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

Type of publication Peer-reviewed
Publikationsform Original article (peer-reviewed)
Author Huemer Markus, Mairpady Shambat Srikanth, Bergada-Pijuan Judith, Söderholm Sandra, Boumasmoud Mathilde, Vulin Clément, Gómez-Mejia Alejandro, Antelo Varela Minia, Tripathi Vishwachi, Götschi Sandra, Marques Maggio Ewerton, Hasse Barbara, Brugger Silvio D., Bumann Dirk, Schuepbach Reto A., Zinkernagel Annelies S.,
Project Infectious Diseases Biobank Zurich
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Original article (peer-reviewed)

Journal Proceedings of the National Academy of Sciences
Volume (Issue) 118(7)
Page(s) e201492011 - e201492011
Title of proceedings Proceedings of the National Academy of Sciences
DOI 10.1073/pnas.2014920118


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.