Plasmid classification in an era of whole-genome sequencing: application in studies of antibiotic resistance epidemiology

A Orlek, N Stoesser, MF Anjum, M Doumith… - Frontiers in …, 2017 - frontiersin.org
Plasmids are extra-chromosomal genetic elements ubiquitous in bacteria, and commonly
transmissible between host cells. Their genomes include variable repertoires of 'accessory …

[HTML][HTML] Ordering the mob: Insights into replicon and MOB typing schemes from analysis of a curated dataset of publicly available plasmids

A Orlek, H Phan, AE Sheppard, M Doumith, M Ellington… - Plasmid, 2017 - Elsevier
Plasmid typing can provide insights into the epidemiology and transmission of plasmid-
mediated antibiotic resistance. The principal plasmid typing schemes are replicon typing …

Universal whole-sequence-based plasmid typing and its utility to prediction of host range and epidemiological surveillance

J Robertson, K Bessonov, J Schonfeld… - Microbial …, 2020 - microbiologyresearch.org
Bacterial plasmids play a large role in allowing bacteria to adapt to changing environments
and can pose a significant risk to human health if they confer virulence and antimicrobial …

[HTML][HTML] Plasmid classifications

MP Garcillán-Barcia, S Redondo-Salvo, F de la Cruz - Plasmid, 2023 - Elsevier
Plasmids are universally present in bacteria and play key roles in the dissemination of
genes such as antibiotic resistance determinants. Major concepts in Plasmid Biology derive …

Identification of bacterial plasmids based on mobility and plasmid population biology

MP Garcillán-Barcia, A Alvarado… - FEMS microbiology …, 2011 - academic.oup.com
Plasmids contain a backbone of core genes that remains relatively stable for long
evolutionary periods, making sense to speak about plasmid species. The identification and …

In Silico Detection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing

A Carattoli, E Zankari, A García-Fernández… - Antimicrobial agents …, 2014 - Am Soc Microbiol
In the work presented here, we designed and developed two easy-to-use Web tools for in
silico detection and characterization of whole-genome sequence (WGS) and whole-plasmid …

COPLA, a taxonomic c lassifier of pla smids

S Redondo-Salvo, R Bartomeus-Peñalver, L Vielva… - BMC …, 2021 - Springer
Background Plasmids are mobile genetic elements, key in the dissemination of antibiotic
resistance, virulence determinants and other adaptive traits in bacteria. Obtaining a robust …

PlaScope: a targeted approach to assess the plasmidome from genome assemblies at the species level

G Royer, JW Decousser, C Branger… - Microbial …, 2018 - microbiologyresearch.org
Plasmid prediction may be of great interest when studying bacteria of medical importance
such as Enterobacteriaceae as well as Staphylococcus aureus or Enterococcus. Indeed …

PlasForest: a homology-based random forest classifier for plasmid detection in genomic datasets

L Pradier, T Tissot, AS Fiston-Lavier, S Bedhomme - BMC bioinformatics, 2021 - Springer
Background Plasmids are mobile genetic elements that often carry accessory genes, and
are vectors for horizontal transfer between bacterial genomes. Plasmid detection in large …

Platon: identification and characterization of bacterial plasmid contigs in short-read draft assemblies exploiting protein sequence-based replicon distribution scores

O Schwengers, P Barth, L Falgenhauer… - Microbial …, 2020 - microbiologyresearch.org
Plasmids are extrachromosomal genetic elements that replicate independently of the
chromosome and play a vital role in the environmental adaptation of bacteria. Due to …