COPLA, a taxonomic classifier of plasmids
Santiago Redondo-Salvo,Roger Bartomeus-Peñalver,Luis Vielva,Kaitlin A. Tagg,Hattie E. Webb,Raul Fernandez-Lopez,Fernando de la Cruz +6 more
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TLDR
COPLA as mentioned in this paper is a bioinformatic tool for universal, species-independent, plasmid classification, which can assign plasmids to known and novel taxonomic units based on their genomic sequence.Abstract:
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. 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. 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.read more
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Evolution of Plasmid Mobility: Origin and Fate of Conjugative and Nonconjugative Plasmids
TL;DR: The evolution of plasmid mobility is frequent, shapes the patterns of gene flow in bacteria, the dynamics of gene repertoires, and the ecology ofplasmids, according to a source-sink dynamic.
Journal ArticleDOI
Origins of transfer establish networks of functional dependencies for plasmid transfer by conjugation
TL;DR: In this paper , the authors identify hundreds of plasmids and chromosomes with conjugative origins of transfer in Escherichia coli and Staphylococcus aureus and propose a putative mechanism of transfer for ∼90% of them.
Posted ContentDOI
The mobilome associated with Gram-negative bloodstream infections: A large-scale observational hybrid sequencing based study
Samuel Lipworth,W L Matlock,Liam P. Shaw,Gillian Rodger,K K Chau,Leanne Barker,Senator George,James Kavanagh,Tim Davies,Alison Vaughan,Madelen Andersson,Katie Jeffery,Sarah Oakley,Marcus Morgan,Sussie Hopkins,Tim E. A. Peto,D Crook,A. Sarah Walker,Nicole Stoesser +18 more
TL;DR: 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.
Journal ArticleDOI
Rapid emergence of extensively drug-resistant Shigella sonnei in France
Sophie D. Lefevre,Elisabeth Njamkepo,Sarah Feldman,Corinne Ruckly,Isabelle Carle,Monique Lejay-Collin,Laetitia Fabre,Iman Yassine,Lise Frézal,Maria Pardos de la Gandara,Arnaud Fontanet,François-Xavier Weill +11 more
TL;DR: In this article , the authors detected a dramatic increase in the proportion of isolates simultaneously resistant to ciprofloxacin (CIP), third-generation cephalosporins (3GCs) and azithromycin (AZM) from 2015.
Posted ContentDOI
Improved detection and classification of plasmids from circularized and fragmented assemblies
TL;DR: PlaSquid, a dockerized tool developed in Nextflow that expands plasmid detection and improves replicon typing and mobility groups classification schemes, outperforming previously available methods in both precision and sensitivity is presented.
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Sergio Arredondo-Alonso,Rob J. L. Willems,Willem van Schaik,Willem van Schaik,Anita C. Schürch +4 more
TL;DR: This study shows that it is possible to automatically predict small plasmids, and benchmark algorithms for automated plasmid sequence reconstruction from short-read sequencing data had the highest precision, but was restricted by the contents of its database and the contig length obtained from de novo assembly.