## 3 Results and Discussion
### Search for Resistance and Virulence Genes in Reference Genomes
Resistance mechanisms are restricted to the functions of efflux and alteration of the target of action, the latter being expressed from the _arnA_ gene in the three species. Regarding the efflux function, a similarity was observed between the _Mex_ and _Opr_ family genes. These families of efflux pumps (_Mex_ and _Opr_, mainly) function in three states: Loose (L), Tight (T), and Open (O). Thus, they confer resistance to antibiotics through the electrochemical potential of protons [112]. A single gene found in this group, _arnA_, was correlated with the mechanism of antibiotic change, mainly the type of peptides (polymyxin). In a recent study using in vivo methodology, isolated species of _Staphylococcus_ were present in sheep's cheese produced with raw milk, with resistance to multiple antimicrobial agents, 46% of which were multi-resistant. Furthermore, most isolates had at least one resistance gene in their genome [29]. In this in silico analysis, 16 resistance genes were detected in 3 species of _Staphylococcus_ (_S. equorum_ FDARGOS 1068, _S. simulans_ IVB6189, and _S. chromogenes_ 22). The genes _arlR_, _mgrA_, _norA_, _Saur_norA_, _norC_, _sepA_, _tet(38)_ (efflux)_, _dfC_ (substitution of the antibiotic target), _mpH_C (inactivation), and _msrA_ (protection) are resistant to 7 classes of antibiotics (fluoroquinoline, cephalospor, tetracycline, diaminopyrimidine, macrolide, streptogramin B, and streptogramin). The _mpH_C and _msrA_ genes were only identified in the species _S. equorum_ FDARGOS 1068. The species _A. jolnsonii_ ANC3681, _A. ursingii_ NIPH706, _A. otitis_ ATCC51267, _B. thermosphata_ D337, _F. necrohorum_ subsp. _Funduliforme_ F1260, and _T. pyogenes_ TP6375 did not present resistance genes in the analysis and, therefore, are not represented in Figure 10.  
With the clustermap of virulence genes, we can observe the correlation between the number of genes and their presence/absence in the reference genomes (Figure 10B). In general, 12 types of virulence mechanisms were identified in 247 different genes in the analysis (totaling 522 genes identified) with functions of adherence (n = 86), antimicrobial activity (n = 4), biofilm formation (n = 40), effector delivery system (n = 93), exoenzyme (n = 1), exotoxins (n = 1), immune modulation (n = 81), invasion (n = 5), motility (n = 127), nutritional factor/metabolic (n = 56), regulation (n = 18), and stress survival (n = 10). According to Figure 10B, immune modulation and adherence processes were the main types found in the genomes of the BPP group. For immune modulation, the genes _ACICU_RS00400_, _ACICU_RS00475_, _ACICU_RS00500_, _galE_, _galF_, _galU_, _gmuA_/_lpcA_, _gndA_, _KPI_RS17355_, _KPI_RS17345_, _KPI_RS17340_, _KPI_RS17240_, _KPI_RS17225_, _kdsA_, _KPI_RS17280_, _lpsA_, _lpxB_, _lpxC_, _lpxD_, _lpxL_, _phpG_, _pgi_, _ftbA_, _rfbB_, _rfabT_, _rfaE_, _rfbD_, _rfbK1_, _ftvB_, _ugd_, and _twal_ were identified. For the adhesion process, the genes _fmA_, _fmB_, _fmD_, _fmE_, _fmF_, _fmG_, _fmH_, _fmD_, _pilB_, _pilC_, _pilF_, _pilG_, _pilH_, _pilP_, _pilP_, _pilP_, _pilP_, _pilQ_, _pilR_, _pilT_, _pilU_, _rpoS_, _strC_-_1/_strB_, _tufA_, _yagX_/_ccpX_, _yagW_/_ccpD_, _yagY_/_ccpB_, and _yagZ_/_ccpA_ were found.The process of immune modulation is considered one of the main types of virulence mechanisms used by microorganisms. Bacterial capsules and lipopolysaccharidesaccharides stand out in this type of mechanism. Bacterial capsules in the cell wall provide a niche for the microorganism, favoring its response to stress and survival over time. Lipopolysaccharide, part of the structure of the microbial wall, act as an immunological barrier, controlling the passage of antibiotics and contributing to cellular integrity [113]. The virulence mechanism correlated with adherence is considered a crucial process, which can facilitate the fixation and internalization of the microorganism in the host's epithelial cells, inducing several factors that can be apoptotic and lead to the death of host cells.