PlasmidFinder

PlasmidFinder identifies and types plasmid replicons in whole-genome sequencing (WGS) data from Enterobacteriaceae to characterize plasmid-mediated antimicrobial resistance.

Key Features:

• Database Composition: A reference database of 133 unique plasmid replicon sequences initially compiled from fully sequenced plasmids in the NCBI nucleotide database as of 2014 and continuously updated.
• Input Data: Detection and typing work on both raw and assembled WGS datasets, including draft genomes.
• Target Organisms: Focused analysis for plasmid replicons associated with Enterobacteriaceae, including multi-drug-resistant isolates.
• Integration with pMLST: In silico plasmid multiLocus sequence typing (pMLST) integration using a weekly updated database sourced from www.pubmlst.org for sequence-based plasmid typing.

Scientific Applications:

• Antimicrobial Resistance Surveillance: Identification and typing of plasmid replicons to track and characterize plasmid-borne resistance determinants in Enterobacteriaceae.
• Epidemiology and Strain Tracking: Comparative plasmid replicon profiles to support investigations of plasmid distribution and transmission among bacterial strains.

Methodology:

Analyzes WGS data (raw or assembled) to detect known plasmid replicon sequences and performs in silico pMLST-based multi-locus sequence typing using the referenced databases.