{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T18:26:23Z","timestamp":1790792783778,"version":"4.1.0"},"reference-count":31,"publisher":"Microbiology Society","issue":"9","license":[{"start":{"date-parts":[[2018,9,1]],"date-time":"2018-09-01T00:00:00Z","timestamp":1535760000000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,9,1]]},"abstract":"<jats:p>\n                    Plasmid prediction may be of great interest when studying bacteria of medical importance such as\n                    <jats:italic>Enterobacteriaceae<\/jats:italic>\n                    as well as\n                    <jats:italic>Staphylococcus aureus<\/jats:italic>\n                    or\n                    <jats:italic>Enterococcus<\/jats:italic>\n                    . Indeed, many resistance and virulence genes are located on such replicons with major impact in terms of pathogenicity and spreading capacities. Beyond strain outbreak, plasmid outbreaks have been reported in particular for some extended-spectrum beta-lactamase- or carbapenemase-producing\n                    <jats:italic>Enterobacteriaceae<\/jats:italic>\n                    . Several tools are now available to explore the \u2018plasmidome\u2019 from whole-genome sequences with various approaches, but none of them are able to combine high sensitivity and specificity. With this in mind, we developed PlaScope, a targeted approach to recover plasmidic sequences in genome assemblies at the species or genus level. Based on Centrifuge, a metagenomic classifier, and a custom database containing complete sequences of chromosomes and plasmids from various curated databases, PlaScope classifies contigs from an assembly according to their predicted location. Compared to other plasmid classifiers, PlasFlow and cBar, it achieves better recall (0.87), specificity (0.99), precision (0.96) and accuracy (0.98) on a dataset of 70 genomes of\n                    <jats:italic>Escherichia coli<\/jats:italic>\n                    containing plasmids. In a second part, we identified 20 of the 21 chromosomal integrations of the extended-spectrum beta-lactamase coding gene in a clinical dataset of\n                    <jats:italic>E. coli<\/jats:italic>\n                    strains. In addition, we predicted virulence gene and operon locations in agreement with the literature. We also built a database for\n                    <jats:italic>Klebsiella<\/jats:italic>\n                    and correctly assigned the location for the majority of resistance genes from a collection of 12\n                    <jats:italic>Klebsiella pneumoniae<\/jats:italic>\n                    strains. Similar approaches could also be developed for other well-characterized bacteria.\n                  <\/jats:p>","DOI":"10.1099\/mgen.0.000211","type":"journal-article","created":{"date-parts":[[2018,9,28]],"date-time":"2018-09-28T13:41:39Z","timestamp":1538142099000},"source":"Crossref","is-referenced-by-count":49,"title":["PlaScope: a targeted approach to assess the plasmidome from genome assemblies at the species level"],"prefix":"10.1099","volume":"4","author":[{"given":"G.","family":"Royer","sequence":"first","affiliation":[{"name":"2\u200bUniversit\u00e9 Paris Diderot, INSERM, IAME, UMR 1137, Sorbonne Paris Cit\u00e9, F-75018 Paris, France"},{"name":"3\u200bLABGeM, G\u00e9nomique M\u00e9tabolique, Genoscope, Institut Fran\u00e7ois Jacob, CEA, CNRS, Univ Evry, Universit\u00e9 Paris-Saclay, 91057 Evry, France"},{"name":"1\u200bD\u00e9partement de Microbiologie, Assistance Publique-H\u00f4pitaux de Paris, H\u00f4pital Henri Mondor, Universit\u00e9 Paris Est Cr\u00e9teil, F-94000 Cr\u00e9teil, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"J. W.","family":"Decousser","sequence":"additional","affiliation":[{"name":"2\u200bUniversit\u00e9 Paris Diderot, INSERM, IAME, UMR 1137, Sorbonne Paris Cit\u00e9, F-75018 Paris, France"},{"name":"1\u200bD\u00e9partement de Microbiologie, Assistance Publique-H\u00f4pitaux de Paris, H\u00f4pital Henri Mondor, Universit\u00e9 Paris Est Cr\u00e9teil, F-94000 Cr\u00e9teil, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"C.","family":"Branger","sequence":"additional","affiliation":[{"name":"2\u200bUniversit\u00e9 Paris Diderot, INSERM, IAME, UMR 1137, Sorbonne Paris Cit\u00e9, F-75018 Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"M.","family":"Dubois","sequence":"additional","affiliation":[{"name":"3\u200bLABGeM, G\u00e9nomique M\u00e9tabolique, Genoscope, Institut Fran\u00e7ois Jacob, CEA, CNRS, Univ Evry, Universit\u00e9 Paris-Saclay, 91057 Evry, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"C.","family":"M\u00e9digue","sequence":"additional","affiliation":[{"name":"3\u200bLABGeM, G\u00e9nomique M\u00e9tabolique, Genoscope, Institut Fran\u00e7ois Jacob, CEA, CNRS, Univ Evry, Universit\u00e9 Paris-Saclay, 91057 Evry, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"E.","family":"Denamur","sequence":"additional","affiliation":[{"name":"4\u200bAssistance Publique-H\u00f4pitaux de Paris, H\u00f4pital Bichat, Laboratoire de G\u00e9n\u00e9tique Mol\u00e9culaire, F-75018 Paris, France"},{"name":"2\u200bUniversit\u00e9 Paris Diderot, INSERM, IAME, UMR 1137, Sorbonne Paris Cit\u00e9, F-75018 Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"D.","family":"Vallenet","sequence":"additional","affiliation":[{"name":"3\u200bLABGeM, G\u00e9nomique M\u00e9tabolique, Genoscope, Institut Fran\u00e7ois Jacob, CEA, CNRS, Univ Evry, Universit\u00e9 Paris-Saclay, 91057 Evry, France"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"345","reference":[{"key":"R1","doi-asserted-by":"publisher","DOI":"10.1099\/mgen.0.000128"},{"key":"R2","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbx162"},{"key":"R3","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btw493"},{"key":"R4","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.02412-14"},{"key":"R5","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkx1321"},{"key":"R6","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btw651"},{"key":"R7","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btq299"},{"key":"R8","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1004766"},{"key":"R9","doi-asserted-by":"publisher","DOI":"10.1016\/j.dib.2017.04.024"},{"key":"R10","doi-asserted-by":"publisher","DOI":"10.1101\/gr.210641.116"},{"key":"R11","doi-asserted-by":"publisher","DOI":"10.1089\/cmb.2012.0021"},{"key":"R12","article-title":"Extended-spectrum \u03b2-lactamase-genes are spreading on a wide range of Escherichia coli plasmids existing prior the use of third generation cephalosporins","volume":"4","author":"Branger","year":"2018","journal-title":"Microb Genom"},{"key":"R13","article-title":"ident-16s Rapid identification of bacterial species from FASTA contigs [Internet]. 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