Epidemiology of Streptococcus pneumoniae serotypes in children before and after pneumococcal vaccination

Aim. To investigate how the pneumococcal vaccination affects the distribution of Streptococcus pneumoniae serotypes.Materials and Methods. In 2011-2019, 1,852 healthy children (1,354 aged ≤ 5 years and 480 aged from 6 to 17 years) were examined for the nasopharyngeal pneumococcal carriage. Of them, 539 children were tested before the start of pneumococcal vaccination (2011-2014), while 1,313 were tested during the vaccine campaign (2015-2019). Pneumococcal strains were serotyped using multiplex polymerase chain reaction.Results. Streptococcus pneumoniae serotype distribution considerably differed between children ≤ 5 and 6-17 years of age. Serotypes 23F, 19F, 19A, 6AB, and 15BC were prevalent in children ≤ 5 years of age while the older children were characterised by a high prevalence of capsular serotypes (3 and 33AF/37), serogroup 9 (9AV and 9LN), non-typeable streptococci, as well as 19F, 6AB and 6CD serotypes. Vaccination was associated with a significantly decreased prevalence of Streptococcus pneumoniae carriage (from 41.5% to 19.2%) among children ≤ 5 years of age, while this reduction was less pronounced (from 13.5 to 9.0%) in older children. Vaccination led to the shift in the distribution of pneumococcal serotypes towards an increased prevalence of non-vaccine serotypes that was particularly prominent in children ≤ 5 years of age. In particular, vaccination reduced the prevalence of 23F and 19A pneumococcal serotypes but heightened prevalence of 11AD serotype and to the appearance of previously undetected serotypes such as 8, 10A, 17F, 22F, 24ABF, 34, and 39.Conclusion. Pneumococcal vaccination decreased prevalence of pneumococcal carriage, yet causing a serotype replacement effect requiring improved microbiological monitoring in children of all age groups.

High-throughput nanofluidic real-time PCR to discriminate Pneumococcal Conjugate Vaccine (PCV)-associated serogroups 6, 18, and 22 to serotypes using modified oligonucleotides

Current real-time high-throughput Polymerase Chain Reaction (qPCR) methods do not distinguish serotypes 6A from 6B, 18C from 18A/B and 22F from 22A. We established a nanofluidic real-time PCR (Fluidigm) for serotyping that included Dual-Priming-Oligonucleotides (DPO), a Locked-Nucleic-Acid (LNA) probe and TaqMan assay-sets for high-throughput serotyping. The designed assay-sets target capsular gene wciP in serogroup 6, wciX and wxcM in serogroup 18, and wcwA in serogroup 22. An algorithm combining results from published assay-sets (6A/B/C/D; 6C/D; 18A/B/C; 22A/F) and designed assay-sets for 6A/C; 18B/C/F; 18C/F, 18F and 22F was validated through blind analysis of 1973 archived clinical samples collected from South African children ≤ 5-years-old (2009–2011), previously serotyped with the culture-based Quellung method. All assay-sets were efficient (92–101%), had low variation between replicates (R2 > 0.98), and were able to detect targets at a limit of detection (LOD) of < 100 Colony-Forming-Units (CFU)/mL of sample. There was high concordance (Kappa = 0.73–0.92); sensitivity (85–100%) and specificity (96–100%) for Fluidigm compared with Quellung for serotyping 6A; 6B; 6C; 18C and 22F. Fluidigm distinguishes vaccine-serotypes 6A, 6B, 18C, next-generation PCV-serotype 22F and non-vaccine-serotypes 6C, 6D, 18A, 18B, 18F and 22A. Discriminating single serotypes is important for assessing serotype replacement and the impact of PCVs on vaccine- and non-vaccine serotypes.

Emergence of a multidrug resistant and virulent Streptococcus pneumoniae lineage mediates serotype replacement after PCV13

Background Pneumococcal Conjugate Vaccine (PCV) which targets up to 13 serotypes of Streptococcus pneumoniae is very effective at reducing disease in young children; however, rapid increases in replacement with non-PCV serotypes remains a concern. Serotype 24F is one of the major invasive serotypes that mediates serotype replacement in France and multiple other countries. We aimed to identify the major pneumococcal lineage that has driven the increase of serotype 24F in France, and provide context for the findings by investigating the global diversity of serotype 24F pneumococci and characterise the driver lineage from a global perspective and elucidate its spatiotemporal transmission in France and across the world. Methods We whole-genome sequenced a collection of 419 serotype 24F S. pneumoniae from asymptomatic carriers and invasive disease cases among individuals <18 years old in France between 2003 and 2018. Genomes were clustered into Global Pneumococcal Sequence Clusters (GPSCs) and clonal complexes (CCs) so as to identify the lineages that drove the increase in serotype 24F in France. For each serotype 24F lineage, we evaluated the invasive disease potential and propensity to cause meningitis by comparing the proportion of invasive disease cases with that of carriers. To provide a global context of serotype 24F and the driver lineage, we extracted relevant genomes and metadata from the Global Pneumococcal Sequencing (GPS) project database (n=25,590) and additionally sequenced a collection of 91 pneumococcal isolates belonging to the lineage that were responsible for the serotype 24F increase in Spain during the PCV introduction for comparison. Phylogenetic, evolutionary, and spatiotemporal analysis were conducted to understand the mechanism underlying the global spread of serotype 24F, evolutionary history and long-range transmissions of the driver lineage. Findings A multidrug-resistant pneumococcal lineage GPSC10 (CC230) drove the serotype 24F increase in both carriage and invasive disease in France after PCV13 introduction. When compared with other serotype 24F lineages, it exhibited a 1.4-fold higher invasive disease potential and 1.6-fold higher propensity to cause meningitis. Globally, serotype 24F was widespread, largely due to clonal dissemination of GPSC10, GPSC16 (CC66) and GPSC206 (CC7701) rather than recent capsular switching. Among these lineages, only GPSC10 was multidrug-resistant. It expressed 17 serotypes, with only 6 included in PCV13 and none of the expected PCVs covered all serotypes expressed by this lineage. Global phylogeny of GPSC10 showed that all serotype 24F isolates except for one were clustered together, regardless of its country of origin. Long-range transmissions of GPSC10-24F from Europe to Israel, Morocco and India were detected. Spatiotemporal analysis revealed that it took ~5 years for GPSC10-24F to spread across French provinces. In Spain, we detected that the serotype 24F driver lineage GPSC10 underwent a rapid change of serotype composition from serotype 19A to 24F during the introduction of PCV13 (targets 19A but not 24F), indicating that pre-existence of serotype variants enabled GPSC10 to survive and expand under vaccine-selective pressure. Interpretation Our work further shows the utility of bacterial genome sequencing to better understand the pneumococcal lineages behind the serotype changes and reveals that GPSC10 alone is a challenge for serotype-based vaccine strategy. More systematic investigation to identify lineages like GPSC10 will better inform and improve next-generation preventive strategies against pneumococcal diseases. Funding Bill & Melinda Gates Foundation, Wellcome Sanger Institute, and the US Centers for Disease Control.

Pneumococcal Vaccines: Past Findings, Present Work, and Future Strategies

The importance of Streptococcus pneumoniae has been well established. These bacteria can colonize infants and adults without symptoms, but in some cases can spread, invade other tissues and cause disease with high morbidity and mortality. The development of pneumococcal conjugate vaccines (PCV) caused an enormous impact in invasive pneumococcal disease and protected unvaccinated people by herd effect. However, serotype replacement is a well-known phenomenon that has occurred after the introduction of the 7-valent pneumococcal conjugate vaccine (PCV7) and has also been reported for other PCVs. Therefore, it is possible that serotype replacement will continue to occur even with higher valence formulations, but the development of serotype-independent vaccines might overcome this problem. Alternative vaccines are under development in order to improve cost effectiveness, either using proteins or the pneumococcal whole cell. These approaches can be used as a stand-alone strategy or together with polysaccharide vaccines. Looking ahead, the next generation of pneumococcal vaccines can be impacted by the new technologies recently approved for human use, such as mRNA vaccines and viral vectors. In this paper, we will review the advantages and disadvantages of the addition of new polysaccharides in the current PCVs, mainly for low- and middle-income countries, and we will also address future perspectives.

Recent Topics of Pneumococcal Vaccination: Indication of Pneumococcal Vaccine for Individuals at a Risk of Pneumococcal Disease in Adults

Pneumococcal disease is one of the most common and severe vaccine-preventable diseases (VPDs). Despite the advances in antimicrobial treatment, pneumococcal disease still remains a global burden and exhibits a high mortality rate among people of all ages worldwide. The immunization program of the pneumococcal conjugate vaccine (PCV) in children has decreased pneumococcal disease incidence in several countries. However, there are several problems regarding the pneumococcal vaccine, such as indications for immunocompetent persons with underlying medical conditions with a risk of pneumococcal disease, the balance of utility and cost, i.e., cost-effectiveness, vaccine coverage rate, serotype replacement, and adverse events. Especially for individuals aged 19–64 at risk of pneumococcal disease, physicians and vaccine providers should make a rational decision whether the patients should be vaccinated or not, since there is insufficient evidence supporting it. We describe this review regarding topics and problems regarding pneumococcal vaccination from the clinician’s point of view.

High-throughput nanofluidic real-time PCR to discriminate Pneumococcal Conjugate Vaccine (PCV)-associated serogroups 6, 18, and 22 to serotypes using modified oligonucleotides.

Current real-time Polymerase Chain Reaction (qPCR) methods are unable to distinguish serotypes 6A from 6B, 18C from 18A/B and 22F from 22A. We established a nanofluidic real-time PCR (Fluidigm) for serotyping that included Dual-Priming-Oligonucleotides (DPO), a Locked-Nucleic-Acid (LNA) probe and TaqMan assay-sets for high-throughput serotyping. The designed assay-sets target capsular gene wciP in serogroup 6, wciX and wxcM in serogroup 18, and wcwA in serogroup 22. An algorithm combining results from published assay-sets (6A/B/C/D; 6C/D; 18A/B/C; 22A/F) and designed assay-sets for 6A/C; 18B/C/F; 18C/F, 18F and 22F was validated through blind analysis of 1973 archived clinical samples collected from South African children ≤ 5-years-old (2009-11), previously serotyped with the culture-based Quellung method. All assay-sets were efficient (92–101%), had low variation between replicates (R2 > 0.98), and were able to detect targets at a limit of detection (LOD) of < 100 Colony-Forming-Units (CFU)/ml of sample. There was high concordance (Kappa = 0.73–0.92); sensitivity (85–100%) and specificity (96–100%) for Fluidigm compared with Quellung for serotyping 6A; 6B; 6C; 18C and 22F. Fluidigm distinguishes vaccine-serotypes 6A, 6B, 18C, next-generation PCV-serotype 22F and non-vaccine-serotypes 6C, 6D, 18A, 18B, 18F and 22A. Discriminating single serotypes is important for assessing serotype replacement and the impact of PCVs on vaccine- and non-vaccine serotypes.

The metabolic, virulence and antimicrobial resistance profiles of colonizing Streptococcus pneumoniae shift after pneumococcal vaccine introduction in urban Malawi

Streptococcus pneumoniae accounts for at least 300,000 deaths from pneumonia, septicaemia and meningitis among children under 5-years-old worldwide. Protein-polysaccharide conjugate vaccines (PCVs) are highly effective at reducing vaccine serotype disease but emergence of non-vaccine serotypes and persistent nasopharyngeal carriage threaten to undermine this success. Here, we address the hypothesis that following vaccine introduction in high disease and carriage burden settings, adapted pneumococcal genotypes emerge with the potential to facilitate vaccine escape. We show that beyond serotype replacement, there are marked changes in S. pneumoniae carriage population genetics amongst 2804 isolates sampled 4-8 years after the 2011 introduction of PCV-13 in urban Malawi. These changes are characterised by metabolic genotypes with distinct virulence and antimicrobial resistance (AMR) profiles. This included exclusive genes responsible for metabolism and carbohydrate transport, and toxin-antitoxin systems located in an integrative-conjugative region suggestive of horizontal gene transfer. These emergent genotypes were found to have differential growth, haemolytic, or epithelial adhesion/invasion traits that may confer advantage in the nasopharyngeal niche. Together these data show that in the context of PCV13 introduction in a high burden population, there has been a shift in the pneumococcal population dynamics with the emergence of genotypes that have undergone multiple adaptations extending beyond simple serotype replacement, a process that could further undermine vaccine control and promote the spread of AMR.

Insights Into the Effects of Mucosal Epithelial and Innate Immune Dysfunction in Older People on Host Interactions With Streptococcus pneumoniae

In humans, nasopharyngeal carriage of Streptococcus pneumoniae is common and although primarily asymptomatic, is a pre-requisite for pneumonia and invasive pneumococcal disease (IPD). Together, these kill over 500,000 people over the age of 70 years worldwide every year. Pneumococcal conjugate vaccines have been largely successful in reducing IPD in young children and have had considerable indirect impact in protection of older people in industrialized country settings (herd immunity). However, serotype replacement continues to threaten vulnerable populations, particularly older people in whom direct vaccine efficacy is reduced. The early control of pneumococcal colonization at the mucosal surface is mediated through a complex array of epithelial and innate immune cell interactions. Older people often display a state of chronic inflammation, which is associated with an increased mortality risk and has been termed ‘Inflammageing’. In this review, we discuss the contribution of an altered microbiome, the impact of inflammageing on human epithelial and innate immunity to S. pneumoniae, and how the resulting dysregulation may affect the outcome of pneumococcal infection in older individuals. We describe the impact of the pneumococcal vaccine and highlight potential research approaches which may improve our understanding of respiratory mucosal immunity during pneumococcal colonization in older individuals.

Global Landscape Review of Serotype-Specific Invasive Pneumococcal Disease Surveillance among Countries Using PCV10/13: The Pneumococcal Serotype Replacement and Distribution Estimation (PSERENADE) Project

Serotype-specific surveillance for invasive pneumococcal disease (IPD) is essential for assessing the impact of 10- and 13-valent pneumococcal conjugate vaccines (PCV10/13). The Pneumococcal Serotype Replacement and Distribution Estimation (PSERENADE) project aimed to evaluate the global evidence to estimate the impact of PCV10/13 by age, product, schedule, and syndrome. Here we systematically characterize and summarize the global landscape of routine serotype-specific IPD surveillance in PCV10/13-using countries and describe the subset that are included in PSERENADE. Of 138 countries using PCV10/13 as of 2018, we identified 109 with IPD surveillance systems, 76 of which met PSERENADE data collection eligibility criteria. PSERENADE received data from most (n = 63, 82.9%), yielding 240,639 post-PCV10/13 introduction IPD cases. Pediatric and adult surveillance was represented from all geographic regions but was limited from lower income and high-burden countries. In PSERENADE, 18 sites evaluated PCV10, 42 PCV13, and 17 both; 17 sites used a 3 + 0 schedule, 38 used 2 + 1, 13 used 3 + 1, and 9 used mixed schedules. With such a sizeable and generally representative dataset, PSERENADE will be able to conduct robust analyses to estimate PCV impact and inform policy at national and global levels regarding adult immunization, schedule, and product choice, including for higher valency PCVs on the horizon.