Anna S. Tocheva

Declining serotype coverage of new pneumococcal conjugate vaccines relating to the carriage of Streptococcus pneumoniae in young children

BACKGROUND Asymptomatic carriage of the opportunistic pathogen Streptococcus pneumoniae is known to precede the development of invasive disease. Young children are one of the major reservoirs for pneumococci and worldwide over 700,000 children under two years old die due to invasive pneumococcal disease each year. Heptavalent conjugate vaccine (PCV-7) was introduced into the UK childhood immunisation schedule in September 2006. Our objective was to assess the emergence of colonising serotypes in young children in the three years following PCV-7 implementation. METHODS Time-series prevalence survey set in the paediatric outpatients department of a large UK teaching hospital. Participants were children aged four years and under attending the outpatients department during PCV-7 introduction (October 2006-February 2007) and in the same months of the two subsequent years. The main outcome measure was prevalence of pneumococcal carriage by serotype. RESULTS The rate of pneumococcal nasopharyngeal carriage remained stable during the three year period. We observed a significant 69% (95% CI, -40% to -118%, p<0.0001) decrease in carriage of PCV-7 serotypes during PCV-7 implementation and a concomitant increase in the proportion of non PCV-7 serotypes. The most prevalent emerging non-vaccine serotypes were 6C, 11A, 19A and 22F. By March 2009, PCV-13 was predicted to cover only 33.3% (95% CI, 24.2-42.5%) of strains carried in the study population. CONCLUSIONS Although the overall pneumococcal carriage rate remained stable between 2006 and 2009, we observed a significant decrease in the serotype coverage of PCV-7 and PCV-13. PCV-7 was highly successful in reducing carriage of vaccine serotypes. However, the increase in the proportion of non-vaccine serotypes found both in our study and causing invasive disease currently in the UK, underlines the importance of continued surveillance of carriage and disease.

Five winters of pneumococcal serotype replacement in UK carriage following PCV introduction

Highlights • PCV7 serotype replacement was near complete 5 years after PCV7 introduction.• The carriage rate remained stable through out the 5 year period.• Serotypes unique to PCV13 significantly decreased by the final winter.• Clonal expansion of existing genotypes was primarily responsible for replacement.• Continued surveillance is needed to monitor replacement until equilibrium is reached.

Increase in serotype 6C pneumococcal carriage, United Kingdom.

To the Editor: Streptococcus pneumoniae is a major human pathogen. In 2007, Park et al. identified a novel serotype, 6C (1), which emerged from serotype 6A. A study of children in the Netherlands who had not previously received a pneumococcal vaccine found low prevalence of this newly identified serotype before the heptavalent pneumococcal conjugate vaccine Prevnar/Prevenar (PCV7) (Wyeth, Taplow, UK) was introduced (2). Studies have shown cross-protection between vaccine serotype 6B and vaccine-related serotype 6A. However, PCV7 elicits no cross-protection against serotype 6C. The potential exists for the emergence of nonvaccine serotypes or novel clones. These serotypes and clones may be better adapted to colonize the nasopharynx, evade the human immune response, and cause disease. A recent study showed an increase in prevalence of serotype 6C pneumococci in children and a corresponding decrease in serotype 6A after introduction of PCV7 (3). We studied the underlying genetic basis for expansion of serotype 6C. Initial data from an ongoing study of pneumococcal carriage are presented. This study was reviewed and approved by the Southampton and South West Hampshire Research Ethics Committee (B) (reference 06/Q1704/105). A total of 697 nasopharyngeal swab specimens were collected from unselected (not selected by a method) children Appendix Figure Appendix Figure. Appendix Figure. Genotypes of serotype 6C pneumococci isolated from children in 2006–2007 (year 1) and 2007–2008 (year 2), United Kingdom. ST, sequence type. In the first year of this study, we identified 3 (3.1%) serotype 6C pneumococci belonging to 3 sequence types (STs): ST65, ST1714, and ST1692 (Appendix Figure). ST1714 and ST 1692 shared a common clonal complex. Only ST 65 was shared between serotype 6C and serotype 6A. In the second year, we identified 14 (13.6%) serotype 6C pneumococci belonging to 6 STs (Appendix Figure). Two of these STs, of the same ST, were from siblings. Three of them (ST1692 [n = 8], ST1714 [n = 2], and ST395 [n = 1]) were members of a common clonal complex with a predicted founder of ST395. Each of the remaining 3 STs (ST398, ST1862, and ST3460) was isolated only once. One serotype 6A isolate of ST1692 was also observed. No serotype 6C ST65 was observed in the second year. We isolated more serotype 6C pneumococci in year 2 than in year 1 (p Our study showed a large increase in ST1692 in serotype 6C pneumococci during the implementation of PCV7 and an increase in serotype 6C. Depending on the extent of cross-protection between vaccine-related serotypes, introduction of conjugate vaccines could induce clearance or emergence of vaccine-related serotypes. This introduction could also contribute to their substitution with novel or existing serotypes that are better adapted to the ecologic niche. However, our data may only be relevant to carried pneumococci and not reflected in pneumococcal disease epidemiology. Nevertheless, the increase in serotype 6C pneumococci in the United Kingdom, which is supported by a similar observation in the United States (3), highlights the potential for emergence of serotypes not included in the current study and newly developed pneumococcal conjugate vaccines.

Current methods for capsular typing of Streptococcus pneumoniae

Streptococcus pneumoniae is a major respiratory tract pathogen causing pneumococcal disease mainly in children aged less than five years and in the elderly. Ninety-eight different capsular types (serotypes) of pneumococci have been reported, but pneumococcal conjugate vaccines (PCV) include polysaccharide antigens against only 7, 10 or 13 serotypes. It is therefore important to track the emergence of serotypes due to the clonal expansion of non-vaccine serotypes. Increased numbers of carried and disease-causing pneumococci are now being analysed as part of the post-PCV implementation surveillance studies and hence rapid, accurate and cost-effective typing methods are important. Here we describe serotyping methods published prior to 10th November 2014 for pneumococcal capsule typing. Sixteen methods were identified; six were based on serological tests using immunological properties of the capsular epitopes, eight were semi-automated molecular tests, and one describes the identification of capsular type directly from whole genome data, which also allows for further intra and inter-genome analyses. There was no single method that could be recommended for all pneumococcal capsular typing applications. Although the Quellung reaction is still considered to be the gold-standard, laboratories should take into account the number of pneumococcal isolates and the type of samples to be used for testing, the time frame for the results and the resources available in order to select the most appropriate method. Most likely, a combination of phenotypic and genotypic methods would be optimal to monitor and evaluate the impact of pneumococcal conjugate vaccines and to provide information for future vaccine formulations.

Cholesteryl esters stabilize human CD1c conformations for recognition by self-reactive T cells

Significance T cells autoreactive to cluster of differentiation 1c (CD1c) are abundant in human blood but lipid antigens recognized by these T cells remained poorly understood. A new 2.4-Å structure of CD1c and computational simulations thereof indicated substantial conformational plasticity of CD1c with ligand-induced formation of an F′ roof and G′ portal, as well as the potential of CD1c to present acylated sterols. Confirming these predictions we demonstrated CD1c loading and biophysical interaction of CD1c–lipid complexes with self-reactive human T-cell receptors for two lipid classes: cholesteryl esters similar to those accumulating in foamy macrophages (e.g., in atherosclerosis) and acylated steryl glycosides from Borrelia burgdorferi. These findings differentiate CD1c from other CD1 isoforms and open up new avenues for research into the role of CD1c in human immunity. Cluster of differentiation 1c (CD1c)-dependent self-reactive T cells are abundant in human blood, but self-antigens presented by CD1c to the T-cell receptors of these cells are poorly understood. Here we present a crystal structure of CD1c determined at 2.4 Å revealing an extended ligand binding potential of the antigen groove and a substantially different conformation compared with known CD1c structures. Computational simulations exploring different occupancy states of the groove reenacted these different CD1c conformations and suggested cholesteryl esters (CE) and acylated steryl glycosides (ASG) as new ligand classes for CD1c. Confirming this, we show that binding of CE and ASG to CD1c enables the binding of human CD1c self-reactive T-cell receptors. Hence, human CD1c adopts different conformations dependent on ligand occupancy of its groove, with CE and ASG stabilizing CD1c conformations that provide a footprint for binding of CD1c self-reactive T-cell receptors.

Clonal Expansion within Pneumococcal Serotype 6C after Use of Seven-Valent Vaccine

Streptococcus pneumoniae causes invasive infections, primarily at the extremes of life. A seven-valent conjugate vaccine (PCV7) is used to protect against invasive pneumococcal disease in children. Within three years of PCV7 introduction, we observed a fourfold increase in serotype 6C carriage, predominantly due to a single clone. We determined the whole-genome sequences of nineteen S. pneumoniae serotype 6C isolates, from both carriage (n = 15) and disease (n = 4) states, to investigate the emergence of serotype 6C in our population, focusing on a single multi-locus sequence type (MLST) clonal complex 395 (CC395). A phylogenetic network was constructed to identify different lineages, followed by analysis of variability in gene sets and sequences. Serotype 6C isolates from this single geographical site fell into four broad phylogenetically distinct lineages. Variation was seen in the 6C capsular locus and in sequences of genes encoding surface proteins. The largest clonal complex was characterised by the presence of lantibiotic synthesis locus. In our population, the 6C capsular locus has been introduced into multiple lineages by independent capsular switching events. However, rapid clonal expansion has occurred within a single MLST clonal complex. Worryingly, plasticity exists within current and potential vaccine-associated loci, a consideration for future vaccine use, target selection and design.

Structural and Functional Changes of the Invariant NKT Clonal Repertoire in Early Rheumatoid Arthritis.

Invariant NKT cells (iNKT) are potent immunoregulatory T cells that recognize CD1d via a semi-invariant TCR (iNKT-TCR). Despite the knowledge of a defective iNKT pool in several autoimmune conditions, including rheumatoid arthritis (RA), a clear understanding of the intrinsic mechanisms, including qualitative and structural changes of the human iNKT repertoire at the earlier stages of autoimmune disease, is lacking. In this study, we compared the structure and function of the iNKT repertoire in early RA patients with age- and gender-matched controls. We analyzed the phenotype and function of the ex vivo iNKT repertoire as well as CD1d Ag presentation, combined with analyses of a large panel of ex vivo sorted iNKT clones. We show that circulating iNKTs were reduced in early RA, and their frequency was inversely correlated to disease activity score 28. Proliferative iNKT responses were defective in early RA, independent of CD1d function. Functional iNKT alterations were associated with a skewed iNKT-TCR repertoire with a selective reduction of high-affinity iNKT clones in early RA. Furthermore, high-affinity iNKTs in early RA exhibited an altered functional Th profile with Th1- or Th2-like phenotype, in treatment-naive and treated patients, respectively, compared with Th0-like Th profiles exhibited by high-affinity iNKTs in controls. To our knowledge, this is the first study to provide a mechanism for the intrinsic qualitative defects of the circulating iNKT clonal repertoire in early RA, demonstrating defects of iNKTs bearing high-affinity TCRs. These defects may contribute to immune dysregulation, and our findings could be exploited for future therapeutic intervention.

Identification of novel pneumolysin alleles from paediatric carriage isolates of Streptococcus pneumoniae

Pneumolysin (Ply) is a major virulence factor of Streptococcus pneumoniae and is produced by all known clinical isolates of pneumococci. Pneumolysin toxoids are being considered as vaccine candidates. We investigated the diversity of pneumolysin among 194 nasopharyngeal pneumococci characterized by serotyping and multilocus sequence typing (MLST). Eight Ply protein alleles were identified, four of which were novel. The 4 novel alleles varied at 10 different amino acid positions, from a total of 147, 3 of these substitutions have been previously reported in different combinations. The protein allele correlated closely with MLST. It is critical that the presence of pneumolysin variants is considered with regards to the potential use of Ply in future vaccine formulations, as variation in Ply amino acid sequence may influence the immunogenicity of vaccines based on the presence of an individual Ply allele.

Distribution of carried pneumococcal clones in UK children following the introduction of the 7-valent pneumococcal conjugate vaccine: A 3-year cross-sectional population based analysis

The success of Streptococcus pneumoniae (pneumococcus) in both colonisation and disease is associated with the increased prevalence of genetic clones expressing virulence factors that assist host invasion. We studied the distribution of pneumococcal clones in paediatric carriage as part of an ongoing longitudinal study of pneumococcal carriage in children less than 5 years of age. Across three years, 87 different sequence types (STs) were found amongst 310 pneumococci. A decline in PCV-7 related STs was observed during the study period. STs 62, 199, 433 and 1692 increased after the implementation of PCV-7 and were related to increases in serotypes 11A, 19A, 22F, and to serotype 6C, respectively. Overall, a strong correlation was observed between ST and serotype. Thirteen STs contained multiple serotypes and 74 STs were associated with only one serotype. On-going molecular epidemiological surveillance of pneumococcal carriage is warranted during the implementation of pneumococcal conjugate vaccines.

CD1b-restricted GEM T cell responses are modulated by Mycobacterium tuberculosis mycolic acid meromycolate chains

Significance Tuberculosis is a major global pandemic responsible for more deaths than any other infectious disease, yet no effective vaccine exists. Here, we demonstrate CD1b expression within human tuberculous granulomas, supporting a role for CD1b lipid antigen presentation in host immunity to infection. CD1b presents mycolates, the dominant Mycobacterium tuberculosis (Mtb) cell wall lipid class and key virulence factors, to αβ T cells. We reveal that mycolate tail moieties, distal to the head group, are antigenic determinants for the conserved human germline-encoded mycolyl lipid-reactive (GEM) T cell receptors (TCRs). Computational simulations suggest a putative mechanism whereby lipid-ligand dynamics within CD1b regulate GEM-TCR activity. This work provides insights for the development of major histocompatibility complex (MHC)-independent Mtb lipid vaccines, including those that target GEM T cells. Tuberculosis (TB), caused by Mycobacterium tuberculosis, remains a major human pandemic. Germline-encoded mycolyl lipid-reactive (GEM) T cells are donor-unrestricted and recognize CD1b-presented mycobacterial mycolates. However, the molecular requirements governing mycolate antigenicity for the GEM T cell receptor (TCR) remain poorly understood. Here, we demonstrate CD1b expression in TB granulomas and reveal a central role for meromycolate chains in influencing GEM-TCR activity. Meromycolate fine structure influences T cell responses in TB-exposed individuals, and meromycolate alterations modulate functional responses by GEM-TCRs. Computational simulations suggest that meromycolate chain dynamics regulate mycolate head group movement, thereby modulating GEM-TCR activity. Our findings have significant implications for the design of future vaccines that target GEM T cells.