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

Area of Science:

• Microbiology
• Genomics
• Molecular Biology

Background:

• Plasmids are mobile DNA elements crucial for bacterial adaptation and trait dissemination.
• Antimicrobial resistance and virulence factors are often plasmid-borne, impacting bacterial evolution.
• Understanding plasmid diversity is key to combating infectious diseases.

Purpose of the Study:

• To investigate fundamental differences between plasmid populations from clinical/isolate and environmental/metagenome sources.
• To assess how plasmid origin influences characteristics like mobility, gene content, and host association.
• To compare plasmid datasets from RefSeq, IMG/PR (isolates), and IMG/PR (microbiomes).

Main Methods:

• Comparative analysis of three distinct plasmid genome datasets: RefSeq, Integrated Microbial Genomes & Microbiomes (IMG/PR) from bacterial isolates (I), and IMG/PR from microbiomes (M).
• Assessment of plasmid characteristics including mobility types, antimicrobial resistance genes (ARGs), virulence genes (VGs), and host taxonomy.
• Statistical comparison of plasmid features based on their origin (isolate vs. metagenome).

Main Results:

• Plasmids from bacterial isolates (enriched in clinical samples) are fundamentally distinct from those assembled from metagenomes.
• Isolate plasmids are larger, more frequently conjugative, and exhibit higher frequencies of ARGs and VGs compared to metagenome-derived plasmids.
• Antimicrobial resistance genes are more commonly associated with highly mobile plasmids, especially conjugative plasmids (pCONJ).

Conclusions:

• Plasmid origin is a critical factor influencing plasmid epidemiology, functional potential, and mobility.
• Distinguishing between isolate and metagenome plasmid populations is essential for accurate interpretation of plasmid data.
• These findings have implications for understanding the spread of adaptive traits in bacterial communities.