## 1 Introduction
### S. aureus in Biofilms and Resistance and Tolerance Mechanisms  
What inflames the bacterial antibiotic resistance or tolerance puzzle is the existence of biofilms in most chronic bacterial infections (i.e., medical implant- and wound-associated infections) [51; 53; 54; 55; 56]. S. _aureus_ is a key biofilm producer [1; 57; 58; 59], utilizing a system ofcell-to-cell communication called quorum sensing (QS). The chromosomal locus regulating QS in _S. aureus_ is called accessory gene regulator (_agr_), encoding the production of a diffusive distinct autoinducer molecule (indicating local cell density). This _agr_ quorum-sensing system plays a pivotal role in the pathogenicity of _S. aureus_[6; 60; 61] via coordinating the architecture, bacterial growth rates, species interactions, and virulence factors (toxin production and exoenzymes) of biofilms [6; 56; 62]. Biofilms are sessile microbial cell communities embedded in an extracellular polymeric substance, forming a matrix and exhibiting a sophisticated altered phenotype concerning bacterial physiology, metabolism, and gene transcription [8; 63; 64; 65; 66]. The extracellular polymeric substance (EPS) matrix adheres to periprosthetic tissue and surfaces of medical implants [1; 53; 63; 65; 67] and wounds [68; 69] or enables cell-cell adhesion and aggregation, forming mobile biofilms (flocs) without substrate [56; 70; 71], as shown in Figure 1. The matrix is composed of bacterial secreted polymers, e.g., exopolysaccharides, lipids, proteins, and extracellular deoxyribonucle acid (e-DNA), arming bacteria with intricate three-dimensional (3D) structure and excessive resistance or tolerance against antibiotics. The e-DNA could prompt the expression of resistance genes and the horizontal gene transfer between bacterial cells within biofilms [1; 72; 73; 74]. With the advent of emergent resistant bacteria and their tolerant biofilms, there is a need to explicitly elaborate on the difference between'resistance' and 'tolerance'. The term'resistance' refers to a permanent genetic change in bacteria that could be acquired through point mutation or horizontal gene transfer. As a result of this permanent genetic alteration, the resistance continues with bacterial cells in biofilms and their dispersed planktonic cells. Moreover, resistance paves the way for bacteria not only to survive in the presence of drugs but also to replicate and is tied to the minimum inhibitory concentration (MIC), as a higher MIC confers a higher resistance. Comparatively, 'tolerance' describes a transient characteristic feature enabling bacterial cells' survival in the presence of antibiotics (e.g., the complex lag phase of bacterial growth as a transient non-replicative evolvable phenotype tolerates antibiotics [75]) without an increase in the MIC. Tolerance is mostly linked to bacterial cells growing in the biofilm phenotype. Therefore, tolerance could be lost when biofilms are dispersed into their planktonic cells [51; 56; 70; 71; 73; 76]. The biofilm matrix structure contains open fluid channels, resembling the circulatory system and delivering nutrients to deeply embedded bacterial cells [62; 63; 77]. The matrix also provides local heterogeneous, compartmentalized chemical and physical microenvironments that resemble the heterogenous compartmentalized tumor ECM [70; 78]. The biofilm matrix structures are seen in Figure 2. Biofilm formation could be classified into four consecutive steps (as formed in Figure 1 on the hip implant): (i) initial bacterial adhesion to tissue or surfaces (starting as reversible adhesion; then, cells undergo species-specific behavior and secrete exopolysaccharides, changing to irreversible adhesion) via cell-surface-associated adhesins. (ii) Initial biofilm formation, where microcolonies and fluid channel architecture are formed within the produced EPS. (iii) Biofilm maturation, where EPS develops into a 3D scaffold, facilitating the formation of heterogeneous chemical and physical microenvironments.