PlaScope

PlaScope classifies contigs from bacterial genome assemblies to localize plasmid and chromosomal sequences and thereby identify plasmid-borne resistance and virulence genes in species such as Enterobacteriaceae, Staphylococcus aureus, and Enterococcus.

Key Features:

• High Sensitivity and Specificity: Uses the Centrifuge metagenomic classifier with a custom database of complete sequences from curated databases to classify contigs by predicted genomic location, achieving recall 0.87, specificity 0.99, precision 0.96, and accuracy 0.98 and outperforming PlasFlow and cBar.
• Targeted Approach: Recovers plasmidic sequences from genome assemblies at the species or genus level for focused plasmidome analysis.
• Database Integration: Utilizes a custom database of chromosomes and plasmids to enable accurate classification and identification of genetic elements within bacterial genomes.

Scientific Applications:

• Plasmid Outbreak Analysis: Supports investigation of plasmid outbreaks including extended-spectrum beta-lactamase (ESBL) and carbapenemase-producing Enterobacteriaceae and can detect chromosomal integrations of resistance genes such as ESBL genes in Escherichia coli.
• Virulence Gene Prediction: Predicts the genomic locations of virulence genes and operons to inform studies of pathogenic mechanisms.
• Resistance Gene Mapping: Assigns the location of resistance genes in Klebsiella pneumoniae strains to aid analysis of resistance patterns.

Methodology:

Contig classification using Centrifuge against a custom database of complete chromosome and plasmid sequences curated from public databases.