In Silico Detection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing
Citations
9 citations
Cites methods from "In Silico Detection and Typing of P..."
...were identified using BLASTn search of the PlasmidFinder database (40)....
[...]
9 citations
9 citations
9 citations
Cites methods from "In Silico Detection and Typing of P..."
...No plasmid was detected in the genome by using Plasmid Finder (15)....
[...]
9 citations
Cites methods from "In Silico Detection and Typing of P..."
...…and acquired antimicrobial resistance genes using the pipelines mlst (version 1.7), plasmidfinder (version 1.2, 80% threshold for %ID) and resfinder (version 2.1, 80% threshold for %ID/60% minimum length) available from CGE (Carattoli et al., 2014; Larsen et al., 2012; Zankari et al., 2012)....
[...]
...Single nucleotide polymorphisms (SNPs) were determined using the pipeline csi phylogeny (version 1.4) available from the CGE (http://cge.cbs.dtu.dk/services/all.php)....
[...]
...The assembled sequences were analysed to identify the MLST sequence type (ST) for Salmonella enterica, plasmid replicons and acquired antimicrobial resistance genes using the pipelines mlst (version 1.7), plasmidfinder (version 1.2, 80% threshold for %ID) and resfinder (version 2.1, 80% threshold for %ID/60% minimum length) available from CGE (Carattoli et al., 2014; Larsen et al., 2012; Zankari et al., 2012)....
[...]
...The quality of the reads was assessed using the FastQC quality control tool (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), reads with a quality score of below 20 were filtered out, and all the remaining reads were assembled using the assembler pipeline (version 1.4) available from the Center for Genomic Epidemiology (CGE) (http://cge.cbs.dtu.dk/services/all.php)....
[...]
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)....
[...]
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)....
[...]
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....
[...]
...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)....
[...]
...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....
[...]
...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....
[...]
...This method was initially developed to detect the replicons of plasmids belonging to the 18 major incompatibility (Inc) groups of Enterobacteriaceae species (3)....
[...]
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)....
[...]