COPLA

COPLA classifies plasmids into plasmid taxonomic units (PTUs) using average nucleotide identity to provide a universal, species-independent classification framework for plasmids that mobilize antibiotic resistance, virulence factors, and other adaptive traits.

Key Features:

• Plasmid Taxonomic Units (PTUs): Uses a formal definition of PTUs to organize plasmid diversity across bacterial taxa.
• Average Nucleotide Identity (ANI): Employs ANI metrics to delineate plasmid relatedness and define PTU boundaries.
• Sequence-based assignment: Assigns plasmids to known or novel PTUs based on plasmid genomic sequences.
• Automated pipeline: Provides an automated computational pipeline for PTU assignment.
• Performance evaluation: Evaluated on 1,000 unclassified plasmids, assigning 41% to previously defined PTUs overall and 63% within Enterobacterales, with the remainder identified as novel PTUs.
• Species-independent applicability: Designed to operate across all bacterial taxa for universal plasmid classification.

Scientific Applications:

• Plasmid epidemiology: Enables tracking of plasmid-mediated spread of antibiotic resistance and virulence factors among bacteria.
• Bacterial genetics: Supports characterization of plasmid backbones and diversity in genetic studies.
• Clinical microbiology: Facilitates classification of clinical plasmids relevant to antimicrobial resistance surveillance.
• Microbial genomics and public health: Contributes to genomic surveillance efforts across bacterial taxa to inform public health initiatives.

Methodology:

Defines PTUs using average nucleotide identity comparisons of plasmid genomic sequences and assigns plasmids to known or novel PTUs via an automated pipeline; evaluation used 1,000 unclassified plasmids with reported assignment rates of 41% overall and 63% within Enterobacterales.