Abstract

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.

Details

Title
COPLA, a taxonomic classifier of plasmids
Author
Redondo-Salvo, Santiago; Bartomeus-Peñalver, Roger; Vielva, Luis; Tagg, Kaitlin A; Webb, Hattie E; Fernández-López, Raúl; de la Cruz, Fernando  VIAFID ORCID Logo 
Pages
1-9
Section
Software
Publication year
2021
Publication date
2021
Publisher
BioMed Central
e-ISSN
14712105
Source type
Scholarly Journal
Language of publication
English
ProQuest document ID
2562429440
Copyright
© 2021. This work is licensed under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.