In Silico Detection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing
Citations
25 citations
25 citations
Cites background from "In Silico Detection and Typing of P..."
...…factors (VirulenceFinder), and species confirmation for VRE and ESBL-E. coli (KmerFinder), and serotype (SerotypeFinder) and plasmid replicons (PlasmidFinder) for ESBL-E. coli (Zankari et al., 2012; Carattoli et al., 2014; Hasman et al., 2014; Joensen et al., 2014, 2015; Larsen et al., 2014)....
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25 citations
Cites methods from "In Silico Detection and Typing of P..."
...Plasmid incompatibility types and subtypes were identified using PlasmidFinder[15] and established methods for IncC subtyping[16,17]....
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25 citations
Cites methods from "In Silico Detection and Typing of P..."
...Contiguous sequences containing antimicrobial resistance genes were extracted from assemblies and the presence of plasmid incompatibility groups on these contiguous sequences was determined by using PlasmidFinder (33)....
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25 citations
Cites methods from "In Silico Detection and Typing of P..."
...com/phac-nml/staramr) against known plasmid sequences in the PlasmidFinder database [36] with 98% minimum identity and 60% minimum coverage....
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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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