{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,5]],"date-time":"2026-10-05T19:05:37Z","timestamp":1791227137126,"version":"4.1.0"},"reference-count":43,"publisher":"National Academy of Sciences","issue":"26","content-domain":{"domain":["www.pnas.org"],"crossmark-restriction":true},"short-container-title":["Proc. Natl. Acad. Sci. U.S.A."],"published-print":{"date-parts":[[2006,6,27]]},"abstract":"<jats:p>\n                    <jats:italic>Helicobacter pylori<\/jats:italic>\n                    produces acute superficial gastritis in nearly all of its human hosts. However, a subset of individuals develops chronic atrophic gastritis (ChAG), a condition characterized in part by diminished numbers of acid-producing parietal cells and increased risk for development of gastric adenocarcinoma. Previously, we used a gnotobiotic transgenic mouse model with an engineered ablation of parietal cells to show that loss of parietal cells provides an opportunity for a\n                    <jats:italic>H. pylori<\/jats:italic>\n                    isolate from a patient with ChAG (HPAG1) to bind to, enter, and persist within gastric stem cells. This finding raises the question of how ChAG influences\n                    <jats:italic>H. pylori<\/jats:italic>\n                    genome evolution, physiology, and tumorigenesis. Here we describe the 1,596,366-bp HPAG1 genome. Custom HPAG1 Affymetrix GeneChips, representing 99.6% of its predicted ORFs, were used for whole-genome genotyping of additional\n                    <jats:italic>H. pylori<\/jats:italic>\n                    ChAG isolates obtained from Swedish patients enrolled in a case-control study of gastric cancer, as well as ChAG- and cancer-associated isolates from an individual who progressed from ChAG to gastric adenocarcinoma. The results reveal a shared gene signature among ChAG strains, as well as genes that may have been lost or gained during progression to adenocarcinoma. Whole-genome transcriptional profiling of HPAG1\u2019s response to acid during\n                    <jats:italic>in vitro<\/jats:italic>\n                    growth indicates that genes encoding components of metal uptake and utilization pathways, outer membrane proteins, and virulence factors are among those associated with\n                    <jats:italic>H. pylori<\/jats:italic>\n                    \u2019s adaptation to ChAG.\n                  <\/jats:p>","DOI":"10.1073\/pnas.0603784103","type":"journal-article","created":{"date-parts":[[2006,6,20]],"date-time":"2006-06-20T23:57:39Z","timestamp":1150847859000},"page":"9999-10004","update-policy":"https:\/\/doi.org\/10.1073\/pnas.cm10313","source":"Crossref","is-referenced-by-count":207,"title":["The complete genome sequence of a chronic atrophic gastritis\n                    <i>Helicobacter pylori<\/i>\n                    strain: Evolution during disease progression"],"prefix":"10.1073","volume":"103","author":[{"given":"Jung D.","family":"Oh","sequence":"first","affiliation":[{"name":"*Center for Genome Sciences,"},{"name":"Molecular Biology and Pharmacology and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Helene","family":"Kling-B\u00e4ckhed","sequence":"additional","affiliation":[{"name":"*Center for Genome Sciences,"},{"name":"Molecular Biology and Pharmacology and"},{"name":"Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, 171 77 Stockholm, Sweden; and"},{"name":"Swedish Institute for Infectious Disease Control, 171 82 Solna, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marios","family":"Giannakis","sequence":"additional","affiliation":[{"name":"*Center for Genome Sciences,"},{"name":"Genome Sequencing Center, and Departments of"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jian","family":"Xu","sequence":"additional","affiliation":[{"name":"*Center for Genome Sciences,"},{"name":"Genome Sequencing Center, and Departments of"},{"name":"**Genetics, Washington University School of Medicine, St. Louis, MO 63108;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robert S.","family":"Fulton","sequence":"additional","affiliation":[{"name":"Genome Sequencing Center, and Departments of"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lucinda A.","family":"Fulton","sequence":"additional","affiliation":[{"name":"Genome Sequencing Center, and Departments of"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Holland S.","family":"Cordum","sequence":"additional","affiliation":[{"name":"Genome Sequencing Center, and Departments of"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chunyan","family":"Wang","sequence":"additional","affiliation":[{"name":"Genome Sequencing Center, and Departments of"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Glendoria","family":"Elliott","sequence":"additional","affiliation":[{"name":"Genome Sequencing Center, and Departments of"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jennifer","family":"Edwards","sequence":"additional","affiliation":[{"name":"Genome Sequencing Center, and Departments of"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elaine R.","family":"Mardis","sequence":"additional","affiliation":[{"name":"Genome Sequencing Center, and Departments of"},{"name":"**Genetics, Washington University School of Medicine, St. Louis, MO 63108;"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lars G.","family":"Engstrand","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, 171 77 Stockholm, Sweden; and"},{"name":"Swedish Institute for Infectious Disease Control, 171 82 Solna, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jeffrey I.","family":"Gordon","sequence":"additional","affiliation":[{"name":"*Center for Genome Sciences,"},{"name":"Molecular Biology and Pharmacology and"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"341","published-online":{"date-parts":[[2006,6,27]]},"reference":[{"key":"e_1_3_3_1_2","doi-asserted-by":"publisher","DOI":"10.1093\/oxfordjournals.epirev.a018040"},{"key":"e_1_3_3_2_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0188-4409(00)00099-0"},{"key":"e_1_3_3_3_2","doi-asserted-by":"publisher","DOI":"10.1016\/S1286-4579(03)00112-6"},{"key":"e_1_3_3_4_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0016-5085(98)70475-5"},{"key":"e_1_3_3_5_2","doi-asserted-by":"publisher","DOI":"10.1086\/314785"},{"key":"e_1_3_3_6_2","doi-asserted-by":"publisher","DOI":"10.1093\/jnci\/djh057"},{"key":"e_1_3_3_7_2","doi-asserted-by":"publisher","DOI":"10.1016\/S1470-2045(01)00486-7"},{"key":"e_1_3_3_8_2","doi-asserted-by":"publisher","DOI":"10.1053\/j.gastro.2003.08.033"},{"key":"e_1_3_3_9_2","doi-asserted-by":"publisher","DOI":"10.1002\/ijc.11680"},{"key":"e_1_3_3_10_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-2036.2005.02582.x"},{"key":"e_1_3_3_11_2","doi-asserted-by":"publisher","DOI":"10.1097\/00042737-199701000-00002"},{"key":"e_1_3_3_12_2","doi-asserted-by":"publisher","DOI":"10.1158\/1055-9965.EPI-03-0124"},{"key":"e_1_3_3_13_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.251551698"},{"key":"e_1_3_3_14_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1735481100"},{"key":"e_1_3_3_15_2","doi-asserted-by":"publisher","DOI":"10.1172\/JCI12672"},{"key":"e_1_3_3_16_2","doi-asserted-by":"publisher","DOI":"10.1038\/41483"},{"key":"e_1_3_3_17_2","doi-asserted-by":"publisher","DOI":"10.1038\/16495"},{"key":"e_1_3_3_18_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.96.17.9721"},{"key":"e_1_3_3_19_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0334340100"},{"key":"e_1_3_3_20_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.36.12.708"},{"key":"e_1_3_3_21_2","doi-asserted-by":"publisher","DOI":"10.1093\/genetics\/123.4.887"},{"key":"e_1_3_3_22_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0506758102"},{"key":"e_1_3_3_23_2","first-page":"981","volume":"9","author":"Enroth H.","year":"2000","unstructured":"H. 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