COPLA, a taxonomic classifier of plasmids

Details

• Alternative Title:
  BMC Bioinformatics
• Personal Author:
  Redondo-Salvo, Santiago ; Bartomeus-Peñalver, Roger ; Vielva, Luis ; Tagg, Kaitlin A. ; Webb, Hattie E. ; Fernández-López, Raúl ; de la Cruz, Fernando
• Description:
  Background ; Plasmids 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. ; Results ; We 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. ; Conclusions ; COPLA 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. ; Supplementary Information ; The online version contains supplementary material available at 10.1186/s12859-021-04299-x.
• Subjects:
  • Software
  • Horizontal gene transfer
  • Plasmid
  • Antibiotic resistance genes
  • Average nucleotide identity
  • Plasmid epidemiology
  • Drug Resistance, Microbial
  • Gene Transfer, Horizontal
  • Genomics
  • Plasmids
  More +
• Source:
  BMC Bioinformatics. 22
• Pubmed ID:
  34332528
• Pubmed Central ID:
  PMC8325299
• Document Type:
  Journal Article
• Funding:
  BFU2017-86378-P/Ministerio de Ciencia, Innovación y Universidades/ ; DI-17-09164/Ministerio de Ciencia, Innovación y Universidades/ ; 200-2019-06679/CC/CDC HHSUnited States/
• Volume:
  22
• Download URL:
  https://stacks.cdc.gov/view/cdc/111608/cdc_111608_DS1.pdf
• File Type:
  [PDF - 1.20 MB]
• Collection(s):
  CDC Public Access
• Main Document Checksum:
  urn:sha-512:57ec67903b5fe60c4ff3c4c33f04ba0c99c3b1b6bc2ac1a151f44013a904458df1548aaff20d6621986d2125aa818659e17a85dc19662cae5791104c1c8a01be