COPLA, a taxonomic classifier of plasmids

Area of Science:

• Microbiology
• Bioinformatics
• Genetics

Background:

• Plasmids are crucial mobile genetic elements driving bacterial adaptation and the spread of traits like antibiotic resistance.
• Current plasmid classification methods lack universality and precision, hindering pathogen genetics and epidemiology studies.
• Plasmid taxonomic units (PTUs) offer a universal classification framework based on average nucleotide identity.

Purpose of the Study:

• To develop and present COPLA, a software tool for universal, species-independent plasmid classification.
• To enable the assignment of plasmids to known and novel plasmid taxonomic units (PTUs) based on genomic sequences.

Main Methods:

• Implementation of an automated bioinformatics pipeline for plasmid classification.
• Assessment of the pipeline's performance on a dataset of 1000 unclassified plasmid DNA sequences.
• Utilizing average nucleotide identity metrics for PTU definition and assignment.

Main Results:

• COPLA successfully assigned 41% of tested plasmids to previously defined PTUs.
• Classification accuracy reached 63% for plasmids within well-characterized bacterial orders like Enterobacterales.
• A significant proportion of plasmids represent novel PTUs, indicating extensive uncharacterized plasmid diversity.

Conclusions:

• COPLA provides a universal and species-independent method for plasmid classification.
• The software is available as an automated pipeline and a web service, facilitating rapid plasmid analysis.
• COPLA will aid bacterial geneticists and clinical microbiologists in classifying plasmids, advancing research in bacterial genetics and epidemiology.