In Silico Detection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing
Citations
54 citations
Cites methods from "In Silico Detection and Typing of P..."
...Separated DNA was transferred to a nylon membrane and probed with a digoxigenin-labeled DNA probe (Roche Diagnostics, Basel, Switzerland) specific to blaNDM and plasmid replicon IncFII, IncX3, IncFII(pRSB107), IncFIB(pQil), or IncL/M (42)....
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...We found five different replicon types among the plasmids harboring blaNDM-1: IncFIB(pQil), IncL/M, IncFII(pRSB107), IncA/C2, and a multireplicon-type plasmid harboring the IncFII(K), IncQ1, and IncR replication genes (Fig....
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...Assembled contig sequences of these two isolates were mapped with high confidence (93% coverage and 99% nucleotide identity) to a previously reported IncL/M plasmid carried by a clinical K. pneumoniae isolate of Omani origin, pNDM-OM (21), which was recently reclassified as IncM2 (22)....
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...It was found in other types of plasmids, such as IncFIB(pQil), IncFII(pRSB107)-like, IncL/M, and IncA/C2, indicating their independent acquisition of the gene rather than the dissemination of the gene with major transferable plasmids....
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...Two blaNDM-1-harboring plasmids carried by phylogenetically distant isolates (1,377 SNPs), M211 and M414, were determined as the IncL/M type....
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54 citations
53 citations
53 citations
Cites background from "In Silico Detection and Typing of P..."
...…context, multiples Blast-based tools have been designed for fast genome screening and comparison to detect mobile elements such as resistance markers, transposons, phage-like elements/remnants and plasmids (Zankari et al., 2012; Cosentino et al., 2013; Carattoli et al., 2014; Joensen et al., 2014)....
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53 citations
Cites methods from "In Silico Detection and Typing of P..."
...The assembled contigs were analysed for the presence of resistance genes, genes encoding virulence factors, replicon types and multilocus sequence type (ST) by ResFinder, VirulenceFinder, PlasmidFinder, and multilocus sequence typing (MLST) available from the Center for Genomic Epidemiology (DTU, Copenhagen, Denmark) [17-20]....
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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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