Molecular reprogramming and phenotype switching in Staphylococcus aureus lead to high antibiotic persistence and affect therapy success

Abstract

Staphylococcus aureus causes invasive infections and easily acquires antibiotic resistance. Even antibiotic-susceptible S. aureus can survive antibiotic therapy and persist, requiring prolonged treatment and surgical interventions. These so-called persisters display an arrested-growth phenotype, tolerate high antibiotic concentrations, and are associated with chronic and recurrent infections. To characterize these persisters, we assessed S. aureus recovered directly from a patient suffering from a persistent infection. We show that host-mediated stress, including acidic pH, abscess environment, and antibiotic exposure promoted persister formation in vitro and in vivo. Multiomics analysis identified molecular changes in S. aureus in response to acid stress leading to an overall virulent population. However, further analysis of a persister-enriched population revealed major molecular reprogramming in persisters, including down-regulation of virulence and cell division and up-regulation of ribosomal proteins, nucleotide-, and amino acid-metabolic pathways, suggesting their requirement to fuel and maintain the persister phenotype and highlighting that persisters are not completely metabolically inactive. Additionally, decreased aconitase activity and ATP levels and accumulation of insoluble proteins involved in transcription, translation, and energy production correlated with persistence in S. aureus, underpinning the molecular mechanisms that drive the persister phenotype. Upon regrowth, these persisters regained their virulence potential and metabolically active phenotype, including reduction of insoluble proteins, exhibiting a reversible state, crucial for recurrent infections. We further show that a targeted antipersister combination therapy using retinoid derivatives and antibiotics significantly reduced lag-phase heterogeneity and persisters in a murine infection model. Our results provide molecular insights into persisters and help explain why persistent S. aureus infections are so difficult to treat.

Bacterial persisters are a stochastically formed subpopulation of low-energy cells

“…In agreement with this, antibiotic efficacy positively correlates with metabolic activity in the cell [44,45]. Interestingly, it has also been shown that in the infection environment, interactions of S. aureus with other pathogens or with the host immune system can both impact its metabolic activity and induce a decrease in ATP level and an increase in antibiotic tolerance [46][47][48].…”

Ser/Thr phospho-regulation by PknB and Stp mediates bacterial quiescence and antibiotic persistence inStaphylococcus aureus

“…We recently found elevated levels of proteins involved in protein, nucleotide and aminoacid biosynthesis in a persister-enriched population of a clinical isolate of S. aureus that was isolated from a difficult-to-treat infection, 38 . Higher levels of PknB might lead to increased phosphorylation levels that in turn can reduce translation, alter cell wall synthesis and can lead to decreased intracellular ATP levels.…”

“…4A). Here, we used the less cytotoxic Cowan I to induce abscess formation and pus production in the mice as described previously 13,38 . Five days post-infection, mice were sacrificed, abscess size measured, and the pus harvested for further analysis.…”

Shooting yourself in the foot: How immune cells induce antibiotic tolerance in microbial pathogens

“…MAU : Pleasecheckwhethertheeditstothesentence acrophages induce antibiotic tolerance of internalized S. aureus through reactive oxygen species (ROS) that cause collapse of the tricarboxylic acid (TAU : PleasenotethatTCAhasbeendefinedastricarboxylicacidinthesentenceMacropha CA) cycle an entrance to a low ATP state [6]. Additionally, activation of the stringent response has also been shown to contribute to S. aureus intracellular tolerance [7], while neutrophil interaction as well as acid stress have also been shown to induce antibiotic tolerance in S. aureus abscess patient isolates [21]. In Salmonella Typhimurium, antibiotic-tolerant persister subpopulations are induced intracellularly through acid stress, nutritional deprivation, and the activation of toxin-antitoxin modules [9].…”