COPLA, a taxonomic classifier of plasmids

BMC Bioinformatics

Hattie E. Webb¹  Kaitlin A. Tagg¹  Luis Vielva²  Fernando de la Cruz³  Santiago Redondo-Salvo³  Roger Bartomeus-Peñalver³  Raúl Fernández-López³ 

[1] Centers for Disease Control and Prevention, Atlanta, USA;WDS, Inc., Atlanta, USA;Departamento de Ingeniería de las Comunicaciones, Universidad de Cantabria, Santander, Spain;Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, Santander, Spain;

关键词: Horizontal gene transfer;    Plasmid;    Antibiotic resistance genes;    Average nucleotide identity;    Plasmid epidemiology;   

DOI  :  10.1186/s12859-021-04299-x

来源: Springer

【 摘 要 】

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

【 授权许可】

CC BY