## 3 Results
### Presence of Resistance Genes  
Analysis with Abricate and the Resfinder database revealed the presence of 124 RGs in the collection of _Enterococcus_ spp., conferring resistance to aminoglycos, macrolides, limosamides and streptogramines (MLS), drug and biocide resistance (efflux pumps) and tetracyclines (Figure 2). Less frequent types of resistance were those to trimethoprim, nucleosides and of efflux pumps conferring multi-drug resistance (MDR). _Enterococcus_ spp. \begin{table}
\begin{tabular}{l l c c c c c c c} \hline \hline \multirow{2}{*}{**Strain ID**} & **Genus \&** & \multicolumn{2}{c}{**Genome**} & \multicolumn{2}{c}{**GC**} & \multirow{2}{*}{**No of**} & \multirow{2}{*}{**N50 (Mb)**} & \multirow{2}{*}{**No of**} & \multirow{2}{*}{**Contamination**} & \multirow{2}{*}{**Completeness**} \\  & **Species** & **Size (Mb)** & & & & & & \\ \hline ent\_C22 & _E. faecium_ & 2.81 & 37.88 & 49 & 2.14 & 2951 & 3.6 & 97.2 \\ ent\_C25 & _E. faecium_ & 2.79 & 37.83 & 17 & 1.47 & 2832 & 4.6 & 95.4 \\ ent\_C28 & _E. faecalis_ & 2.95 & 37.42 & 18 & 2.86 & 2933 & 2.3 & 97.5 \\ ent\_C29 & _E. faecium_ & 2.77 & 37.86 & 13 & 1.64 & 2803 & 4.5 & 95.7 \\ ent\_C3 & _E. faecium_ & 2.76 & 37.88 & 8 & 2.57 & 2806 & 3.4 & 97.2 \\ ent\_C4 & _E. faecium_ & 2.79 & 37.86 & 11 & 1.20 & 2867 & 3.1 & 98.7 \\ ent\_C5 & _E. faecium_ & 2.75 & 37.9 & 6 & 1.48 & 2784 & 4.1 & 97.5 \\ ent\_C57 & _E. faecium_ & 2.75 & 37.9 & 4 & 2.41 & 2793 & 2.9 & 98.7 \\ ent\_C6 & _E. faecium_ & 2.79 & 37.87 & 7 & 2.59 & 2865 & 2.2 & 98.4 \\ ent\_C62 & _E. faecium_ & 2.85 & 37.83 & 38 & 2.42 & 2897 & 2.2 & 95.8 \\ ent\_C7 & _E. faecium_ & 2.79 & 37.87 & 12 & 1.63 & 2846 & 4.1 & 95.1 \\ ent\_C71 & _E. faecium_ & 2.76 & 37.87 & 15 & 2.08 & 2795 & 3.7 & 98.4 \\ ent\_C74 & _E. italicus_ & 2.39 & 39.36 & 29 & 1.43 & 2442 & 3.2 & 97.4 \\ ent\_C78 & _E. faecalis_ & 2.96 & 37.46 & 18 & 2.43 & 2918 & 2.8 & 98.0 \\ ent\_C8 & _E. faecium_ & 2.74 & 37.94 & 5 & 1.64 & 2798 & 3.2 & 98.9 \\ \hline \hline \end{tabular}
\begin{tabular}{l l} \hline \multicolumn{2}{c}{\# species} & \multicolumn{2}{c}{\# Cellular processes} \\ \multicolumn{2}{c}{\# Cell envelope} & \multicolumn{2}{c}{\# Regulation \& cell signaling} \\ \multicolumn{2}{c}{\# RNA processing} & \multicolumn{2}{c}{\# Miscellaneous} \\ \multicolumn{2}{c}{\# Metabolism} & \multicolumn{2}{c}{\# Stress response, defense \& virulence} \\ \multicolumn{2}{c}{\# Energy} & \multicolumn{2}{c}{\# DNA processing} \\ \multicolumn{2}{c}{\# Protein processing} \\ \hline \hline \end{tabular}
\end{table} 
Table 1: _Cont._  
Figure 1: Overview of the subsystems in _Enterococcus_ spp. genomes. isolates carried four AMR genes, on average, while all (n = 30) isolates carried at least one AMR gene. Details on the RG-content per isolate are presented in Supplementary File S1. The most prevalent types of resistance were those to drug and biocide resistance and MLS, with 90.0% of isolates carrying at least one related gene, followed closely by aminoglycoside resistance (86.7%). Within the MLS category the _msrC_ gene, encoding for an ABC efflux pump, was the most prevalent (71% of MLS genes), followed by _lsa_ efflux pump (18%) and the _ermB_ 23S methyltransferase (12%). The drug & biocide category was dominated by the _efmA_ group efflux pumps. Acquired, high-level aminoglycoside resistance is particularly problematic in clinical Enterococci isolates [44] and within this category we found _aac(6')-Im_ in 83.3% of isolates. This acetyltransferase alters the 6-prime amino group of the aminoglycoside molecule by transferring an acetyl group from acetyl-CoA to the aminoglycoside drug and is the most common resistance type to aminoglycosides used in microbial chemotherapy [45]. The _ant(6)_, _ant(9)_ nucleotidyltransferase and _aph(2'')_ Phosphotransferase were also found but were less frequent. Tetracycline resistance genes were present in one-third of _Enterococcus_ spp. More specifically, the _tetM_ and _tetL_ genes, encoding tetracycline ribosomal protection proteins, were present in eight and six strains, respectively.