Identification and typing of plasmid replicons in whole-genome sequencing (WGS).
About
Plasmidfinder allows for the detection of plasmid replicons in total or partial sequenced isolates of bacteria. The tool utilizes the BLASTn algorithm to map the input genome sequence against a curated database of plasmid replicons. It is primarily intended for the identification of plasmids in WGS data originating from Enterobacteriaceae and Gram-positive species, enabling the assignment of plasmids to lineages (Inc groups) based on existing knowledge.
PlasmidFinder in Pathogenwatch
The species assignment from Speciator is used to select the Inc type library (Enterobacteriaceae or Gram positive). Please contact us if wrong library has been run or results are missing.
Genome Report
Contig Inc annotations
In the Plasmid section of the genome report, each row corresponds to an individual match to an Inc marker. The first field in each row shows the complete set of Inc types for that single contig. A contig may have multiple matches, and hence, complex Inc types. In this case the first cell spans each row corresponding to the same contig.
An example of a single contig with 2 Inc matches, both at 100%.
Contig AMR genes
An extra column showing presence of antimicrobial resistance genes on the same contig is included If AMR assignments are available, though that currently excludes Kleborate. If no genes were found in the contig then a dash is shown. If the linked AMR gene is a core chromosomal gene, then it is marked with an asterix, and noted at the bottom of the table. This is likely indicative of either assembly error or a chromosomally integrated plasmid ("episome").
The rep22-containing contig may be chromosomal, as gyrA is a core gene.
Collection View
The identified Inc types are displayed in the "Typing" table as a comma-separated list and are available for download in the associated CSV.
How to cite
Carattoli A, Zankari E, García-Fernández A, Voldby Larsen M, Lund O, Villa L, Møller Aarestrup F, Hasman H. In Silico Detection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing. Antimicrob Agents Chemother. 2014;58(7):3895-3903. doi:10.1128/AAC.02412-14.
