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Dengler Haunreiter V, Tarnutzer A, Bär J, von Matt M, Hertegonne S, Andreoni F, Vulin C, Künzi L, Menzi C, Kiefer P, Christen P, Vorholt JA, Zinkernagel AS. C-di-AMP levels modulate Staphylococcus aureus cell wall thickness, response to oxidative stress, and antibiotic resistance and tolerance. Microbiol Spectr 2023; 11:e0278823. [PMID: 37948390 PMCID: PMC10715141 DOI: 10.1128/spectrum.02788-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 10/12/2023] [Indexed: 11/12/2023] Open
Abstract
IMPORTANCE Antibiotic resistance and tolerance are substantial healthcare-related problems, hampering effective treatment of bacterial infections. Mutations in the phosphodiesterase GdpP, which degrades cyclic di-3', 5'-adenosine monophosphate (c-di-AMP), have recently been associated with resistance to beta-lactam antibiotics in clinical Staphylococcus aureus isolates. In this study, we show that high c-di-AMP levels decreased the cell size and increased the cell wall thickness in S. aureus mutant strains. As a consequence, an increase in resistance to cell wall targeting antibiotics, such as oxacillin and fosfomycin as well as in tolerance to ceftaroline, a cephalosporine used to treat methicillin-resistant S. aureus infections, was observed. These findings underline the importance of investigating the role of c-di-AMP in the development of tolerance and resistance to antibiotics in order to optimize treatment in the clinical setting.
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Affiliation(s)
- Vanina Dengler Haunreiter
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Andrea Tarnutzer
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Julian Bär
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Manuela von Matt
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Sanne Hertegonne
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Federica Andreoni
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Clément Vulin
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Lisa Künzi
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Carmen Menzi
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Patrick Kiefer
- Department of Biology, Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Philipp Christen
- Department of Biology, Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Julia A. Vorholt
- Department of Biology, Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Annelies S. Zinkernagel
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
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Huemer M, Mairpady Shambat S, Hertegonne S, Bergada-Pijuan J, Chang CC, Pereira S, Gómez-Mejia A, Van Gestel L, Bär J, Vulin C, Pfammatter S, Stinear TP, Monk IR, Dworkin J, Zinkernagel AS. Serine-threonine phosphoregulation by PknB and Stp contributes to quiescence and antibiotic tolerance in Staphylococcus aureus. Sci Signal 2023; 16:eabj8194. [PMID: 36595572 DOI: 10.1126/scisignal.abj8194] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 12/06/2022] [Indexed: 01/05/2023]
Abstract
Staphylococcus aureus can cause infections that are often chronic and difficult to treat, even when the bacteria are not antibiotic resistant because most antibiotics act only on metabolically active cells. Subpopulations of persister cells are metabolically quiescent, a state associated with delayed growth, reduced protein synthesis, and increased tolerance to antibiotics. Serine-threonine kinases and phosphatases similar to those found in eukaryotes can fine-tune essential bacterial cellular processes, such as metabolism and stress signaling. We found that acid stress-mimicking conditions that S. aureus experiences in host tissues delayed growth, globally altered the serine and threonine phosphoproteome, and increased threonine phosphorylation of the activation loop of the serine-threonine protein kinase B (PknB). The deletion of stp, which encodes the only annotated functional serine-threonine phosphatase in S. aureus, increased the growth delay and phenotypic heterogeneity under different stress challenges, including growth in acidic conditions, the intracellular milieu of human cells, and abscesses in mice. This growth delay was associated with reduced protein translation and intracellular ATP concentrations and increased antibiotic tolerance. Using phosphopeptide enrichment and mass spectrometry-based proteomics, we identified targets of serine-threonine phosphorylation that may regulate bacterial growth and metabolism. Together, our findings highlight the importance of phosphoregulation in mediating bacterial quiescence and antibiotic tolerance and suggest that targeting PknB or Stp might offer a future therapeutic strategy to prevent persister formation during S. aureus infections.
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Affiliation(s)
- Markus Huemer
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Srikanth Mairpady Shambat
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Sanne Hertegonne
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Judith Bergada-Pijuan
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Chun-Chi Chang
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Sandro Pereira
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Alejandro Gómez-Mejia
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Lies Van Gestel
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Julian Bär
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Clément Vulin
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Sibylle Pfammatter
- Functional Genomics Center Zurich, ETH/University of Zurich, Zurich, Switzerland
| | - Timothy P Stinear
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Ian R Monk
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Jonathan Dworkin
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Annelies S Zinkernagel
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
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Schweizer TA, Hertegonne S, Vulin C, Zinkernagel AS, Mairpady Shambat S. Antibacterial Neutrophil Effector Response: Ex Vivo Quantification of Regulated Cell Death Associated with Extracellular Trap Release. Methods Mol Biol 2023; 2674:235-250. [PMID: 37258972 DOI: 10.1007/978-1-0716-3243-7_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Regulated cell death (RCD) and the concomitant release of extracellular traps by neutrophils (NETs) constitute an important antibacterial effector response. Usually, the dynamic processes of RCD and NETs release are assessed independently of each other by either unspecific or time-consuming methods. Here, we describe a flow cytometry-based high-throughput analysis method incorporating neutrophil RCD and NETs release with visual live-imaging conformation upon ex vivo bacterial challenge. This combined approach allows to quantify and closely follow the kinetics of the dynamic neutrophil effector response towards bacterial infection.
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Affiliation(s)
- Tiziano A Schweizer
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Sanne Hertegonne
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Clément Vulin
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Annelies S Zinkernagel
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Srikanth Mairpady Shambat
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich and University of Zurich, Zurich, Switzerland.
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Mairpady Shambat S, Gómez-Mejia A, Schweizer TA, Huemer M, Chang CC, Acevedo C, Bergada-Pijuan J, Vulin C, Hofmaenner DA, Scheier TC, Hertegonne S, Parietti E, Miroshnikova N, Wendel Garcia PD, Hilty MP, Buehler PK, Schuepbach RA, Brugger SD, Zinkernagel AS. Hyperinflammatory environment drives dysfunctional myeloid cell effector response to bacterial challenge in COVID-19. PLoS Pathog 2022; 18:e1010176. [PMID: 35007290 PMCID: PMC8782468 DOI: 10.1371/journal.ppat.1010176] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 01/21/2022] [Accepted: 12/06/2021] [Indexed: 02/06/2023] Open
Abstract
COVID-19 displays diverse disease severities and symptoms including acute systemic inflammation and hypercytokinemia, with subsequent dysregulation of immune cells. Bacterial superinfections in COVID-19 can further complicate the disease course and are associated with increased mortality. However, there is limited understanding of how SARS-CoV-2 pathogenesis and hypercytokinemia impede the innate immune function against bacterial superinfections. We assessed the influence of COVID-19 plasma hypercytokinemia on the functional responses of myeloid immune cells upon bacterial challenges from acute-phase COVID-19 patients and their corresponding recovery-phase. We show that a severe hypercytokinemia status in COVID-19 patients correlates with the development of bacterial superinfections. Neutrophils and monocytes derived from COVID-19 patients in their acute-phase showed an impaired intracellular microbicidal capacity upon bacterial challenges. The impaired microbicidal capacity was reflected by abrogated MPO and reduced NETs production in neutrophils along with reduced ROS production in both neutrophils and monocytes. Moreover, we observed a distinct pattern of cell surface receptor expression on both neutrophils and monocytes, in line with suppressed autocrine and paracrine cytokine signaling. This phenotype was characterized by a high expression of CD66b, CXCR4 and low expression of CXCR1, CXCR2 and CD15 in neutrophils and low expression of HLA-DR, CD86 and high expression of CD163 and CD11b in monocytes. Furthermore, the impaired antibacterial effector function was mediated by synergistic effect of the cytokines TNF-α, IFN-γ and IL-4. COVID-19 patients receiving dexamethasone showed a significant reduction of overall inflammatory markers in the plasma as well as exhibited an enhanced immune response towards bacterial challenge ex vivo. Finally, broad anti-inflammatory treatment was associated with a reduction in CRP, IL-6 levels as well as length of ICU stay and ventilation-days in critically ill COVID-19 patients. Our data provides insights into the transient functional dysregulation of myeloid immune cells against subsequent bacterial infections in COVID-19 patients and describe a beneficial role for the use of dexamethasone in these patients.
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Affiliation(s)
- Srikanth Mairpady Shambat
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Alejandro Gómez-Mejia
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Tiziano A. Schweizer
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Markus Huemer
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Chun-Chi Chang
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Claudio Acevedo
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Judith Bergada-Pijuan
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Clément Vulin
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Daniel A. Hofmaenner
- Institute of Intensive Care, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Thomas C. Scheier
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Sanne Hertegonne
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Elena Parietti
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Nataliya Miroshnikova
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Pedro D. Wendel Garcia
- Institute of Intensive Care, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Matthias P. Hilty
- Institute of Intensive Care, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Philipp Karl Buehler
- Institute of Intensive Care, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Reto A. Schuepbach
- Institute of Intensive Care, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Silvio D. Brugger
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Annelies S. Zinkernagel
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
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Schweizer TA, Mairpady Shambat S, Vulin C, Hoeller S, Acevedo C, Huemer M, Gomez‐Mejia A, Chang C, Baum J, Hertegonne S, Hitz E, Scheier TC, Hofmaenner DA, Buehler PK, Moch H, Schuepbach RA, Brugger SD, Zinkernagel AS. Blunted sFasL signalling exacerbates TNF-driven neutrophil necroptosis in critically ill COVID-19 patients. Clin Transl Immunology 2021; 10:e1357. [PMID: 34938538 PMCID: PMC8665925 DOI: 10.1002/cti2.1357] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 10/26/2021] [Accepted: 11/03/2021] [Indexed: 12/15/2022] Open
Abstract
OBJECTIVES Critically ill coronavirus disease 2019 (COVID-19) patients are characterised by a severely dysregulated cytokine profile and elevated neutrophil counts, impacting disease severity. However, it remains unclear how neutrophils contribute to pathophysiology during COVID-19. Here, we assessed the impact of the dysregulated cytokine profile on the regulated cell death (RCD) programme of neutrophils. METHODS Regulated cell death phenotype of neutrophils isolated from critically ill COVID-19 patients or healthy donors and stimulated with COVID-19 or healthy plasma ex vivo was assessed by flow cytometry, time-lapse microscopy and cytokine multiplex analysis. Immunohistochemistry of COVID-19 patients and control biopsies were performed to assess the in situ neutrophil RCD phenotype. Plasma cytokine levels of COVID-19 patients and healthy donors were measured by multiplex analysis. Clinical parameters were correlated to cytokine levels of COVID-19 patients. RESULTS COVID-19 plasma induced a necroptosis-sensitive neutrophil phenotype, characterised by cell lysis, elevated release of damage-associated molecular patterns (DAMPs), increased receptor-interacting serine/threonine-protein kinase (RIPK) 1 levels and mixed lineage kinase domain-like pseudokinase (MLKL) involvement. The occurrence of neutrophil necroptosis MLKL axis was further confirmed in COVID-19 thrombus and lung biopsies. Necroptosis was induced by the tumor necrosis factor receptor 1 (TNFRI)/TNF-α axis. Moreover, reduction of soluble Fas ligand (sFasL) levels in COVID-19 patients and hence decreased signalling to Fas directly increased RIPK1 levels, exacerbated TNF-driven necroptosis and correlated with disease severity, which was abolished in patients treated with glucocorticoids. CONCLUSION Our results suggest a novel role for sFasL signalling in the TNF-α-induced RCD programme in neutrophils during COVID-19 and a potential therapeutic target to curb inflammation and thus influence disease severity and outcome.
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Affiliation(s)
- Tiziano A Schweizer
- Department of Infectious Diseases and Hospital EpidemiologyUniversity Hospital of ZurichUniversity of ZurichZurichSwitzerland
| | - Srikanth Mairpady Shambat
- Department of Infectious Diseases and Hospital EpidemiologyUniversity Hospital of ZurichUniversity of ZurichZurichSwitzerland
| | - Clement Vulin
- Department of Infectious Diseases and Hospital EpidemiologyUniversity Hospital of ZurichUniversity of ZurichZurichSwitzerland
| | - Sylvia Hoeller
- Department of Pathology and Molecular PathologyUniversity Hospital of ZurichUniversity of ZurichZurichSwitzerland
| | - Claudio Acevedo
- Department of Infectious Diseases and Hospital EpidemiologyUniversity Hospital of ZurichUniversity of ZurichZurichSwitzerland
| | - Markus Huemer
- Department of Infectious Diseases and Hospital EpidemiologyUniversity Hospital of ZurichUniversity of ZurichZurichSwitzerland
| | - Alejandro Gomez‐Mejia
- Department of Infectious Diseases and Hospital EpidemiologyUniversity Hospital of ZurichUniversity of ZurichZurichSwitzerland
| | - Chun‐Chi Chang
- Department of Infectious Diseases and Hospital EpidemiologyUniversity Hospital of ZurichUniversity of ZurichZurichSwitzerland
| | - Jeruscha Baum
- Department of Infectious Diseases and Hospital EpidemiologyUniversity Hospital of ZurichUniversity of ZurichZurichSwitzerland
| | - Sanne Hertegonne
- Department of Infectious Diseases and Hospital EpidemiologyUniversity Hospital of ZurichUniversity of ZurichZurichSwitzerland
| | - Eva Hitz
- Department of Infectious Diseases and Hospital EpidemiologyUniversity Hospital of ZurichUniversity of ZurichZurichSwitzerland
| | - Thomas C Scheier
- Department of Infectious Diseases and Hospital EpidemiologyUniversity Hospital of ZurichUniversity of ZurichZurichSwitzerland
| | - Daniel A Hofmaenner
- Institute for Intensive Care MedicineUniversity Hospital of ZurichUniversity of ZurichZurichSwitzerland
| | - Philipp K Buehler
- Institute for Intensive Care MedicineUniversity Hospital of ZurichUniversity of ZurichZurichSwitzerland
| | - Holger Moch
- Department of Pathology and Molecular PathologyUniversity Hospital of ZurichUniversity of ZurichZurichSwitzerland
| | - Reto A Schuepbach
- Institute for Intensive Care MedicineUniversity Hospital of ZurichUniversity of ZurichZurichSwitzerland
| | - Silvio D Brugger
- Department of Infectious Diseases and Hospital EpidemiologyUniversity Hospital of ZurichUniversity of ZurichZurichSwitzerland
| | - Annelies S Zinkernagel
- Department of Infectious Diseases and Hospital EpidemiologyUniversity Hospital of ZurichUniversity of ZurichZurichSwitzerland
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