Streptococcus pneumoniae: virulence factors, pathogenesis, and vaccines

Routine immunization against Streptococcus pneumoniae and Haemophilus influenzae type B and antibiotic consumption in India: a dynamic modeling analysis

Background

Childhood vaccinations can reduce disease burden and associated antibiotic use, in turn reducing the risk of antimicrobial resistance (AMR). We retrospectively estimated the population-level reductions in antibiotic use in India following the introduction of vaccines against Streptococcus pneumoniae and Haemophilius influenzae type B in the national immunization program for children in the mid-2010s and projected future gains to 2028 if vaccination coverage were to be increased.

Methods

Using IndiaSim, a dynamic agent-based microsimulation model (ABM) for India, we simulated the spread of Streptococcus pneumoniae and Haemophilius influenzae type B (Hib) among children to estimate reductions in antibiotic use under the scenarios of: (i) pneumococcal and Hib vaccine coverage levels equivalent to the national coverage of pentavalent diphtheria-pertussis-tetanus third dose (DPT3) compared to a baseline of no vaccination, and (ii) near-universal (90%) coverage of the vaccines compared to pre-COVID national DPT3-level coverage. Model parameters, including national DPT3 coverage rates, were based on data from the National Family Household Survey 2015-2016 and other published sources. We quantified reductions in antibiotic consumption nationally and by state and wealth quintiles.

Findings

We estimate that coverage of S. pneumoniae and Hib vaccines at the same level as DPT3 in India would translate to a 61.4% [95% UI: 43.8-69.5] reduction in attributable antibiotic use compared to a baseline of zero vaccination coverage. Increases in childhood vaccination coverage between 2004 and 2016 have likely reduced attributable antibiotic demand by as much as 93.4% among the poorest quintile. Increasing vaccination coverage by an additional 11 percentage points from 2016 levels results in mortality and antibiotic use across wealth quintiles becoming increasingly similar (p < 0.05), reducing in health inquities. We project that near-universal vaccine coverage would further reduce inequities in antibiotic demand and may eliminate of outbreak-associated antibiotic use from S. pneumoniae and Hib.

Interpretation

Though vaccination has a complex relationship with antibiotic use because both are modulated by socioeconomic factors, increasing vaccinations for S. pneumoniae and Hib may have a significant impact on reducing antibiotic use and improving health outcomes among the poorest individuals.

Funding

The Bill & Melinda Gates Foundation (grant numbers OPP1158136 and OPP1190803).

Pneumococcal antibody response in children with recurrent respiratory tract infections: A descriptive study

BACKGROUND

The pneumococcal antibody response after vaccination with unconjugated pneumococcal vaccine can be evaluated as part of the diagnostic work-up of children with recurrent respiratory tract infections to detect an underlying polysaccharide antibody deficiency. Little is known about the prevalence of polysaccharide antibody deficiency in this population and its therapeutic consequences.

OBJECTIVES

This study aimed to investigate the prevalence of polysaccharide antibody deficiency in children with recurrent respiratory tract infections and to correlate polysaccharide responsiveness with clinical severity. In addition, we aimed to evaluate differences in the immunoglobulin (Ig)G2/IgG ratio, IgA level, and age in relation to the number of deficient serotype-specific antibody responses.

METHODS

Polysaccharide antibody titers for pneumococcal serotypes 8, 9N, and 15B; clinical characteristics; and immunoglobulin levels of 103 children with recurrent respiratory tract infections were retrospectively assessed. American Academy of Allergy, Asthma, and Immunology guidelines were used for the interpretation of the polysaccharide antibody response.

RESULTS

Overall, 28 children (27.2 %) were diagnosed with polysaccharide antibody deficiency. No correlation was found between the number of deficient serotype-specific antibody responses and clinical severity. The study participants with a normal response to all three serotypes had a higher IgG2/IgG ratio than those with one or more deficient responses (p < 0.003). No significant correlation between IgA levels and polysaccharide responsiveness was found. The median age of children with normal polysaccharide responsiveness for the three tested serotypes was higher than that of children with a deficient response to one or more serotypes (p < 0.0025).

CONCLUSION

For a large group of children (18.4 %) with recurrent respiratory tract infections, an underlying mechanism for their susceptibility was defined thanks to diagnostic unconjugated pneumococcal polysaccharide vaccination. Further research is needed to formulate age-specific normal values for polysaccharide responsiveness and to investigate the usefulness of the IgG2/IgG ratio in determining the need for diagnostic unconjugated pneumococcal polysaccharide vaccination.

Demodex Species and Culturable Microorganism Co-Infestations in Patients with Blepharitis

We aimed to determine the prevalence of Demodex spp. and bacterial infection in patients with blepharitis and also to investigate the relationship between culturable microorganisms and Demodex spp. in this study. The study included patients diagnosed with blepharitis (n = 128) and volunteers without ocular problems (n = 113). Eyelash sampling was performed by epilating eight lashes, which were then tested for Demodex spp. using a light microscope. The examination consisted of assessing the patient's vision with and without ocular correction and tonus in both eyes and a careful examination of the anterior segment of both eyes. Bacterial identification was performed based on morphological, physiological, and biochemical methods. The prevalence of Demodex spp. was 8.0% in patients from the control group and all patients with blepharitis. Isolated forms of Demodex spp. were detected in all infested patients in the control group and in 58% of patients with blepharitis. A total of 35% of patients with blepharitis had from three to nine forms of Demodex spp., and 7% of patients with blepharitis had more than 10 mites in every field of vision. We found a statistically significant relationship between Demodex spp. infestation and the occurrence of eye dryness and sensations of burning and tearing, redness of the conjunctiva, feeling of a foreign body, loss of eyelashes, Meibomian gland dysfunction, and cylindrical dandruff. There were statistically significant relationships between Demodex sp. infestation and the presence of hyperopia, Meibomian cysts, chronic eyelid inflammation, and the use of eyeglasses. There was also a statistically significant relationship between the occurrence of Demodex spp. and seborrheic dermatitis and diabetes mellitus. Culturable microorganisms of the ocular surface were found in 8.7% of participants who were uninfested and in all patients infested with D. folliculorum. We isolated Staphylococcus aureus, Acinetobacter baumannii, Streptococcus pneumoniae, Klebsiella oxytoca, and Bacillus spp. from the conjunctival sac only in patients infested with D. folliculorum. This indicates an increased probability of colonization by pathogenic bacteria in patients with demodicosis. Therefore, patients infested with D. folliculorum should undergo a microbiological examination of conjunctival swabs.

Emerging vaccine strategies against the incessant pneumococcal disease

The incidence of invasive pneumococcal disease (IPD) caused by infection with the pathogen Streptococcus pneumoniae (Spn) has been on a downward trend for decades due to worldwide vaccination programs. Despite the clinical successes observed, the Center for Disease Control (CDC) reports that the continued global burden of S. pneumoniae will be in the millions each year, with a case-fatality rate hovering around 5%. Thus, it is a top priority to continue developing new Spn vaccination strategies to harness immunological insight and increase the magnitude of protection provided. As emphasized by the World Health Organization (WHO), it is also crucial to broaden the implementation of vaccines that are already obtainable in the clinical setting. This review focuses on the immune mechanisms triggered by existing pneumococcal vaccines and provides an overview of the current and upcoming clinical strategies being employed. We highlight the associated challenges of serotype selectivity and using pneumococcal-derived proteins as alternative vaccine antigens.

Comparative genomic analysis of two ST320 Streptococcus pneumoniae isolates, representing serotypes 19A and 19F

BACKGROUND

Streptococcus pneumoniae (pneumococcus) represents an important human pathogen, responsible for respiratory and invasive infections in the community. The efficacy of polysaccharide conjugate vaccines formulated against pneumococci is reduced by the phenomenon of serotype replacement in population of this pathogen. The aim of the current study was to obtain and compare complete genomic sequences of two pneumococcal isolates, both belonging to ST320 but differing by the serotype.

RESULTS

Here, we report genomic sequences of two isolates of important human pathogen, S. pneumoniae. Genomic sequencing resulted in complete sequences of chromosomes of both isolates, 2,069,241 bp and 2,103,144 bp in size, and confirmed the presence of cps loci specific for serotypes 19A and 19F. The comparative analysis of these genomes revealed several instances of recombination, which involved not only S. pneumoniae but also presumably other streptococci as donors.

CONCLUSIONS

We report the complete genomic sequences of two S. pneumoniae isolates of ST320 and serotypes 19A and 19F. The detailed comparative analysis of these genomes revealed the history of several recombination events, clustered in the region including the cps locus.

Microbiome-scale analysis of aerosol facemask contamination during nebulization therapy in hospital

BACKGROUND

Microbial contamination of aerosol facemasks could be a source of nosocomial infections during nebulization therapy in hospital, prompting efforts to identify these contaminants. Identification of micro-organisms in medical devices has traditionally relied on culture-dependent methods, which are incapable of detecting the majority of these microbial contaminants. This challenge could be overcome with culture-independent sequencing-based techniques that are suited for the profiling of complex microbiomes.

AIM

To characterize the microbial contaminants in aerosol facemasks used for nebulization therapy, and identify factors influencing the composition of these microbial contaminants with the acquisition and analysis of comprehensive microbiome-scale profiles using culture-independent high-throughput sequencing.

METHODS

Used aerosol facemasks collected from hospitalized patients were analysed with culture-independent 16S rRNA gene-based amplicon sequencing to acquire microbiome-scale comprehensive profiles of the microbial contaminants. Microbiome-based analysis was performed to identify potential sources of microbial contamination in facemasks.

FINDINGS

Culture-independent high-throughput sequencing was demonstrated for the capacity to acquire microbiome-scale profiles of microbial contaminants on aerosol facemasks. Microbial source identification enabled by the microbiome-scale profiles linked microbial contamination on aerosol facemasks to the human skin and oral microbiota. Antibiotic treatment with levofloxacin was found to reduce contamination of the facemasks by oral microbiota.

CONCLUSION

Sequencing-based microbiome-scale analysis is capable of providing comprehensive characterization of microbial contamination in aerosol facemasks. Insight gained from microbiome-scale analysis facilitates the development of effective strategies for the prevention and mitigation of the risk of nosocomial infections arising from exposure to microbial contamination of aerosol facemasks, such as targeted elimination of potential sources of contamination.

Conjugation Mechanism for Pneumococcal Glycoconjugate Vaccines: Classic and Emerging Methods

Licensed glycoconjugate vaccines are generally prepared using native or sized polysaccharides coupled to a carrier protein through random linkages along the polysaccharide chain. These polysaccharides must be chemically modified before covalent linking to a carrier protein in order to obtain a more defined polysaccharide structure that leads to a more rational design and safer vaccines. There are classic and new methods for site-selective glycopolysaccharide conjugation, either chemical or enzymatic modification of the polysaccharide length or of specific amino acid residues of the protein carrier. Here, we discuss the state of the art and the advancement of conjugation of S. pneumoniae glycoconjugate vaccines based on pneumococcal capsular polysaccharides to improve existing vaccines.

Manipulation and exploitation of host immune system by pathogenic Mycobacterium tuberculosis for its advantage

Mycobacterium tuberculosis (Mtb) can become a long-term infection by evading the host immune response. Coevolution of Mtb with humans has resulted in its ability to hijack the host's immune systems in a variety of ways. So far, every Mtb defense strategy is essentially dependent on a subtle balance that, if shifted, can promote Mtb proliferation in the host, resulting in disease progression. In this review, the authors summarize many important and previously unknown mechanisms by which Mtb evades the host immune response. Besides recently found strategies by which Mtb manipulates the host molecular regulatory machinery of innate and adaptive immunity, including the intranuclear regulatory machinery, costimulatory molecules, the ubiquitin system and cellular intrinsic immune components will be discussed. A holistic understanding of these immune-evasion mechanisms is of foremost importance for the prevention, diagnosis and treatment of tuberculosis and will lead to new insights into tuberculosis pathogenesis and the development of more effective vaccines and treatment regimens.

Biochemical Characterization and Synthetic Application of WciN and Its Mutants From Streptococcus pneumoniae Serotype 6B

The biochemical properties of α-1,3-galactosyltransferase WciN from Streptococcus pneumoniae serotype 6B were systemically characterized with the chemically synthesized Glcα-PP-(CH₂)₁₁-OPh as an acceptor substrate. The in vitro site-directed mutation of D38 and A150 residues of WciN was further investigated, and the enzymatic activities of those WciN mutants revealed that A150 residue was the pivotal residue responsible for nucleotide donor recognition and the single-site mutation could completely cause pneumococcus serotype switch. Using WciN_A150P and WciN_A150D mutants as useful tool enzymes, the disaccharides Galα1,3Glcα-PP-(CH₂)₁₁-OPh and Glcα1,3Glcα-PP-(CH₂)₁₁-OPh were successfully prepared in multi-milligram scale in high yields.

Food-web and metabolic interactions of the lung inhabitants Streptococcus pneumoniae and Pseudomonas aeruginosa

Bacteria that successfully adapt to different substrates and environmental niches within the lung and overcome the immune defence can cause serious lung infections. Such infections are generally complex, and recognised as polymicrobial in nature. Both Pseudomonas aeruginosa and Streptococcus pneumoniae can cause chronic lung infections and were both detected in cystic fibrosis (CF) lung at different stages. In this study, single and dual species cultures of Pseudomonas aeruginosa and Streptococcus pneumoniae were studied under well controlled planktonic growth conditions. Under pH-controlled conditions, both species apparently benefited from the presence of the other. In co-culture with P. aeruginosa, S. pneumoniae grew efficiently under aerobic conditions, whereas in pure S. pneumoniae culture, growth inhibition occurred in bioreactors with dissolved oxygen concentrations above the microaerobic range. Lactic acid and acetoin that are produced by S. pneumoniae was efficiently utilised by P. aeruginosa. In pH-uncontrolled co-cultures, the low pH triggered by S. pneumoniae assimilation of glucose and lactic acid production negatively affected the growth of both strains. Nevertheless, ammonia production improved significantly, and P. aeruginosa growth dominated at later growth stages. This study revealed unreported metabolic interactions of two important pathogenic microorganisms and shed new lights into pathophysiology of bacterial lung infection. This article is protected by copyright. All rights reserved.

Pneumolysin/Plasma Protein Adsorption, Bacterial Adherence, and Cell Adhesion Characteristics of a Cell-Membrane-Mimicking Polymer System

This study delivers the first report on a cell-membrane-mimicking polymer system, poly[oxy(4-(13-cholenoatenonyl)-1,2,3-triazoyl-1-methyl)ethylene-random-oxy(4-(13-phosphorylcholinenonyl)-1,2,3-triazoyl-1-methyl)ethylene] (PGA-Chol_mPC_n) films in various compositions in terms of physicochemical properties, protein adsorptions, bacterial adherences, and human cell adhesions. Higher Chol-containing PGA-Chol_mPC_n in a self-assembled multi-bilayer membrane structure is confirmed to show excellently high affinity to pneumolysin (a cytolysin) and its C-terminal fragment (domain 4) but substantially suppressed affinity to the N-terminal fragment (domains 1-3) and further to plasma proteins. Furthermore, the adherences of pathogenic bacteria are increased favorably; however, the adhesion and proliferation of a human HEp-2 cell line are hindered severely. In contrast, higher-PC-containing PGA-Chol_mPC_n membranes promote HEp-2 cell adhesion and proliferation but significantly suppress the adsorptions of pneumolysin and its fragments and plasma proteins as well as bacterial adherence. The results collectively confirm that PGA-Chol_mPC_n can yield a membrane platform enriched with hydrophobic Chol and hydrophilic and zwitterionic PC moieties in any desired compositions, providing highly selective and sensitive physicochemical characters and biocompatibilities which are demanded for applications in various fields including biomedicine, cosmetics, and environmentally friendly consumer products.

Pneumococcal carriage in unvaccinated children at the time of vaccine implementation into the national immunization program in Poland

We investigated pneumococcal carriage among unvaccinated children under five years of age at a time when the conjugate polysaccharide vaccine (PCV) was introduced in Poland into the national immunization program (NIP). Paired nasopharyngeal swab (NPS) and saliva samples collected between 2016 and 2020 from n = 394 children were tested with conventional culture and using qPCR. The carriage rate detected by culture was 25.4% (97 of 394), by qPCR 39.1% (155 of 394), and 40.1% (158 of 394) overall. The risk of carriage was significantly elevated among day care center attendees, and during autumn/winter months. Among isolates cultured, the most common serotypes were: 23A, 6B, 15BC, 10A, 11A. The coverage of PCV10 and PCV13 was 23.2% (23 of 99) and 26.3% (26 of 99), respectively. Application of qPCR lead to detection of 168 serotype carriage events, with serogroups 15, 6, 9 and serotype 23A most commonly detected. Although the highest number of carriers was identified by testing NPS with qPCR, saliva significantly contributed to the overall number of detected carriers. Co-carriage of multiple serotypes was detected in 25.3% (40 of 158) of carriers. The results of this study represent a baseline for the future surveillance of effects of pneumococcal vaccines in NIP in Poland.

Microbiome Profiles of Nebulizers in Hospital Use

Background: Nebulizers are used to provide treatment to respiratory patients. Concerns over nosocomial infection risks from contaminated nebulizers raise the critical need to identify all microbial populations in nebulizers used by patients. However, conventional culture-dependent techniques are inadequate with the ability to identify specific microbial populations only. Therefore, the aims of this study were to acquire complete profiles of microbiomes in nebulizers used by in-patients with culture-independent high-throughput sequencing and identify sources of microbial contaminants for the development of effective practices to reduce microbial contamination in nebulizer devices. Methods: This study was conducted at the University of Tennessee Medical Center in Knoxville, TN. Nebulizers were collected between May 2018 and October 2018 from inpatients admitted to the floors for pneumonia or chronic obstructive pulmonary disease exacerbations. Nebulizers were sampled for 16S rRNA gene-based amplicon sequencing to profile nebulizer microbiomes and perform phylogenetic analysis. A Bayesian community-wide culture-independent microbial source tracking technique was used to quantify the contribution of human-associated microbiota as potential sources of nebulizer contamination. Results: Culture-independent sequencing detected diverse microbial populations in nebulizers, represented by 18 abundant genera. Stenotrophomonas was identified as the most abundant genus, accounting for 12.4% of the nebulizer microbiome, followed by Rhizobium, Staphylococcus, Streptococcus, and Ralstonia. Phylogenetic analysis revealed the presence of multiple phylotypes with close relationship to potential pathogens. Contributing up to 15% to nebulizer microbiomes, human-associated microbiota was not identified as the primary sources of nebulizer contamination. Conclusion: Culture-independent sequencing was demonstrated to be capable of acquiring comprehensive profiles of microbiomes in nebulizers used by in-patients. Phylogenetic analysis identified differences in pathogenicity between closely related phylotypes. Microbiome profile-enabled community-wide culture-independent microbial source tracking suggested greater importance of environmental sources than human sources as contributors to nebulizer microbiomes, providing important insight for the development of effective strategies for the monitoring and control of nebulizer devices to mitigate infection risks in the hospital.

Glucocorticoid-Induced Leucine Zipper Alleviates Lung Inflammation and Enhances Bacterial Clearance During Pneumococcal Pneumonia

Pneumonia is a leading cause of morbidity and mortality. While inflammation is a host protective response that ensures bacterial clearance, a finely regulated response is necessary to prevent bystander tissue damage. Glucocorticoid (GC)-induced leucine zipper (GILZ) is a GC-induced protein with anti-inflammatory and proresolving bioactions, yet the therapeutical role of GILZ in infectious diseases remains unexplored. Herein, we investigate the role and effects of GILZ during acute lung injury (ALI) induced by LPS and Streptococcus pneumoniae infection. GILZ deficient mice (GILZ^−/−) presented more severe ALI, characterized by increased inflammation, decreased macrophage efferocytosis and pronounced lung damage. In contrast, pulmonary inflammation, and damage were attenuated in WT mice treated with TAT-GILZ fusion protein. During pneumococcal pneumonia, TAT-GILZ reduced neutrophilic inflammation and prevented the associated lung damage. There was also enhanced macrophage efferocytosis and bacterial clearance in TAT-GILZ-treated mice. Mechanistically, TAT-GILZ enhanced macrophage phagocytosis of pneumococcus, which was lower in GILZ^−/− macrophages. Noteworthy, early treatment with TAT-GILZ rescued 30% of S. pneumoniae-infected mice from lethal pneumonia. Altogether, we present evidence that TAT-GILZ enhances host resilience and resistance to pneumococcal pneumonia by controlling pulmonary inflammation and bacterial loads leading to decreased lethality. Exploiting GILZ pathways holds promise for the treatment of severe respiratory infections.

Pneumococcal Serotype Identification by Capsular Sequence Typing (CST): A Modified Novel Approach for Serotyping Directly in Clinical Samples

As almost 60-70% of Invasive Pneumococcal Disease (IPD) is identified by nonculture methods in Greece, serotyping is of high importance for the better monitoring of pneumococcal serotypes due to the availability of conjugate vaccines. The aim of the study was the modification and direct application of the Capsular Sequence Typing (CST) assay in clinical samples in order to serotype Streptococcus pneumoniae culture-negative, Polymerase Chain Reaction (PCR_-positive samples, followed by CST group specific single-tube PCR assays. A two-step PCR modified assay was applied on a total of 306 samples (such as CSF, blood, pleural and middle ear fluids, isolates) obtained from 283 patients with IPD. The overall performance permits a rapid, accurate and cost-effective method for nonculture pneumococcal serotyping. As the management of IPD is closely related to the continuous monitoring of pneumococcal serotypes, the proposed approach proved to be a valuable tool for the typing and epidemiological monitoring of S. pneumoniae, for the evaluation of the overall impact of vaccination programs in the era of pneumococcal conjugate vaccines, in order to initiate the appropriate vaccination strategy.

Contribution of Nε-lysine Acetylation towards Regulation of Bacterial Pathogenesis

N^ε-lysine acetylation is an important, dynamic regulatory posttranslational modification (PTM) that is common in bacteria. Protein acetylomes have been characterized for more than 30 different species, and it is known that acetylation plays important regulatory roles in many essential biological processes. The levels of acetylation are enzymatically controlled by the opposing actions of lysine acetyltransferases and deacetylases. In bacteria, a second mechanism of acetylation exists and occurs via an enzyme-independent manner using the secondary metabolite acetyl-phosphate. Nonenzymatic acetylation accounts for global low levels of acetylation. Recently, studies concerning the role of protein acetylation in bacterial virulence have begun. Acetylated virulence factors have been identified and further characterized. The roles of the enzymes that acetylate and deacetylate proteins in the establishment of infection and biofilm formation have also been investigated. In this review, we discuss the acetylomes of human bacterial pathogens. We highlight examples of known acetylated virulence proteins and examine how they affect survival in the host. Finally, we discuss how acetylation might influence host-pathogen interactions and look at the contribution of acetylation to antimicrobial resistance.

Synthetic Analogs of Streptococcus pneumoniae Capsular Polysaccharides and Immunogenic Activities of Glycoconjugates

Streptococcus pneumoniae is a Gram-positive bacterium (pneumococcus) that causes severe diseases in adults and children. It was established that some capsular polysaccharides of the clinically significant serotypes of S. pneumoniae in the composition of commercial pneumococcal polysaccharide or conjugate vaccines exhibit low immunogenicity. The review considers production methods and structural features of the synthetic oligosaccharides from the problematic pneumococcal serotypes that are characterized with low immunogenicity due to destruction or detrimental modification occurring in the process of their preparation and purification. Bacterial serotypes that cause severe pneumococcal diseases as well as serotypes not included in the composition of the pneumococcal conjugate vaccines are also discussed. It is demonstrated that the synthetic oligosaccharides corresponding to protective glycotopes of the capsular polysaccharides of various pneumococcal serotypes are capable of inducing formation of the protective opsonizing antibodies and immunological memory. Optimal constructs of oligosaccharides from the epidemiologically significant pneumococcal serotypes are presented that can be used for designing synthetic pneumococcal vaccines, as well as test systems for diagnosis of S. pneumoniae infections and monitoring of vaccination efficiency .

Sequential Linkage of Carbohydrate Antigens to Mimic Capsular Polysaccharides: Toward Semisynthetic Glycoconjugate Vaccine Candidates against Streptococcus pneumoniae Serotype 14

Vaccines based on isolated polysaccharides successfully protect humans from bacterial pathogens such as Streptococcus pneumoniae. Because polysaccharide production and isolation can be technically challenging, glycoconjugates containing synthetic antigens are an attractive alternative. Typically, the shortest possible oligosaccharide antigen is preferable as syntheses of longer structures are more difficult and time-consuming. Combining several protective epitopes or polysaccharide repeating units as blocks by bonds other than glycosidic linkages would greatly reduce the synthetic effort if the immunological response to the polysaccharide could be retained. To explore this concept, we bridged the well-understood and immunologically potent RU of S. pneumoniae serotype 14 (ST14) with an aliphatic spacer and conjugated it to the carrier protein CRM197. Mice immunized with the spacer-bridged glycan conjugates produced high levels of specific antibodies after just one or two vaccine doses, while the tetrasaccharide repeating unit alone required three doses. The antibodies recognized specifically ST14 CPS, while no significant antibody levels were raised against the spacer or unrelated CPS. Synthetic vaccines generated antibodies with opsonic activity. Mimicking polysaccharides by coupling repeating unit antigens via an aliphatic spacer may prove useful also for the development of other glycoconjugate vaccine candidates, thereby reducing the synthetic complexity while enhancing a faster immune response.

Recent progress and challenges on the bioassay of pathogenic bacteria

The present review (containing 242 references) illustrates the importance and application of optical and electrochemical methods as well as their performance improvement using various methods for the detection of pathogenic bacteria. The application of advanced nanomaterials including hyper branched nanopolymers, carbon-based materials and silver, gold and so on. nanoparticles for biosensing of pathogenic bacteria was also investigated. In addition, a summary of the applications of nanoparticle-based electrochemical biosensors for the identification of pathogenic bacteria has been provided and their advantages, detriments and future development capabilities was argued. Therefore, the main focus in the present review is to investigate the role of nanomaterials in the development of biosensors for the detection of pathogenic bacteria. In addition, type of nanoparticles, analytes, methods of detection and injection, sensitivity, matrix and method of tagging are also argued in detail. As a result, we have collected electrochemical and optical biosensors designed to detect pathogenic bacteria, and argued outstanding features, research opportunities, potential and prospects for their development, according to recently published research articles.

Estimating the impact of pneumococcal conjugate vaccines on childhood pneumonia in sub-Saharan Africa: A systematic review

Background: This study aimed to summarise the evidence on the impact of routine administration of 10-valent and 13-valent pneumococcal conjugate vaccines on pneumonia in children under five years of age in sub-Saharan Africa. Methods: A systematic search of the literature was conducted including primary research reporting on the impact of 10- or 13-valent pneumococcal vaccines on childhood pneumonia in a sub-Saharan African country. Case-control, cohort, pre-post and time-series study designs were eligible for inclusion. Thematic narrative synthesis was carried out to summarise the findings. Results: Eight records were included in the final analysis, 6 records were pre-post or time-series studies, 1 was a case-control study and 1 report combined pre-post and case-control studies. Vaccine impact on clinical pneumonia measured as percentage reduction in risk (%RR) was mostly non-significant. The reduction in risk was more consistent in radiological and pneumococcal pneumonia. Conclusions: Evidence of the positive impact of routine infant pneumococcal vaccination on clinical pneumonia incidence in sub-Saharan Africa is inconclusive. Ongoing surveillance and further research is required to establish the long term trend in pneumonia epidemiology and aetiology after PCV introduction. PROSPERO registration: CRD42019142369 30/09/19.

Estimating the impact of pneumococcal conjugate vaccines on childhood pneumonia in sub-Saharan Africa: A systematic review

Background: This study aimed to summarise the evidence on the impact of routine administration of 10-valent and 13-valent pneumococcal conjugate vaccines on pneumonia in children under five years of age in sub-Saharan Africa. Methods: A systematic search of the literature was conducted including primary research reporting on the impact of 10- or 13-valent pneumococcal vaccines on childhood pneumonia in a sub-Saharan African country. Case-control, cohort, pre-post and time-series study designs were eligible for inclusion. Thematic narrative synthesis was carried out to summarise the findings. Results: Eight records were included in the final analysis, 6 records were pre-post or time-series studies, 1 was a case-control study and 1 report combined pre-post and case-control studies. Vaccine impact on clinical pneumonia measured as percentage reduction in risk (%RR) was mostly non-significant. The reduction in risk was more consistent in radiological and pneumococcal pneumonia. Conclusions: Evidence of the positive impact of routine infant pneumococcal vaccination on clinical pneumonia incidence in sub-Saharan Africa is inconclusive. Ongoing surveillance and further research is required to establish the long term trend in pneumonia epidemiology and aetiology after PCV introduction. PROSPERO registration: CRD42019142369 30/09/19.

Synthesis of Streptococcus pneumoniae serotype 9V oligosaccharide antigens

Streptococcus pneumoniae (SP) bacteria cause serious invasive diseases. SP bacteria are covered by a capsular polysaccharide (CPS) that is a virulence factor and the basis for SP polysaccharide and glycoconjugate vaccines. The serotype 9V is part of the currently marketed conjugate vaccine and contains an acetate modification. To better understand the importance of glycan modifications in general and acetylation in particular, defined oligosaccharide antigens are needed for serological and immunological studies. Here, we demonstrate a convergent [2 + 3] synthetic strategy to prepare the pentasaccharide repeating unit of 9V with and without an acetate group at the C-6 position of mannosamine.

Antibacterial mechanism of gold nanoparticles on Streptococcus pneumoniae

Streptococcus pneumoniae is a causal agent of otitis media, pneumonia, meningitis and severe cases of septicemia. This human pathogen infects elderly people and children with a high mortality rate of approximately one million deaths per year worldwide. Antibiotic-resistance of S. pneumoniae strains is an increasingly serious health problem; therefore, new therapies capable of combating pneumococcal infections are indispensable. The application of gold nanoparticles has emerged as an option in the control of bacterial infections; however, the mechanism responsible for bacterial cell lysis remains unclear. Specifically, it has been observed that gold nanoparticles are capable of crossing different structures of the S. pneumoniae cells, reaching the cytosol where inclusion bodies of gold nanoparticles are noticed. In this work, a novel process for the separation of such inclusion bodies that allowed the analysis of the biomolecules such as carbohydrates, lipids and proteins associated with the gold nanoparticles was developed. Then, it was possible to separate and identify proteins associated with the gold nanoparticles, which were suggested as possible candidates that facilitate the interaction and entry of gold nanoparticles into S. pneumoniae cells.

In vitro and in vivo characterization of the interaction, proinflammatory, immunomodulatory and antigenic properties of capsular polysaccharide from Streptococcus pneumoniae serotype 1

Pneumococcal capsular polysaccharide (PCP) is the major virulence determinant of Streptococcus pneumoniae (pneumococcus). Strains devoid of the capsule are avirulent or highly attenuated. PCP is present in soluble form and on pneumococci in infected individuals. The present study was undertaken to study the interaction of PCP from serotype 1 (PCP1) with immune cells, and its proinflammatory, immunomodulatory and antigenic properties. Binding of PCP1 to the surface of immune cells led to proinflammatory cytokine production which was not cell line or cytokine restricted. HEK293T transfectants expressing TLR1 and TLR2 produced IL-8 upon stimulation with PCP1, untransfected cells did not do so. PCP1 failed to induce TNF-α production from RAW264.7 cells when pre-incubated with a TLR2 blocking antibody. The surface binding of PCP1 was abrogated in the presence of TLR2 blocking antibody. PCP1 failed to bind TLR2 deficient RAW264.7 cells and induce TNF-α production. Unlike PCP1, alkali-treated PCP1 failed to stimulate RAW264.7 cells to produce TNF-α indicating the importance of alkali-sensitive moieties like O-acetyl groups. Alkali-treated PCP1 elicited lower anti-PCP1 antibody response. Mice experiments suggested that alkali-sensitive groups are significant target of protective antibodies in PCP1 immunized mice. Our findings demonstrate that PCP1 is an important modulator of immune response against pneumococci.

PspA facilitates evasion of pneumococci from bactericidal activity of neutrophil extracellular traps (NETs)

Pneumococcal strains are variably resistant to killing by neutrophil extracellular traps (NETs). We hypothesize that this variability in resistance is due to heterogeneity in pneumococcal surface protein A (PspA), a structurally diverse virulence factor of Streptococcus pneumoniae. Pneumococcal strains showed variability in induction of NETs and in susceptibility to killing by NETs. The variability in susceptibility to NETs-mediated killing of pneumococcal strains is attributed to PspA, as strains lacking the surface expression of PspA were significantly more sensitive to NETs-mediated killing compared to the wild-type strains. Using pspA switch mutants we were further able to demonstrate that NETs induction and killing by NETs is a function of PspA as mutants with switch PspA demonstrated donor phenotype. Antibody to PspA alone showed an increase in induction of NETs, and NETs thus generated were able to trap and kill pneumococci. Pneumococci opsonized with antibody to PspA showed increase adherence to NETs but a decrease susceptibility to killing by NETs. In conclusion we demonstrate a novel role for pneumococcal PspA in resisting NETs mediated killing and allowing the bacteria to escape containment by blocking binding of pneumococci to NETs.

Next-Generation Whole-Cell Pneumococcal Vaccine

Streptococcus pneumoniae remains a major public health hazard. Although Pneumococcal Conjugate Vaccines (PCVs) are available and have significantly reduced the rate of invasive pneumococcal diseases, there is still a need for new vaccines with unlimited serotype coverage, long-lasting protection, and lower cost to be developed. One of the most promising candidates is the Whole-Cell Pneumococcal Vaccine (WCV). The new generation of whole-cell vaccines is based on an unencapsulated serotype that allows the expression of many bacterial antigens at a lower cost than a recombinant vaccine. These vaccines have been extensively studied, are currently in human trial phase 1/2, and seem to be the best treatment choice for pneumococcal diseases, especially for developing countries.

Serotypes & penicillin susceptibility of Streptococcus pneumoniae isolated from children admitted to a tertiary teaching hospital in Malaysia

Background & objectives:

Streptococcus pneumoniae (pneumococcus) is a highly invasive extracellular pathogen that causes diseases such as pneumonia, otitis media and meningitis. This study was undertaken to determine the serotype diversity and penicillin susceptibility of S. pneumoniae isolated from paediatric patients in a tertiary teaching hospital in Malaysia.

Methods:

A total of 125 clinical isolates collected from January 2013 to May 2015 were serotyped using seven sequential multiplex polymerase chain reactions. The susceptibility of these isolates to penicillin was also investigated.

Results:

Serotypes detected among the isolates were serotypes 3, 6A/B, 6C, 11/A/D/F, 15A/F, 19A, 19F, 23A, 23F, 34. Serotypes 19F and 6A/B were the most prevalent serotypes detected. Most of the S. pneumoniae were isolated from nasopharyngeal samples of children below five years of age. Majority of the isolates were penicillin susceptible. Only 5.6 per cent of the isolates were non-susceptible to penicillin, mostly of serotype 19F.

Interpretation & conclusions:

Our study revealed the distribution of various serotypes in S. pneumoniae isolates obtained from children in a teaching hospital at Kuala Lumpur, Malaysia and decreasing rates of penicillin resistance among them. The shifts in serotypes and susceptibility to penicillin from time to time have been observed. Continuous monitoring and surveillance are pivotal for better infection control and management of pneumococcal infections among children.

Asymptomatic carriage of Streptococcus pneumoniae detected by qPCR on the palm of hands of populations in rural Senegal

Aside from malaria, infectious diseases are an important cause of death in sub-Saharan Africa and continue to pose major public health problems in African countries, notably pneumonia. Streptococcus pneumoniae remains the most common bacterial cause of pneumonia in all age groups. The skin is one of the main infection sites followed by the oropharynx. The skin carriage of certain pathogenic bacteria such as S. pneumoniae is often ignored or under-diagnosed. Finally, the mode of transmission of these infections remains uncertain. Here, we hypothesized that skin could play a role in the transmission of these infections. We collected 649 cotton swabs from a healthy population in Dielmo and Ndiop, rural Senegal. The sampling was carried out on the palm of the hands. After DNA extraction and actin control, qPCR targeting eight different bacteria was performed on 614 skin samples. We detected Streptococcus pneumoniae in 33.06% (203/614), Staphylococcus aureus in 18.08% (111/614) and Streptococcus pyogenes in 1.95% (12/614) of samples. A skin S. pneumoniae carriage was detected in more than a third of a rural population in rural Africa, highlighting the need to develop hand disinfection programs in order to reduce the burden of infections.

Purification of Capsular Polysaccharides of Streptococcus pneumoniae: Traditional and New Methods

Pneumonia caused by Streptococcus pneumoniae is a major bacterial disease responsible for many deaths worldwide each year and is particularly dangerous in children under 5 years old and adults over 50. The capsular polysaccharide (CPS) constitutes the outermost layer of the bacterial cell and is the main virulence factor. Regardless of whether pharmaceutical agents are composed of CPS alone or protein-conjugated CPS, CPS purification is essential for the development of vaccines against S. pneumoniae. These vaccines are effective and safe but remain quite expensive. This review describes the methods currently available for CPS purification. Advances in CPS purification methods are aimed at improvements in quality and yield and, above all, process simplification.

Structural Characteristics of Pneumolysin and Its Domains in a Biomimetic Solution

Pneumolysin (PLY) and its truncated fragments, domains 1-3 (D_1-3), and domain 4 (D₄), were purified as recombinant proteins after being cloned and over-expressed in Escherichia coli. The three-dimensional structures of these proteins were quantitatively investigated in a biomimetic condition, phosphate buffered saline (PBS) by synchrotron X-ray scattering. X-ray scattering analysis revealed important structural features including structural parameters. PLY was present as a monomeric form in PBS. The monomeric form resembled its crystallographic structure with a discrepancy of only 6.3%, confirming that PLY forms a stable structure and, thus, retains its structure in the crystalline state and even in PBS solution. D₄ was also present as a monomeric form, but its structure was very different from that of the corresponding part in the crystallographic PLY structure; the discrepancy was 92.0%. Such a dissimilar structure might originate from a less folded-chain conformation. This result suggested that the structure of D₄ is highly dependent on the crystalline or solution state and further on the presence or absence of the D_1-3 unit. In contrast, D_1-3 was dimeric rather than monomeric. Its structure was close to the most probable dimeric form of the corresponding part in the crystallographic PLY structure with 13.1% discrepancy. This fact indicated that the D_1-3 unit forms a stable structure and, indeed, such structure is well maintained in the crystalline state as well as in PBS although presented as a dimer. This result further supported that the whole structural stability of PLY is mainly attributed to the structure of D_1-3. All of PLY, D_1-3, and D₄ revealed aggregation tendencies during purification and storage. Overall, the structural characteristics of PLY and its domains in PBS may correlate to the PLY oligomer formation yielding large pore structures for the penetration of cell membranes.

Structural investigation of human S. aureus-targeting antibodies that bind wall teichoic acid

Infections caused by methicillin-resistant Staphylococcus aureus (MRSA) are a growing health threat worldwide. Efforts to identify novel antibodies that target S. aureus cell surface antigens are a promising direction in the development of antibiotics that can halt MRSA infection. We biochemically and structurally characterized three patient-derived MRSA-targeting antibodies that bind to wall teichoic acid (WTA), which is a polyanionic surface glycopolymer. In S. aureus, WTA exists in both α- and β-forms, based on the stereochemistry of attachment of a N-acetylglucosamine residue to the repeating phosphoribitol sugar unit. We identified a panel of antibodies cloned from human patients that specifically recognize the α or β form of WTA, and can bind with high affinity to pathogenic wild-type strains of S. aureus bacteria. To investigate how the β-WTA specific antibodies interact with their target epitope, we determined the X-ray crystal structures of the three β-WTA specific antibodies, 4462, 4497, and 6078 (Protein Data Bank IDs 6DWI, 6DWA, and 6DW2, respectively), bound to a synthetic WTA epitope. These structures reveal that all three of these antibodies, while utilizing distinct antibody complementarity-determining region sequences and conformations to interact with β-WTA, fulfill two recognition principles: binding to the β-GlcNAc pyranose core and triangulation of WTA phosphate residues with polar contacts. These studies reveal the molecular basis for targeting a unique S. aureus cell surface epitope and highlight the power of human patient-based antibody discovery techniques for finding novel pathogen-targeting therapeutics.

Streptococcus pneumoniae's Virulence and Host Immunity: Aging, Diagnostics, and Prevention

Streptococcus pneumoniae is an infectious pathogen responsible for millions of deaths worldwide. Diseases caused by this bacterium are classified as pneumococcal diseases. This pathogen colonizes the nasopharynx of its host asymptomatically, but overtime can migrate to sterile tissues and organs and cause infections. Pneumonia is currently the most common pneumococcal disease. Pneumococcal pneumonia is a global health concern and vastly affects children under the age of five as well as the elderly and individuals with pre-existing health conditions. S. pneumoniae has a large selection of virulence factors that promote adherence, invasion of host tissues, and allows it to escape host immune defenses. A clear understanding of S. pneumoniae's virulence factors, host immune responses, and examining the current techniques available for diagnosis, treatment, and disease prevention will allow for better regulation of the pathogen and its diseases. In terms of disease prevention, other considerations must include the effects of age on responses to vaccines and vaccine efficacy. Ongoing work aims to improve on current vaccination paradigms by including the use of serotype-independent vaccines, such as protein and whole cell vaccines. Extending our knowledge of the biology of, and associated host immune response to S. pneumoniae is paramount for our improvement of pneumococcal disease diagnosis, treatment, and improvement of patient outlook.

Current status and future directions of invasive pneumococcal diseases and prophylactic approaches to control them

Streptococcus pneumoniae is a major human bacterial pathogen responsible for millions of deaths each year and significantly more illnesses worldwide. With over 90 different serotypes, providing effective vaccine programs has been a continuing challenge. Since 1983, the world has been introduced to four different pneumococcal vaccines (PPSV23, PCV7, PCV10, and PCV13) each with their own complications and successes. Since vaccination programs began, a decrease in the overall rate of pneumococcal pneumonia and associated diseases has been observed, notably in higher risk populations. However, with a decrease in incidence of vaccine type pneumococcal serotypes, increases in non-vaccine serotypes of the bacteria have been observed along with serotype switching. Additionally, a rise in antibiotic resistant strains of S. pneumoniae is noted. Here we discuss both the positive and negative clinical manifestations of pneumonia vaccine programs and discuss the challenges in pneumococcal vaccine design.

A novel extracellular vesicle-associated endodeoxyribonuclease helps Streptococcus pneumoniae evade neutrophil extracellular traps and is required for full virulence

Streptococcus pneumoniae (pneumococcus) is a major bacterial pathogen that causes pneumonia and septicemia in humans. Pneumococci are cleared from the host primarily by antibody dependent opsonophagocytosis by phagocytes like neutrophils. Neutrophils release neutrophil extracellular traps (NETs) on contacting pneumococci. NETs immobilize pneumococci and restrict its dissemination in the host. One of the strategies utilized by pneumococci to evade the host immune response involves use of DNase(s) to degrade NETs. We screened the secretome of autolysin deficient S. pneumoniae to identify novel DNase(s). Zymogram analysis revealed 3 bands indicative of DNase activity. Mass spectrometric analysis led to the identification of TatD as a potential extracellular DNase. Recombinant TatD showed nucleotide sequence-independent endodeoxyribonuclease activity. TatD was associated with extracellular vesicles. Pneumococcal secretome degraded NETs from human neutrophils. Extracellular vesicle fraction from tatD deficient strain showed little NET degrading activity. Recombinant TatD efficiently degraded NETs. tatD deficient pneumococci showed lower bacterial load in lungs, blood and spleen in a murine sepsis model compared to wildtype strain, and showed less severe lung pathology and compromised virulence. This study provides insights into the role of a novel extracellular DNase in evasion of the innate immune system.

Synthetic avenues towards a tetrasaccharide related to Streptococcus pneumonia of serotype 6A

Streptococcus pneumonia (SPn) is a Gram-positive bacterium which causes life threatening diseases. The bacteria protect themselves against non-specific host defence by an external polysaccharide (PS) capsule which bears a repeating unit, α-D-Galp(1->3)-α-D-Glcp(1->3)-α-L-Rhap(1->3)-D-Rib (SPn 6A). A closer look at the structure reveals the presence of α-linked galactose and glucose residues. The synthesis of these 1,2-cis glycosidic linkages are considered challenging particularly in the context of a one-pot oligosaccharide synthesis. We have synthesized the aforesaid tetrasaccharide (SPn 6A) based on both stepwise and sequential one-pot glycosylation reactions using easily accessible common building blocks; eventually similar overall yields were obtained in both cases.

Bacterial Adherence and Dwelling Probability: Two Drivers of Early Alveolar Infection by Streptococcus pneumoniae Identified in Multi-Level Mathematical Modeling

Pneumococcal infection is the most frequent cause of pneumonia, and one of the most prevalent diseases worldwide. The population groups at high risk of death from bacterial pneumonia are infants, elderly and immunosuppressed people. These groups are more vulnerable because they have immature or impaired immune systems, the efficacy of their response to vaccines is lower, and antibiotic treatment often does not take place until the inflammatory response triggered is already overwhelming. The immune response to bacterial lung infections involves dynamic interactions between several types of cells whose activation is driven by intracellular molecular networks. A feasible approach to the integration of knowledge and data linking tissue, cellular and intracellular events and the construction of hypotheses in this area is the use of mathematical modeling. For this paper, we used a multi-level computational model to analyse the role of cellular and molecular interactions during the first 10 h after alveolar invasion of Streptococcus pneumoniae bacteria. By “multi-level” we mean that we simulated the interplay between different temporal and spatial scales in a single computational model. In this instance, we included the intracellular scale of processes driving lung epithelial cell activation together with the scale of cell-to-cell interactions at the alveolar tissue. In our analysis, we combined systematic model simulations with logistic regression analysis and decision trees to find genotypic-phenotypic signatures that explain differences in bacteria strain infectivity. According to our simulations, pneumococci benefit from a high dwelling probability and a high proliferation rate during the first stages of infection. In addition to this, the model predicts that during the very early phases of infection the bacterial capsule could be an impediment to the establishment of the alveolar infection because it impairs bacterial colonization.

Allergic Rhinitis Augments the Response to a Bacterial Sinus Infection in Mice: A Review of an Animal Model

Background

Sinusitis is a poorly understood disease. Despite the significant morbidity and the enormous cost of treating sinusitis, little progress has been made at improving our understanding of its pathophysiology. One reason for restricted progress in understanding the disease is the lack of a satisfactory animal model that mimics sinusitis in man.

Objective

We review data establishing the development of sinusitis in mice after instillation of Streptococcus pneumoniae, the most common pathogen responsible for acute sinusitis in man. We also review data showing that allergic inflammation in mice worsens a subsequent bacterial sinusitis. We use this data to hypothesize how allergic inflammation worsens a bacterial sinus infection.

Methods

Different strains of mice were made allergic and/or infected.

Results

We show our ability to generate an allergic reaction in the nose after sensitization to ovalbumin. Our data further show that an ongoing allergic nasal reaction worsens acute sinusitis.

Conclusion

A mouse model has been created for a study of the interaction of allergic rhinitis and acute bacterial sinusitis.

Antigenic Variation in Streptococcus pneumoniae PspC Promotes Immune Escape in the Presence of Variant-Specific Immunity

Genomic analysis reveals extensive sequence variation and hot spots of recombination in surface proteins of Streptococcus pneumoniae. While this phenomenon is commonly attributed to diversifying selection by host immune responses, there is little mechanistic evidence for the hypothesis that diversification of surface protein antigens produces an immune escape benefit during infection with S. pneumoniae. Here, we investigate the biological significance of sequence variation within the S. pneumoniae cell wall-associated pneumococcal surface protein C (PspC) protein antigen. Using pspC allelic diversity observed in a large pneumococcal collection, we produced variant-specific protein constructs that span the sequence variability within the pspC locus. We show that antibodies raised against these PspC constructs are variant specific and prevent association between PspC and the complement pathway mediator, human factor H. We found that PspC variants differ in their capacity to bind factor H, suggesting that sequence variation within pspC reflects differences in biological function. Finally, in an antibody-dependent opsonophagocytic assay, S. pneumoniae expressing a PspC variant matching the antibody specificity was killed efficiently. In contrast, killing efficacy was not evident against S. pneumoniae expressing mismatched PspC variants. Our data suggest that antigenic variation within the PspC antigen promotes immune evasion and could confer a fitness benefit during infection.

Loci encoding surface protein antigens in Streptococcus pneumoniae are highly polymorphic. It has become a truism that these polymorphisms are the outcome of selective pressure on S. pneumoniae to escape host immunity. However, there is little mechanistic evidence to support the hypothesis that diversifying protein antigens produces a benefit for the bacteria. Using the highly diverse pspC locus, we have now characterized the functional and immune implications of sequence diversity within the PspC protein. We have characterized the spectrum of biological function among diverse PspC variants and show that pspC sequence diversity reflects functional differences. Further, we show that sequence variation in PspC confers an immune escape benefit in the presence of anti-PspC variant-specific immunity. Overall, the results of our studies provide insights into the functional implications of protein sequence diversity and the role of variant-specific immunity in its maintenance.

Comparative genomic analysis of ten clinical Streptococcus pneumoniae collected from a Malaysian hospital reveal 31 new unique drug-resistant SNPs using whole genome sequencing

Background

Streptococcus pneumoniae or pneumococcus is a leading cause of morbidity and mortality worldwide, specifically in relation to community-acquired pneumonia. Due to the overuse of antibiotics, S. pneumoniae has developed a high degree of resistance to a wide range of antibacterial drugs.

Methods

In this study, whole genome sequencing (WGS) was performed for 10 clinical strains of S. pneumoniae with different levels of sensitivity to standard antibiotics. The main objective was to investigate genetic changes associated with antibiotic resistance in S. pneumoniae.

Results

Our results showed that resistant isolates contain a higher number of non-synonymous single nucleotide polymorphisms (SNPs) as compared to susceptible isolates. We were able to identify SNPs that alter a single amino acid in many genes involved in virulence and capsular polysaccharide synthesis. In addition, 90 SNPs were only presented in the resistant isolates, and 31 SNPs were unique and had not been previously reported, suggesting that these unique SNPs could play a key role in altering the level of resistance to different antibiotics.

Conclusion

Whole genome sequencing is a powerful tool for comparing the full genome of multiple isolates, especially those closely related, and for analysing the variations found within antibiotic resistance genes that lead to differences in antibiotic sensitivity. We were able to identify specific mutations within virulence genes related to resistant isolates. These findings could provide insights into understanding the role of single nucleotide mutants in conferring drug resistance.

Electronic supplementary material

The online version of this article (10.1186/s12929-018-0414-8) contains supplementary material, which is available to authorized users.

The variome of pneumococcal virulence factors and regulators

BACKGROUND

In recent years, the idea of a highly immunogenic protein-based vaccine to combat Streptococcus pneumoniae and its severe invasive infectious diseases has gained considerable interest. However, the target proteins to be included in a vaccine formulation have to accomplish several genetic and immunological characteristics, (such as conservation, distribution, immunogenicity and protective effect), in order to ensure its suitability and effectiveness. This study aimed to get comprehensive insights into the genomic organization, population distribution and genetic conservation of all pneumococcal surface-exposed proteins, genetic regulators and other virulence factors, whose important function and role in pathogenesis has been demonstrated or hypothesized.

RESULTS

After retrieving the complete set of DNA and protein sequences reported in the databases GenBank, KEGG, VFDB, P2CS and Uniprot for pneumococcal strains whose genomes have been fully sequenced and annotated, a comprehensive bioinformatic analysis and systematic comparison has been performed for each virulence factor, stand-alone regulator and two-component regulatory system (TCS) encoded in the pan-genome of S. pneumoniae. A total of 25 S. pneumoniae strains, representing different pneumococcal phylogenetic lineages and serotypes, were considered. A set of 92 different genes and proteins were identified, classified and studied to construct a pan-genomic variability map (variome) for S. pneumoniae. Both, pneumococcal virulence factors and regulatory genes, were well-distributed in the pneumococcal genome and exhibited a conserved feature of genome organization, where replication and transcription are co-oriented. The analysis of the population distribution for each gene and protein showed that 49 of them are part of the core genome in pneumococci, while 43 belong to the accessory-genome. Estimating the genetic variability revealed that pneumolysin, enolase and Usp45 (SP_2216 in S. p. TIGR4) are the pneumococcal virulence factors with the highest conservation, while TCS08, TCS05, and TCS02 represent the most conserved pneumococcal genetic regulators.

CONCLUSIONS

The results identified well-distributed and highly conserved pneumococcal virulence factors as well as regulators, representing promising candidates for a new generation of serotype-independent protein-based vaccine(s) to combat pneumococcal infections.

Cell Invasion and Pyruvate Oxidase-Derived H2O2 Are Critical for Streptococcus pneumoniae-Mediated Cardiomyocyte Killing

Streptococcus pneumoniae (the pneumococcus) is the leading cause of community-acquired pneumonia and is now recognized to be a direct contributor to adverse acute cardiac events. During invasive pneumococcal disease, S. pneumoniae can gain access to the myocardium, kill cardiomyocytes, and form bacterium-filled "microlesions" causing considerable acute and long-lasting cardiac damage. While the molecular mechanisms responsible for bacterial translocation into the heart have been elucidated, the initial interactions of heart-invaded S. pneumoniae with cardiomyocytes remain unclear. In this study, we used a model of low multiplicity of S. pneumoniae infection with HL-1 mouse cardiomyocytes to investigate these early events. Using adhesion/invasion assays and immunofluorescent and transmission electron microscopy, we showed that S. pneumoniae rapidly adhered to and invaded cardiomyocytes. What is more, pneumococci existed as intravacuolar bacteria or escaped into the cytoplasm. Pulse-chase assays with BrdU confirmed intracellular replication of pneumococci within HL-1 cells. Using endocytosis inhibitors, bacterial isogenic mutants, and neutralizing antibodies against host proteins recognized by S. pneumoniae adhesins, we showed that S. pneumoniae uptake by cardiomyocytes is not through the well-studied canonical interactions identified for vascular endothelial cells. Indeed, S. pneumoniae invasion of HL-1 cells occurred through clathrin-mediated endocytosis (CME) and independently of choline binding protein A (CbpA)/laminin receptor, CbpA/polymeric immunoglobulin receptor, or cell wall phosphorylcholine/platelet-activating factor receptor. Subsequently, we determined that pneumolysin and streptococcal pyruvate oxidase-derived H₂O₂ production were required for cardiomyocyte killing. Finally, we showed that this cytotoxicity could be abrogated using CME inhibitors or antioxidants, attesting to intracellular replication of S. pneumoniae as a key first step in pneumococcal pathogenesis within the heart.

Spectrum of pathogen- and model-specific histopathologies in mouse models of acute pneumonia

Pneumonia may be caused by a wide range of pathogens and is considered the most common infectious cause of death in humans. Murine acute lung infection models mirror human pathologies in many aspects and contribute to our understanding of the disease and the development of novel treatment strategies. Despite progress in other fields of tissue imaging, histopathology remains the most conclusive and practical read out tool for the descriptive and semiquantitative evaluation of mouse pneumonia and therapeutic interventions. Here, we systematically describe and compare the distinctive histopathological features of established models of acute pneumonia in mice induced by Streptococcus (S.) pneumoniae, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Legionella pneumophila, Escherichia coli, Middle East respiratory syndrome (MERS) coronavirus, influenza A virus (IAV) and superinfection of IAV-incuced pneumonia with S. pneumoniae. Systematic comparisons of the models revealed striking differences in the distribution of lesions, the characteristics of pneumonia induced, principal inflammatory cell types, lesions in adjacent tissues, and the detectability of the pathogens in histological sections. We therefore identified core criteria for each model suitable for practical semiquantitative scoring systems that take into account the pathogen- and model-specific patterns of pneumonia. Other critical factors that affect experimental pathologies are discussed, including infectious dose, time kinetics, and the genetic background of the mouse strain. The substantial differences between the model-specific pathologies underscore the necessity of pathogen- and model-adapted criteria for the comparative quantification of experimental outcomes. These criteria also allow for the standardized validation and comparison of treatment strategies in preclinical models.

Pneumococcal 23B Molecular Subtype Identified Using Whole Genome Sequencing

The polysaccharide capsule is a major virulence factor of Streptococcus pneumoniae and the target of all currently licensed pneumococcal vaccines. At present, there are 92 serologically distinct pneumococcal serotypes. Structural and antigenic variation of capsular types is the result of genetic variation within the capsular polysaccharide synthesis (CPS) locus; however, genetic variation may not always result in phenotypic differences which produce novel serotypes. With the introduction of high throughput whole genome sequencing, discovery of novel genotypic variants is not unexpected and this study describes a novel variant of the serotype 23B CPS operon. This novel variant was characterized as a novel genotypic subtype (23B1) with ∼70% homology to the published 23B CPS sequence. High sequence variability was determined in eight cps genes involved in sugar biosynthesis. However, there was no distinction between the classic 23B serotype and 23B1 serologically or in terms of polysaccharide structure. Phylogenetic and eBURST analysis revealed a distinct lineage for 23B1 with multiple clones (UK, Thailand, and USA) that arose at different points during pneumococcal evolution. Analysis of the UK S. pneumoniae isolates (n = 121) revealed an upsurge of 23B1 ST2372 in 2011, after which this previously unseen ST increased to reach 50% proportion of the 23B sequenced isolates from 2013 and remained prevalent within our sequenced isolates from later years. Therefore, although the 23B1 variant appears to have no phenotypic impact and cannot be considered as novel serotype, it appears to have led to a genetic restructuring of the UK serotype 23B population.

A Streptococcus pneumoniae Type 2 Oligosaccharide Glycoconjugate Elicits Opsonic Antibodies and Is Protective in an Animal Model of Invasive Pneumococcal Disease

Invasive pneumococcal diseases (IPDs) remain the leading cause of vaccine-preventable childhood death, even though highly effective pneumococcal conjugate vaccines (PCVs) are used in national immunization programs in many developing countries. Licensed PCVs currently cover only 13 of the over 90 serotypes of Streptococcus pneumoniae (Sp), so nonvaccine serotypes are a major obstacle to the effective control of IPD. Sp serotype 2 (ST2) is such a nonvaccine serotype that is the main cause of IPD in many countries, including Nepal, Bangladesh, and Guatemala. Glycoconjugate vaccines based on synthetic oligosaccharides instead of isolated polysaccharides offer an attractive alternative to the traditional process for PCV development. To prevent the IPDs caused by ST2, we identified an effective ST2 neoglycoconjugate vaccine candidate that was identified using a medicinal chemistry approach. Glycan microarrays containing a series of synthetic glycans resembling portions of the ST2 capsular polysaccharide (CPS) repeating unit were used to screen human and rabbit sera and identify epitope hits. Synthetic hexasaccharide 2, resembling one repeating unit (RU) of ST2 CPS, emerged as a hit from the glycan array screens. Vaccination with neoglycoconjugates consisting of hexasaccharide 2 coupled to carrier protein CRM197 stimulates a T-cell-dependent B-cell response that induced CPS-specific opsonic antibodies in mice, resulting in killing of encapsulated bacteria by phagocytic activity. Subcutaneous immunization with neoglycoconjugate protected mice from transnasal challenge with the highly virulent ST2 strain NCTC 7466 by reducing the bacterial load in lung tissue and blood.

Oligosaccharide ligand tuning in design of third generation carbohydrate pneumococcal vaccines

Streptococcus pneumoniae can cause many types of dangerous infectious diseases such as otitis media, pneumonia, meningitis and others that are more common in the very young and very old age. Available to date commercial vaccines based on capsular polysaccharides of S. pneumoniae of clinically important strains (first generation carbohydrate vaccines) and conjugated vaccines based on these polysaccharides (second generation carbohydrate vaccines) have certain limitations in protective efficiency. However, the efficiency of vaccines can be increased by the use of third generation vaccines based on synthetic oligosaccharide ligands representing in their structures the protective epitopes of capsular polysaccharides. The proper choice of an optimal oligosaccharide ligand is the most important step in the design of third generation carbohydrate vaccines. Herein we overview our works on the synthesis of three oligosaccharides corresponding to one, “one and a half” and two repeating units of S. pneumoniae type 14 capsular polysaccharide, immunogenic conjugates thereof and comparative immunological study of their conjugates with bovine serum albumin, which was used as a model protein carrier. The ability of obtained products to raise antibodies specific to capsular polysaccharide and homologous oligosaccharides, the induction of phagocytosis by immune antisera and active protection of immunized animals from S. pneumoniae type 14 infection were evaluated. On the basis of the results obtained tetrasaccharide comprising the repeating unit of S. pneumoniae type 14 capsular polysaccharide is an optimal carbohydrate ligand to be used as a part of the third generation carbohydrate pneumococcal vaccine.

Polysaccharide-Specific Memory B Cells Predict Protection against Experimental Human Pneumococcal Carriage

RATIONALE

We have previously demonstrated that experimental pneumococcal carriage enhances immunity and protects healthy adults against carriage reacquisition after rechallenge with a homologous strain.

OBJECTIVES

To investigate the role of naturally acquired pneumococcal protein and polysaccharide (PS)-specific immunity in protection against carriage acquisition using a heterologous challenge model.

METHODS

We identified healthy volunteers that were naturally colonized with pneumococcus and, after clearance of their natural carriage episode, challenged them with a heterologous 6B strain. In another cohort of volunteers we assessed 6BPS-specific, PspA-specific, and PspC-specific IgG and IgA plasma and memory B-cell populations before and 7, 14, and 35 days after experimental pneumococcal inoculation.

MEASUREMENTS AND MAIN RESULTS

Heterologous challenge with 6B resulted in 50% carriage among volunteers with previous natural pneumococcal carriage. Protection from carriage was associated with a high number of circulating 6BPS IgG-secreting memory B cells at baseline. There were no associations between protection from carriage and baseline levels of 6BPS IgG in serum or nasal wash, PspA-specific, or PspC-specific memory B cells or plasma cells. In volunteers who did not develop carriage, the number of circulating 6BPS memory B cells decreased and the number of 6BPS plasma cells increased postinoculation.

CONCLUSIONS

Our data indicate that naturally acquired PS-specific memory B cells, but not levels of circulating IgG at time of pneumococcal exposure, are associated with protection against carriage acquisition.

CRH Affects the Phenotypic Expression of Sepsis-Associated Virulence Factors by Streptococcus pneumoniae Serotype 1 In vitro

Sepsis is a life-threatening health condition caused by infectious pathogens of the respiratory tract, and accounts for 28–50% of annual deaths in the US alone. Current treatment regimen advocates the use of corticosteroids as adjunct treatment with antibiotics, for their broad inhibitory effect on the activity and production of pro-inflammatory mediators. However, despite their use, corticosteroids have not proven to be able to reverse the death incidence among septic patients. We have previously demonstrated the potential for neuroendocrine factors to directly influence Streptococcus pneumoniae virulence, which may in turn mediate disease outcome leading to sepsis and septic shock. The current study investigated the role of Corticotropin-releasing hormone (CRH) in mediating key markers of pneumococcal virulence as important phenotypic determinants of sepsis and septic shock risks. In vitro cultures of serotype 1 pneumococcal strain with CRH promoted growth rate, increased capsule thickness and penicillin resistance, as well as induced pneumolysin gene expression. These results thus provide significant insights of CRH–pathogen interactions useful in understanding the underlying mechanisms of neuroendocrine factor's role in the onset of community acquired pneumonias (CAP), sepsis and septic shock.