In Silico Detection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing
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Cites methods from "In Silico Detection and Typing of P..."
...2017) with the PlasmidFinder database (Carattoli et al. 2014) (accessed 05-12-2017) to identify all of the Incompatibility (Inc) groups in each sample....
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...PlasmidFinder successfully identified one plasmid Inc group, IncFIIS, as present in 89.5% of all samples tested....
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...To provide a point of comparison, and determine what plasmids were present in the input dataset, all of the samples were compared to the PlasmidFinder (Carattoli et al. 2014) database (retrieved 2017-07-25) using Ariba (v2....
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...“In Silico Detection and Typing of Plasmids Using PlasmidFinder and Plasmid Multilocus Sequence Typing.”...
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...The K. pneumoniae dataset from Holt et al. (Holt et al. 2015) was analysed using ARIBA (version 2.10.3) (Hunt et al. 2017) with the PlasmidFinder database (Carattoli et al. 2014) (accessed 05-12-2017) to identify all of the Incompatibility (Inc) groups in each sample....
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7 citations
7 citations
References
3,956 citations
"In Silico Detection and Typing of P..." refers methods in this paper
...To extract the relevant information from the large amount of data generated, a Web-based tool, ResFinder, for the identification of acquired or intrinsically present antimicrobial resistance genes in whole-genome data was recently developed (15)....
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2,934 citations
"In Silico Detection and Typing of P..." refers background in this paper
...In particular, the replicase proteins showing the pfam02387 or pfam01051 conserved domains were assigned to the FII and FIB groups, respectively (31)....
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2,163 citations
"In Silico Detection and Typing of P..." refers methods in this paper
...A collection of 24 previously characterized and fully FIG 1 Numbers of fully sequenced plasmids (y axis) classified into incompatibility groups occurring in the different bacterial species of the Enterobacteriaceae family....
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...Since 2005, a PCR-based replicon typing (PBRT) scheme has been available that targets in multiplex PCRs the replicons of the major plasmid families occurring in members of the family Enterobacteriaceae (2)....
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...Here, we present two free, easy-to-use Web tools, PlasmidFinder and pMLST, to analyze and classify plasmids from bacterial species of the family Enterobacteriaceae....
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...Here, we describe the design of two new easy-to-use Web tools useful for the rapid identification of plasmids in Enterobacteriaceae species that are of interest for epidemiological and clinical microbiology investigations of the plasmid-associated spread of antimicrobial resistance....
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...This method was initially developed to detect the replicons of plasmids belonging to the 18 major incompatibility (Inc) groups of Enterobacteriaceae species (3)....
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1,943 citations
1,620 citations
"In Silico Detection and Typing of P..." refers methods in this paper
...If raw sequence reads are uploaded, they are first assembled (after the sequencing platform is given by the user) as described previously (16)....
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