COPLA, a taxonomic classifier of plasmids

Abstract Background Plasmids are mobile genetic elements, key in the dissemination of antibiotic resistance, virulence determinants and other adaptive traits bacteria. Obtaining a robust method for plasmid classification is necessary to better understand genetics epidemiology many pathogens. Until now, systems focused on specific traits, which limited their precision universality. The definition taxonomic units (PTUs), based average nucleotide identity metrics, allows generation universal scheme, applicable all bacterial taxa. Here we present COPLA, software able assign plasmids known novel PTUs, genomic sequence. Results We implemented an automated pipeline given DNA sequence its cognate PTU, assessed performance using sample 1000 unclassified plasmids. Overall, 41% samples could be assigned previously defined number that reached 63% well-known taxa such as Enterobacterales order. remaining represent indicating large fraction backbones still uncharacterized. Conclusions COPLA bioinformatic tool universal, species-independent, classification. Offered both automatable open web service, will help geneticists clinical microbiologists quickly classify