In Silico Detection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing
Citations
24 citations
24 citations
Cites methods from "In Silico Detection and Typing of P..."
...There are a number of tools that can be used to detect plasmid sequences including PlasmidFinder [2], cBar [3], gPlas [4], PlasFlow [5], and others....
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24 citations
24 citations
Cites methods from "In Silico Detection and Typing of P..."
...In contrast, plasmid genes were not identified to be lost or acquired in any lineage (the PlasmidFinder database was used to define plasmid genes)....
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...Finally, the absence of Pseudomonas plasmid annotations in the PlasmidFinder database could have led to a low number of identified plasmids among our isolates....
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...The PlasmidFinder (61) database (263 sequences; retrieved 21 March 2018) was used for plasmid gene identification, the VFDB database (2,597 genes; retrieved 21 March 2018) (62) was used for virulence gene identification, the Resfinder database (2,280 genes; retrieved 21 March 2018) (63) was used for resistance gene identification, and the ACLAME database (54,945 genes; retrieved 7 June 2018) (64) was used for prophage origin sequence identification....
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24 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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