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 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.

PlasmidHostFinder: Prediction of Plasmid Hosts Using Random Forest

“…Overall, PlasmidFinder correctly identified the hosts of 336 plasmids, incorrectly identified the hosts of 16 plasmids, and identified no host for 39 plasmids at the species level. The COPLA tool classifies plasmids by assigning them to PTUs, where each PTU establishes a characteristic host range ( 16 , 21 ). COPLA correctly identified the hosts of 292 plasmids, incorrectly identified the hosts of 12 plasmids and identified no host for 87 plasmids at the species level.…”

“…We compared our model performance to PlasmidFinder and COPLA for the Enterobacteriaceae species that are present in the PATRIC hold-out data set ( 3 , 16 , 21 , 41 ). Moreover, the hold-out plasmids that present in the PlasmidFinder database were excluded from this comparison.…”

“…To our knowledge, the PlasFlow tool is not currently maintained. Recently, in 2021, Redondo-Salvo et al ( 16 ) developed an automated plasmid classification tool called COPLA that works by assigning plasmid taxonomic units (PTUs) based on total average nucleotide identity.…”

Enterobacteralesplasmid sharing amongst human bloodstream infections, livestock, wastewater, and waterway niches in Oxfordshire, UK

“…We contextualised our plasmids within known plasmid diversity using COPLA to determine each plasmid’s ‘plasmid taxonomic unit’ (PTU; see Methods), which is designed to be equivalent to a ‘species’ concept for plasmids 41 . Briefly, COPLA classifies query plasmids based on average nucleotide identity (ANI) against a non-redundant reference plasmid database where most plasmids have been assigned to a reference PTU 40 .…”

Complete sequence of classic F-type plasmid pRK100 shows unique conservation over time and geographic location

“…Recent efforts were made to review, to organize and to propose unifying nomenclature of the conjugative transfer or plasmid genes ( Fernandez-Lopez et al, 2017 ; Orlek et al, 2017 ; Thomas et al, 2017 ). Several types of classification of plasmids are currently in use or proposed: (1) based on replication mechanisms and incompatibility groups ( Carattoli et al, 2005 ); (2) Mob families for conjugative plasmids using conservation of key transfer protein – relaxase ( Francia et al, 2004 ; Orlek et al, 2017 ); (3) partitioning mechanism ( Bousquet et al, 2015 ), (4) based on ANI via a taxonomic c lassifier o f pla smids tool (COPLA) for plasmid taxonomic units (PTUs) ( Redondo-Salvo et al, 2021 ). Unfortunately, these classifications cannot capture all essential plasmid features, for example, Mob-based classification does not relate to nonconjugative plasmids; replicon typing gets complicated by abundant multireplicon plasmids, such as pRK100.…”