Table 2 Plasmids characteristics and their closest counterparts

pNN-1

155,772 bp

Enterococcus faecium isolate E8440 genome assembly, plasmid: 2 (query cover: 99%; Identity: 99.97%)

Antibiotic Tolerance: Encodes two-component response regulator VncR for vancomycin tolerance and several toxin-antitoxin systems for survival.

Metabolic Functions: Includes PTS systems and ABC transporters for carbohydrate uptake, enhancing adaptability to nutrient availability.

Stress Response: Encodes DNA topoisomerase and glyoxalase proteins for DNA integrity and oxidative stress protection.

pNN-1B

129,445 bp

Enterococcus faecium isolate E8440 genome assembly, plasmid: 2 (query cover: 98%; Identity: 99.97%)

All the main characteristics of pNN-1 are retained in pNN-1B (21-kb deletion variant).

pNN-2

28,557 bp

Enterococcus faecium isolate E7356 genome assembly, plasmid: 4 (query cover: 100%; Identity: 100%)

Antibiotic Resistance: Contains genes for 23 S rRNA dimethyltransferase (ermB), aminoglycoside 3’-phosphotransferase (aph(3’)-III), aminoglycoside 6-nucleotidyltransferase (ant(6)-Ia), and acetyltransferase (sat-4), conferring resistance against macrolide, aminoglycoside, streptomycin, and streptothricin antibiotics, respectively.

Enzymatic Functions: Encodes DNA polymerase (beta-like region), DNA topoisomerase III, and DNA-directed RNA polymerase beta subunit, all involved in nucleic acid synthesis and processing.

Toxin-Antitoxin Systems: Features the Epsilon antitoxin and Zeta toxin, which may contribute to stability and survival under stress conditions.

pNN-3

102,041 bp

Enterococcus faecium strain VVEswe-R plasmid pVVEswe-R2 (query cover: 87%; Identity: 99.99%)

Antibiotic Resistance: Contains gene aac(6’)-aph(2’’) that provide resistance against aminoglycosides.

Enzymatic Functions: Encodes several enzymes, including alpha-N-arabinofuranosidase and ketopantoate reductase, involved in carbohydrate metabolism and essential biochemical pathways.

Stability Mechanisms: Features the RelE/StbE toxin for plasmid stabilization and a variety of hypothetical proteins that may contribute to unknown functions.

pNN-4

4,462 bp

Enterococcus faecium strain 2016C07-254 plasmid p2016C07-254-6 (query cover: 100%; Identity: 99.98%)

Contains 6 CDS, including one plasmid replication initiation protein and five hypothetical proteins.

pNN-5

4,372 bp

Enterococcus faecium JARB-OU2352 plasmid pJAOU2352_5 (query cover: 100%; Identity: 100%)

Contains 7 CDS, including one plasmid replication initiation protein and six hypothetical proteins.

pNN-6

1,979 bp

Enterococcus faecium strain VRE-WC072 plasmid unnamed4 (query cover: 100%; Identity: 99.60%)

Contains 2 CDS, including one plasmid replication initiation protein and one hypothetical protein.

pNN-7

6,173 bp

Enterococcus faecium strain A15023 plasmid pA15023_P4 (query cover: 100%; Identity: 100%)

Bacteriocin Production: Prebacteriocin and predicted prebacteriocin proteins suggest involvement in bacteriocin production, providing competitive advantages to bacterial species or strains in its environment.