## Stress Responses and Persistence: The SOS Response  
The stringent response is not the sole stressor implicated in persistence development. Under biofilm conditions, stringent response activation increases basal expression of the SOS DNA repair regulon [97]. The SOS response is a highly conserved gene pathway that allows cells to survive genotoxic stressors, including \(\beta\)-lactam and fluoroquinolone antibiotics, and is well-known to be involved in persistence development in a variety of clinically relevant species [12; 29].  
A pivotal study by [PERSON] et al. challenged the previous contention that persister formation was only due to stochastic dormancy [29]. Instead, they proposed that persister cells are actively able to survive antibiotic stress via an increase in efficient drug efflux and DNA lesion repair via either transient overexpression or environmental activation of the SOS pathway [29]. Experimental knockdown of _recA_ and _recBC_, key players in the SOS response, caused complete ablation of persister formation after 6 hours of antibiotic exposure, suggesting that persisters experienced and were unable to mitigate antibiotic-induced DNA lesions. _E. coli_ strains that constitutively express the SOS regulon had a 20-fold increase in persister formation upon ciprofloxacin challenge. When challenged with mitomycin C, these mutants demonstrated a 180-fold increased induction of persistence, suggesting a functional SOS response is necessary for antibiotic persistence [29]. [PERSON] et al. expanded upon this work and found that SOS induction is necessary for ofloxacin tolerance, and proposed that SOS induction might lead to persistence development in biofilms [59]. Their findings support the complex interconnectedness between metabolic flux systems, the stringent response, and SOS repair pathways in promoting persistence development.  
A major trigger for persistence development is exposure to sub-inhibitory concentrations of antibiotics, which mimics in vivo drug accumulation after clinical administration [1]. Daily dosing of aminoglycos selects for almost complete persister enrichment in _Klebsiella pneumoniae_ and periodic daptomycin exposure leads to high persister enrichment in _S. aureus_[106]. When challenged to multi-antibiotic panels, _E. coli_ persister formation was enhanced by both ciprofloxacin and gentamicin treatment while _S. aureus_ persistence activity increased under ampicillin treatment. These findings suggest some interspecies variation or drug-specific variation in persistence mechanisms. Interestingly, ampicillin pretreatment increased the rate of cross-tolerance to non-related drug classes due to \(\beta\)-lactam activation of the SOS pathway in _S. aureus_[26]. SOS-deficient _E. coli_ strains failed to produce persisters during ciprofloxacin challenge but were able to produce gentamicin persisters since gentamicin does not directly cause DNA lesions [26]. This suggests that persisters are actively synthesizing DNA and are sensitive to perturbations in DNA integrity.  
Sub-inhibitory drug concentrations are of high clinical relevance. Realistically, serum antibiotic levels are only at inhibitory concentrations for a short portion of the regimen [107]. As a result, bacteria spend most therapeutic time at sub-inhibitory concentrations while inside a host, and this is drastically exaggerated in biofilm antibiotic exposure. Interestingly, it is this transient concentration that elicits and selects for tolerance [108]. However, insufficient data is available regarding bacterial responses during these transient, sub-therapeutic concentrations. Significant insight can be gained by profiling physiological and transcriptional responses of pathogens isolated from the site of infection as the effective antibiotic concentration is reduced by host metabolism.