The global distribution and diversity of protein vaccine candidate antigens in the highly virulent Streptococcus pnuemoniae serotype 1

Streptococcus pneumoniae serotype 19A from carriers and invasive disease: virulence gene profile and pathogenicity in a Galleria mellonella model

PURPOSE

This study aimed to evaluate and compare the presence of genes related to surface proteins between isolates of Streptococcus pneumoniae from healthy carriers (HC) and invasive pneumococcal disease (IPD) with a particular focus on serotype 19A.

METHODS

The presence of these genes was identified by real-time PCR. Subsequently, we employed the Galleria mellonella larval infection model to study their effect on pathogenicity in vivo.

RESULTS

The percentage of selected virulence genes was similar between the HC and IPD groups (p > 0.05), and the genes lytA, nanB, pavA, pcpA, phtA, phtB, phtE, rrgA, and sipA were all present in both groups. However, the virulence profile of the isolates differed individually between HC and IPD groups. The highest lethality in G. mellonella was for IPD isolates (p < 0.01), even when the virulence profile was the same as compared to the HC isolates or when the nanA, pspA, pspA-fam1, and pspC genes were not present.

CONCLUSIONS

The occurrence of the investigated virulence genes was similar between HC and IPD S. pneumoniae serotype 19A groups. However, the IPD isolates showed a higher lethality in the alternative G. mellonella model than the HC isolates, regardless of the virulence gene composition, indicating that other virulence factors may play a decisive role in virulence. Currently, this is the first report using the in vivo G. mellonella model to study the virulence of clinical isolates of S. pneumoniae.

Characterization of the innate immune response to Streptococcus pneumoniae infection in zebrafish

Streptococcus pneumoniae (pneumococcus) is one of the most frequent causes of pneumonia, sepsis and meningitis in humans, and an important cause of mortality among children and the elderly. We have previously reported the suitability of the zebrafish (Danio rerio) larval model for the study of the host-pathogen interactions in pneumococcal infection. In the present study, we characterized the zebrafish innate immune response to pneumococcus in detail through a whole-genome level transcriptome analysis and revealed a well-conserved response to this human pathogen in challenged larvae. In addition, to gain understanding of the genetic factors associated with the increased risk for severe pneumococcal infection in humans, we carried out a medium-scale forward genetic screen in zebrafish. In the screen, we identified a mutant fish line which showed compromised resistance to pneumococcus in the septic larval infection model. The transcriptome analysis of the mutant zebrafish larvae revealed deficient expression of a gene homologous for human C-reactive protein (CRP). Furthermore, knockout of one of the six zebrafish crp genes by CRISPR-Cas9 mutagenesis predisposed zebrafish larvae to a more severe pneumococcal infection, and the phenotype was further augmented by concomitant knockdown of a gene for another Crp isoform. This suggests a conserved function of C-reactive protein in anti-pneumococcal immunity in zebrafish. Altogether, this study highlights the similarity of the host response to pneumococcus in zebrafish and humans, gives evidence of the conserved role of C-reactive protein in the defense against pneumococcus, and suggests novel host genes associated with pneumococcal infection.

<i>In silico</i> Research at the Stages of Designing Modern Means for Prevention of Plague (by the Example of Subunit Vaccines)

The purpose of this review was to analyze the findings of domestic and foreign researchers on the development of modern drugs for the specific prevention of plague and to illustrate the possibilities of using bioinformatics analysis at the design stages to create an effective and safe vaccine. Work on the creation of an effective new-generation plague vaccine is hampered by several factors associated primarily with the presence of mechanisms of evasion from the immune system of the macroorganism, as well as a large number of pathogenicity determinants in the plague agent. Due to the development of approaches that are based on in silico studies, there is a progressive development of vaccine technologies oriented primarily to the use of the most important immunogens of the plague microbe (F1 and V antigen). Studies aimed at improving the antigenic properties of F1 and LcrV, as well as work on bioinformatic search and analysis of additional promising components to be included in the composition of subunit vaccines are considered as topical applications of bioinformatics data analysis in developing the tools for enhancing the effectiveness of protection through vaccination with subunit preparations.

Serotype 1 pneumococcus: epidemiology, genomics, and disease mechanisms

Streptococcus pneumoniae (the 'pneumococcus') is a significant cause of morbidity and mortality worldwide, causing life-threatening diseases such as pneumonia, bacteraemia, and meningitis, with an annual death burden of over one million. Discovered over a century ago, pneumococcal serotype 1 (S1) is a significant cause of these life-threatening diseases. Our understanding of the epidemiology and biology of pneumococcal S1 has significantly improved over the past two decades, informing the development of preventative and surveillance strategies. However, many questions remain unanswered. Here, we review the current state of knowledge of pneumococcal S1, with a special emphasis on clinical epidemiology, genomics, and disease mechanisms.

A Jack of All Trades: The Role of Pneumococcal Surface Protein A in the Pathogenesis of Streptococcus pneumoniae

Streptococcus pneumoniae (Spn), or the pneumococcus, is a Gram-positive bacterium that colonizes the upper airway. Spn is an opportunistic pathogen capable of life-threatening disease should it become established in the lungs, gain access to the bloodstream, or disseminate to vital organs including the central nervous system. Spn is encapsulated, allowing it to avoid phagocytosis, and current preventative measures against infection include polyvalent vaccines composed of capsular polysaccharide corresponding to its most prevalent serotypes. The pneumococcus also has a plethora of surface components that allow the bacteria to adhere to host cells, facilitate the evasion of the immune system, and obtain vital nutrients; one family of these are the choline-binding proteins (CBPs). Pneumococcal surface protein A (PspA) is one of the most abundant CBPs and confers protection against the host by inhibiting recognition by C-reactive protein and neutralizing the antimicrobial peptide lactoferricin. Recently our group has identified two new roles for PspA: binding to dying host cells via host-cell bound glyceraldehyde 3-phosphate dehydrogenase and co-opting of host lactate dehydrogenase to enhance lactate availability. These properties have been shown to influence Spn localization and enhance virulence in the lower airway, respectively. Herein, we review the impact of CBPs, and in particular PspA, on pneumococcal pathogenesis. We discuss the potential and limitations of using PspA as a conserved vaccine antigen in a conjugate vaccine formulation. PspA is a vital component of the pneumococcal virulence arsenal - therefore, understanding the molecular aspects of this protein is essential in understanding pneumococcal pathogenesis and utilizing PspA as a target for treating or preventing pneumococcal pneumonia.

Subcutaneous immunization with the fusion protein ΔA146Ply-SP0148 confers protection against Streptococcus pneumoniae infection

Pneumococcal SP0148 and pneumolysin (Ply) derivatives are important vaccine candidates. SP0148 is a conserved lipoprotein with high immunogenicity produced by Streptococcus pneumoniae. We have previously demonstrated that SP0148 can confer protection against fatal infections caused by S. pneumoniae. ΔA146Ply is a noncytotoxic mutant of Ply that retains the TLR4 agonistic effect and has mucosal and subcutaneous adjuvant activities suggested to induce protective immunity against S. pneumoniae infection. In this study, we constructed the fusion protein ΔA146Ply-SP0148, composed of ΔA146Ply and SP0148, and evaluated the immunoprotective effect of the fusion protein. When mice were subcutaneously immunized with the fusion protein ΔA146Ply-SP0148, high levels of anti-ΔA146Ply and anti-SP0148 IgG antibodies were induced in the serum. Specific antibodies can bind to a variety of different serotypes of S. pneumoniae. Compared with mice immunized with ΔA146Ply and SP0148 alone, mice immunized subcutaneously with the fusion protein ΔA146Ply-SP0148 with Al(OH)₃ had a higher survival rate when challenged by a lethal dose of S. pneumoniae, and they also had significantly lower lung bacterial loads and milder lung inflammation. In addition, mice immunized subcutaneously with the fusion protein ΔA146Ply-SP0148 stimulated strong Th1, Th2, and Th17 cell responses. In summary, these results suggest that subcutaneous immunization with the ΔA146Ply-SP0148 fusion protein can protect mice against fatal pneumococcal infection and lung infection. The fusion protein ΔA146ply-SP0148 can be a new pneumococcal vaccine target.

Post-Vaccination Streptococcus pneumoniae Carriage and Virulence Gene Distribution among Children Less Than Five Years of Age, Cape Coast, Ghana

In 2012, Ghana introduced PCV13 into its childhood immunization program. To monitor the pneumococcus after PCV13 vaccination, we analyzed serotypes, antibiotic resistance, and virulence genes of pneumococcal carriage isolates among children under five years of age. We obtained nasopharyngeal swabs from 513 children from kindergartens and immunization centers in Cape Coast, Ghana. Pneumococcal serotypes were determined by multiplex-PCR and Quellung reaction. Antibiotic resistance and virulence genes prevalence were determined by disc diffusion and PCR respectively. Overall, carriage prevalence was 29.4% and PCV13 coverage was 38.4%. Over 60% of the isolates were non-PCV13 serotypes and serotype 23B was the most prevalent. One isolate showed full resistance to penicillin, while 35% showed intermediate resistance. Resistance to erythromycin and clindamycin remained low, while susceptibility to ceftriaxone, levofloxacin and vancomycin remained high. Penicillin resistance was associated with PCV13 serotypes. Forty-three (28.5%) strains were multidrug-resistant. Virulence genes pavB, pcpA, psrP, pilus-1, and pilus-2 were detected in 100%, 87%, 62.9%, 11.9%, and 6.6% of the strains, respectively. The pilus islets were associated with PCV13 and multidrug-resistant serotypes. PCV13 vaccination had impacted on pneumococcal carriage with a significant increase in non-PCV13 serotypes and lower penicillin resistance. Including PcpA and PsrP in pneumococcal protein-based vaccines could be beneficial to Ghanaian children.

Role of BgaA as a Pneumococcal Virulence Factor Elucidated by Molecular Evolutionary Analysis

Streptococcus pneumoniae is a major cause of pneumonia, sepsis, and meningitis. Previously, we identified a novel virulence factor by investigating evolutionary selective pressure exerted on pneumococcal choline-binding cell surface proteins. Herein, we focus on another pneumococcal cell surface protein. Cell wall-anchoring proteins containing the LPXTG motif are conserved in Gram-positive bacteria. Our evolutionary analysis showed that among the examined genes, nanA and bgaA had high proportions of codon that were under significant negative selection. Both nanA and bgaA encode a multi-functional glycosidase that aids nutrient acquisition in a glucose-poor environment, pneumococcal adherence to host cells, and evasion from host immunity. However, several studies have shown that the role of BgaA is limited in a mouse pneumonia model, and it remains unclear if BgaA affects pneumococcal pathogenesis in a mouse sepsis model. To evaluate the distribution and pathogenicity of bgaA, we performed phylogenetic analysis and intravenous infection assay. In both Bayesian and maximum likelihood phylogenetic trees, the genetic distances between pneumococcal bgaA was small, and the cluster of pneumococcal bgaA did not contain other bacterial orthologs except for a Streptococcus gwangjuense gene. Evolutionary analysis and BgaA structure indicated BgaA active site was not allowed to change. The mouse infection assay showed that the deletion of bgaA significantly reduced host mortality. These results indicated that both nanA and bgaA encode evolutionally conserved pneumococcal virulence factors and that molecular evolutionary analysis could be a useful alternative strategy for identification of virulence factors.

High residual carriage of vaccine-serotype Streptococcus pneumoniae after introduction of pneumococcal conjugate vaccine in Malawi

There are concerns that pneumococcal conjugate vaccines (PCVs) in sub-Saharan Africa sub-optimally interrupt Streptococcus pneumoniae vaccine-serotype (VT) carriage and transmission. Here we assess PCV carriage using rolling, prospective nasopharyngeal carriage surveys between 2015 and 2018, 3.6–7.1 years after Malawi’s 2011 PCV13 introduction. Carriage decay rate is analysed using non-linear regression. Despite evidence of reduction in VT carriage over the study period, there is high persistent residual carriage. This includes among PCV-vaccinated children 3–5-year-old (16.1% relative reduction from 19.9% to 16.7%); PCV-unvaccinated children 6–8-year-old (40.5% reduction from 26.4% to 15.7%); HIV-infected adults 18-40-years-old on antiretroviral therapy (41.4% reduction from 15.2% to 8.9%). VT carriage prevalence half-life is similar among PCV-vaccinated and PCV-unvaccinated children (3.26 and 3.34 years, respectively). Compared with high-income settings, there is high residual VT carriage 3.6–7.1 years after PCV introduction. Rigorous evaluation of strategies to augment vaccine-induced control of carriage, including alternative schedules and catch-up campaigns, is required.

Impact of pneumococcal conjugate vaccines (PCV) in controlling carriage needs to be evaluated to inform vaccine policy. Here, Swarthout et al. show in a prospective rolling cross-sectional study in Malawi a high residual prevalence of vaccine-serotype S. pneumoniae 7 years after PCV introduction.

Epidemiology Characteristics of Streptococcus pneumoniae From Children With Pneumonia in Shanghai: A Retrospective Study

Background: Streptococcus pneumoniae is the most common pathogen causing death in children under 5 years old. This retrospective surveillance aimed to analyze serotype distribution, drug resistance, virulence factors, and molecular characteristics of pneumonia isolates from children in Shanghai, China. Methods: A total of 287 clinical pneumococcal isolates were collected from January to December in 2018 and were divided into community-acquired pneumonia (CAP) and healthcare-associated pneumonia (HAP) two groups according to where someone contracts the infection. All isolates were serotyped by multiplex sequential PCR and antimicrobial susceptibility testing was performed using E-test or disk diffusion method. The molecular epidemiology was analyzed using multilocus sequence typing and seven housekeeping genes were sequenced to identified the sequence types (STs). In addition, we investigated the presence of virulence genes via PCR. Results: The most common serotypes were 19F, 6A, 19A, 23F, 14, and 6B, and the coverage rates of the 7-, 10- and 13-valent pneumococcal conjugate vaccines were 58.9, 58.9, and 80.5%, respectively. More PCV13/non-PCV7 serotypes and higher rate of penicillin non-susceptible S. pneumoniae were seen in HAP. Molecular epidemiological typing showed a high level of diversity and five international antibiotic-resistant clones were found, including Taiwan^19F-14, Spain^23F-1, Spain^6B-2, Taiwan^23F-15 and Sweden^15A-25. No significant difference was observed in the presence of virulence genes among the isolates obtained from CAP and HAP. All of the S. pneumoniae isolates carried lytA, ply, psaA, pavA, spxB, htrA, and clpP, and the carriage rate of nanA and piaA were 96.2 and 99.0%. Conversely, cps2A, cbpA, and pspA were present in 33.8-44.3% of the isolates. Conclusions: Serotype changes and emerging multidrug-resistant international clones were found in current study. lytA, ply, psaA, pavA, spxB, htrA, and clpP may be good protein vaccine candidates. Long-term high-quality surveillance should be conducted to assess impact and effectiveness brought by vaccines, and provide a foundation for prevention strategies and vaccine policies.

Identification of evolutionarily conserved virulence factor by selective pressure analysis of Streptococcus pneumoniae

Evolutionarily conserved virulence factors can be candidate therapeutic targets or vaccine antigens. Here, we investigated the evolutionary selective pressures on 16 pneumococcal choline-binding cell-surface proteins since Streptococcus pneumoniae is one of the pathogens posing the greatest threats to human health. Phylogenetic and molecular analyses revealed that cbpJ had the highest codon rates to total numbers of codons under considerable negative selection among those examined. Our in vitro and in vivo assays indicated that CbpJ functions as a virulence factor in pneumococcal pneumonia by contributing to evasion of neutrophil killing. Deficiency of cbpL under relaxed selective pressure also caused a similar tendency but showed no significant difference in mouse intranasal infection. Thus, molecular evolutionary analysis is a powerful tool that reveals the importance of virulence factors in real-world infection and transmission, since calculations are performed based on bacterial genome diversity following transmission of infection in an uncontrolled population.

Protection against fatal pneumonia through mucosal and subcutaneous immunization with the pneumococcal SP0148 protein

Streptococcus pneumoniae infection is associated with very high morbidity and mortality throughout the world. Vaccines are an effective measure for the reduction of S. pneumoniae infection. In particular, protein vaccines are attracting increasing attention because of their good immunogenicity and wide coverage of serotypes. Therefore, identifying effective protein vaccine targets is important for protein vaccine development. SP0148 is a promising protein vaccine target for S. pneumoniae and is capable of reducing S. pneumoniae colonization in the nasopharynx of mice through the IL-17A pathway. However, the protective effects of SP0148 in fatal pneumococcal infection have not been evaluated. This study used subcutaneous and nasal immunization routes to systematically evaluate the protective effects of the SP0148 protein in fatal pneumococcal infection. Subcutaneous and nasal mucosal immunization with recombinant SP0148 protein produced effective immune protection against infection with a lethal dose of S. pneumoniae and significantly prolonged survival time and increased the survival rate of mice. Furthermore, nasal immunization with SP0148 induced mouse splenocytes to secrete high levels of the cytokines IFN-γ and IL-17A. Both recombinant SP0148 protein and its antiserum inhibited the adhesion of S.pneumoniae D39 to A549 human lung epithelial cells in a dose-dependent manner. In summary, SP0148 induced mice to produce protective immune responses to fatal S. pneumoniae infection, and our results could contribute to the accumulating data on the use of SP0148 protein vaccines.

A recombinant conjugated pneumococcal vaccine that protects against murine infections with a similar efficacy to Prevnar-13

The pneumococcal conjugate vaccine (PCV) strongly protects against vaccine serotypes, but the rapid expansion of non-vaccine serotype disease and the vaccine's high expense has reduced its overall impact. We have developed Protein Glycan Coupling Technology (PGCT) as a flexible methodology for making low-cost polysaccharide/protein glycoconjugates recombinantly in Escherichia coli. We have used PGCT to make a recombinant PCV containing serotype 4 capsular polysaccharide linked to the Streptococcus pneumoniae proteins NanA, PiuA, and Sp0148. The introduction of the Campylobacter jejuni UDP-glucose 4-epimerase gene GalE (gne) into E. coli improved the yield of the resulting glycoprotein. PGCT glycoconjugate vaccination generated strong antibody responses in mice to both the capsule and the carrier protein antigens, with the PiuA/capsule glycoconjugate inducing similar anti-capsular antibody responses as the commercial PCV Prevnar-13. Antibody responses to PGCT glycoconjugates opsonised S. pneumoniae and Streptococcus mitis expressing the serotype 4 capsule and promoted neutrophil phagocytosis of S. pneumoniae to a similar level as antisera generated by vaccination with Prevnar-13. Vaccination with the PGCT glycoconjugates protected mice against meningitis and septicaemia with the same efficacy as vaccination with Prevnar-13. In addition, vaccination with the protein antigen components from PGCT glycoconjugates alone provided partial protection against septicaemia and colonisation. These data demonstrate that a vaccine made by PGCT is as effective as Prevnar-13, identifies PiuA as a carrier protein for glycoconjugate vaccines, and demonstrates that linking capsular antigen to S. pneumoniae protein antigens has additional protective benefits that could provide a degree of serotype-independent immunity.

Novel Immunoprotective Proteins of Streptococcus pneumoniae Identified by Opsonophagocytosis Killing Screen

The success of polysaccharide conjugate vaccines represents a major advance in the prevention of pneumococcal disease, but the power of these vaccines is limited by partial spectrum of coverage and high cost. Vaccines using immunoprotective proteins are a promising alternative type of pneumococcal vaccines. In this study, we constructed a library of antisera against conserved pneumococcal proteins predicted to be associated with cell surface or virulence using a combination of bioinformatic prediction and immunization of rabbits with recombinant proteins. Screening of the library by an opsonophagocytosis killing (OPK) assay identified the OPK-positive antisera, which represented 15 (OPK-positive) proteins. Further tests showed that virtually all of these OPK-positive antisera conferred passive protection against lethal infection of virulent pneumococci. More importantly, immunization with recombinant forms of three OPK-positive proteins (SP148, PBP2b, and ScpB), alone or in combination, conferred significant protection against lethal challenge of pneumococcal strains representing capsular serotypes 3, 4, and 6A in a mouse sepsis model. To our best knowledge, this work represents the first example in which novel vaccine candidates are successfully identified by the OPK screening. Our data have also provided further confirmation that the OPK activity may serve as a reliable in vitro surrogate for evaluating vaccine efficacy of pneumococcal proteins.

Immunization with pneumococcal neuraminidases NanA, NanB and NanC to generate neutralizing antibodies and to increase survival in mice

Purpose. Pneumococcal virulence protein-based vaccines can provide serotype-independent protection against pneumococcal infections. Many studies, including clinical observational studies on Thomsen-Friedenrich antigen exposure and haemolytic uremic syndrome, defined the role of neuraminidases NanA, NanB and NanC in host-pneumococcus interaction. Since neuraminidases are major virulence proteins, they are potential targets for both vaccines and small molecule inhibitors. Here we explored the utility of three neuraminidases as protein vaccine antigens to generate neutralizing antibodies and to increase survival following pneumococcal infections.Methodology. Rabbits and mice were immunized subcutaneously with enzymatically active recombinant NanA, NanB and NanC as individual or a combination of the three neuraminidases. Antisera titres were determined by ELISA. Neuraminidase activity inhibition by antiserum was tested by peanut lectin and flow cytometry. Clinical isolates with serotype 3, 6B, 14, 15B, 19A and 23F were used to infect immunized mice by tail vein injection.Results/Key findings. Presence of high levels of IgG antibodies in antisera against NanA, NanB and NanC indicates that all of the three neuraminidases are immunogenic vaccine antigens. To generate potent NanA neutralizing antibodies, both lectin and catalytic domains are essential, whereas for NanB and NanC a single lectin domain is sufficient. Immunization with triple neuraminidases increased the survival of mice when intravenously challenged with clinical isolates of serotype 3 (40 %), 6B (60 %), 15B (60 %), 19A (40 %) and 23F (30 %).Conclusion. We recommend the inclusion of three pneumococcal neuraminidases in future protein vaccine formulations to prevent invasive pneumococcal infection caused by various serotypes.

Towards Identifying Protective B-Cell Epitopes: The PspA Story

Pneumococcal surface protein A (PspA) is one of the most abundant cell surface protein of Streptococcus pneumoniae (S. pneumoniae). PspA variants are structurally and serologically diverse and help evade complement-mediated phagocytosis of S. pneumoniae, which is essential for its survival in the host. PspA is currently been screened for employment in the generation of more effective (serotype independent) vaccine to overcome the limitations of polysaccharide based vaccines, providing serotype specific immune responses. The cross-protection eliciting regions of PspA localize to the α-helical and proline rich regions. Recent data indicate significant variation in the ability of antibodies induced against the recombinant PspA variants to recognize distinct S. pneumoniae strains. Hence, screening for the identification of the topographical repertoire of B-cell epitopes that elicit cross-protective immune response seems essential in the engineering of a superior PspA-based vaccine. Herein, we revisit epitope identification in PspA and the utility of hybridoma technology in directing the identification of protective epitope regions of PspA that can be used in vaccine research.