COPLA, a taxonomic classifier of plasmids

Redondo-Salvo, Santiago; Bartomeus, Roger; Vielva, Luis; Tagg, Kaitlin A.; Webb, Hattie E.; Fernández-López, Raúl; Cruz, Fernando de la

doi:10.1101/2020.12.15.422809

Cited by 12 publications

(21 citation statements)

References 10 publications

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“…At the plasmid-level, 17% (317/1880) plasmids could not be assigned a replicon type and 33% (622/1880) had no identifiable relaxase-type. Similarly 26% (487/1880) plasmids were not typable using the recently described Plasmid Taxonomic Unit (PTU) scheme (15). Whilst overall there was a strong correlation between the number of plasmids in hybrid assemblies and replicon types detected in the short read assemblies (Pearson correlation 0.83, 95%CI 0.81-0.86, p<0.001), there were a substantial number of isolates 69% (507/738) for which counting replicon types misrepresented the true number of plasmids, consistent with the presence of multi-replicon plasmids (Figure 1b).…”

Section: Hybrid Assembly Demonstrates the Limitations Of Existing Typ...mentioning

confidence: 99%

The mobilome associated with Gram-negative bloodstream infections: A large-scale observational hybrid sequencing based study

Lipworth

Matlock

Shaw

et al. 2022

Preprint

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Plasmids carry genes conferring antimicrobial resistance (AMR), and other clinically important traits; their ability to move within and between species may provide the machinery for rapid dissemination of such genes. Despite this, existing studies using complete plasmid assemblies, which are essential for reliable inference, have been small and/or limited to those carrying particularly antimicrobial resistance genes (ARGs). In this study, we sequenced 1,880 complete plasmids from 738 isolates from bloodstream infections (BSI) in 2009 (194 isolates) and 2018 (368 isolates) in Oxfordshire, UK, plus a stratified selection from intervening years (176 isolates). We demonstrate that plasmids are largely, but not entirely, constrained to host species, although there is substantial overlap between species of plasmid gene-repertoire. Plasmids carrying ARGs (including those encoding carbapenemases) share a putative "backbone" of core genes with those carrying no such genes. Most ARGs are carried by a relatively small number of plasmid groups with biological features that are predictable. These findings suggest that future surveillance should, in addition to tracking plasmids currently associated with clinically important genes, focus on identifying and monitoring the dissemination of high-risk plasmid groups with the potential to rapidly acquire and disseminate these genes.

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Section: Hybrid Assembly Demonstrates the Limitations Of Existing Typ...mentioning

confidence: 99%

The mobilome associated with Gram-negative bloodstream infections: A large-scale observational hybrid sequencing based study

Lipworth

Matlock

Shaw

et al. 2022

Preprint

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“…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 .…”

Section: Highlighting the Extent Of Plasmid Diversitymentioning

confidence: 99%

“…Plasmids were assigned a plasmid taxonomic unit (PTU) using COPLA 41 (default parameters except -t circular, -k Bacteria, -p Pseudomonadota, -c Gammaproteobacteria, and -o Enterobacterales), based on the classification system developed in Redondo-Salvo et al, 2021 29 . COPLA compares query plasmids to a database of PTU reference plasmids, assigning a PTU when both (i) the ANI>0.7 along 50% of the length of the smallest plasmid in the comparison, and (ii) a graph-neighbouring condition to existing PTU clusters is satisfied.…”

Section: Ptu Classificationmentioning

confidence: 99%

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

Matlock

Lipworth

Chau

et al. 2022

Preprint

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Horizontal gene transfer in Enterobacterales allows mobile genetic elements to move between strains, species, and genera. In particular, the movement of plasmids is a known route for rapid dissemination of antimicrobial resistance (AMR) genes. However, it is difficult to establish to what extent plasmids are shared between Enterobacterales causing human infections and those from non-human sources, such as livestock or the environment. While some previous studies have found only limited evidence for genetic overlap, these have often been limited in size, restricted to drug-resistant isolates, and have used fragmented genome assemblies. Here, we report a collection of geographically and temporally restricted isolates from human bloodstream infections (BSI), environmental soils, livestock (cattle, pigs, poultry, sheep), wastewater (influent, effluent), and rivers. Isolates were all collected between 2008-2018 from sampling sites <60km apart. The combined dataset contains 1,458 complete Enterobacterales genomes, including 3,697 circularised plasmids of which one third were unclassifiable. We find eight groups of near-identical plasmids seen in both human BSI and non-human isolates, of which two are conjugative F-type plasmids carrying AMR genes. We cluster plasmids based on alignment-free distances and find that 73/247 (30%) plasmid clusters contain plasmids from both human BSI and non-human isolates. Pangenome-style analyses of the 69 most prevalent clusters (1,832/3,697 plasmids) reveals sets of shared core genes alongside accessory gene repertoires. Core-gene phylogenies suggest an intertwined ecology where well-conserved putative plasmid 'backbones' carry diverse accessory functions, potentially linked to niche adaptation. Furthermore, we show that closely related human and non-human plasmids are frequently found across distantly related bacterial hosts. Our findings underline the importance of diverse sampling in 'One Health' approaches for AMR management.

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“…The taxonomic classifier of plasmids, COPLA, was used to assign plasmids to taxonomic units (Redondo-Salvo et al 2021).…”

Section: Ptu Predictionsmentioning

confidence: 99%

Evolution of plasmid mobility: origin and fate of non-conjugative plasmids

Coluzzi

Garcillán-Barcia

Cruz

et al. 2021

Preprint

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Conjugation drives horizontal gene transfer of many adaptive traits across prokaryotes. Yet, only a fourth of the plasmids encode the functions necessary to conjugate autonomously, others being non-mobile or mobilizable by other elements. How these different plasmids evolve is poorly understood. Here, we studied plasmid evolution in terms of their gene repertoires and relaxases. We observed that gene content in plasmid varies rapidly in relation to the rate of evolution of relaxases, such that plasmids with 95% identical relaxases have on average fewer than 50% of homologs. The identification of 249 recent transitions in terms of mobility types revealed that they are associated with even greater changes in gene repertoires, possibly mediated by transposable elements that are more abundant in such plasmids. These changes include pseudogenization of the conjugation locus, exchange of replication initiators, and extensive gene loss. In some instances, the transition between mobility types also leads to the genesis of novel plasmid taxonomic units. Most of these transitions are short-lived, suggesting a source-sink dynamic, where conjugative plasmids constantly generate mobilizable and putatively non-mobilizable plasmids by gene deletion. Yet, in few cases such transitions resulted in the emergence of large clades of relaxases present only in mobilizable plasmids, suggesting successful specialization of these families in the hijacking of diverse conjugative systems. Our results shed further light on the huge plasticity of plasmids, suggest that many non-conjugative plasmids emerged recently from conjugative elements and allowed to quantify how changes in plasmid mobility shape the variation of their gene repertoires.

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COPLA, a taxonomic classifier of plasmids

Cited by 12 publications

References 10 publications

The mobilome associated with Gram-negative bloodstream infections: A large-scale observational hybrid sequencing based study

The mobilome associated with Gram-negative bloodstream infections: A large-scale observational hybrid sequencing based study

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

Evolution of plasmid mobility: origin and fate of non-conjugative plasmids

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