CD4 T cell antigens from Staphylococcus aureus Newman strain identified following immunization with heat-killed bacteria

Immunoinformatic prediction to identify Staphylococcus aureus peptides that bind to CD8+ T-cells as potential vaccine candidates

Background and Aim

Staphylococcus aureus, with its diverse virulence factors and immune response evasion mechanisms, presents a formidable challenge as an opportunistic pathogen. Developing an effective vaccine against S. aureus has proven elusive despite extensive efforts. Autologous Staphylococcus lysate (ASL) treatment has proven effective in triggering an immune response against bovine mastitis. Peptides that stimulate the immune response can be the subject of further research. The study aimed to use immunoinformatics tools to identify epitopes on S. aureus surface and secretory proteins that can bind to major histocompatibility complex class I (MHC I) and CD8+ T-cells. This method aids in discovering prospective vaccine candidates and elucidating the rationale behind ASL therapy's efficacy.

Materials and Methods

Proteins were identified using both literature search and the National Center for Biotechnology Information search engine Entrez. Self and non-self peptides, allergenicity predictions, epitope locations, and physicochemical characteristics were determined using sequence alignment, AllerTOP, SVMTriP, and Protein-Sol tools. Hex was employed for simulating the docking interactions between S. aureus proteins and the MHC I + CD8+ T-cells complex. The binding sites of S. aureus proteins were assessed using Computer Atlas of Surface Topography of Proteins (CASTp) while docked with MHC I and CD8+ T-cells.

Results

Nine potential S. aureus peptides and their corresponding epitopes were identified in this study, stimulating cytotoxic T-cell mediated immunity. The peptides were analyzed for similarity with self-antigens and allergenicity. 1d20, 2noj, 1n67, 1nu7, 1amx, and 2b71, non-self and stable, are potential elicitors of the cytotoxic T-cell response. The energy values from docking simulations of peptide-MHC I complexes with the CD8+ and T-cell receptor (TCR) indicate the stability and strength of the formed complexes. These peptides - 2noj, 1d20, 1n67, 2b71, 1nu7, 1yn3, 1amx, 2gi9, and 1edk - demonstrated robust MHC I binding, as evidenced by their low binding energies. Peptide 2gi9 exhibited the lowest energy value, followed by 2noj, 1nu7, 1n67, and 1d20, when docked with MHC I and CD8 + TCR, suggesting a highly stable complex. CASTp analysis indicated substantial binding pockets in the docked complexes, with peptide 1d20 showing the highest values for area and volume, suggesting its potential as an effective elicitor of immunological responses. These peptides - 2noj, 2gi9, 1d20, and 1n67 - stand out for vaccine development and T-cell activation against S. aureus.

Conclusion

This study sheds light on the design and development of S. aureus vaccines, highlighting the significance of employing computational methods in conjunction with experimental verification. The significance of T-cell responses in combating S. aureus infections is emphasized by this study. More experiments are needed to confirm the effectiveness of these vaccine candidates and discover their possible medical uses.

Screening for immune biomarkers associated with infection or protection against Ehrlichia ruminantium by RNA-sequencing analysis

Heartwater is one of the most economically important tick-borne fatal diseases of livestock. The disease is caused by the bacteria Ehrlichia ruminantium transmitted by Amblyomma ticks. Although there is evidence that interferon-gamma controls E. ruminantium growth and that cellular immune responses are protective, an effective recombinant vaccine for this disease is lacking. Analyses of markers associated with infection as well as protection will lead to a better understanding of the E. ruminantium immune response and corresponding pathways induced in sheep peripheral blood mononuclear cells (PBMC) will assist in development of such a vaccine. In this study, Biomarkers of infection (BMI) were identified as uniquely expressed genes during primary infection and biomarkers of protection (BMP) associated with immune to heartwater were identified post challenge. Sheep were experimentally infected and challenged with E. ruminantium infected ticks. The immune phenotypic and transcriptome profile of their PBMC were compared to their own naïve PBMC collected before infection. The study revealed 305 differentially expressed genes (DEGs) as BMI, of these 17 were upregulated at all three time-points investigated. These DEGs, form part of the bacterial invasion of epithelial cells Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway, and others detected from day 1 post infection and are considered predictive markers for early heartwater infection in ruminants. Similarly, a total of 332 DEGs were identified as BMP, of these 100 were upregulated and 75 were downregulated at all three time-points investigated. However, at D1PC most DEGs were downregulated (n = 1312) that correlated with a reduction in the % CD4 and CD8 T cells detected with flow cytometry. KEGG pathway analyses showed complete down regulation of T cell specific pathways possibly due to homing of immune cells to the site of infection after acquired immunity developed. At D4PC, expression levels of most of these downregulated genes increased and by D6PC they were upregulated. This indicates that the sampling time-point for biomarker analyses is important when results for acquired immune responses are inferred. This data identified DEGs that could be considered as biomarkers of protective immunity that can be used for identification of vaccine antigens and provides a strong foundation to further development of heartwater recombinant vaccines.

T cell activation and bacterial infection in skin wounds of recessive dystrophic epidermolysis bullosa patients

Recessive dystrophic epidermolysis bullosa (RDEB) patients develop poorly healing skin wounds that are frequently colonized with microbiota. Because T cells play an important role in clearing such pathogens, we aimed to define the status of adaptive T cell‐mediated immunity in RDEB wounds. Using a non‐invasive approach for sampling of wound‐associated constituents, we evaluated microbial contaminants in cellular fraction and exudates obtained from RDED wounds. Infectivity and intracellular trafficking of inactivated Staphylococcus aureus was accessed in RDEB keratinocytes. S. aureus and microbial antigen‐specific activation of RDEB wound‐derived T cells were investigated by fluorescence‐activated cell sorting‐based immune‐phenotyping and T‐cell functional assays. We found that RDEB wounds and epithelial cells are most frequently infected with Staphylococcus sp. and Pseudomonas sp. and that S. aureus essentially infects more RDEB keratinocytes and RDEB‐derived squamous cell carcinoma cells than keratinocytes from healthy donors. The RDEB wound‐associated T cells contain populations of CD4⁺ and CD8⁺ peripheral memory T cells that respond to soluble microbial antigens by proliferating and secreting interferon gamma (IFNγ). Moreover, CD8⁺ cytotoxic T lymphocytes recognize S. aureus‐infected RDEB keratinocytes and respond by producing interleukin‐2 (IL‐2) and IFNγ and degranulating and cytotoxically killing infected cells. Prolonged exposure of RDEB‐derived T cells to microbial antigens in vitro does not trigger PD‐1‐mediated T‐cell exhaustion but induces differentiation of the CD4^high population into CD4^highCD25⁺FoxP3⁺ regulatory T cells. Our data demonstrated that adaptive T cell‐mediated immunity could clear infected cells from wound sites, but these effects might be inhibited by PD‐1/Treg‐mediated immuno‐suppression in RDEB.

Virulence Gene Expression of Staphylococcus aureus in Human Skin

Staphylococcus aureus is the main cause of human skin and soft tissue infections. However, S. aureus pathogenicity within the skin is not fully characterized. Here, we implemented an S. aureus cutaneous infection model using human skin explants and performed a time-course infection to study the gene expression profile of a large panel of virulence-related factors of S. aureus USA300 LAC strain, by high-throughput RT-PCR. We pinpointed the genes that were differentially regulated by the bacteria in the skin tissues and identified 12 virulence factors that were upregulated at all time points assessed. Finally, using confocal microscopy, we show that the expression of alpha-hemolysin by S. aureus varies dependent on the skin niche and that the bacteria preferentially accumulates inside sweat glands and ducts. Taken together, our study gives insights about the pathogenic lifestyle of S. aureus within human skin tissues, which may contribute for the development of anti-S. aureus therapeutic strategies.

Identification of CD4+ T cell epitopes from Staphylococcus aureus secretome using immunoinformatic prediction and molecular docking

One major reason for the lack of clinical success of Staphylococcus aureus vaccine candidates is the inability of the antigens to develop a CD4⁺ T cell-mediated immune response. Hence, it is important to identify CD4⁺ T cell antigens from S. aureus. CD4⁺ T cells are activated following the presentation of epitopes derived from exogenous proteins on HLA class II molecules. Fifty-nine secretory proteins of S. aureus were analyzed computationally for the presence of HLA class II binding peptides. Fifteen-mer peptides were generated, and their binding to 26 HLA class II alleles was predicted. The structural feasibility of the peptides binding to HLA-II was studied using molecular docking. Of the 16,724 peptides generated, 6991 (41.8%) were predicted to bind to any one of the alleles with an IC₅₀ value below 50 nM. Comparative sequence analysis revealed that only 545 of the strong binding peptides are non-self in the human system. Approximately 50% of the binding peptides were monoallele-specific. Moreover, approximately 95% of the predicted strong binding non-self peptides interacted with the binding groove of at least one HLA class II molecule with a glide score better than -10 kcal/mol. On the basis of the analysis of the strength of binding, non-self presentation in the human host, propensity to bind to a higher number of alleles, and energetically favorable interactions with HLA molecules, a set of 11 CD4⁺ T cell epitopes that can be used as vaccine candidates was identified.

Immunogenicity and protective efficacy of recombinant alkaline shock protein 23 from Staphylococcus aureus in a murine model

The diversity and severity of infections caused and the rapid emergence of antibiotic resistance necessitates the development of a vaccine against Staphylococcus aureus. None of the antigens tried as vaccine candidates so far has been translated into a clinically viable vaccine. Recent research data suggest that antigens with the potential to activate cell mediated immunity along with humoral immunity would be the key to the development of a vaccine. Alkaline shock protein 23, a membrane-anchored protein involved in the stress response, has been identified as a CD4⁺ T cell antigen from S. aureus. In the present study, we report the evaluation of immunogenicity and protective efficacy of a recombinant alkaline shock protein 23 from S. aureus in mouse models. The gene coding for the protein was cloned and expressed in Escherichia coli, purified using immobilized metal iron affinity chromatography, sequence-confirmed using mass spectrometry and intraperitoneally administered to BALB/c mice. Serum titers of IgG, IgG1, and IgG2a in response to the protein were measured on post-immunization days 21, 35 and 42 using indirect ELISA and compared to control mice injected with PBS. Our results showed that the protein induced significantly higher (p < 0.01) antibody responses in immunized mice compared to the control mice. The mean serum antibody titers of IgG, IgG1 and IgG2a three weeks after the last immunization were found to be 25600, 25600 and 12800 respectively. Moreover, we found that immunization with Asp23 protected mice from a lethal dose of S. aureus strain USA300.

Adaptive immune response to lipoproteins of Staphylococcus aureus in healthy subjects

Staphylococcus aureus is a frequent commensal but also a dangerous pathogen, causing many forms of infection ranging from mild to life‐threatening conditions. Among its virulence factors are lipoproteins, which are anchored in the bacterial cell membrane. Lipoproteins perform various functions in colonization, immune evasion, and immunomodulation. These proteins are potent activators of innate immune receptors termed Toll‐like receptors 2 and 6. This study addressed the specific B‐cell and T‐cell responses directed to lipoproteins in human S. aureus carriers and non‐carriers. 2D immune proteomics and ELISA approaches revealed that titers of antibodies (IgG) binding to S. aureus lipoproteins were very low. Proliferation assays and cytokine profiling data showed only subtle responses of T cells; some lipoproteins did not elicit proliferation. Hence, the robust activation of the innate immune system by S. aureus lipoproteins does not translate into a strong adaptive immune response. Reasons for this may include inaccessibility of lipoproteins for B cells as well as ineffective processing and presentation of the antigens to T cells.

Probiotic Lactobacilli Modulate Staphylococcus aureus-Induced Activation of Conventional and Unconventional T cells and NK Cells

Lactobacilli are probiotic commensal bacteria and potent modulators of immunity. When present in the gut or supplemented as probiotics, they beneficially modulate ex vivo immune responsiveness. Further, factors derived from several lactobacilli strains act immune regulatory in vitro. In contrast, Staphylococcus aureus (S. aureus) is known to induce excessive T cell activation. In this study, we aimed to investigate S. aureus-induced activation of human mucosal-associated invariant T cells (MAIT cells), γδ T cells, NK cells, as well as of conventional CD4⁺ and CD8⁺ T cells in vitro. Further, we investigated if lactobacilli-derived factors could modulate their activation. PBMC were cultured with S. aureus 161:2 cell-free supernatants (CFS), staphylococcal enterotoxin A or CD3/CD28-beads alone, or in combination with Lactobacillus rhamnosus GG-CFS or Lactobacillus reuteri DSM 17938-CFS and activation of T and NK cells was evaluated. S. aureus-CFS induced IFN-γ and CD107a expression as well as proliferation. Costimulation with lactobacilli-CFS dampened lymphocyte-activation in all cell types analyzed. Preincubation with lactobacilli-CFS was enough to reduce subsequent activation, and the absence of APC or APC-derived IL-10 did not prevent lactobacilli-mediated dampening. Finally, lactate selectively dampened activation of unconventional T cells and NK cells. In summary, we show that molecules present in the lactobacilli-CFS are able to directly dampen in vitro activation of conventional and unconventional T cells and of NK cells. This study provides novel insights on the immune-modulatory nature of probiotic lactobacilli and suggests a role for lactobacilli in the modulation of induced T and NK cell activation.

The T Cell Response to Staphylococcus aureus

Staphylococcus aureus (S. aureus) is a dangerous pathogen and a leading cause of both nosocomial and community acquired bacterial infection worldwide. However, on the other hand, we are all exposed to this bacterium, often within the first hours of life, and usually manage to establish equilibrium and coexist with it. What does the adaptive immune system contribute toward lifelong control of S. aureus? Will it become possible to raise or enhance protective immune memory by vaccination? While in the past the S. aureus-specific antibody response has dominated this discussion, the research community is now coming to appreciate the role that the cellular arm of adaptive immunity, the T cells, plays. There are numerous T cell subsets, each with differing functions, which together have the ability to orchestrate the immune response to S. aureus and hence to tip the balance between protection and pathology. This review summarizes the state of the art in this dynamic field of research.

Memory Th1 Cells Are Protective in Invasive Staphylococcus aureus Infection

Mechanisms of protective immunity to Staphylococcus aureus infection in humans remain elusive. While the importance of cellular immunity has been shown in mice, T cell responses in humans have not been characterised. Using a murine model of recurrent S. aureus peritonitis, we demonstrated that prior exposure to S. aureus enhanced IFNγ responses upon subsequent infection, while adoptive transfer of S. aureus antigen-specific Th1 cells was protective in naïve mice. Translating these findings, we found that S. aureus antigen-specific Th1 cells were also significantly expanded during human S. aureus bloodstream infection (BSI). These Th1 cells were CD45RO⁺, indicative of a memory phenotype. Thus, exposure to S. aureus induces memory Th1 cells in mice and humans, identifying Th1 cells as potential S. aureus vaccine targets. Consequently, we developed a model vaccine comprising staphylococcal clumping factor A, which we demonstrate to be an effective human T cell antigen, combined with the Th1-driving adjuvant CpG. This novel Th1-inducing vaccine conferred significant protection during S. aureus infection in mice. This study notably advances our understanding of S. aureus cellular immunity, and demonstrates for the first time that a correlate of S. aureus protective immunity identified in mice may be relevant in humans.

Staphylococcus aureus is a leading cause of skin, soft tissue and bone infections and, most seriously, bloodstream infection. When S. aureus does get into the bloodstream, it is more likely to kill than any other bacterial infection, despite all the treatments modern medicine has to offer. It has thus far developed resistance to all antibiotics licensed to treat it. Thus, there is an urgent need to develop a vaccine against S. aureus. However, such a vaccine remains elusive. This is largely due to the fact that we have a very limited understanding of how our immune system fights this infection. Here, we examine how certain T cells of the mouse immune system effectively recognise and respond to S. aureus, and show that transferring these cells to other mice improves their ability to clear infection. We then demonstrate that a vaccine which drives these specific T cells also improves clearance of infection. Until recently, it was not known if human T cells could recognise and respond to S. aureus. Here we show, for the first time, that these cells are expanded in patients with S. aureus bloodstream infection, and suggest that they should be targeted in anti-S. aureus vaccines.

Generation of a Novel Staphylococcus aureus Ghost Vaccine and Examination of Its Immunogenicity against Virulent Challenge in Rats

Staphylococcus aureus is a Gram-positive pathogen that causes a wide range of infections in humans and animals. Bacterial ghosts are nonliving, empty cell envelopes and are well represented as novel vaccine candidates. In this study, we examined the immunogenicity and protective efficacy of S. aureus ghosts (SAGs) against a virulent challenge in rats. Nonliving SAGs were generated by using the MIC of sodium hydroxide. The formation of a transmembrane lysis tunnel structure in SAGs was visualized by scanning electron microscopy. To investigate these SAGs as a vaccine candidate, rats were divided into four groups, A (nonimmunized control), B (orally immunized), C (subcutaneously immunized), and D (intravenously immunized). The IgG antibody responses were significantly stronger in the SAG-immunized groups than in the nonimmunized control group (P < 0.05). Moreover, a significant increase in the populations of CD4(+) and CD8(+) T cells was observed in all three immunized groups (P < 0.05). We also found that serum bactericidal antibodies were significantly elicited in the SAG-immunized groups (P < 0.05). Most importantly, the bacterial loads in the immunized groups were significantly lower than those in the nonimmunized control group (P < 0.01). These results suggest that immunization with SAGs induces immune responses and provides protection against a virulent S. aureus challenge.

Staphylococcus aureus Colonization: Modulation of Host Immune Response and Impact on Human Vaccine Design

In apparent contrast to its invasive potential Staphylococcus aureus colonizes the anterior nares of 20–80% of the human population. The relationship between host and microbe appears particularly individualized and colonization status seems somehow predetermined. After decolonization, persistent carriers often become re-colonized with their prior S. aureus strain, whereas non-carriers resist experimental colonization. Efforts to identify factors facilitating colonization have thus far largely focused on the microorganism rather than on the human host. The host responds to S. aureus nasal colonization via local expression of anti-microbial peptides, lipids, and cytokines. Interplay with the co-existing microbiota also influences colonization and immune regulation. Transient or persistent S. aureus colonization induces specific systemic immune responses. Humoral responses are the most studied of these and little is known of cellular responses induced by colonization. Intriguingly, colonized patients who develop bacteremia may have a lower S. aureus-attributable mortality than their non-colonized counterparts. This could imply a staphylococcal-specific immune “priming” or immunomodulation occurring as a consequence of colonization and impacting on the outcome of infection. This has yet to be fully explored. An effective vaccine remains elusive. Anti-S. aureus vaccine strategies may need to drive both humoral and cellular immune responses to confer efficient protection. Understanding the influence of colonization on adaptive response is essential to intelligent vaccine design, and may determine the efficacy of vaccine-mediated immunity. Clinical trials should consider colonization status and the resulting impact of this on individual patient responses. We urgently need an increased appreciation of colonization and its modulation of host immunity.

Biofilm matrix exoproteins induce a protective immune response against Staphylococcus aureus biofilm infection

The Staphylococcus aureus biofilm mode of growth is associated with several chronic infections that are very difficult to treat due to the recalcitrant nature of biofilms to clearance by antimicrobials. Accordingly, there is an increasing interest in preventing the formation of S. aureus biofilms and developing efficient antibiofilm vaccines. Given the fact that during a biofilm-associated infection, the first primary interface between the host and the bacteria is the self-produced extracellular matrix, in this study we analyzed the potential of extracellular proteins found in the biofilm matrix to induce a protective immune response against S. aureus infections. By using proteomic approaches, we characterized the exoproteomes of exopolysaccharide-based and protein-based biofilm matrices produced by two clinical S. aureus strains. Remarkably, results showed that independently of the nature of the biofilm matrix, a common core of secreted proteins is contained in both types of exoproteomes. Intradermal administration of an exoproteome extract of an exopolysaccharide-dependent biofilm induced a humoral immune response and elicited the production of interleukin 10 (IL-10) and IL-17 in mice. Antibodies against such an extract promoted opsonophagocytosis and killing of S. aureus. Immunization with the biofilm matrix exoproteome significantly reduced the number of bacterial cells inside a biofilm and on the surrounding tissue, using an in vivo model of mesh-associated biofilm infection. Furthermore, immunized mice also showed limited organ colonization by bacteria released from the matrix at the dispersive stage of the biofilm cycle. Altogether, these data illustrate the potential of biofilm matrix exoproteins as a promising candidate multivalent vaccine against S. aureus biofilm-associated infections.