Plasmid classifications

• Published in: Plasmid 2023-05, Vol.126, p.102684-102684, Article 102684
• Main Authors: Garcillán-Barcia, M. Pilar, Redondo-Salvo, Santiago, de la Cruz, Fernando
• Format: Article
• Language: English
• Subjects: Anti-Bacterial Agents - pharmacology; Bacteria - genetics; Gene Transfer, Horizontal; Global plasmidome structure; Horizontal gene transfer; Network-based analyses of the bacterial plasmidome; Plasmid classification; Plasmid incompatibility; Plasmid taxonomic units; Plasmids - genetics; Relaxase MOB class; Replicon formula
• ISSN: 0147-619X; 1095-9890
• DOI: 10.1016/j.plasmid.2023.102684

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 from the efforts to classify plasmids. Here, we review the main plasmid classification systems, starting by phenotype-based methods, such as fertility inhibition and incompatibility, followed by schemes based on a single gene (replicon type and MOB class), and finishing with recently developed approaches that use genetic distances between whole plasmid sequences. A comparison of the latter highlights significant differences between them. We further discuss the need for an operational definition of plasmid species that reveals their biological features, akin to plasmid taxonomic units (PTUs). •Plasmid classification has been at the center of Plasmid Biology research•The initial classification attempts were based on phenotype-based methods, being Inc groups the most prominent•Schemes based on a single gene (replicon type and MOB class), both in vitro and in silico, have been broadly used•Current classification methods use genetic distances between whole plasmid sequences•We propose Plasmid Taxonomic Units (PTUs) as an operational definition of plasmid species