.4% vs 9.8%, <jats:italic>P<\/jats:italic>\u2009=\u20090.038) and CG patients (28.2% vs 7.7%, <jats:italic>P<\/jats:italic>\u2009=\u20090.024). cagPAI and complete <jats:italic>tfs3<\/jats:italic> increased the risk of DU compared to NCGC (OR\u2009=\u20093.56, 95%CI: 1.1\u201314.1, <jats:italic>P<\/jats:italic>\u2009=\u20090.038) and CG (OR\u2009=\u20094.64, 95%CI: 1.1\u201327.6, <jats:italic>P<\/jats:italic>\u2009=\u20090.024). A complete cluster of <jats:italic>tfs3<\/jats:italic> ICE was associated with gastroduodenal diseases in Vietnam. However, there was a low prevalence of the <jats:italic>dupA<\/jats:italic>\/complete <jats:italic>dupA<\/jats:italic> cluster (15.4%) in the Vietnam strains. The prevalence of cagPAI in Vietnam strains was significantly higher than in US (<jats:italic>P<\/jats:italic>\u2009=\u20090.01) and Indonesia (<jats:italic>P<\/jats:italic>\u2009&lt;\u20090.0001); the prevalence of the <jats:italic>dupA<\/jats:italic> cluster was also higher in the Vietnam strains than in the Indonesian strains (<jats:italic>P<\/jats:italic>\u2009&lt;\u20090.05). In addition, the prevalence of <jats:italic>ctkA<\/jats:italic>, an accessory gene of <jats:italic>tfs3<\/jats:italic>, was significantly different between Vietnam and US strains (28% vs 2%, <jats:italic>P<\/jats:italic>\u2009=\u20090.0002). In summary, the acquisition of <jats:italic>tfs3\/4<\/jats:italic> ICE was common in <jats:italic>H. pylori<\/jats:italic> strains in patients with gastroduodenal disease in Vietnam, and the complete cluster of <jats:italic>tfs3<\/jats:italic> ICE was a reliable marker for the severity of disease in the <jats:italic>H. pylori<\/jats:italic> infected population.<\/jats:p>","DOI":"10.1038\/s41598-021-83862-1","type":"journal-article","created":{"date-parts":[[2021,2,25]],"date-time":"2021-02-25T11:04:11Z","timestamp":1614251051000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":16,"title":["Helicobacter pylori type 4 secretion systems as gastroduodenal disease markers"],"prefix":"10.1038","volume":"11","author":[{"given":"Bui Hoang","family":"Phuc","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vo Phuoc","family":"Tuan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ho Dang Quy","family":"Dung","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tran Thanh","family":"Binh","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pham Huu","family":"Tung","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tran Dinh","family":"Tri","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ngo Phuong Minh","family":"Thuan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vu","family":"Van Khien","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tran Thi Huyen","family":"Trang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Junko","family":"Akada","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Takeshi","family":"Matsumoto","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yoshio","family":"Yamaoka","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2021,2,25]]},"reference":[{"issue":"11","key":"83862_CR1","doi-asserted-by":"publisher","first-page":"784","DOI":"10.1056\/NEJMoa001999","volume":"345","author":"N Uemura","year":"2001","unstructured":"Uemura, N. et al. 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