Design of Staphylococcus aureus New Vaccine Candidates with B and T Cell Epitope Mapping, Reverse Vaccinology, and Immunoinformatics

Bioinformatics-Driven mRNA-Based Vaccine Design for Controlling Tinea Cruris Induced by Trichophyton rubrum

Tinea cruris, a dermatophyte fungal infection predominantly caused by Trichophyton rubrum and Epidermophyton floccosum, primarily affects the groin, pubic region, and adjacent thigh. Its recurrence is frequent, attributable to repeated fungal infections in susceptible individuals, especially those with onychomycosis or tinea pedis, which act as reservoirs for dermatophytes. Given the persistent nature of tinea cruris, vaccination emerges as a promising strategy for fungal infection management, offering targeted, durable protection against various fungal species. Vaccines stimulate both humoral and cell-mediated immunity and are administered prophylactically to prevent infections while minimizing the risk of antifungal resistance development. Developing fungal vaccines is challenging due to the thick fungal cell wall, similarities between fungal and human cells, antigenic variation, and evolutionary resemblance to animals, complicating non-toxic target identification and T-cell response variability. No prior research has shown an mRNA vaccine for T. rubrum. Hence, this study proposes a novel mRNA-based vaccine for tinea cruris, potentially offering long-term immunity and reducing reliance on antifungal medications. This study explores the complete proteome of T. rubrum, identifying potential protein candidates for vaccine development through reverse vaccinology. Immunogenic epitopes from these candidates were mapped and integrated into multitope vaccines and reverse translated to construct mRNA vaccines. Then, the mRNA was translated and computationally assessed for physicochemical, chemical, and immunological attributes. Notably, 1,3-beta-glucanosyltransferase, CFEM domain-containing protein, cell wall galactomannoprotein, and LysM domain-containing protein emerged as promising vaccine targets. Antigenic, immunogenic, non-toxic, and non-allergenic cytotoxic T lymphocyte, helper T lymphocyte, and B lymphocyte epitopes were selected and linked with appropriate linkers and Toll-like receptor (TLR) agonist adjuvants to formulate vaccine candidates targeting T. rubrum. The protein-based vaccines underwent reverse translation to construct the mRNA vaccines, which, after inoculation, were translated again by host ribosomes to work as potential components for triggering the immune response. After that, molecular docking, normal mode analysis, and molecular dynamic simulation confirmed strong binding affinities and stable complexes between vaccines and TLR receptors. Furthermore, immune simulations of vaccines with and without adjuvant demonstrated activation of immune responses, evidenced by elevated levels of IgG1, IgG2, IgM antibodies, cytokines, and interleukins. There was no significant change in antibody production between vaccines with and without adjuvants, but adjuvants are crucial for activating the innate immune response via TLRs. Although mRNA vaccines hold promise against fungal infections, further research is essential to assess their safety and efficacy. Experimental validation is crucial for evaluating their immunogenicity, effectiveness, and safety.

Emerging strategies and therapeutic innovations for combating drug resistance in Staphylococcus aureus strains: A comprehensive review

In recent years, antibiotic therapy has encountered significant challenges due to the rapid emergence of multidrug resistance among bacteria responsible for life-threatening illnesses, creating uncertainty about the future management of infectious diseases. The escalation of antimicrobial resistance in the post-COVID era compared to the pre-COVID era has raised global concern. The prevalence of nosocomial-related infections, especially outbreaks of drug-resistant strains of Staphylococcus aureus, have been reported worldwide, with India being a notable hotspot for such occurrences. Various virulence factors and mutations characterize nosocomial infections involving S. aureus. The lack of proper alternative treatments leading to increased drug resistance emphasizes the need to investigate and examine recent research to combat future pandemics. In the current genomics era, the application of advanced technologies such as next-generation sequencing (NGS), machine learning (ML), and quantum computing (QC) for genomic analysis and resistance prediction has significantly increased the pace of diagnosing drug-resistant pathogens and insights into genetic intricacies. Despite prompt diagnosis, the elimination of drug-resistant infections remains unattainable in the absence of effective alternative therapies. Researchers are exploring various alternative therapeutic approaches, including phage therapy, antimicrobial peptides, photodynamic therapy, vaccines, host-directed therapies, and more. The proposed review mainly focuses on the resistance journey of S. aureus over the past decade, detailing its resistance mechanisms, prevalence in the subcontinent, innovations in rapid diagnosis of the drug-resistant strains, including the applicants of NGS and ML application along with QC, it helps to design alternative novel therapeutics approaches against S. aureus infection.

In silico epitope prediction of Borrelia burgdorferi sensu lato antigens for the detection of specific antibodies

Despite many years of research, serodiagnosis of Lyme disease still faces many obstacles. Difficulties arise mainly due to the low degree of amino acid sequence conservation of the most immunogenic antigens among B. burgdorferi s.l. genospecies, as well as differences in protein production depending on the environment in which the spirochete is located. Mapping B-cell epitopes located on antigens allows for a better understanding of antibody-pathogen interactions which is essential for the development of new and more effective diagnostic tools. In this study, in silico B-cell epitope mapping was performed to determine the theoretical diagnostic potential of selected B. burgdorferi s.l. proteins (BB0108, BB0126, BB0298, BB0689, BB0323, FliL, PstS, SecD, EF-Tu). Bioinformatics software predicted 35 conserved linear and 31 conformational epitopes with the degree of identity among B. burgdorferi s.l. of at least 85%, which may prove to be useful in the development of a new tool for the diagnosis of Lyme disease.

Reverse vaccinology & immunoinformatics approach to design a multiepitope vaccine (CV3Ag-antiMRSA) against methicillin resistant Staphylococcus aureus (MRSA) - a pathogen affecting both human and animal health

Infections caused by drug resistant bacteria is a silent detrimental pandemic affecting the global health care profoundly. Methicillin resistant Staphylococcus aureus (MRSA) is a pathogen that causes serious infections in different settings (community, hospital & veterinary) whose treatment remains highly challenging due to its powerful characteristics (antibiotic resistance strategies, virulence factors). In this study, we used reverse vaccinology (RV) approach and designed an immunogenic multi epitope vaccine (CV3Ag-antiMRSA) targeting three potential antigen candidates viz., mecA encoding transpeptidase (PBP2a) protein responsible for conferring methicillin resistance and two virulence determinants - hlgA encoding gamma-hemolysin component A (a pore forming toxin) and isdB encoding iron regulated surface determinant B (heme transport component that allows S. aureus to scavenge iron from host hemoglobin and myoglobin). We employed an array of immunoinformatic tools/server to identify and use immunogenic epitopes (B cell and MHC class) to develop the chimeric subunit vaccine V4 (CV3Ag-antiMRSA) with immune modulating adjuvant and linkers. Based on different parameters, the vaccine construct V4 (CV3Ag-antiMRSA) was determined to be suitable vaccine (antigenic and non-allergen). Molecular docking and simulation of CV3Ag-antiMRSA with Toll Like Receptor (TLR2) predicted its immuno-stimulating potential. Finally, in silico cloning of CV3Ag-antiMRSA construct into pet28a and pet30 vector displayed its feasibility for the heterologous expression in the E. coli expression system. This vaccine candidate (CV3Ag-antiMRSA) designed based on the MRSA genomes obtained from both animal and human hosts can be experimentally validated and thereby contribute to vaccine development to impart protection to both animal and human health.Communicated by Ramaswamy H. Sarma.

The Promising Potential of Reverse Vaccinology-Based Next-Generation Vaccine Development over Conventional Vaccines against Antibiotic-Resistant Bacteria

The clinical use of antibiotics has led to the emergence of multidrug-resistant (MDR) bacteria, leading to the current antibiotic resistance crisis. To address this issue, next-generation vaccines are being developed to prevent antimicrobial resistance caused by MDR bacteria. Traditional vaccine platforms, such as inactivated vaccines (IVs) and live attenuated vaccines (LAVs), were effective in preventing bacterial infections. However, they have shown reduced efficacy against emerging antibiotic-resistant bacteria, including MDR M. tuberculosis. Additionally, the large-scale production of LAVs and IVs requires the growth of live pathogenic microorganisms. A more promising approach for the accelerated development of vaccines against antibiotic-resistant bacteria involves the use of in silico immunoinformatics techniques and reverse vaccinology. The bioinformatics approach can identify highly conserved antigenic targets capable of providing broader protection against emerging drug-resistant bacteria. Multi-epitope vaccines, such as recombinant protein-, DNA-, or mRNA-based vaccines, which incorporate several antigenic targets, offer the potential for accelerated development timelines. This review evaluates the potential of next-generation vaccine development based on the reverse vaccinology approach and highlights the development of safe and immunogenic vaccines through relevant examples from successful preclinical and clinical studies.

Immunoproteomic and immunoinformatic approaches identify secreted antigens and epitopes from Staphylococcus saprophyticus

Urinary tract infections (UTIs) are common human infections that compromise women's health around the world, even though they can affect men and women of all ages. Bacterial species are the primary causative agents of UTIs, while Staphylococcus saprophyticus, a gram-positive bacterium, is especially important for uncomplicated infections in young women. Despite the number of antigenic proteins identified in Staphylococcus aureus and other bacteria of the genus, there is no immunoproteomic study in S. saprophyticus. In this context, since pathogenic microorganisms secrete important proteins that interact with hosts during infection, the present work aims to identify the exoantigens from S. saprophyticus ATCC 15305 by immunoproteomic and immunoinformatic approaches. We identified 32 antigens on the exoproteome of S. saprophyticus ATCC 15305 by immunoinformatic tools. By using 2D-IB immunoproteomic analysis, it was possible to identify 3 antigenic proteins: transglycosylase IsaA, enolase and the secretory antigen Q49ZL8. In addition, 5 antigenic proteins were detected by immunoprecipitation (IP) approach, where the most abundant were bifunctional autolysin and transglycosylase IsaA proteins. The transglycosylase IsaA was the only protein detected by all the tools approaches used in this study. In this work it was possible to describe a total of 36 S. saprophyticus exoantigens. Immunoinformatic analysis allowed the identification of 5 exclusive linear B cell epitopes from S. saprophyticus and 5 epitopes presenting homology with other bacteria that cause UTIs. This work describes, for the first time, the profile of exoantigens secreted by S. saprophyticus and can contribute to the identification of new diagnostic targets of UTIs, as well as to develop vaccines and immunotherapies against bacterial urinary infections.

Designing a Next-Generation Multiepitope-Based Vaccine against Staphylococcus aureus Using Reverse Vaccinology Approaches

Staphylococcus aureus is a human bacterial pathogen that can cause a wide range of symptoms. As virulent and multi-drug-resistant strains of S. aureus have evolved, invasive S. aureus infections in hospitals and the community have become one of the leading causes of mortality and morbidity. The development of novel techniques is therefore necessary to overcome this bacterial infection. Vaccines are an appropriate alternative in this context to control infections. In this study, the collagen-binding protein (CnBP) from S. aureus was chosen as the target antigen, and a series of computational methods were used to find epitopes that may be used in vaccine development in a systematic way. The epitopes were passed through a filtering pipeline that included antigenicity, toxicity, allergenicity, and cytokine inducibility testing, with the objective of identifying epitopes capable of eliciting both T and B cell-mediated immune responses. To improve vaccine immunogenicity, the final epitopes and phenol-soluble modulin α4 adjuvant were fused together using appropriate linkers; as a consequence, a multiepitope vaccine was developed. The chosen T cell epitope ensemble is expected to cover 99.14% of the global human population. Furthermore, docking and dynamics simulations were used to examine the vaccine's interaction with the Toll-like receptor 2 (TLR2), revealing great affinity, consistency, and stability between the two. Overall, the data indicate that the vaccine candidate may be extremely successful, and it will need to be evaluated in experimental systems to confirm its efficiency.

A Structural View at Vaccine Development against M. tuberculosis

Tuberculosis (TB) is still the leading global cause of death from an infectious bacterial agent. Limiting tuberculosis epidemic spread is therefore an urgent global public health priority. As stated by the WHO, to stop the spread of the disease we need a new vaccine, with better coverage than the current Mycobacterium bovis BCG vaccine. This vaccine was first used in 1921 and, since then, there are still no new licensed tuberculosis vaccines. However, there is extremely active research in the field, with a steep acceleration in the past decades, due to the advance of technologies and more rational vaccine design strategies. This review aims to gather latest updates in vaccine development in the various clinical phases and to underline the contribution of Structural Vaccinology (SV) to the development of safer and effective antigens. In particular, SV and the development of vaccine adjuvants is making the use of subunit vaccines, which are the safest albeit the less antigenic ones, an achievable goal. Indeed, subunit vaccines overcome safety concerns but need to be rationally re-engineered to enhance their immunostimulating effects. The larger availability of antigen structural information as well as a better understanding of the complex host immune response to TB infection is a strong premise for a further acceleration of TB vaccine development.

Integration of immunoinformatics and cheminformatics to design and evaluate a multitope vaccine against Klebsiella pneumoniae and Pseudomonas aeruginosa coinfection

Introduction: Klebsiella pneumoniae (K. pneumoniae) and Pseudomonas aeruginosa (P. aeruginosa) are the most common Gram-negative bacteria associated with pneumonia and coinfecting the same patient. Despite their high virulence, there is no effective vaccine against them. Methods: In the current study, the screening of several proteins from both pathogens highlighted FepA and OmpK35 for K. pneumonia in addition to HasR and OprF from P. aeruginosa as promising candidates for epitope mapping. Those four proteins were linked to form a multitope vaccine, that was formulated with a suitable adjuvant, and PADRE peptides to finalize the multitope vaccine construct. The final vaccine's physicochemical features, antigenicity, toxicity, allergenicity, and solubility were evaluated for use in humans. Results: The output of the computational analysis revealed that the designed multitope construct has passed these assessments with satisfactory scores where, as the last stage, we performed a molecular docking study between the potential vaccine construct and K. pneumonia associated immune receptors, TLR4 and TLR2, showing affinitive to both targets with preferentiality for the TLR4 receptor protein. Validation of the docking studies has proceeded through molecular dynamics simulation, which estimated a strong binding and supported the nomination of the designed vaccine as a putative solution for K. pneumoniae and P. aeruginosa coinfection. Here, we describe the approach for the design and assessment of our potential vaccine.

Identification of a Potential Vaccine against Treponema pallidum Using Subtractive Proteomics and Reverse-Vaccinology Approaches

Syphilis, a sexually transmitted infection, is a deadly disease caused by Treponema pallidum. It is a Gram-negative spirochete that can infect nearly every organ of the human body. It can be transmitted both sexually and perinatally. Since syphilis is the second most fatal sexually transmitted disease after AIDS, an efficient vaccine candidate is needed to establish long-term protection against infections by T. pallidum. This study used reverse-vaccinology-based immunoinformatic pathway subtractive proteomics to find the best antigenic proteins for multi-epitope vaccine production. Six essential virulent and antigenic proteins were identified, including the membrane lipoprotein TpN32 (UniProt ID: O07950), DNA translocase FtsK (UniProt ID: O83964), Protein Soj homolog (UniProt ID: O83296), site-determining protein (UniProt ID: F7IVD2), ABC transporter, ATP-binding protein (UniProt ID: O83930), and Sugar ABC superfamily ATP-binding cassette transporter, ABC protein (UniProt ID: O83782). We found that the multiepitope subunit vaccine consisting of 4 CTL, 4 HTL, and 11 B-cell epitopes mixed with the adjuvant TLR-2 agonist ESAT6 has potent antigenic characteristics and does not induce an allergic response. Before being docked at Toll-like receptors 2 and 4, the developed vaccine was modeled, improved, and validated. Docking studies revealed significant binding interactions, whereas molecular dynamics simulations demonstrated its stability. Furthermore, the immune system simulation indicated significant and long-lasting immunological responses. The vaccine was then reverse-transcribed into a DNA sequence and cloned into the pET28a (+) vector to validate translational activity as well as the microbial production process. The vaccine developed in this study requires further scientific consensus before it can be used against T. pallidum to confirm its safety and efficacy.

Development and evaluation of a multi-epitope subunit vaccine against group B Streptococcus infection

Streptococcus agalactiae (Group B Streptococcus, GBS) is a multi-host pathogen, even causing life-threatening infections in newborns. Vaccination with GBS crossed serotypes vaccine is one of the best options for long-term infection control. Here we built a comprehensive in silico epitope-prediction workflow pipeline to design a multivalent multiepitope-based subunit vaccine containing 11 epitopes against Streptococcus agalactiae (MVSA). All epitopes in MVSA came from the proteins which were antigenic-confirmed, virulent-associated, surface-exposed and conserved in ten GBS serotypes. The in-silico analysis showed MVSA had potential to evoke strong immune responses and enable worldwide population coverage. To validate MVSA protection efficacy against GBS infection, immune protection experiments were performed in a mouse model. Importantly, MVSA induced a high titre of antibodies, significant proliferation of mice splenocytes and elicited strong protection against lethal-dose challenge with a survival rate of 100% in mice after three vaccinations. Meanwhile, the polyclonal antibody against MVSA did not only inhibit for growth of GBS from six crucial serotypes in vitro, but also protect 100% naive mice from GBS lethal challenge. These active and passive immunity assay results suggested that MVSA could therefore be an efficacious multi-epitope vaccine against GBS infection.

Modern vaccine development via reverse vaccinology to combat antimicrobial resistance

With the continuous evolution of bacteria, the global antimicrobial resistance health threat is causing millions of deaths yearly. While depending on antibiotics as a primary treatment has its merits, there are no effective alternatives thus far in the pharmaceutical market against some drug-resistant bacteria. In recent years, vaccinology has become a key topic in scientific research. Combining with the growth of technology, vaccine research is seeing a new light where the process is made faster and more efficient. Although less discussed, bacterial vaccine is a feasible strategy to combat antimicrobial resistance. Some vaccines have shown promising results with good efficacy against numerous multidrug-resistant strains of bacteria. In this review, we aim to discuss the findings from studies utilizing reverse vaccinology for vaccine development against some multidrug-resistant bacteria, as well as provide a summary of multi-year bacterial vaccine studies in clinical trials. The advantages of reverse vaccinology in the generation of new bacterial vaccines are also highlighted. Meanwhile, the limitations and future prospects of bacterial vaccine concludes this review.

Mining of Marburg Virus Proteome for Designing an Epitope-Based Vaccine

Marburg virus (MARV) is one of the most harmful zoonotic viruses with deadly effects on both humans and nonhuman primates. Because of its severe outbreaks with a high rate of fatality, the world health organization put it as a risk group 4 pathogen and focused on the urgent need for the development of effective solutions against that virus. However, up to date, there is no effective vaccine against MARV in the market. In the current study, the complete proteome of MARV (seven proteins) was analyzed for the antigenicity score and the virulence or physiological role of each protein where we nominated envelope glycoprotein (Gp), Transcriptional activator (VP30), and membrane-associated protein (VP24) as the candidates for epitope prediction. Following that, a vaccine construct was designed based on CTL, HTL, and BCL epitopes of the selected protein candidates and to finalize the vaccine construct, several amino acid linkers, β-defensin adjuvant, and PADRE peptides were incorporated. The generated potential vaccine was assessed computationally for several properties such as antigenicity, allergenicity, stability, and other structural features where the outcomes of these assessments nominated this potential vaccine to be validated for its binding affinity with two molecular targets TLR-8 and TLR-4. The binding score and the stability of the vaccine-receptor complex, which was deeply studied through molecular docking-coupled dynamics simulation, supported the selection of our designed vaccine as a putative solution for MARV that should be validated through future wet-lab experiments. Here, we describe the computational approach for designing and analysis of this potential vaccine.

Identification of Putative Vaccine and Drug Targets against the Methicillin-Resistant Staphylococcus aureus by Reverse Vaccinology and Subtractive Genomics Approaches

Methicillin-resistant Staphylococcus aureus (MRSA) is an opportunistic pathogen and responsible for causing life-threatening infections. The emergence of hypervirulent and multidrug-resistant (MDR) S. aureus strains led to challenging issues in antibiotic therapy. Consequently, the morbidity and mortality rates caused by S. aureus infections have a substantial impact on health concerns. The current worldwide prevalence of MRSA infections highlights the need for long-lasting preventive measures and strategies. Unfortunately, effective measures are limited. In this study, we focus on the identification of vaccine candidates and drug target proteins against the 16 strains of MRSA using reverse vaccinology and subtractive genomics approaches. Using the reverse vaccinology approach, 4 putative antigenic proteins were identified; among these, PrsA and EssA proteins were found to be more promising vaccine candidates. We applied a molecular docking approach of selected 8 drug target proteins with the drug-like molecules, revealing that the ZINC4235426 as potential drug molecule with favorable interactions with the target active site residues of 5 drug target proteins viz., biotin protein ligase, HPr kinase/phosphorylase, thymidylate kinase, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-L-lysine ligase, and pantothenate synthetase. Thus, the identified proteins can be used for further rational drug or vaccine design to identify novel therapeutic agents for the treatment of multidrug-resistant staphylococcal infection.

In silico Designing of an Epitope-Based Vaccine Against Common E. coli Pathotypes

Escherichia coli (E. coli) is a Gram-negative bacterium that belongs to the family Enterobacteriaceae. While E. coli can stay as an innocuous resident in the digestive tract, it can cause a group of symptoms ranging from diarrhea to live threatening complications. Due to the increased rate of antibiotic resistance worldwide, the development of an effective vaccine against E. coli pathotypes is a major health priority. In this study, a reverse vaccinology approach along with immunoinformatics has been applied for the detection of potential antigens to develop an effective vaccine. Based on our screening of 5,155 proteins, we identified lipopolysaccharide assembly protein (LptD) and outer membrane protein assembly factor (BamA) as vaccine candidates for the current study. The conservancy of these proteins in the main E. coli pathotypes was assessed through BLASTp to make sure that the designed vaccine will be protective against major E. coli pathotypes. The multitope vaccine was constructed using cytotoxic T lymphocyte (CTL), helper T lymphocyte (HTL), and B cell lymphocyte (BCL) epitopes with suitable linkers and adjuvant. Following that, it was analyzed computationally where it was found to be antigenic, soluble, stable, and non-allergen. Additionally, the adopted docking study, as well as all-atom molecular dynamics simulation, illustrated the promising predicted affinity and free binding energy of this constructed vaccine against the human Toll-like receptor-4 (hTLR-4) dimeric state. In this regard, wet lab studies are required to prove the efficacy of the potential vaccine construct that demonstrated promising results through computational validation.

Investigation of novel putative immunogenic targets against Staphylococcus aureus using a reverse vaccinology strategy

BACKGROUND

The emergence of methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant S. aureus (VRSA) strains is a significant public health concern. Considering the high morbidity and mortality of invasive S. aureus infections and multi-drug resistant strains, there is an urgent need for non-antibiotic immune-based approaches to cure these infections. Despite all efforts, vaccine candidates targeting S. aureus failed in human clinical trials, and no approved vaccine is available against this pathogen. Therefore, this study aimed to introduce suitable candidates for immunization against S. aureus using a comprehensive reverse vaccinology approach.

METHODS

In this study, we retrieved putative immunogenic targets from three different levels (literature review, automated reverse vaccinology, and manual reverse vaccinology) and evaluated them using several immunoinformatics analyses including antigenicity, allergenicity, PSI-BLAST to human proteome, physiochemical properties, B-cell, and T-cell epitopes. In the next step, the quartile method scoring was used to the shortlisted proteins. Finally, the molecular docking and immune simulation of immunogenic targets were performed.

RESULTS

This study presents 12 vaccine candidates, including three enzymatic proteins (WP_000222271.1, WP_001170274, and WP_000827736.1), three cell wall-associated proteins (WP_001125631.1, WP_000731642, and WP_000751265.1), two hemolysins (WP_000594517.1, and WP_000916697.1), one secretion involved protein (WP_000725226.1), one heme‑iron binding protein (WP_001041573.1), one superantigen like protein (WP_000668994.1) and one hypothetical proteins (WP_000737711.1).

CONCLUSION

Through quartile scoring method, immune simulation and molecular docking, four promising targets including lytic transglycosylase IsaA, HlgA, secretory antigen precursor SsaA, and heme uptake protein IsdB were selected as the shortlisted proteins. It seems that a polarized immunization (Th1/Th17) response is needed for protection against this bacterium. An optimized formulation based on these putative immunogenic proteins and a wisely adjuvant selection may drive the immune system toward a full protection.

In Silico Designing of a Multitope Vaccine against Rhizopus microsporus with Potential Activity against Other Mucormycosis Causing Fungi

During the current era of the COVID-19 pandemic, the dissemination of Mucorales has been reported globally, with elevated rates of infection in India, and because of the high rate of mortality and morbidity, designing an effective vaccine against mucormycosis is a major health priority, especially for immunocompromised patients. In the current study, we studied shared Mucorales proteins, which have been reported as virulence factors, and after analysis of several virulent proteins for their antigenicity and subcellular localization, we selected spore coat (CotH) and serine protease (SP) proteins as the targets of epitope mapping. The current study proposes a vaccine constructed based on top-ranking cytotoxic T lymphocyte (CTL), helper T lymphocyte (HTL), and B cell lymphocyte (BCL) epitopes from filtered proteins. In addition to the selected epitopes, β-defensins adjuvant and PADRE peptide were included in the constructed vaccine to improve the stimulated immune response. Computational tools were used to estimate the physicochemical and immunological features of the proposed vaccine and validate its binding with TLR-2, where the output data of these assessments potentiate the probability of the constructed vaccine to stimulate a specific immune response against mucormycosis. Here, we demonstrate the approach of potential vaccine construction and assessment through computational tools, and to the best of our knowledge, this is the first study of a proposed vaccine against mucormycosis based on the immunoinformatics approach.

A Perspective on Nanotechnology and COVID-19 Vaccine Research and Production in South Africa

Advances in nanotechnology have enabled the development of a new generation of vaccines, which are playing a critical role in the global control of the COVID-19 pandemic and the return to normalcy. Vaccine development has been conducted, by and large, by countries in the global north. South Africa, as a major emerging economy, has made extensive investments in nanotechnology and bioinformatics and has the expertise and resources in vaccine development and manufacturing. This has been built at a national level through decades of investment. In this perspective article, we provide a synopsis of the investments made in nanotechnology and highlight how these could support innovation, research, and development for vaccines for this disease. We also discuss the application of bioinformatics tools to support rapid and cost-effective vaccine development and make recommendations for future research and development in this area to support future health challenges.

Staphylococcus aureus Putative Vaccines Based on the Virulence Factors: A Mini-Review

Since the 1960s, the frequency of methicillin-resistant Staphylococcus aureus as a recurrent cause of nosocomial infections has increased. Since multidrug-resistant Staphylococcus has overcome antimicrobial treatment, the development of putative vaccines based on virulence factors could be a great help in controlling the infections caused by bacteria and are actively being pursued in healthcare settings. This mini-review provides an overview of the recent progress in vaccine development, immunogenicity, and therapeutic features of some S. aureus macromolecules as putative vaccine candidates and their implications against human S. aureus-related infections. Based on the reviewed experiments, multivalent vaccines could prevent the promotion of the diseases caused by this bacterium and enhance the prevention chance of S. aureus infections.

Proteome Based Approach Defines Candidates for Designing a Multitope Vaccine against the Nipah Virus

Nipah virus is one of the most harmful emerging viruses with deadly effects on both humans and animals. Because of the severe outbreaks, in 2018, the World Health Organization focused on the urgent need for the development of effective solutions against the virus. However, up to date, there is no effective vaccine against the Nipah virus in the market. In the current study, the complete proteome of the Nipah virus (nine proteins) was analyzed for the antigenicity score and the virulence role of each protein, where we came up with fusion glycoprotein (F), glycoprotein (G), protein (V), and protein (W) as the candidates for epitope prediction. Following that, the multitope vaccine was designed based on top-ranking CTL, HTL, and BCL epitopes from the selected proteins. We used suitable linkers, adjuvant, and PADRE peptides to finalize the constructed vaccine, which was analyzed for its physicochemical features, antigenicity, toxicity, allergenicity, and solubility. The designed vaccine passed these assessments through computational analysis and, as a final step, we ran a docking analysis between the designed vaccine and TLR-³ and validated the docked complex through molecular dynamics simulation, which estimated a strong binding and supported the nomination of the designed vaccine as a putative solution for Nipah virus. Here, we describe the computational approach for design and analysis of this vaccine.

In Silico Prediction of a Multitope Vaccine against Moraxella catarrhalis: Reverse Vaccinology and Immunoinformatics

Moraxella catarrhalis (M. catarrhalis) is a Gram-negative bacterium that can cause serious respiratory tract infections and middle ear infections in children and adults. M. catarrhalis has demonstrated an increasing rate of antibiotic resistance in the last few years, thus development of an effective vaccine is a major health priority. We report here a novel designed multitope vaccine based on the mapped epitopes of the vaccine candidates filtered out of the whole proteome of M. catarrhalis. After analysis of 1615 proteins using a reverse vaccinology approach, only two proteins (outer membrane protein assembly factor BamA and LPS assembly protein LptD) were nominated as potential vaccine candidates. These proteins were found to be essential, outer membrane, virulent and non-human homologs with appropriate molecular weight and high antigenicity score. For each protein, cytotoxic T lymphocyte (CTL), helper T lymphocyte (HTL) and B cell lymphocyte (BCL) epitopes were predicted and confirmed to be highly antigenic and cover conserved regions of the proteins. The mapped epitopes constituted the base of the designed multitope vaccine where suitable linkers were added to conjugate them. Additionally, beta defensin adjuvant and pan-HLA DR-binding epitope (PADRE) peptide were also incorporated into the construct to improve the stimulated immune response. The constructed multitope vaccine was analyzed for its physicochemical, structural and immunological characteristics and it was found to be antigenic, soluble, stable, non-allergenic and have a high affinity to its target receptor. Although the in silico analysis of the current study revealed that the designed multitope vaccine has the ability to trigger a specific immune response against M. catarrhalis, additional translational research is required to confirm the effectiveness of the designed vaccine.

Evasion of Immunological Memory by S. aureus Infection: Implications for Vaccine Design

Recurrent S. aureus infections are common, suggesting that natural immune responses are not protective. All candidate vaccines tested thus far have failed to protect against S. aureus infections, highlighting an urgent need to better understand the mechanisms by which the bacterium interacts with the host immune system to evade or prevent protective immunity. Although there is evidence in murine models that both cellular and humoral immune responses are important for protection against S. aureus, human studies suggest that T cells are critical in determining susceptibility to infection. This review will use an “anatomic” approach to systematically outline the steps necessary in generating a T cell-mediated immune response against S. aureus. Through the processes of bacterial uptake by antigen presenting cells, processing and presentation of antigens to T cells, and differentiation and proliferation of memory and effector T cell subsets, the ability of S. aureus to evade or inhibit each step of the T-cell mediated response will be reviewed. We hypothesize that these interactions result in the redirection of immune responses away from protective antigens, thereby precluding the establishment of “natural” memory and potentially inhibiting the efficacy of vaccination. It is anticipated that this approach will reveal important implications for future design of vaccines to prevent these infections.

Emerging Strategies to Combat β-Lactamase Producing ESKAPE Pathogens

Since the discovery of penicillin by Alexander Fleming in 1929 as a therapeutic agent against staphylococci, β-lactam antibiotics (BLAs) remained the most successful antibiotic classes against the majority of bacterial strains, reaching a percentage of 65% of all medical prescriptions. Unfortunately, the emergence and diversification of β-lactamases pose indefinite health issues, limiting the clinical effectiveness of all current BLAs. One solution is to develop β-lactamase inhibitors (BLIs) capable of restoring the activity of β-lactam drugs. In this review, we will briefly present the older and new BLAs classes, their mechanisms of action, and an update of the BLIs capable of restoring the activity of β-lactam drugs against ESKAPE (Enterococcus spp., Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.) pathogens. Subsequently, we will discuss several promising alternative approaches such as bacteriophages, antimicrobial peptides, nanoparticles, CRISPR (clustered regularly interspaced short palindromic repeats) cas technology, or vaccination developed to limit antimicrobial resistance in this endless fight against Gram-negative pathogens.