{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,12]],"date-time":"2026-04-12T06:14:25Z","timestamp":1775974465792,"version":"3.50.1"},"reference-count":31,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2022,5,7]],"date-time":"2022-05-07T00:00:00Z","timestamp":1651881600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2018YFE0102400"],"award-info":[{"award-number":["2018YFE0102400"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32070572"],"award-info":[{"award-number":["32070572"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003399","name":"Science and Technology Commission of Shanghai Municipality","doi-asserted-by":"publisher","award":["19JC1413000"],"award-info":[{"award-number":["19JC1413000"]}],"id":[{"id":"10.13039\/501100003399","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003399","name":"Science and Technology Commission of Shanghai Municipality","doi-asserted-by":"publisher","award":["19430750600"],"award-info":[{"award-number":["19430750600"]}],"id":[{"id":"10.13039\/501100003399","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Medicine and Engineering Interdisciplinary Research Fund of Shanghai Jiao Tong University","award":["19x190020171"],"award-info":[{"award-number":["19x190020171"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,7,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>VRprofile2 is an updated pipeline that rapidly identifies diverse mobile genetic elements in bacterial genome sequences. Compared with the previous version, three major improvements were made. First, the user-friendly visualization could aid users in investigating the antibiotic resistance gene cassettes in conjunction with various mobile elements in the multiple resistance region with mosaic structure. VRprofile2 could compare the predicted mobile elements to the collected known mobile elements with similar architecture. A new mobilome indicator was proposed to give an overall estimation of the mobilome size in individual bacterial genomes. Second, the relationship between antibiotic resistance genes, mobile elements, and host strains would be efficiently examined with the aid of predicted strain's sequence typing, the incompatibility group and the transferability of plasmids. Finally, the updated back-end database, MobilomeDB2, now collected nearly a thousand active mobile elements retrieved from literature or based on prediction. The pre-computed results of the antibiotic resistance gene-carrying mobile elements of &amp;gt;5500 ESKAPEE genomes were also provided. We expect that VRprofile2 will provide better support for researchers interested in bacterial mobile elements and the dissemination of antibiotic resistance. VRprofile2 is freely available to all users without any login requirement at https:\/\/tool2-mml.sjtu.edu.cn\/VRprofile.<\/jats:p>","DOI":"10.1093\/nar\/gkac321","type":"journal-article","created":{"date-parts":[[2022,4,21]],"date-time":"2022-04-21T11:17:40Z","timestamp":1650539860000},"page":"W768-W773","source":"Crossref","is-referenced-by-count":127,"title":["VRprofile2: detection of antibiotic resistance-associated mobilome in bacterial pathogens"],"prefix":"10.1093","volume":"50","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4805-2144","authenticated-orcid":false,"given":"Meng","family":"Wang","sequence":"first","affiliation":[{"name":"State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University , Shanghai \u00a0 200030 , China"}]},{"given":"Ying-Xian","family":"Goh","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University , Shanghai \u00a0 200030 , China"}]},{"given":"Cui","family":"Tai","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University , Shanghai \u00a0 200030 , China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4011-9631","authenticated-orcid":false,"given":"Hui","family":"Wang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Microbiology and Epidemiology , Beijing \u00a0 100071 , China"}]},{"given":"Zixin","family":"Deng","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University , Shanghai \u00a0 200030 , China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9439-1660","authenticated-orcid":false,"given":"Hong-Yu","family":"Ou","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University , Shanghai \u00a0 200030 , China"}]}],"member":"286","published-online":{"date-parts":[[2022,5,7]]},"reference":[{"key":"2022070423583385400_B1","doi-asserted-by":"crossref","first-page":"e3","DOI":"10.1093\/nar\/gni005","article-title":"ArrayOme: a program for estimating the sizes of microarray-visualized bacterial genomes","volume":"33","author":"Ou","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2022070423583385400_B2","doi-asserted-by":"crossref","first-page":"W194","DOI":"10.1093\/nar\/gkq326","article-title":"mGenomeSubtractor: a web-based tool for parallel in silico subtractive hybridization analysis of multiple bacterial genomes","volume":"38","author":"Shao","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"2022070423583385400_B3","doi-asserted-by":"crossref","first-page":"e0008817","DOI":"10.1128\/CMR.00088-17","article-title":"Mobile genetic elements associated with antimicrobial resistance","volume":"31","author":"Partridge","year":"2018","journal-title":"Clin. 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