In Silico Detection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing
Citations
12 citations
Cites methods from "In Silico Detection and Typing of P..."
...The bacterial analysis pipeline of GoSeqIt tools was also used to annotate and identify known acquired antibiotic‐resistant genes via ResFinder (Zankari et al., 2012), virulence factors using VirulenceFinder (Joensen et al., 2014) and plasmids through PlasmidFinder (Carattoli et al., 2014) with 95% identity and 90× coverage....
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...…of GoSeqIt tools was also used to annotate and identify known acquired antibiotic‐resistant genes via ResFinder (Zankari et al., 2012), virulence factors using VirulenceFinder (Joensen et al., 2014) and plasmids through PlasmidFinder (Carattoli et al., 2014) with 95% identity and 90× coverage....
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...PlasmidFinder revealed that the plasmid replicon types repL(pDLK1), rep(SAP101A) and repC(Cassette) were detected in all isolates....
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...In silico detection and typing of plas‐ mids using PlasmidFinder and plasmid multilocus sequence typing....
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12 citations
Cites background from "In Silico Detection and Typing of P..."
...Using plasmid multilocus sequence typing (pMLST) (18, 19), specific ESBL/pAmpC variants were found to be associated with particular IncI1-I STs (12, 13, 16, 17)....
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...Information regarding the source, isolation year, and in silico characterization of all plasmids (19, 25) and strains (26, 27) is...
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12 citations
Cites background from "In Silico Detection and Typing of P..."
...Each contained two plasmids belonging to IncF1B and IncHI2, respectively (25)....
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12 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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