{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T00:51:46Z","timestamp":1791334306725,"version":"4.3.1"},"reference-count":50,"publisher":"BMJ","issue":"4","content-domain":{"domain":["bmj.com"],"crossmark-restriction":true},"short-container-title":["Gut"],"accepted":{"date-parts":[[2014,6,16]]},"published-print":{"date-parts":[[2015,4]]},"abstract":"<jats:sec>\n                  <jats:title>Objective<\/jats:title>\n                  <jats:p>To study the detailed nature of genomic microevolution during mixed infection with multiple <jats:italic>Helicobacter pylori<\/jats:italic> strains in an individual.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Design<\/jats:title>\n                  <jats:p>We sampled 18 isolates from a single biopsy from a patient with chronic gastritis and nephritis. Whole-genome sequencing was applied to these isolates, and statistical genetic tools were used to investigate their evolutionary history.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>The genomes fall into two clades, reflecting colonisation of the stomach by two distinct strains, and these lineages have accumulated diversity during an estimated 2.8 and 4.2\u2005years of evolution. We detected about 150 clear recombination events between the two clades. Recombination between the lineages is a continuous ongoing process and was detected on both clades, but the effect of recombination in one clade was nearly an order of magnitude higher than in the other. Imputed ancestral sequences also showed evidence of recombination between the two strains prior to their diversification, and we estimate that they have both been infecting the same host for at least 12\u2005years. Recombination tracts between the lineages were, on average, 895\u2005bp in length, and showed evidence for the interspersion of recipient sequences that has been observed in in vitro experiments. The complex evolutionary history of a phage-related protein provided evidence for frequent reinfection of both clades by a single phage lineage during the past 4\u2005years.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Conclusions<\/jats:title>\n                  <jats:p>Whole genome sequencing can be used to make detailed conclusions about the mechanisms of genetic change of <jats:italic>H. pylori<\/jats:italic> based on sampling bacteria from a single gastric biopsy.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1136\/gutjnl-2014-307345","type":"journal-article","created":{"date-parts":[[2014,7,9]],"date-time":"2014-07-09T22:04:20Z","timestamp":1404943460000},"page":"554-561","update-policy":"https:\/\/doi.org\/10.1136\/crossmarkpolicy","source":"Crossref","is-referenced-by-count":54,"title":["Progressive genomic convergence of two <i>Helicobacter pylori<\/i> strains during mixed infection of a patient with chronic gastritis"],"prefix":"10.1136","volume":"64","author":[{"given":"Qizhi","family":"Cao","sequence":"first","affiliation":[{"name":"State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China"},{"name":"Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China"},{"name":"Department of Immunology, Binzhou Medical University, Yantai, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xavier","family":"Didelot","sequence":"additional","affiliation":[{"name":"Department of Infectious Disease Epidemiology, Imperial College London, London, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhongbiao","family":"Wu","sequence":"additional","affiliation":[{"name":"The First People's Hospital of Wenling, the Affiliated Wenling Hospital of Wenzhou Medical College, Zhejiang, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zongwei","family":"Li","sequence":"additional","affiliation":[{"name":"Beijing Institute of Radiation Medicine, Beijing, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lihua","family":"He","sequence":"additional","affiliation":[{"name":"State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China"},{"name":"Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yunsheng","family":"Li","sequence":"additional","affiliation":[{"name":"The First People's Hospital of Wenling, the Affiliated Wenling Hospital of Wenzhou Medical College, Zhejiang, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ming","family":"Ni","sequence":"additional","affiliation":[{"name":"Beijing Institute of Radiation Medicine, Beijing, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuanhai","family":"You","sequence":"additional","affiliation":[{"name":"State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China"},{"name":"Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xi","family":"Lin","sequence":"additional","affiliation":[{"name":"The First People's Hospital of Wenling, the Affiliated Wenling Hospital of Wenzhou Medical College, Zhejiang, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhen","family":"Li","sequence":"additional","affiliation":[{"name":"Beijing Institute of Radiation Medicine, Beijing, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanan","family":"Gong","sequence":"additional","affiliation":[{"name":"State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China"},{"name":"Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Minqiao","family":"Zheng","sequence":"additional","affiliation":[{"name":"The First People's Hospital of Wenling, the Affiliated Wenling Hospital of Wenzhou Medical College, Zhejiang, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Minli","family":"Zhang","sequence":"additional","affiliation":[{"name":"Beijing Institute of Radiation Medicine, Beijing, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jie","family":"Liu","sequence":"additional","affiliation":[{"name":"State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China"},{"name":"Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Weijun","family":"Wang","sequence":"additional","affiliation":[{"name":"The First People's Hospital of Wenling, the Affiliated Wenling Hospital of Wenzhou Medical College, Zhejiang, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaochen","family":"Bo","sequence":"additional","affiliation":[{"name":"Beijing Institute of Radiation Medicine, Beijing, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel","family":"Falush","sequence":"additional","affiliation":[{"name":"Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany"},{"name":"Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shengqi","family":"Wang","sequence":"additional","affiliation":[{"name":"Beijing Institute of Radiation Medicine, Beijing, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jianzhong","family":"Zhang","sequence":"additional","affiliation":[{"name":"State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China"},{"name":"Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"239","published-online":{"date-parts":[[2014,7,9]]},"reference":[{"key":"2025090714321314000_64.4.554.1","doi-asserted-by":"publisher","DOI":"10.1126\/science.284.5418.1328"},{"key":"2025090714321314000_64.4.554.2","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMra020542"},{"key":"2025090714321314000_64.4.554.3","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.251396098"},{"key":"2025090714321314000_64.4.554.4","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1001036"},{"key":"2025090714321314000_64.4.554.5","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1018444108"},{"key":"2025090714321314000_64.4.554.6","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1304681110"},{"key":"2025090714321314000_64.4.554.7","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0003797"},{"key":"2025090714321314000_64.4.554.8","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1000337"},{"key":"2025090714321314000_64.4.554.9","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2180-12-67"},{"key":"2025090714321314000_64.4.554.10","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1113219109"},{"key":"2025090714321314000_64.4.554.11","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0061319"},{"key":"2025090714321314000_64.4.554.12","doi-asserted-by":"publisher","DOI":"10.1101\/gr.097261.109"},{"key":"2025090714321314000_64.4.554.13","doi-asserted-by":"publisher","DOI":"10.1101\/gr.074492.107"},{"key":"2025090714321314000_64.4.554.14","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2164-9-75"},{"key":"2025090714321314000_64.4.554.15","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkm160"},{"key":"2025090714321314000_64.4.554.16","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gki366"},{"key":"2025090714321314000_64.4.554.17","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0011147"},{"key":"2025090714321314000_64.4.554.18","doi-asserted-by":"publisher","DOI":"10.1099\/ijs.0.01472-0"},{"key":"2025090714321314000_64.4.554.19","doi-asserted-by":"publisher","DOI":"10.1534\/genetics.106.063305"},{"key":"2025090714321314000_64.4.554.20","doi-asserted-by":"publisher","DOI":"10.1016\/j.syapm.2009.01.001"},{"key":"2025090714321314000_64.4.554.21","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1002191"},{"key":"2025090714321314000_64.4.554.22","doi-asserted-by":"publisher","DOI":"10.1111\/mec.12162"},{"key":"2025090714321314000_64.4.554.23","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2180-11-104"},{"key":"2025090714321314000_64.4.554.24","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2004-5-2-r12"},{"key":"2025090714321314000_64.4.554.25","doi-asserted-by":"publisher","DOI":"10.1101\/gr.5512906"},{"key":"2025090714321314000_64.4.554.26","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/25.17.3389"},{"key":"2025090714321314000_64.4.554.27","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkp874"},{"key":"2025090714321314000_64.4.554.28","doi-asserted-by":"publisher","DOI":"10.1111\/j.1523-5378.1997.tb00058.x"},{"key":"2025090714321314000_64.4.554.29","doi-asserted-by":"publisher","DOI":"10.3748\/wjg.v16.i40.5118"},{"key":"2025090714321314000_64.4.554.30","doi-asserted-by":"publisher","DOI":"10.1111\/hel.12046"},{"key":"2025090714321314000_64.4.554.31","doi-asserted-by":"publisher","DOI":"10.1038\/41483"},{"key":"2025090714321314000_64.4.554.32","doi-asserted-by":"publisher","DOI":"10.1126\/science.1080857"},{"key":"2025090714321314000_64.4.554.33","doi-asserted-by":"publisher","DOI":"10.1093\/oxfordjournals.molbev.a026061"},{"key":"2025090714321314000_64.4.554.34","doi-asserted-by":"publisher","DOI":"10.1038\/nrg3226"},{"key":"2025090714321314000_64.4.554.35","doi-asserted-by":"publisher","DOI":"10.1016\/j.tim.2010.04.002"},{"key":"2025090714321314000_64.4.554.36","doi-asserted-by":"publisher","DOI":"10.1046\/j.1365-2958.2000.02049.x"},{"key":"2025090714321314000_64.4.554.37","doi-asserted-by":"publisher","DOI":"10.1179\/136485911X12899838683485"},{"key":"2025090714321314000_64.4.554.38","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.00517-12"},{"key":"2025090714321314000_64.4.554.39","doi-asserted-by":"publisher","DOI":"10.1086\/315173"},{"key":"2025090714321314000_64.4.554.40","doi-asserted-by":"publisher","DOI":"10.1128\/JB.05006-11"},{"key":"2025090714321314000_64.4.554.41","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.251551698"},{"key":"2025090714321314000_64.4.554.42","doi-asserted-by":"publisher","DOI":"10.1093\/infdis\/174.3.631"},{"key":"2025090714321314000_64.4.554.43","doi-asserted-by":"publisher","DOI":"10.1080\/003655201750065861"},{"key":"2025090714321314000_64.4.554.44","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0043370"},{"key":"2025090714321314000_64.4.554.45","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.95.21.12619"},{"key":"2025090714321314000_64.4.554.46","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0306629101"},{"key":"2025090714321314000_64.4.554.47","doi-asserted-by":"publisher","DOI":"10.1038\/nature05562"},{"key":"2025090714321314000_64.4.554.48","doi-asserted-by":"publisher","DOI":"10.1126\/science.1166083"},{"key":"2025090714321314000_64.4.554.49","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/mst055"},{"key":"2025090714321314000_64.4.554.50","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro1528"}],"container-title":["Gut"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.1136\/gutjnl-2014-307345","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,9,7]],"date-time":"2025-09-07T21:32:19Z","timestamp":1757280739000},"score":1,"resource":{"primary":{"URL":"https:\/\/gut.bmj.com\/lookup\/doi\/10.1136\/gutjnl-2014-307345"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,7,9]]},"references-count":50,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2015,3,6]]},"published-print":{"date-parts":[[2015,4]]}},"alternative-id":["10.1136\/gutjnl-2014-307345"],"URL":"https:\/\/doi.org\/10.1136\/gutjnl-2014-307345","relation":{},"ISSN":["0017-5749","1468-3288"],"issn-type":[{"value":"0017-5749","type":"print"},{"value":"1468-3288","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,7,9]]}}}