{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T00:16:14Z","timestamp":1790036174755,"version":"4.0.1"},"reference-count":42,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2021,8,2]],"date-time":"2021-08-02T00:00:00Z","timestamp":1627862400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:p>\n                    <jats:italic>Helicobacter pylori<\/jats:italic>\n                    exhibit specific geographic distributions that are related to clinical outcomes. Despite the high infection rate of\n                    <jats:italic>H. pylori<\/jats:italic>\n                    throughout the world, the genetic epidemiology surveillance of\n                    <jats:italic>H. pylori<\/jats:italic>\n                    still needs to be improved. This study used the single nucleotide polymorphisms (SNPs) profiling approach based on whole genome sequencing (WGS) to facilitate genomic population analyses of\n                    <jats:italic>H. pylori<\/jats:italic>\n                    and encourage the dissemination of microbial genotyping strategies worldwide. A total number of 1,211 public\n                    <jats:italic>H. pylori<\/jats:italic>\n                    genomes were downloaded and used to construct the typing tool, named\n                    <jats:italic>Hp<\/jats:italic>\n                    TT (\n                    <jats:italic>H. pylori<\/jats:italic>\n                    Typing Tool). Combined with the metadata, we developed two levels of genomic typing, including a continent-scale and a country scale that nested in the continent scale. Results showed that Asia was the largest isolate source in our dataset, while isolates from Europe and Oceania were comparatively more widespread. More specifically, Switzerland and Australia are the main sources of widespread isolates in their corresponding continents. To integrate all the typing information and enable researchers to compare their dataset against the existing global database easily and rapidly, a user-friendly website (\n                    <jats:ext-link>https:\/\/db.cngb.org\/HPTT\/<\/jats:ext-link>\n                    ) was developed with both genomic typing tools and visualization tools. To further confirm the validity of the website, ten newly assembled genomes were downloaded and tested precisely located on the branch as we expected. In summary, the\n                    <jats:italic>H. pylori<\/jats:italic>\n                    typing tool (\n                    <jats:italic>Hp<\/jats:italic>\n                    TT) is a novel genomic epidemiological tool that can achieve high-resolution analysis of genomic typing and visualizing simultaneously, providing insights into the genetic population structure, evolution analysis, and epidemiological surveillance of\n                    <jats:italic>H. pylori<\/jats:italic>\n                    .\n                  <\/jats:p>","DOI":"10.3389\/fmicb.2021.687259","type":"journal-article","created":{"date-parts":[[2021,8,2]],"date-time":"2021-08-02T11:50:20Z","timestamp":1627905020000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":16,"title":["Whole-Genome-Based Helicobacter pylori Geographic Surveillance: A Visualized and Expandable Webtool"],"prefix":"10.3389","volume":"12","author":[{"given":"Xiaosen","family":"Jiang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zheng","family":"Xu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tongda","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuan","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wei","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hongdong","family":"Tan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2021,8,2]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"459","DOI":"10.1046\/j.1365-2958.1999.01382.x","article-title":"Recombination and clonal groupings within Helicobacter pylori from different geographical regions.","volume":"32","author":"Achtman","year":"1999","journal-title":"Mole. Microb."},{"key":"B2","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41467-019-10050-1","article-title":"Within-host evolution of Helicobacter pylori shaped by niche-specific adaptation, intragastric migrations and selective sweeps.","volume":"10","author":"Ailloud","year":"2019","journal-title":"Nat. Comm."},{"key":"B3","doi-asserted-by":"publisher","first-page":"176","DOI":"10.1038\/16495","article-title":"Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori.","volume":"397","author":"Alm","year":"1999","journal-title":"Nature"},{"key":"B4","doi-asserted-by":"publisher","first-page":"298","DOI":"10.3855\/jidc.11877","article-title":"Upper socioeconomic status is associated with lower Helicobacter pylori infection rate among patients undergoing gastroscopy.","volume":"14","author":"Attila","year":"2020","journal-title":"J. Infect. Dev. Count."},{"key":"B5","first-page":"1","article-title":"Genome-based Salmonella serotyping as the new gold standard.","volume":"10","author":"Banerji","year":"2020","journal-title":"Sci. Rep."},{"key":"B6","doi-asserted-by":"publisher","first-page":"1899","DOI":"10.1016\/j.meegid.2011.08.007","article-title":"Expansion of European vacA and cagA alleles to East-Asian Helicobacter pylori strains in Cambodia.","volume":"11","author":"Breurec","year":"2011","journal-title":"Infect. Genet. Evol."},{"key":"B7","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/ncomms11995","article-title":"Genome-wide analysis of chromosomal import patterns after natural transformation of Helicobacter pylori.","volume":"7","author":"Bubendorfer","year":"2016","journal-title":"Nat. Comm."},{"key":"B8","doi-asserted-by":"publisher","first-page":"263","DOI":"10.1046\/j.1083-4389.2001.00047.x","article-title":"The African enigma: low prevalence of gastric atrophy, high prevalence of chronic inflammation in West African adults and children.","volume":"6","author":"Campbell","year":"2001","journal-title":"Helicobacter"},{"key":"B9","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/ncomms5812","article-title":"A robust SNP barcode for typing Mycobacterium tuberculosis complex strains.","volume":"5","author":"Coll","year":"2014","journal-title":"Nat. Comm."},{"key":"B10","doi-asserted-by":"publisher","first-page":"13880","DOI":"10.1073\/pnas.1304681110","article-title":"Genomic evolution and transmission of Helicobacter pylori in two South African families.","volume":"110","author":"Didelot","year":"2013","journal-title":"Proc. Natl. Acad. Sci."},{"key":"B11","article-title":"Unraveling antimicrobial resistance in Helicobacter pylori: Global resistome meets global phylogeny.","volume":"2021","author":"Domanovich-Asor","year":"2021","journal-title":"Helicobacter"},{"key":"B12","doi-asserted-by":"publisher","first-page":"615","DOI":"10.1146\/annurev.micro.54.1.615","article-title":"The disease spectrum of Helicobacter pylori: the immunopathogenesis of gastroduodenal ulcer and gastric cancer.","volume":"54","author":"Ernst","year":"2000","journal-title":"Ann. Rev. Microbiol."},{"key":"B13","doi-asserted-by":"publisher","first-page":"1582","DOI":"10.1126\/science.1080857","article-title":"Traces of human migrations in Helicobacter pylori populations.","volume":"299","author":"Falush","year":"2003","journal-title":"Science"},{"key":"B14","doi-asserted-by":"publisher","first-page":"4121","DOI":"10.1093\/bioinformatics\/bty407","article-title":"Nextstrain: real-time tracking of pathogen evolution.","volume":"34","author":"Hadfield","year":"2018","journal-title":"Bioinformatics"},{"key":"B15","article-title":"Open-access bacterial population genomics: BIGSdb software, the PubMLST. org website and their applications.","volume":"2018","author":"Jolley","year":"2018","journal-title":"Wellcome Open Res."},{"key":"B16","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1471-2105-11-595","article-title":"BIGSdb: scalable analysis of bacterial genome variation at the population level.","volume":"11","author":"Jolley","year":"2010","journal-title":"BMC Bioinform."},{"key":"B17","doi-asserted-by":"publisher","first-page":"826","DOI":"10.1038\/nrmicro1528","article-title":"Bacterial populations as perfect gases: genomic integrity and diversification tensions in Helicobacter pylori.","volume":"4","author":"Kang","year":"2006","journal-title":"Nat. Rev. Microbiol."},{"key":"B18","author":"Kans","year":"2020","journal-title":"Entrez direct: E-utilities on the UNIX command line in Entrez Programming Utilities Help [Internet]."},{"key":"B19","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1471-2180-11-104","article-title":"Evolution in an oncogenic bacterial species with extreme genome plasticity: Helicobacter pylori East Asian genomes.","volume":"11","author":"Kawai","year":"2011","journal-title":"BMC Microbiol."},{"key":"B20","doi-asserted-by":"crossref","first-page":"5033","DOI":"10.1073\/pnas.1018444108","article-title":"Helicobacter pylori genome evolution during human infection.","volume":"108","author":"Kennemann","year":"2011","journal-title":"Proc. Natl. Acad. Sci."},{"key":"B21","doi-asserted-by":"crossref","first-page":"1455","DOI":"10.1073\/pnas.1318093111","article-title":"Human and Helicobacter pylori coevolution shapes the risk of gastric disease.","volume":"111","author":"Kodaman","year":"2014","journal-title":"Proc. Nat. Acad. Sci."},{"key":"B22","doi-asserted-by":"crossref","DOI":"10.1186\/gb-2004-5-2-r12","article-title":"Versatile and open software for comparing large genomes.","volume":"5","author":"Kurtz","year":"2004","journal-title":"Genome Biol."},{"key":"B23","doi-asserted-by":"publisher","first-page":"278","DOI":"10.1111\/eva.12864","article-title":"A novel taxon selection method, aimed at minimizing recombination, clarifies the discovery of a new sub-population of Helicobacter pylori from Australia.","volume":"13","author":"Lamichhane","year":"2020","journal-title":"Evol. Appl."},{"key":"B24","doi-asserted-by":"publisher","first-page":"947","DOI":"10.1534\/genetics.115.176404","article-title":"Worldwide population structure, long-term demography, and local adaptation of Helicobacter pylori.","volume":"200","author":"Montano","year":"2015","journal-title":"Genetics"},{"key":"B25","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2017.00050","article-title":"Whole genome sequence and phylogenetic analysis show Helicobacter pylori strains from Latin America have followed a unique evolution pathway.","volume":"7","author":"Mu\u00f1oz-Ram\u00edrez","year":"2017","journal-title":"Front. Cell. Infect. Microb."},{"key":"B26","doi-asserted-by":"publisher","first-page":"78","DOI":"10.1038\/s41396-020-00758-0","article-title":"A 500-year tale of co-evolution, adaptation, and virulence: Helicobacter pylori in the Americas.","volume":"15","author":"Mu\u00f1oz-Ram\u00edrez","year":"2021","journal-title":"ISME J."},{"key":"B27","doi-asserted-by":"publisher","first-page":"268","DOI":"10.1093\/molbev\/msu300","article-title":"IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies.","volume":"32","author":"Nguyen","year":"2015","journal-title":"Mole. Biol. Evol."},{"key":"B28","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2019.01902","article-title":"Shifts in the human gut microbiota structure caused by quadruple Helicobacter pylori eradication therapy.","volume":"10","author":"Olekhnovich","year":"2019","journal-title":"Front. Microb."},{"key":"B29","doi-asserted-by":"publisher","first-page":"1533","DOI":"10.1038\/s41564-017-0012-7","article-title":"Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life.","volume":"2","author":"Parks","year":"2017","journal-title":"Nat. Microb."},{"key":"B30","doi-asserted-by":"publisher","DOI":"10.3748\/wjg.v25.i32.4629","article-title":"Review of current diagnostic methods and advances in Helicobacter pylori diagnostics in the era of next generation sequencing.","volume":"25","author":"Pohl","year":"2019","journal-title":"World J. Gastroent."},{"key":"B31","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0026907","article-title":"Rates of mutation and host transmission for an Escherichia coli clone over 3 years.","volume":"6","author":"Reeves","year":"2011","journal-title":"PLoS One"},{"key":"B32","doi-asserted-by":"publisher","first-page":"3834","DOI":"10.1128\/jb.01696-06","article-title":"Genetic analysis of Helicobacter pylori strain populations colonizing the stomach at different times postinfection.","volume":"189","author":"Salama","year":"2007","journal-title":"J. Bacteriol."},{"key":"B33","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1000180","article-title":"Horizontal versus familial transmission of Helicobacter pylori.","volume":"4","author":"Schwarz","year":"2008","journal-title":"PLoS Pathog."},{"key":"B34","doi-asserted-by":"publisher","DOI":"10.3748\/wjg.v25.i33.4870","article-title":"Helicobacter pylori virulence genes.","volume":"25","author":"\u0160terbenc","year":"2019","journal-title":"World J Gastroenterol."},{"key":"B35","doi-asserted-by":"crossref","DOI":"10.1093\/ve\/vey016","article-title":"Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10.","volume":"4","author":"Suchard","year":"2018","journal-title":"Virus Evol."},{"key":"B36","doi-asserted-by":"crossref","first-page":"1175","DOI":"10.1056\/NEJMra020542","article-title":"Helicobacter pylori infection.","volume":"347","author":"Suerbaum","year":"2002","journal-title":"New Engl. J. Med."},{"key":"B37","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1006546","article-title":"Rapid evolution of distinct Helicobacter pylori subpopulations in the Americas.","volume":"13","author":"Thorell","year":"2017","journal-title":"PLoS Genet."},{"key":"B38","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1038\/41483","article-title":"The complete genome sequence of the gastric pathogen Helicobacter pylori.","volume":"388","author":"Tomb","year":"1997","journal-title":"Nature"},{"key":"B39","doi-asserted-by":"publisher","first-page":"1454","DOI":"10.1093\/molbev\/mst055","article-title":"Chromosome painting in silico in a bacterial species reveals fine population structure.","volume":"30","author":"Yahara","year":"2013","journal-title":"Mole. Biol. Evol."},{"key":"B40","doi-asserted-by":"publisher","first-page":"829","DOI":"10.1111\/j.1469-0691.2009.02967.x","article-title":"Helicobacter pylori typing as a tool for tracking human migration.","volume":"15","author":"Yamaoka","year":"2009","journal-title":"Clinical Microbiol. Infect."},{"key":"B41","doi-asserted-by":"crossref","DOI":"10.1111\/hel.12752","article-title":"CRHP Finder, a webtool for the detection of clarithromycin resistance in Helicobacter pylori from whole-genome sequencing data.","volume":"25","author":"Yusibova","year":"2020","journal-title":"Helicobacter"},{"key":"B42","doi-asserted-by":"publisher","first-page":"1395","DOI":"10.1101\/gr.232397.117","article-title":"GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens.","volume":"28","author":"Zhou","year":"2018","journal-title":"Genome Res."}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2021.687259\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,8,2]],"date-time":"2021-08-02T11:50:51Z","timestamp":1627905051000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2021.687259\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,8,2]]},"references-count":42,"alternative-id":["10.3389\/fmicb.2021.687259"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2021.687259","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2021.03.29.437451","asserted-by":"object"}]},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,8,2]]},"article-number":"687259"}}