{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,31]],"date-time":"2026-03-31T08:56:35Z","timestamp":1774947395734,"version":"3.50.1"},"reference-count":27,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2018,10,31]],"date-time":"2018-10-31T00:00:00Z","timestamp":1540944000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100005690","name":"Saarland University","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100005690","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,1,8]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The study of bacterial isolates or communities requires the analysis of the therein included plasmids in order to provide an extensive characterization of the organisms. Plasmids harboring resistance and virulence factors are of especial interest as they contribute to the dissemination of antibiotic resistance. As the number of newly sequenced bacterial genomes is growing a comprehensive resource is required which will allow to browse and filter the available plasmids, and to perform sequence analyses. Here, we present PLSDB, a resource containing 13 789 plasmid records collected from the NCBI nucleotide database. The web server provides an interactive view of all obtained plasmids with additional meta information such as sequence characteristics, sample-related information and taxonomy. Moreover, nucleotide sequence data can be uploaded to search for short nucleotide sequences (e.g. specific genes) in the plasmids, to compare a given plasmid to the records in the collection or to determine whether a sample contains one or multiple of the known plasmids (containment analysis). The resource is freely accessible under https:\/\/ccb-microbe.cs.uni-saarland.de\/plsdb\/.<\/jats:p>","DOI":"10.1093\/nar\/gky1050","type":"journal-article","created":{"date-parts":[[2018,10,17]],"date-time":"2018-10-17T12:31:50Z","timestamp":1539779510000},"page":"D195-D202","source":"Crossref","is-referenced-by-count":443,"title":["PLSDB: a resource of complete bacterial plasmids"],"prefix":"10.1093","volume":"47","author":[{"given":"Valentina","family":"Galata","sequence":"first","affiliation":[{"name":"Chair for Clinical Bioinformatics, Saarland University, Campus Building E2.1, 66123 Saarbruecken, Germany"}]},{"given":"Tobias","family":"Fehlmann","sequence":"first","affiliation":[{"name":"Chair for Clinical Bioinformatics, Saarland University, Campus Building E2.1, 66123 Saarbruecken, Germany"}]},{"given":"Christina","family":"Backes","sequence":"first","affiliation":[{"name":"Chair for Clinical Bioinformatics, Saarland University, Campus Building E2.1, 66123 Saarbruecken, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5361-0895","authenticated-orcid":false,"given":"Andreas","family":"Keller","sequence":"first","affiliation":[{"name":"Chair for Clinical Bioinformatics, Saarland University, Campus Building E2.1, 66123 Saarbruecken, Germany"}]}],"member":"286","published-online":{"date-parts":[[2018,10,31]]},"reference":[{"key":"2020041422561619600_B1","doi-asserted-by":"crossref","first-page":"375","DOI":"10.1128\/MMBR.52.3.375-395.1988","article-title":"Identification and classification of bacterial plasmids","volume":"52","author":"Couturier","year":"1988","journal-title":"Microbiol. Rev."},{"key":"2020041422561619600_B2","doi-asserted-by":"crossref","first-page":"1121","DOI":"10.1093\/jac\/dkx488","article-title":"Plasmids carrying antimicrobial resistance genes in Enterobacteriaceae","volume":"73","author":"Rozwandowicz","year":"2018","journal-title":"J. Antimicrob. Chemother."},{"key":"2020041422561619600_B3","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1016\/S1473-3099(15)00424-7","article-title":"Emergence of plasmid-mediated colistin resistance mechanism MCR-1 in animals and human beings in China: a microbiological and molecular biological study","volume":"16","author":"Liu","year":"2016","journal-title":"Lancet Infect. Dis."},{"key":"2020041422561619600_B4","doi-asserted-by":"crossref","first-page":"42","DOI":"10.1016\/j.plasmid.2017.03.002","article-title":"Ordering the mob: Insights into replicon and MOB typing schemes from analysis of a curated dataset of publicly available plasmids","volume":"91","author":"Orlek","year":"2017","journal-title":"Plasmid"},{"key":"2020041422561619600_B5","doi-asserted-by":"crossref","first-page":"D1152","DOI":"10.1093\/nar\/gku893","article-title":"The Addgene repository: an international nonprofit plasmid and data resource","volume":"43","author":"Kamens","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"2020041422561619600_B6","doi-asserted-by":"crossref","first-page":"3043","DOI":"10.1099\/mic.0.C0123-0","article-title":"The plasmid genome database","volume":"149","author":"M\u00f8lbak","year":"2003","journal-title":"Microbiology (Reading, Engl.)"},{"key":"2020041422561619600_B7","doi-asserted-by":"crossref","first-page":"423","DOI":"10.1016\/j.dib.2017.04.024","article-title":"A curated dataset of complete Enterobacteriaceae plasmids compiled from the NCBI nucleotide database","volume":"12","author":"Orlek","year":"2017","journal-title":"Data Brief."},{"key":"2020041422561619600_B8","article-title":"MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies","volume":"4","author":"Robertson","year":"2018","journal-title":"Microb. Genome"},{"key":"2020041422561619600_B9","doi-asserted-by":"crossref","first-page":"212","DOI":"10.1128\/AAC.01310-13","article-title":"ARG-ANNOT, a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes","volume":"58","author":"Gupta","year":"2014","journal-title":"Antimicrob. Agents Chemother."},{"key":"2020041422561619600_B10","doi-asserted-by":"crossref","first-page":"D566","DOI":"10.1093\/nar\/gkw1004","article-title":"CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database","volume":"45","author":"Jia","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"2020041422561619600_B11","doi-asserted-by":"crossref","first-page":"2640","DOI":"10.1093\/jac\/dks261","article-title":"Identification of acquired antimicrobial resistance genes","volume":"67","author":"Zankari","year":"2012","journal-title":"J. Antimicrob. 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Agents Chemother."},{"key":"2020041422561619600_B14","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1186\/1471-2105-10-421","article-title":"BLAST+: architecture and applications","volume":"10","author":"Camacho","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"2020041422561619600_B15","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1186\/s13059-016-0997-x","article-title":"Mash: fast genome and metagenome distance estimation using MinHash","volume":"17","author":"Ondov","year":"2016","journal-title":"Genome Biol."},{"key":"2020041422561619600_B16","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1109\/SEQUEN.1997.666900","article-title":"On the resemblance and containment of documents","volume-title":"Proceedings. Compression and Complexity of SEQUENCES 1997 (Cat. 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