Towards quantifying plasmid similarity

Abstract

Plasmids are extrachromosomal replicons which can quickly spread resistance and virulence genes between clinical pathogens. From the tens of thousands of currently available plasmid sequences we know that overall plasmid diversity is structured, with related plasmids sharing a largely conserved 'backbone' of genes while being able to carry very different genetic cargo. Moreover, plasmid genomes can be structurally plastic and undergo frequent rearrangements. So, how can we quantify plasmid similarity? Answering this question requires practical efforts to sample natural variation as well as theoretical considerations of what defines a group of related plasmids. Here we consider the challenges of analysing and rationalising the current plasmid data deluge to define appropriate similarity thresholds.

Keywords: antimicrobial resistance; genomic epidemiology; mobile genetic elements.

Fig. 1.. Structural changes between and within plasmids. These structural changes take place within a host cell. Arrows indicate possible changes, which might be reversible. (a) Gene gain and loss events within a plasmid. (b) Co-integration events between plasmids. (c) Inversions, rearrangements, recombination of sequence within a plasmid. (d) Chromosomal integration of plasmids. Figure made with BioRender.com.