In Silico Detection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing
Citations
16 citations
Cites methods from "In Silico Detection and Typing of P..."
...PlasmidFinder was used to search for plasmids within the genome (Carattoli et al. 2014)....
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16 citations
Cites methods from "In Silico Detection and Typing of P..."
...Resistance genes, virulence genes, plasmid incompatibility groups as well as multilocus sequence types were identified using the Webtools ResFinder (Zankari et al., 2012), PlasmidFinder (Carattoli et al., 2014) and MLST 1.8 (Larsen et al., 2012)....
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..., 2012), PlasmidFinder (Carattoli et al., 2014) and MLST 1....
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16 citations
Cites background from "In Silico Detection and Typing of P..."
...3 and the nucleotide databases CARD (54), VFDB (55), and PlasmidFinder (56)....
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...Genotyping of SG17-135 and other S. Agona genomic assemblies was performed using a custom Snakemake-based workflow which utilized ABRicate (https://github.com/ tseemann/Abricate) version 0.9.3 and the nucleotide databases CARD (54), VFDB (55), and PlasmidFinder (56)....
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16 citations
16 citations
Cites methods from "In Silico Detection and Typing of P..."
...In addition, genomes were analysed for the presence of genomic islands using the online tool IslandViewer 3 (Dhillon et al. 2015) and for plasmid sequences using PlasmidFinder (Carattoli et al. 2014) and custom Python scripts....
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...No matches to plasmid sequences on PlasmidFinder database were found....
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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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