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Protocols

PlasmidFinder specifications

Information


Unique identifier OMICS_11488
Name PlasmidFinder
Interface Web user interface
Restrictions to use None
Input data A sequence must be in one-letter nucleotide code and the filename must not contain spaces.
Input format FASTA
Computer skills Basic
Version 1.3
Stability Stable
Maintained Yes

Maintainer


  • person_outline Henrik Hasman

Additional information


https://cge.cbs.dtu.dk//services/PlasmidFinder/instructions.php

Publication for PlasmidFinder

PlasmidFinder citations

 (191)
call_split

Genomic and functional characterisation of IncX3 plasmids encoding blaSHV 12 in Escherichia coli from human and animal origin

2018
Sci Rep
PMCID: 5955891
PMID: 29769695
DOI: 10.1038/s41598-018-26073-5
call_split See protocol

[…] inst the NCBI non-redundant proteins (NR) database, Pfam, and Interpro scan were used to assess their putative functions by identification of structural features and motifs,. ResFinder (version 2.1), PlasmidFinder (version 1.3) and ISfinder were used to determine the presence of resistance genes, replicon types and insertion sequences, respectively–. Plasmid sequences were hierarchically clustered […]

call_split

Draft Genome Sequencing of an Acinetobacter ursingii Isolate from Healthy Human Skin, Carrying Multidrug Resistance Genes

2018
Genome Announc
PMCID: 5946048
PMID: 29748406
DOI: 10.1128/genomeA.00394-18
call_split See protocol

[…] 3,578,188 bp long and provides 3,473 genes. These include 3,236 coding genes and 78 RNA genes (12 rRNAs, 62 tRNAs, and 4 noncoding RNAs [ncRNAs]). There was no plasmid detected using the online tool PlasmidFinder (https://cge.cbs.dtu.dk/services/PlasmidFinder/).A remarkable finding was the presence of the following resistance genes for heavy metals: copper (multicopper oxidase, copB, copC, copD, […]

library_books

Genome based analysis of Carbapenemase producing Klebsiella pneumoniae isolates from German hospital patients, 2008 2014

2018
PMCID: 5930415
PMID: 29744043
DOI: 10.1186/s13756-018-0352-y

[…] WGS data of all isolates were analysed using Resfinder [], PlasmidFinder and the MLST tool [] provided by the Centre for Genomic Epidemiology (https://cge.cbs.dtu.dk/services/; last access: 25/04/2018). Determination of capsular type for Klebsiella strains wa […]

call_split

Complete Genomic Analysis of a Salmonella enterica Serovar Typhimurium Isolate Cultured From Ready to Eat Pork in China Carrying One Large Plasmid Containing mcr 1

2018
Front Microbiol
PMCID: 5934421
PMID: 29755416
DOI: 10.3389/fmicb.2018.00616
call_split See protocol

[…] A, United States). Annotation of the genomes was performed using RAST, BLASTn and BLASTp programs. The open reading frame (ORF) Finder program was used to identify features of public health interest. PlasmidFinder-1.3 was used to identify plasmid replicon types. The comprehensive antibiotic resistance database (CARD) was used to identify antimicrobial resistance genes. Virulence factor database (V […]

call_split

Complete Genome Sequence of a VIM 1 Producing Salmonella enterica subsp. enterica Serovar Infantis Isolate Derived from Minced Pork Meat

2018
Genome Announc
PMCID: 5920186
PMID: 29700156
DOI: 10.1128/genomeA.00327-18
call_split See protocol

[…] ial chromosome (4,698,699 bp) and the blaVIM-1-carrying plasmid pSE15-SA01028 (310,921 bp), comprising average G+C contents of 52.3% and 47.7%, respectively.Genome analysis using the ResFinder3.0 and PlasmidFinder1.3 tools provided by the Center for Genomic Epidemiology (http://www.genomicepidemiology.org) revealed that the plasmid pSE15-SA01028 belongs to the plasmid incompatibility group IncHI2A […]

library_books

Dissemination of blaNDM 5 gene via an IncX3 type plasmid among non clonal Escherichia coli in China

2018
PMCID: 5918551
PMID: 29713466
DOI: 10.1186/s13756-018-0349-6

[…] 8.0.Incompatibility typing of the blaNDM plasmid was performed by PCR-based replicon typing [, ] and was further identified with the help of PlasmidFinder-1.3 server (https://cge.cbs.dtu.dk/services/PlasmidFinder/).In addition, plasmid stability was determined []. Briefly, the blaNDM-5-positive isolates were individually streaked out in the MH agar, incubated at 37 °C for 24 h, and then transferr […]

Citations

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PlasmidFinder institution(s)
Department of Infectious, Parasitic and Immuno-Mediated Diseases, Istituto Superiore di Sanità, Rome, Italy; Danish Technical University, National Food Institute, Division for Epidemiology and Microbial Genomics, Lyngby, Denmark; Danish Technical University, Center for Biological Sequence Analysis, Department of Systems Biology, Lyngby, Denmark
PlasmidFinder funding source(s)
Supported by the Center for Genomic Epidemiology grant 09-067103/DSF, from the Danish Council for Strategic Research, and by the InterOmics project (PB.P05), funded by the Italian Ministry of Education, University and Research (MIUR).

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