## 3 Results
### Phylogenetic Analysis and Comparative Genomics  
In silico typing revealed the genetic background of the sequenced _E. faccum_ (n = 24) and _E. faecalis_ (n = 3) isolates by assignment to six and three unique sequence types (STs), respectively while for the other species (_E. durans_ and _E. italicus_), no official MLST schemas exist ([[https://pubmlst.org/](https://pubmlst.org/)]([https://pubmlst.org/](https://pubmlst.org/)) accessed on 11 May 2022). For _E. faccum_, most of the isolates (nine in 24) belonged to ST2184, followed by ST545 (n = 5), ST1956 and ST113 (n = 4, each). The three _E. faecalis_ isolates were assigned to ST19, ST205, and ST206. _E. faccum_ ST113 and _E. faecalis_ ST205 have been previously reported to be associated with infections [4,49]. Given that _E. faccum_ was the dominant species isolated from the dairy products of this study, a comparative genomic analysis was conducted to gain deeper insights into the genetic relationships of the _E. faccum_ isolated from various sources. More specifically, genomes of human (n = 81), dairy product (n = 61), chicken (n = 8), pig (n = 7), dog (n = 2), and soy (n = 1) origin as well as one isolate of _M. primigenius_ were parsed from the NCBI database [50] (Figure 4), creating an extension of the dataset initially reported by [PERSON] et al. [51]. All animal isolates were retrieved from the gastrointestinal (GI) tract while those of human origin were isolated from bloodstream infections (n = 39/81), urinary tract infections (n = 9/81) and the GI tract (33 in 81) (Figure 4). The pangenome of the _E. faccum_ isolates (i.e., the total number of unique gene families found) consisted of 15,951 gene families. The core-genome comprised 1327 genes, which is equivalent of 46.6% of the average number of CDSs in each genome, meaning that more than half of the protein-coding genes in each genome had an accessory role. The phylogenetic tree and the hierarchical clusters (n = 16) calculated with hierBAPS revealed the genomic relatedness of the analyzed _E. faccum_ isolates. Isolates clustered primarily according to their isolation origin (Figure 4). The bottom-left part of the tree predominantly comprised clusters that contained mainly to human-origin isolates, retrieved from the GI tract (human-GI) or from clinical cases (human-clinical). Conversely, at the right part of the tree, we found the dairy-origin isolates, including all isolates of this study, organized in six closely related clusters. This arrangement was disrupted by a few isolates from other sources, including three from human GI (Figure 4). Lastly, the top-left of the tree contained isolate clusters with a mixture of human (GI and clinical), dairy, chicken, and pig origin. Nevertheless, the dominant, origin-driven pattern of _E. faccum_ clustering observed in our extensive analysis corroborates the findings from previous studies [8,51,52], which also showed that human pathogenic isolates are generally phylogenetically distinct from environmental and food-related isolates. One additional finding of our analysis, which was visually observable in the annotated tree, was the difference in terms of total RG-content between different origins, with human and pig isolates showing higher numbers of resistance determinants and strong association with vancomycin-resistance genes (Figure 4). We confirmed this pattern statistically with Scoary and found significant differences in the total number of RGs and VGs between source of isolation. More specifically, dairy isolates carried the lowest number of RGs (Figure 4) and their RG content was significantly different (\(p<0.05\)) from all other sources except for dog isolates. Moreover, the RG analysis showed that the _van_-like resistance and regulator genes, which respectively encode and regulate resistance to vancomycin and other glycoptides, were predominant in human _E. faccum_ isolates and even more abundant in isolates from human bloodstream infections and UTIs (Figure 4).