Clinical and Environmental Plasmids: Antibiotic Resistance, Virulence, Mobility, and ESKAPEE Pathogens

Background/Objectives: Plasmids are autonomous DNA molecules that can replicate independently and transfer horizontally between bacterial cells. They play a key role in disseminating adaptive traits, such as antimicrobial resistance and virulence. Our study investigates the fundamental differences between plasmid populations originating from clinical/isolates and environmental/metagenomes. Methods: We compare three distinct plasmid genome datasets—the NCBI Reference Sequence Database (RefSeq), the Integrated Microbial Genomes & Microbiomes system (IMG/PR) from bacterial isolates (I) and microbiomes (M)—to assess how plasmid origin shapes their characteristics, including mobility types, antimicrobial resistance genes (ARGs), virulence genes (VGs) and host taxonomy. Results: We show that plasmids originating from bacterial isolates, more enriched in clinical samples, are fundamentally distinct from recovered from metagenomic data. Plasmids from isolates are larger, enriched in conjugative plasmids and display a higher frequency of ARGs and VGs than the ones assembled from metagenomes. Furthermore, ARGs are more frequently associated with highly mobile plasmids, particularly pCONJ. Conclusions: These findings highlight the importance of plasmid origins in studies of plasmid epidemiology, functional potential and mobility.