Impact of the pentose phosphate pathway on metabolism and pathogenesis of Staphylococcus aureus.

Staphylococcus aureus is an important pathogen that leads to significant disease through multiple routes of infection. We recently published a transposon sequencing (Tn-seq) screen in a mouse acute pneumonia model and identified a hypothetical gene (SAUSA300_1902, pgl) with similarity to a lactonase of Escherichia coli involved in the pentose phosphate pathway (PPP) that was conditionally essential. Limited studies have investigated the role of the PPP in physiology and pathogenesis of S. aureus. We show here that mutation of pgl significantly impacts ATP levels and respiration. RNA-seq analysis of the pgl mutant and parent strains identified compensatory changes in gene expression for glucose and gluconate as well as reductions in the pyrimidine biosynthesis locus. These differences were also evident through unbiased metabolomics studies and 13C labeling experiments that showed mutation of pgl led to reductions in pyrimidine metabolism including decreases in ribose-5P, UMP and GMP. These nucleotide reductions impacted the amount of extracellular DNA in biofilms and reduced biofilm formation. Mutation also limited the capacity of the strain to resist oxidant damage induced by hydrogen peroxide and paraquat and subsequent intracellular survival inside macrophages. Changes in wall teichoic acid impacted susceptibility to hydrogen peroxide. We demonstrated the importance of these changes on virulence in three different models of infection, covering respiratory, skin and septicemia, demonstrating the need for proper PPP function in all models. This work demonstrates the multifaceted role metabolism can play in multiple aspects of S. aureus pathogenesis.

Copper ions inhibit pentose phosphate pathway function in Staphylococcus aureus.

To gain a better insight of how Copper (Cu) ions toxify cells, metabolomic analyses were performed in S. aureus strains that lacks the described Cu ion detoxification systems (ΔcopBL ΔcopAZ; cop-). Exposure of the cop- strain to Cu(II) resulted in an increase in the concentrations of metabolites utilized to synthesize phosphoribosyl diphosphate (PRPP). PRPP is created using the enzyme phosphoribosylpyrophosphate synthetase (Prs) which catalyzes the interconversion of ATP and ribose 5-phosphate to PRPP and AMP. Supplementing growth medium with metabolites requiring PRPP for synthesis improved growth in the presence of Cu(II). A suppressor screen revealed that a strain with a lesion in the gene coding adenine phosphoribosyltransferase (apt) was more resistant to Cu. Apt catalyzes the conversion of adenine with PRPP to AMP. The apt mutant had an increased pool of adenine suggesting that the PRPP pool was being redirected. Over-production of apt, or alternate enzymes that utilize PRPP, increased sensitivity to Cu(II). Increasing or decreasing expression of prs resulted in decreased and increased sensitivity to growth in the presence of Cu(II), respectively. We demonstrate that Prs is inhibited by Cu ions in vivo and in vitro and that treatment of cells with Cu(II) results in decreased PRPP levels. Lastly, we establish that S. aureus that lacks the ability to remove Cu ions from the cytosol is defective in colonizing the airway in a murine model of acute pneumonia, as well as the skin. The data presented are consistent with a model wherein Cu ions inhibits pentose phosphate pathway function and are used by the immune system to prevent S. aureus infections.

Innate Immune Signaling Activated by MDR Bacteria in the Airway.

Health care-associated bacterial pneumonias due to multiple-drug resistant (MDR) pathogens are an important public health problem and are major causes of morbidity and mortality worldwide. In addition to antimicrobial resistance, these organisms have adapted to the milieu of the human airway and have acquired resistance to the innate immune clearance mechanisms that normally prevent pneumonia. Given the limited efficacy of antibiotics, bacterial clearance from the airway requires an effective immune response. Understanding how specific airway pathogens initiate and regulate innate immune signaling, and whether this response is excessive, leading to host-induced pathology may guide future immunomodulatory therapy. We will focus on three of the most important causes of health care-associated pneumonia, Staphylococcus aureus, Pseudomonas aeruginosa, and Klebsiella pneumoniae, and review the mechanisms through which an inappropriate or damaging innate immune response is stimulated, as well as describe how airway pathogens cause persistent infection by evading immune activation.

Type III IFNs: Beyond antiviral protection.

The unexpected discovery of a novel family of antiviral mediators, type III IFNs or IFN-λs, challenged the widely accepted primacy of type I IFNs in antiviral immunity, and it is now well recognized that the IFN-λ-based antiviral system plays a major role in antiviral protection of epithelial barriers. The recent characterization of previously unknown IFN-λ-mediated activities has prompted further reassessment of the role of type I IFNs in innate and adaptive immune and inflammatory responses. Since type I and type III IFNs are co-produced in response to a variety of stimuli, it is likely that many physiological processes are simultaneously and coordinately regulated by these cytokines in pathological conditions, and likely at steady state, as baseline expression of both IFN types is maintained by microbiota. In this review, we discuss emerging differences in the production and signaling of type I and type III IFNs, and summarize results of recent studies describing the involvement of type III IFNs in anti-bacterial and anti-fungal, as well as antiviral, defenses.

Trained immunity and host-pathogen interactions.

Infectious diseases are a leading cause of death worldwide with over 8 million fatalities accounted for in 2016. Solicitation of host immune defenses by vaccination is the treatment of choice to prevent these infections. It has long been thought that vaccine immunity was solely mediated by the adaptive immune system. However, over the past decade, numerous studies have shown that innate immune cells can also retain memory of these encounters. This process, called innate immune memory, is mediated by metabolic and epigenetic changes that make cells either hyperresponsive (trained immunity) or hyporesponsive (tolerance) to subsequent challenges. In this review, we discuss the concepts of trained immunity and tolerance in the context of host-pathogen interactions.

The ClpXP Protease Contributes to Staphylococcus aureus Pneumonia.

Staphylococcus aureus is a leading cause of pneumonia. We show here that the ClpXP protease involved in protein turnover is important for pathogenesis in a murine model of acute pneumonia. Staphylococcus aureus lacking this protease is attenuated in vivo, being rapidly cleared from the airway and leading to decreased immune cell influx and inflammation. Characterization of defined mutations in vitro identified defects in intracellular survival and protection against neutrophil killing. Our results further expand on what is known about ClpXP in the pathogenesis of S. aureus to include the respiratory tract.

Differential Induction of Type I and III Interferons by Staphylococcus aureus.

Staphylococcus aureus is a leading cause of bacterial pneumonia, and we have shown previously that type I interferon (IFN) contributes to the pathogenesis of this disease. In this study, we screened 75 S. aureus strains for their ability to induce type I and III IFN. Both cytokine pathways were differentially stimulated by various S. aureus strains independently of their isolation sites or methicillin resistance profiles. These induction patterns persisted over time, and type I and III IFN generation differentially correlated with tumor necrosis factor alpha production. Investigation of one isolate, strain 126, showed a significant defect in type I IFN induction that persisted over several time points. The lack of induction was not due to differential phagocytosis, subcellular location, or changes in endosomal acidification. A correlation between reduced type I IFN induction levels and decreased autolysis and lysostaphin sensitivity was found between strains. Strain 126 had a decreased rate of autolysis and increased resistance to lysostaphin degradation and host cell-mediated killing. This strain displayed decreased virulence in a murine model of acute pneumonia compared to USA300 (current epidemic strain and commonly used in research) and had reduced capacity to induce multiple cytokines. We observed this isolate to be a vancomycin-intermediate S. aureus (VISA) strain, and reduced Ifnb was observed with a defined mutation in walK that induces a VISA phenotype. Overall, this study demonstrates the heterogeneity of IFN induction by S. aureus and uncovered an interesting property of a VISA strain in its inability to induce type I IFN production.

Dual Gene Expression Analysis Identifies Factors Associated with Staphylococcus aureus Virulence in Diabetic Mice.

Staphylococcus aureus is a major human pathogen of the skin. The global burden of diabetes is high, with S. aureus being a major complication of diabetic wound infections. We investigated how the diabetic environment influences S. aureus skin infection and observed an increased susceptibility to infection in mouse models of both type I and type II diabetes. A dual gene expression approach was taken to investigate transcriptional alterations in both the host and bacterium after infection. While analysis of the host response revealed only minor changes between infected control and diabetic mice, we observed that S. aureus isolated from diabetic mice had significant increases in the levels of genes associated with translation and posttranslational modification and chaperones and reductions in the levels of genes associated with amino acid transport and metabolism. One family of genes upregulated in S. aureus isolated from diabetic lesions encoded the Clp proteases, associated with the misfolded protein response. The Clp proteases were found to be partially glucose regulated as well as influencing the hemolytic activity of S. aureus Strains lacking the Clp proteases ClpX, ClpC, and ClpP were significantly attenuated in our animal model of skin infection, with significant reductions observed in dermonecrosis and bacterial burden. In particular, mutations in clpP and clpX were significantly attenuated and remained attenuated in both normal and diabetic mice. Our data suggest that the diabetic environment also causes changes to occur in invading pathogens, and one of these virulence determinants is the Clp protease system.

IL-1ß activation in response to Staphylococcus aureus lung infection requires inflammasome-dependent and independent mechanisms.

Maintaining balanced levels of IL-1ß is extremely important to avoid host tissue damage during infection. Our goal was to understand the mechanisms behind the reduced pathology and decreased bacterial burdens in Ifnlr1-/- mice during lung infection with Staphylococcus aureus. Intranasal infection of Ifnlr1-/- mice with S. aureus led to significantly improved bacterial clearance, survival and decrease of proinflammatory cytokines in the airway including IL-1ß. Ifnlr1-/- mice treated with recombinant IL-1ß displayed increased bacterial burdens in the airway and lung. IL-1ß levels in neutrophils from Ifnlr1-/- infected mice lungs were decreased when compared to neutrophils from WT mice. Mice lacking NLRP3 and caspase-1 had reduced IL-1ß levels 4 h after infection, due to reductions or absence of active caspase-1 respectively, but levels at 24 h were comparable to WT infected mice. Ifnlr1-/- infected mice had decreases in both active caspase-1 and neutrophil elastase indicating an important role for the neutrophil serine protease in IL-1ß processing. By inhibiting neutrophil elastase, we were able to decrease IL-1ß levels by 39% in Nlrp3-/- infected mice when compared to WT mice. These results highlight the crucial role of both proteases in IL-1ß processing, via inflammasome-dependent and -independent mechanisms.

Inducible Costimulator Contributes to Methicillin-Resistant Staphylococcus aureus Pneumonia.

Staphylococcus aureus is a major cause of both community- and healthcare-acquired pneumonias. Inducible costimulator (ICOS) is part of the CD28 family of proteins and is a target for immune checkpoint therapy. We found ICOS highly expressed on activated CD4 cells in response to S. aureus. In the absence of ICOS, mice had improved survival in a pneumonia model with the methicillin-resistant Staphylococcus aureus (MRSA) strain USA300 and significant reductions in bacterial burden in a nonlethal acute pneumonia model. Infected Icos-/- mice had major reductions in several proinflammatory cytokines, neutrophils, inflammatory monocytes, and eosinophils compared to infected wild-type mice, while there was improved expression of CD11c and macrophage receptor with collagenous structure on the surface of alveolar macrophages. Early during infection infected Icos-/- mice had increased numbers of alveolar macrophages and expression of several surface markers on alveolar macrophages and neutrophils. ICOS signaling also contributed to the pathogenesis of the airway pathogens Klebsiella pneumoniae, Pseudomonas aeruginosa, and Streptococcus pneumoniae, and neutralizing antibody to ICOS led to improved clearance of S. aureus from the airway. Our results indicate that ICOS plays a significant role in orchestrating the innate immune response to S. aureus and other airway pathogens, and could be a potential immunomodulatory target to attenuate S. aureus-related immunopathology.

CD80/CD86 signaling contributes to the proinflammatory response of Staphylococcus aureus in the airway.

It was posited that the initial host response to Staphylococcus aureus is a contributing factor in the pathogenesis of acute pneumonia. Having previously observed that T cells play a negative role in the pathogenesis of acute pneumonia to S. aureus the contribution of the CD80/CD86 pathway in pathogenesis was investigated. Mice lacking CD80 and CD86 had significantly improved survival in a mouse model of acute S. aureus pneumonia. This was accompanied by significant reductions in several proinflammatory cytokines, including TNF, MIP-2, IL-1ß, IL-17 and IL-6, as well as increased numbers of viable alveolar macrophages. Early during infection reductions in cytokine production were evident and cytokine production in response to S. aureus in bone marrow derived macrophages showed decreases in TNF, KC, IL-1α and GM-CSF. Our data suggest that CD80/CD86 signaling plays a significant role in the initial inflammatory response to S. aureus in the airway and could be a potential acute target to reduce the initial inflammatory insult.

Impact of Type I and III Interferons on Respiratory Superinfections Due to Multidrug-Resistant Pathogens.

The increased morbidity and mortality associated with bacterial pneumonias that are acquired following influenza infection are well appreciated by clinicians. One of the major components of the immune response to influenza is the induction of the types I and III interferon cascades, which encompasses the activation of over 300 genes. The immunological consequences of IFN activation, while important for viral clearance, modify the host proinflammatory responses through effects on the inflammasome, Th17 signaling and recruitment of phagocytic cells. IFN signaling affects both susceptibility to subsequent Streptococcus pneumoniae and Staphylococcus aureus infection as well as the intensity of the immune responses associated with pulmonary damage. Appreciation for the effects of IFN activation on anti-bacterial pulmonary defense mechanisms should help to inform therapeutic strategies in an ICU setting.

Humanized Mice Exhibit Increased Susceptibility to Staphylococcus aureus Pneumonia.

Staphylococcus aureus is a highly successful human pathogen that has evolved in response to human immune pressure. The common USA300 methicillin-resistant S. aureus (MRSA) strains express a number of toxins, such as Panton-Valentine leukocidin and LukAB, that have specificity for human receptors. Using nonobese diabetic (NOD)-scid IL2Rγnull (NSG) mice reconstituted with a human hematopoietic system, we were able to discriminate the roles of these toxins in the pathogenesis of pneumonia. We demonstrate that expression of human immune cells confers increased severity of USA300 infection. The expression of PVL but not LukAB resulted in more-severe pulmonary infection by the wild-type strain (with a 30-fold increase in the number of colony-forming units/mL; P < .01) as compared to infection with the lukS/F-PV (Δpvl) mutant. Treatment of mice with anti-PVL antibody also enhanced bacterial clearance. We found significantly greater numbers (by 95%; P < .05) of macrophages in the airways of mice infected with the Δpvl mutant compared with those infected with the wild-type strain, as well as significantly greater expression of human tumor necrosis factor and interleukin 6 (84% and 51% respectively; P < .01). These results suggest that the development of humanized mice may provide a framework to assess the contribution of human-specific toxins and better explore the roles of specific components of the human immune system in protection from S. aureus infection.

Toxin-induced necroptosis is a major mechanism of Staphylococcus aureus lung damage.

Staphylococcus aureus USA300 strains cause a highly inflammatory necrotizing pneumonia. The virulence of this strain has been attributed to its expression of multiple toxins that have diverse targets including ADAM10, NLRP3 and CD11b. We demonstrate that induction of necroptosis through RIP1/RIP3/MLKL signaling is a major consequence of S. aureus toxin production. Cytotoxicity could be prevented by inhibiting either RIP1 or MLKL signaling and S. aureus mutants lacking agr, hla or Hla pore formation, lukAB or psms were deficient in inducing cell death in human and murine immune cells. Toxin-associated pore formation was essential, as cell death was blocked by exogenous K+ or dextran. MLKL inhibition also blocked caspase-1 and IL-1ß production, suggesting a link to the inflammasome. Rip3(-/-) mice exhibited significantly improved staphylococcal clearance and retained an alveolar macrophage population with CD200R and CD206 markers in the setting of acute infection, suggesting increased susceptibility of these leukocytes to necroptosis. The importance of this anti-inflammatory signaling was indicated by the correlation between improved outcome and significantly decreased expression of KC, IL-6, TNF, IL-1α and IL-1ß in infected mice. These findings indicate that toxin-induced necroptosis is a major cause of lung pathology in S. aureus pneumonia and suggest the possibility of targeting components of this signaling pathway as a therapeutic strategy.

Induction of type I interferon signaling determines the relative pathogenicity of Staphylococcus aureus strains.

The tremendous success of S. aureus as a human pathogen has been explained primarily by its array of virulence factors that enable the organism to evade host immunity. Perhaps equally important, but less well understood, is the importance of the intensity of the host response in determining the extent of pathology induced by S. aureus infection, particularly in the pathogenesis of pneumonia. We compared the pathogenesis of infection caused by two phylogenetically and epidemiologically distinct strains of S. aureus whose behavior in humans has been well characterized. Induction of the type I IFN cascade by strain 502A, due to a NOD2-IRF5 pathway, was the major factor in causing severe pneumonia and death in a murine model of pneumonia and was associated with autolysis and release of peptidogylcan. In contrast to USA300, 502A was readily eliminated from epithelial surfaces in vitro. Nonetheless, 502A caused significantly increased tissue damage due to the organisms that were able to invade systemically and trigger type I IFN responses, and this was ameliorated in Ifnar⁻/⁻ mice. The success of USA300 to cause invasive infection appears to depend upon its resistance to eradication from epithelial surfaces, but not production of specific toxins. Our studies illustrate the important and highly variable role of type I IFN signaling within a species and suggest that targeted immunomodulation of specific innate immune signaling cascades may be useful to prevent the excessive morbidity associated with S. aureus pneumonia.

CD4+ T cells promote the pathogenesis of Staphylococcus aureus pneumonia.

We postulated that the activation of proinflammatory signaling by methicillin-resistant Staphylococcus aureus (MRSA) strain USA300 is a major factor in the pathogenesis of severe pneumonia and a target for immunomodulation. Local activation of T cells in the lung was a conserved feature of multiple strains of S. aureus, in addition to USA300. The pattern of Vß chain activation was consistent with known superantigens, but deletion of SelX or SEK and SEQ was not sufficient to prevent T-cell activation, indicating the participation of multiple genes. Using Rag2(-/-), Cd4(-/-), and Cd28(-/-) mice, we observed significantly improved clearance of MRSA from the airways and decreased lung pathology, compared with findings for wild-type controls. The improved outcome correlated with decreased production of proinflammatory cytokines (tumor necrosis factor, KC, interleukin 6, and interleukin 1ß). Our data suggest that T-cell-mediated hypercytokinemia induced by infection with MRSA strain USA300 contributes to pathogenesis and may be a therapeutic target for improving outcomes of this common infection in a clinical setting.

Protection from the acquisition of Staphylococcus aureus nasal carriage by cross-reactive antibody to a pneumococcal dehydrogenase.

Nasal colonization by Staphylococcus aureus is the major risk factor for disease and transmission. Epidemiological studies have reported a reduced risk of S. aureus carriage in immunocompetent but not in immunocompromised children colonized by Streptococcus pneumoniae. We investigate the hypothesis that the immune response to pneumococcal colonization affects S. aureus colonization. We demonstrate that pneumococcal colonization in mice inhibits subsequent S. aureus acquisition in an antibody-dependent manner and elicits antibody that cross-reacts with S. aureus. We identify the staphylococcal target of cross-reactive antibody as 1-pyrroline-5-carboxylate dehydrogenase (P5CDH), and the homologous immunogen in S. pneumoniae as SP_1119, both of which are conserved dehydrogenases. These antigens are necessary and sufficient to inhibit the acquisition of S. aureus colonization in a mouse model. Our findings demonstrate that immune-mediated cross-reactivity between S. pneumoniae and S. aureus protects against S. aureus nasal acquisition and thus reveal a paradigm for identifying protective antigens against S. aureus.

Type I interferon response to extracellular bacteria in the airway epithelium.

The airway epithelium possesses many mechanisms to prevent bacterial infection. Not only does it provide a physical barrier, but it also acts as an extension of the immune system through the expression of innate immune receptors and corresponding effectors. One outcome of innate signaling by the epithelium is the production of type I interferons (IFNs), which have traditionally been associated with activation via viral and intracellular organisms. We discuss how three extracellular bacterial pathogens of the airway activate this intracellular signaling cascade through both surface components as well as via secretion systems, and the differing effects of type I IFN signaling on host defense of the respiratory tract.

Staphylococcus aureus induces type I IFN signaling in dendritic cells via TLR9.

The importance of type I IFN signaling in the innate immune response to viral and intracellular pathogens is well established, with an increasing literature implicating extracellular bacterial pathogens, including Staphylococcus aureus, in this signaling pathway. Airway epithelial cells and especially dendritic cells (DCs) contribute to the production of type I IFNs in the lung. We were interested in establishing how S. aureus activates the type I IFN cascade in DCs. In vitro studies confirmed the rapid uptake of S. aureus by DCs followed promptly by STAT1 phosphorylation and expression of IFN-ß. Signaling occurred using heat-killed organisms and in the absence of PVL and α-toxin. Consistent with the participation of endosomal and not cytosolic receptors, signaling was predominantly mediated by MyD88, TLR9, and IRF1 and blocked by cytochalasin D, dynasore, and chloroquine. To determine the role of TLR9 signaling in the pathogenesis of S. aureus pneumonia, we infected WT and Tlr9(-/-) mice with MRSA USA300. Tlr9(-/-) mice had significantly improved clearance of S. aureus from the airways and lung tissue. Ifnar(-/-) mice also had improved clearance. This enhanced clearance in Tlr9(-/-) mice was not due to differences in the numbers of recruited neutrophils into the airways, but instead correlated with decreased induction of TNF. Thus, we identified TLR9 as the critical receptor mediating the induction of type I IFN signaling in DCs in response to S. aureus, illustrating an additional mechanism through which S. aureus exploits innate immune signaling to facilitate infection.

Type III interferon drives pathogenicity to Staphylococcus aureus via the airway epithelium.

Type III interferon signaling contributes to the pathogenesis of the important human pathogen Staphylococcus aureus in the airway. Little is known of the cellular factors important in this response. Using Ifnl2-green fluorescent protein reporter mice combined with flow cytometry and cellular depletion strategies, we demonstrate that the alveolar macrophage is the primary producer of interferon lambda (IFN-λ) in response to S. aureus in the airway. Bone marrow chimeras showed reduced bacterial burden in IFN-λ receptor (IFNLR1)-deficient recipient mice, indicative that non-hematopoietic cells were important for pathogenesis, in addition to significant reductions in pulmonary inflammation. These observations were confirmed through the use of an airway epithelial-specific IFNLR knockout mouse. Our data suggest that upon entry to the airway, S. aureus activates alveolar macrophages to produce type III IFN that is subsequently sensed by the airway epithelium. Future steps will determine how signaling from the epithelium then exerts its influence on bacterial clearance. These results highlight the important, yet sometimes detrimental, role of type III IFN signaling during infection and the impact the airway epithelium plays during host-pathogen interactions.IMPORTANCEThe contribution of type III interferon signaling to the control of bacterial infections is largely unknown. We have previously demonstrated that it contributes to the pathogenesis of acute Staphylococcus aureus respiratory infection. In this report, we document the importance of two cell types that underpin this pathogenesis. We demonstrate that the alveolar macrophage is the cell that is responsible for the production of type III interferon and that this molecule is sensed by airway epithelial cells, which impacts both bacterial clearance and induction of inflammation. This work sheds light on the first two aspects of this important pathogenic cascade.