Pneumococcal carriage in children and adults two years after introduction of the thirteen valent pneumococcal conjugate vaccine in England

Pneumococcal Serotype Evolution and Burden in European Adults in the Last Decade: A Systematic Review

Pneumococcal disease is a major cause of morbidity/mortality worldwide, and vaccination is an important measure in its prevention. Despite European children being vaccinated with pneumococcal conjugate vaccines (PCVs), pneumococcal infections are still a major cause of morbidity/mortality in adults with risk conditions and their vaccination might be an important prevention strategy. New PCVs have been approved, but information is lacking on their potential impact in European adults. In our review, we searched PubMed, MEDLINE, and Embase for studies on the additional PCV20 serotypes (concerning incidence, prevalence, disease severity, lethality, and antimicrobial resistance) in European adults, between January 2010 and April 2022, having included 118 articles and data from 33 countries. We found that these serotypes have become more prevalent in both invasive and non-invasive pneumococcal disease (IPD and NIPD), representing a significant proportion of cases (serotypes 8, 12F, 22F) and more serious disease and/or lethality (10A, 11A, 15B, 22F), showing antimicrobial resistance (11A, 15B, 33F), and/or affecting more vulnerable individuals such as the elderly, immunocompromised patients, and those with comorbidities (8, 10A, 11A, 15B, 22F). The relevance of pneumococcal adult carriers (11A, 15B, 22F, and 8) was also identified. Altogether, our data showed an increase in the additional PCV20 serotypes' prevalence, accounting for a proportion of approximately 60% of all pneumococcal isolates in IPD in European adults since 2018/2019. Data suggest that adults, as older and/or more vulnerable patients, would benefit from vaccination with higher-coverage PCVs, and that PCV20 may address an unmet medical need.

Serotypes and Antibiotic Resistance of Streptococcus pneumoniae before and after the Introduction of the 13-Valent Pneumococcal Conjugate Vaccine for Adults and Children in a Rural Area in Japan

The increase in non-vaccine serotypes of Streptococcus pneumoniae and their multidrug resistance have become an issue following the introduction of the 13-valent pneumococcal conjugate vaccine (PCV13). In this study, we investigated the serotypes and drug resistance of S. pneumoniae detected in adult and pediatric outpatients at a hospital in a rural area of Japan between April 2012 and December 2016. Serotypes of the bacterium were identified using the capsular swelling test and multiplex polymerase chain reaction testing of DNA extracted from the specimens. Antimicrobial susceptibility was determined using the broth microdilution method. The serotype 15A was classified using multilocus sequence typing. The results showed that the prevalence of non-vaccine serotypes increased significantly in children from 50.0% in 2012-2013 to 74.1% in 2016 (p ≤ 0.006) and in adults from 15.8% in 2012-2013 to 61.5% in 2016 (p ≤ 0.026), but no increase in drug-resistant isolates was evident. However, an increase in the drug-resistant serotypes 15A and 35B was observed in children. Although isolates of these two serotypes showed cefotaxime susceptibility, cefotaxime resistance was confirmed for the serotype 15A isolates. Future trends in the spread of these isolates should be monitored with caution.

Nasopharyngeal Carriage of Pneumococcus in Children in England up to 10 Years After 13-Valent Pneumococcal Conjugate Vaccine Introduction: Persistence of Serotypes 3 and 19A and Emergence of 7C

BACKGROUND

Monitoring changes in pharyngeal carriage of pneumococcus in children following 13-valent pneumococcal conjugate vaccine (PCV13) introduction in the United Kingdom in 2010 informs understanding of patterns of invasive pneumococcal disease (IPD) incidence.

METHODS

Nasopharyngeal swabs from healthy children vaccinated with PCV13 according to schedule (2, 4, and 12 months) were cultured and serotyped. Results for children aged 13-48 months were compared between 2014-2015 and 2017-2019 and with children aged 6-12 months (2017-2020). Blood was obtained from a subset of children for pneumococcal serotype-specific immunoglobulin G (IgG).

RESULTS

Total pneumococcal carriage at 13-48 months was 47.9% (473/988) in 2014-2015 and 51.8% (412/795) in 2017-2019 (P = .10); at age 6-12 months this value was 44.6% (274/615). In 2017-2019, 2.9% (95% confidence interval, 1.8%-4.3%) of children aged 13-48 months carried PCV13 serotypes (mainly 3 [1.5%] and 19A [0.8%]) and >20% carried the additional 20-valent PCV (PCV20) serotypes. Similar proportions of children had IgG ≥0.35 IU/mL for each serotype in 2014-2015 and 2017-2019. Serotype 7C carriage increased significantly (P < .01) between 2014-2015 and 2017-2019. Carriage of PCV20 serotypes 8 and 12F, both major causes of IPD, was rare.

CONCLUSIONS

Introduction of PCV20, if licensed for children, could significantly change the composition of pneumococcal serotypes carried in the pharynx of UK children.

CLINICAL TRIALS REGISTRATION

NCT03102840.

Mathematical modeling of pneumococcal transmission dynamics in response to PCV13 infant vaccination in Germany predicts increasing IPD burden due to serotypes included in next-generation PCVs

INTRODUCTION

Two next-generation pneumococcal conjugate vaccines (PCVs), a 15- and a 20-valent PCV (PCV15 and PCV20), have recently been licensed for use in adults, and PCV15 has also been licensed in children. We developed a dynamic transmission model specific for Germany, with the aim to predict carriage prevalence and invasive pneumococcal disease (IPD) burden for serotypes included in these vaccines.

METHODS

The model allows to follow serotype distributions longitudinally both in the absence and presence of PCV vaccinations. We considered eight age cohorts and seven serotype groups according to the composition of different pneumococcal vaccines. This comprises the additional serotypes contained in PCV15 and PCV20 but not in PCV13.

RESULTS

The model predicted that by continuing the current vaccine policy (standard vaccination with PCV13 in children and with PPSV23 in adults) until 2031, IPD case counts due to any serotype in children <2 years of age will remain unchanged. There will be a continuous decrease of IPD cases in adults aged 16-59y, but a 20% increase in adults ≥60y. Furthermore, there will be a steady decrease of the proportion of carriage and IPD due to serotypes included in PCV7 and PCV13 over the model horizon and a steady rise of non-PCV13 serotypes in carriage and IPD. The highest increase for both pneumococcal carriage and absolute IPD case counts was predicted for serotypes 22F and 33F (included in both PCV15 and PCV20) and serotypes 8, 10A, 11A, 12F, and 15B (included in PCV20 only), particularly in older adults. Between 2022 and 2031, serotypes included in PCV20 only are expected to cause 19.7-25.3% of IPD cases in adults ≥60y.

CONCLUSIONS

We conclude that introduction of next-generation PCVs for adults may prevent a substantial and increasing proportion of adult IPDs, with PCV20 having the potential to provide the broadest protection against pneumococcal disease.

Impact of Temporary Storage Conditions on the Viability of Streptococcus pneumoniae in Saliva

Nasopharyngeal swabs are considered the gold-standard sample type for the detection of Streptococcus pneumoniae carriage, but recent studies have demonstrated the utility of saliva in improving the detection of carriage in adults. Saliva is generally collected in its raw, unsupplemented state, unlike nasopharyngeal swabs, which are collected into stabilizing transport media. Few data exist regarding the stability of pneumococci in unsupplemented saliva during transport and laboratory storage. We therefore evaluated the effect of storage conditions on the detection of pneumococci in saliva samples using strains representing eight pneumococcal serotypes. The bacteria were spiked into raw saliva from asymptomatic individuals, and we assessed sample viability after storage at 4°C, room temperature, and 30°C for up to 72 h; at 40°C for 24 h; and following three freeze-thaw cycles. We observed little decrease in pneumococcal detection following culture enrichment and quantitative PCR (qPCR) detection of the piaB and lytA genes compared to testing fresh samples, indicating the prolonged viability of pneumococci in neat saliva samples. This sample stability makes saliva a viable sample type for pneumococcal carriage studies conducted in remote or low-resource settings and provides insight into the effect of the storage of saliva samples in the laboratory. IMPORTANCE For pneumococcal carriage studies, saliva is a sample type that can overcome some of the issues typically seen with nasopharyngeal and oropharyngeal swabs. Understanding the limitations of saliva as a sample type is important for maximizing its use. This study sought to better understand how different storage conditions and freeze-thaw cycles affect pneumococcal survival over time. These findings support the use of saliva as an alternative sample type for pneumococcal carriage studies, particularly in remote or low-resource settings with reduced access to health care facilities.

Impact of Pneumococcal Vaccination on Nasopharyngeal Carriage of Streptococcus pneumoniae and Microbiota Profiles in Preschool Children in South East Poland

In 2017, Poland introduced the 10-valent pneumococcal conjugate vaccine (PCV) into its national immunization schedule. This prospective study was conducted between March and June 2020 to determine the impact of vaccination on prevalence of the nasopharyngeal carriage of S. pneumoniae in 176 healthy children and to determine how conjugate vaccines indirectly affect colonization of nasopharyngeal microbiota. Pneumococcal isolates were analyzed by serotyping and antimicrobial resistance tests. Nasopharyngeal microbiota were detected and identified using the culture method and real-time PCR amplification primers and hydrolysis-probe detection with the 16S rRNA gene as the target. In the vaccinated group of children, colonization was in 24.2% of children, compared to 21.4% in the unvaccinated group. Serotypes 23A and 23B constituted 41.5% of the isolates. Serotypes belonging to PCV10 and PCV13 constituted 4.9% and 17.1% of the isolates, respectively. S. pneumoniae isolates were resistant to penicillin (34.1%), erythromycin (31.7%), and co-trimoxazole (26.8%). Microbial DNA qPCR array correlated to increased amounts of Streptococcus mitis and S. sanguinis in vaccinated children, with reduced amounts of C. pseudodiphtericum, S. aureus, and M. catarrhalis. Introduction of PCV for routine infant immunization was associated with significant reductions in nasopharyngeal carriage of PCV serotypes and resistant strains amongst vaccine serotypes, yet carriage of non-PCV serotypes increased modestly, particularly serotype 23B.

Clearance of mixed biofilms of Streptococcus pneumoniae and methicillin-susceptible/resistant Staphylococcus aureus by antioxidants N-acetyl-L-cysteine and cysteamine

Biofilm-associated infections are of great concern because they are associated with antibiotic resistance and immune evasion. Co-colonization by Staphylococcus aureus and Streptococcus pneumoniae is possible and a threat in clinical practice. We investigated the interaction between S. aureus and S. pneumoniae in mixed biofilms and tested new antibiofilm therapies with antioxidants N-acetyl-l-cysteine (NAC) and cysteamine (Cys). We developed two in vitro S. aureus–S. pneumoniae mixed biofilms in 96-well polystyrene microtiter plates and we treated in vitro biofilms with Cys and NAC analyzing their effect by CV staining and viable plate counting. S. pneumoniae needed a higher proportion of cells in the inoculum and planktonic culture to reach a similar population rate in the mixed biofilm. We demonstrated the effect of Cys in preventing S. aureus biofilms and S. aureus–S. pneumoniae mixed biofilms. Moreover, administration of 5 mg/ml of NAC nearly eradicated the S. pneumoniae population and killed nearly 94% of MSSA cells and 99% of MRSA cells in the mixed biofilms. The methicillin resistance background did not change the antioxidants effect in S. aureus. These results identify NAC and Cys as promising repurposed drug candidates for the prevention and treatment of mixed biofilms by S. pneumoniae and S. aureus.

Non-diphtheriae Corynebacterium species are associated with decreased risk of pneumococcal colonization during infancy

Streptococcus pneumoniae (pneumococcus) is a leading cause of severe infections among children and adults. Interactions between commensal microbes in the upper respiratory tract and S. pneumoniae are poorly described. In this study, we sought to identify interspecies interactions that modify the risk of S. pneumoniae colonization during infancy and to describe development of the upper respiratory microbiome during infancy in a sub-Saharan African setting. We collected nasopharyngeal swabs monthly (0-6 months of age) or bimonthly (6-12 months of age) from 179 mother-infant dyads in Botswana. We used 16S ribosomal RNA gene sequencing to characterize the nasopharyngeal microbiome and identified S. pneumoniae colonization using a species-specific PCR assay. We detect S. pneumoniae colonization in 144 (80%) infants at a median age of 71 days and identify a strong negative association between the relative abundance of the bacterial genera Corynebacterium within the infant nasopharyngeal microbiome and the risk of S. pneumoniae colonization. Using in vitro cultivation experiments, we demonstrate growth inhibition of S. pneumoniae by secreted factors from strains of several Corynebacterium species isolated from these infants. Finally, we demonstrate that antibiotic exposures and the winter season are associated with a decline in the relative abundance of Corynebacterium within the nasopharyngeal microbiome, while breastfeeding is associated with an increase in the Corynebacterium relative abundance. Our findings provide novel insights into the interspecies interactions that contribute to colonization resistance to S. pneumoniae and suggest that the nasopharyngeal microbiome may be a previously unrecognized mechanism by which environmental factors influence the risk of pneumococcal infections during childhood. Moreover, this work lays the foundation for future studies seeking to use targeted manipulation of the nasopharyngeal microbiome to prevent infections caused by S. pneumoniae.

Evaluation of the indirect impact of the 10-valent pneumococcal Haemophilus influenzae protein D conjugate vaccine in a cluster-randomised trial

Background

In the nation-wide double-blind cluster-randomised Finnish Invasive Pneumococcal disease trial (FinIP, ClinicalTrials.gov NCT00861380, NCT00839254), we assessed the indirect impact of the 10-valent pneumococcal Haemophilus influenzae protein D conjugate vaccine (PHiD-CV10) against five pneumococcal disease syndromes.

Methods

Children 6 weeks to 18 months received PHiD-CV10 in 48 clusters or hepatitis B/A-vaccine as control in 24 clusters according to infant 3+1/2+1 or catch-up schedules in years 2009―2011. Outcome data were collected from national health registers and included laboratory-confirmed and clinically suspected invasive pneumococcal disease (IPD), hospital-diagnosed pneumonia, tympanostomy tube placements (TTP) and outpatient antimicrobial prescriptions. Incidence rates in the unvaccinated population in years 2010―2015 were compared between PHiD-CV10 and control clusters in age groups <5 and ≥5 years (5―7 years for TTP and outpatient antimicrobial prescriptions), and in infants <3 months. PHiD-CV10 was introduced into the Finnish National Vaccination Programme (PCV-NVP) for 3-month-old infants without catch-up in 9/2010.

Results

From 2/2009 to 10/2010, 45398 children were enrolled. Vaccination coverage varied from 29 to 61% in PHiD-CV10 clusters. We detected no clear differences in the incidence rates between the unvaccinated cohorts of the treatment arms, except in single years. For example, the rates of vaccine-type IPD, non-laboratory-confirmed IPD and empyema were lower in PHiD-CV10 clusters compared to control clusters in 2012, 2015 and 2011, respectively, in the age-group ≥5 years.

Conclusions

This is the first report from a clinical trial evaluating the indirect impact of a PCV against clinical outcomes in an unvaccinated population. We did not observe consistent indirect effects in the PHiD-CV10 clusters compared to the control clusters. We consider that the sub-optimal trial vaccination coverage did not allow the development of detectable indirect effects and that the supervening PCV-NVP significantly diminished the differences in PHiD-CV10 vaccination coverage between the treatment arms.

Evolution of pneumococcal serotype epidemiology in Botswana following introduction of 13-valent pneumococcal conjugate vaccine

Pneumococcal conjugate vaccines reduce the burden of invasive pneumococcal disease, but the sustained effect of these vaccines can be diminished by an increase in disease caused by non-vaccine serotypes. To describe pneumococcal serotype epidemiology in Botswana following introduction of 13-valent pneumococcal conjugate vaccine (PCV-13) in July 2012, we performed molecular serotyping of 268 pneumococcal strains isolated from 221 children between 2012 and 2017. The median (interquartile range) age of the children included in this analysis was 6 (3,12) months. Fifty-nine percent of the children had received at least one dose of PCV-13 and 35% were fully vaccinated with PCV-13. While colonization by vaccine serotypes steadily declined following PCV-13 introduction, 25% of strains isolated more than 3 years after vaccine introduction were PCV-13 serotypes. We also observed an increase in colonization by non-vaccine serotypes 21 and 23B, which have been associated with invasive pneumococcal disease and antibiotic resistance in other settings.

Factors associated with pneumococcal nasopharyngeal carriage: A systematic review

Pneumococcal disease is a major contributor to global childhood morbidity and mortality and is more common in low- and middle-income countries (LMICs) than in high-income countries. Pneumococcal carriage is a prerequisite for pneumococcal disease. Pneumococcal conjugate vaccine reduces vaccine-type carriage and disease. However, pneumococcal carriage and disease persist, and it is important to identify other potentially modifiable factors associated with pneumococcal carriage and determine if risk factors differ between low, middle, and high-income countries. This information may help inform pneumococcal disease prevention programs. This systematic literature review describes factors associated with pneumococcal carriage stratified by country income status and summarises pneumococcal carriage rates for included studies. We undertook a systematic search of English-language pneumococcal nasopharyngeal carriage studies up to 30th June 2021. Peer-reviewed studies reporting factors associated with overall pneumococcal nasopharyngeal carriage in healthy, community-based study populations were eligible for inclusion. Two researchers independently reviewed studies to determine eligibility. Results are presented as narrative summaries. This review is registered with PROSPERO, CRD42020186914. Eighty-two studies were included, and 46 (56%) were conducted in LMICs. There was heterogeneity in the factors assessed in each study. Factors positively associated with pneumococcal carriage in all income classification were young age, ethnicity, symptoms of respiratory tract infection, childcare attendance, living with young children, poverty, exposure to smoke, season, and co-colonisation with other pathogens. Breastfeeding and antibiotic use were protective against carriage in all income classifications. Median (interquartile range) pneumococcal carriage rates differed by income classification, ranging from 51% (19.3-70.2%), 38.5% (19.3-51.6%), 31.5% (19.0-51.0%), 28.5% (16.8-35.4%), (P = 0.005) in low-, lower-middle, upper-middle, and high-income classifications, respectively. Our findings suggest that where measured, factors associated with pneumococcal nasopharyngeal carriage are similar across income classifications, despite the highest pneumococcal carriage rates being in low-income classifications. Reducing viral transmission through vaccination and public health interventions to address social determinants of health would play an important role.

Serotypes in Adult Pneumococcal Pneumonia in Spain in the Era of Conjugate Vaccines

We studied changes in serotype distribution and antimicrobial susceptibility in adult pneumococcal pneumonia in Spain (2011–2019). Among 895 pneumococci collected (433 bacteremic [BPP] and 462 non-bacteremic [non-BPP]), serotypes 3 (17%), 19A (10%), 8 (6.7%) and 11A (6.7%) were the most frequent. Serotypes 16F, 19A and 24F were associated with old people (≥65) and serotypes 4, 7F, 8, 12F and 19F to young adults. Serotypes 12F, 24F and 1 were significantly more frequent in BPP and serotypes 11A, 23A and 19F in non-BPP. Amoxicillin resistance was higher in non-BPP (17% vs. 11%) while penicillin non-susceptibility (37% vs. 24%) and macrolide resistance (29% vs. 14%) were higher in older adults. In the period 2017–2019, the vaccine coverages were: 32% (PCV13), 39% (PCV15), 65% (PCV20) and 69% (PPV23). Differences were found in serotype composition and antimicrobial resistance by age and type of infection. The maintenance of serotype 3 as a leading cause of adult pneumococcal pneumonia and the increase in highly invasive (serotype 8) or antimicrobial-resistant (serotype 11A) serotypes is worrisome. Further studies will be required to analyse the impact of the upcoming broader conjugate vaccines.

Clinical and Economic Burden of Pneumococcal Disease Due to Serotypes Contained in Current and Investigational Pneumococcal Conjugate Vaccines in Children Under Five Years of Age

INTRODUCTION

The widespread implementation of pneumococcal conjugate vaccines (PCVs) has significantly reduced the burden of pneumococcal disease around the world. Although licensed 10-valent (PCV10) and 13-valent (PCV13) vaccines have considerably reduced mortality and morbidity, a sizeable disease burden attributable to serotypes not contained in these PCVs remains. This study aimed to estimate the annual clinical and economic burden of pneumococcal disease attributable to licensed (PCV10 and PCV13) and investigational PCVs, notably 15-valent (PCV15) and 20-valent (PCV20) vaccines, in 13 countries in children under 5 years of age.

METHODS

A decision-analytic model was created to aggregate total cases [inclusive of invasive pneumococcal disease (IPD), pneumonia, and otitis media (OM)], deaths, and direct costs in each country of interest [stratified by PCV10/PCV13 countries, depending on national immunization programs (NIPs)] over 1 year, using up to the three most recent years of available serotype coverage data. Data inputs were sourced from local databases, surveillance reports, and published literature.

RESULTS

In 5 PCV10 NIPs (Austria, Finland, Netherlands, New Zealand, Sweden), most remaining PCV20-type disease was due to PCV13-unique serotypes (30-85%), followed by PCV20-unique (9-50%), PCV15-unique (4-15%), and PCV10-unique (2-14%) serotypes. In 8 PCV13 NIPs (Australia, Canada, France, Germany, Italy, South Korea, Spain, United Kingdom), most remaining PCV20-type disease was caused by PCV20-unique serotypes (16-69%), followed by PCV13-unique (11-54%), PCV15-unique (2-33%), and PCV10-unique serotypes (3-19%). Across all countries, PCV20 serotypes caused 3000 to 345,000 cases of disease and cost between $1.3 and $44.9 million USD annually with variability driven by population size, NIP status, and epidemiologic inputs. In aggregate, PCV20 serotypes caused 1,234,000 cases and $213.5 million in annual direct medical costs in children under 5 years of age.

CONCLUSION

Despite the success of PCV10 and PCV13 in reducing pneumococcal disease, a substantial clinical and economic burden remains due to serotypes contained in investigational vaccines.

Association of pneumococcal serotype with susceptibility to antimicrobial drugs: a systematic review and meta-analysis

BACKGROUND

Pneumococcal serotypes differ in antimicrobial susceptibility. However, patterns and causes of this variation are not comprehensively understood.

METHODS

We undertook a systematic review of epidemiologic studies of pneumococci isolated from carriage or invasive disease among children globally from 2000-2019. We evaluated associations of each serotype with nonsusceptibility to penicillin, macrolides, and trimethoprim/sulfamethoxazole. We evaluated differences in the prevalence of nonsusceptibility to major antibiotic classes across serotypes using random effects meta-regression models, and assessed changes in prevalence of nonsusceptibility after implementation of pneumococcal conjugate vaccines (PCVs). We also evaluated associations between biological characteristics of serotypes and their likelihood of nonsusceptibility to each drug.

RESULTS

We included data from 129 studies representing 32,187 isolates across 52 countries. Within serotypes, the proportion of nonsusceptible isolates varied geographically and over time, in settings using and those not using PCVs. Factors predicting enhanced fitness of serotypes in colonization as well as enhanced pathogenicity were each associated with higher likelihood of nonsusceptibility to penicillin, macrolides, and trimethoprim/sulfamethoxazole. Increases in prevalence of nonsusceptibility following PCV implementation were evident among non-PCV serotypes including 6A, 6C, 15A, 15B/C, 19A, and 35B; however, this pattern was not universally evident among non-PCV serotypes. Post-vaccination increases in nonsusceptibility for serotypes 6A and 19A were attenuated in settings that implemented PCV13.

CONCLUSIONS

In pneumococci, nonsusceptibility to penicillin, macrolides, and trimethoprim/sulfamethoxazole is associated with more frequent opportunities for antibiotic exposure during both prolonged carriage episodes and when serotypes cause disease. These findings suggest multiple pathways leading to resistance selection in pneumococci.

Nasopharyngeal Carriage in Children After the Introduction of Generalized Infant Pneumococcal Conjugate Vaccine Immunization in Germany

Epidemiological data on nasopharyngeal (NP) bacterial carriage in children in Germany are scarce. We prospectively characterized NP colonization to evaluate the impact of pneumococcal immunization. We longitudinally collected NP swabs from 2-month-old infants (visit 1; V1) at eight representative pediatric offices 10/2008-06/2009. The second swabs were taken at age 9–12 months (V2); the third swab was taken 3–6 months after the booster vaccination at age 17–19 months (V3), and the fourth swab (V4) at age 59–61 months. Samples were broth enriched, cultured for bacteria, and isolates were serotyped. Demographic risk factors for colonization were evaluated. Among 242 vaccinees, bacterial NP carriage increased with age [from 27.2% (V1) to 70.1% (V4)]; leading isolates were S. pneumoniae, H. influenzae, M. catarrhalis, and S. pyogenes. Overall pneumococcal carriage increased [14.7% (V1), 31.5% (V2), 34.8% (V3), 42.2% (V4)], being even greater among day-care attendees. Serotype distribution changed during the study period, with vaccine serotypes declining. At visit 4, 10-valent pneumococcal conjugate vaccine (PCV10) serotypes were no longer among the NP flora, while some serotypes unique to 13-valent pneumococcal conjugate vaccine (PCV13; 3 and 19A) were found. In Germany, universal infant PCV immunization was associated with an almost complete eradication of PCV-serotypes and concomitant increase of non-PCV-serotypes, mainly 11A, 22F, and 23A.

A review of current data to support decision making for introduction of next generation higher valency pneumococcal conjugate vaccination of immunocompetent older adults in the UK

INTRODUCTION

The burden of pneumococcal disease in older UK adults remains substantial. Higher valency pneumococcal conjugate vaccines (PCVs) are currently in development with adult formulations for two of these anticipated to become available in 2022. This article collates and reviews relevant candidate data now available that may be used to support cost effectiveness assessments of vaccinating immunocompetent UK adults aged ≥65-years with PCVs.

AREAS COVERED

This article uses published data from surveillance systems, randomized controlled trials and observational studies. It focuses on local data from the UK but where these are either limited or not available relevant global data are considered.

EXPERT OPINION

The body of relevant data now available suggests the UK is well placed to assess the cost effectiveness of vaccinating immunocompetent ≥65-year olds with new generation higher valency PCVs. Recent contemporary data provide important new and robust insights into the epidemiology of pneumococcal disease in older UK adults and help to address much of the uncertainty and data gaps associated with previous analyses. Using these data to make informed decisions about use of new higher valency PCVs for routine use in older adults will be important for public health in the UK.

Invasive Pneumococcal Disease in People With Human Immunodeficiency Virus in England, 1999-2017

BACKGROUND

The 7-valent and 13-valent pneumococcal conjugate vaccines (PCVs) were introduced into the UK childhood immunization program in 2006 and 2010, respectively, with high effectiveness and resulting in both direct and indirect protection. We describe the epidemiology of invasive pneumococcal disease (IPD) in adults with human immunodeficiency virus (HIV) in England following the introduction of both PCVs.

METHODS

Data on a national cohort of people with HIV were linked to confirmed IPD cases in adults aged ≥ 15 years during 1999-2017. Date of HIV infection was estimated using a CD4 slope decline algorithm.

RESULTS

Among 133 994 adults with HIV, 1453 developed IPD during 1999-2017, with 70% (1016/1453) developing IPD ≥ 3 months after their HIV diagnosis. IPD and HIV were codiagnosed within 90 days in 345 (24%) individuals. A missed opportunity for earlier HIV diagnosis was identified in 6% (89/1453), mostly in earlier years. IPD incidence in people with HIV increased from 147/100 000 in 1999 to 284/100 000 in 2007 before declining and stabilizing between 92 and 113/100 000 during 2014-2017. Mean annual IPD incidence was lower among those receiving antiretroviral therapy during 2014-17 (68 vs 720/100 000; incidence rate ratio [IRR] 9.3; 95% confidence interval [CI], 7.3-11.8; P < .001) and was markedly lower in those with a suppressed viral load (50 vs 523/100 000; IRR 10.4; 95% CI, 7.6-14.1; P < .001). The latter group still had 4.5-fold higher (95% CI, 3.8-5.3; P < .001) IPD incidence compared to the general population (11.2/100 000).

CONCLUSIONS

IPD incidence among people with HIV reduced after PCV13 introduction and has remained stable. Adults presenting with IPD should continue to be tested for HIV infection.

Impact of private use of the 13-valent pneumococcal conjugate vaccine (PCV13) on pneumococcal carriage among Portuguese children living in urban and rural regions

In Portugal, the 13-valent pneumococcal conjugate vaccine (PCV13) was commercially available between 2010 and 2015, following a decade of private use of PCV7. We evaluated changes on serotype distribution and antimicrobial susceptibility of pneumococci carried by children living in two regions of Portugal (one urban and one rural). Three epidemiological periods were defined: pre-PCV13 (2009-2010), early-PCV13 (2011-2012), and late-PCV13 (2015-2016). Nasopharyngeal samples (n = 4,232) were obtained from children 0-6 years old attending day-care centers. Private use of PCVs was very high in both regions (>75%). Pneumococcal carriage remained stable and high over time (62.1%, 62.4% and 61.6% (p = 0.909) in the urban region; and 59.8%, 62.8%, 59.5% (p = 0.543) in the rural region). Carriage of PCV7 serotypes remained low (5.3%, 7.8% and 4.3% in the urban region; and 2.5%, 3.7% and 4.8% in the rural region). Carriage of PCV13 serotypes not targeted by PCV7 decreased in both the urban (16.4%, 7.3%, and 1.6%; p < 0.001) and rural regions (13.2%, 7.8%, and 1.9%; p < 0.001). This decline was mostly attributable to serotype 19A (14.1%, 4.4% and 1.3% in the urban region; and 11.1%, 3.6% and 0.8% in the rural region, both p < 0.001). Serotype 3 declined over time in the urban region (10.1%, 4.4%, 0.8%; p < 0.001) and had no obvious trend in the rural region (4.2%, 6.7%, 2.4%; p = 0.505). Serotype 6C decreased in both regions while serotypes 11D, 15A/B/C, 16F, 21, 22F, 23A/B, 24F, 35F, and NT were the most prevalent in the late-PCV13 period. Intermediate resistance to penicillin and non-susceptibility to erythromycin decreased significantly in both regions (19.5%, 13.3%, and 9.3%; and 25.4%, 25.9%, and 13.4%; both p < 0.001, respectively in the urban region; and 12.4%, 11.1%, and 2.8% (p < 0.001); and 15.3%, 14.7%, and 9.2% (p = 0.037), respectively, in the rural region). In conclusion, private use of PCV13 led to significant changes on the pneumococcal population carried by children in Portugal.

Serum antibody levels to pneumococcal polysaccharides 22F, 33F, 19A and 6A that correlate with protection from colonization and acute otitis media in children

BACKGROUND

Serotypes 22F and 33F have been added to a new pneumococcal-conjugate vaccine (PCV-15) because of their prevalence in causing invasive pneumococcal diseases (IPD).

METHOD

We measured anti-polysaccharide 22F, 33F, 19A and 6A antibodies in children before and after pneumococcal colonization and acute otitis media (AOM) episodes caused by these specific-serotypes. A two-step method for construction of correlate of protection (COP) models included using a generalized estimating equation for the relationship between antibody level, age and colonization history followed by logistic-regression modelling that included colonization or AOM episodes as independent variables, and age adjusted antibody level as the predictor.

RESULTS

A vaccine-induced serum antibody level of 0.45 μg/ml for 22F, 0.51 μg/ml for 6A and 4.1 μg/ml for 19A correlated with prevention of pneumococcal colonization by respective serotypes (insufficient number of cases for 33F to find COP against colonization). Antibody levels of 0.25 μg/ml for 22F, 33F and 6A and 2 μg/ml for 19A correlated with prevention of AOM by the respective serotypes.

CONCLUSIONS

A COP threshold of anti-22F, 33F, 19A and 6A serum antibodies for NP colonization and AOM in young children can be derived using GEE and logistic regression modelling.

Characteristics of Invasive Pneumococcal Disease Caused by Emerging Serotypes After the Introduction of the 13-Valent Pneumococcal Conjugate Vaccine in England: A Prospective Observational Cohort Study, 2014-2018

BACKGROUND

England is experiencing a rapid increase in invasive pneumococcal disease (IPD) caused by serotypes 8, 12F, and 9N; their clinical characteristics and outcomes have not been described.

METHODS

Public Health England conducts national IPD surveillance. Cases due to emerging serotypes were compared with those included in the 13-valent pneumococcal conjugate vaccine (PCV13) and the remaining non-PCV13 serotypes.

RESULTS

There were 21 592 IPD cases during 2014-15 to 2017-18, including 20 108 (93.1%) with serotyped isolates and 17 450 (86.8%) with completed questionnaires. PCV13 serotypes were responsible for 20.1% (n = 4033), while serotype 8 (3881/20 108 [19.3%]), 12F (2365/20 108 [11.8%]), and 9N (1 296/20 108 [6.4%]) were together responsible for 37.5% of cases. Invasive pneumonia was the most common presentation (11 424/16 346 [69.9%]) and, overall, 67.0% (n = 11 033) had an underlying comorbidity. The median age (interquartile range) at IPD due to serotypes 8 (59 [45-72] years) and 12F (56 [41-70] years) was lower than serotype 9N (67 [53-80] years), PCV13 serotypes (68 [52-81] years), and remaining non-PCV13 serotypes (70 [53-82] years). Serotype 9N IPD cases also had higher comorbidity prevalence (748/1087 [68.8%]) compared to serotype 8 (1901/3228 [58.9%]) or 12F (1042/1994 [52.3%]), and higher case fatality (212/1128 [18.8%]) compared to 8.6% (291/3365) or 10.0% (209/2086), respectively.

CONCLUSIONS

Serotypes 8 and 12F were more likely to cause IPD in younger, healthier individuals and less likely to be fatal, while serotype 9N affected older adults with comorbidities and had higher case fatality.

Pneumonia and Invasive Pneumococcal Diseases: The Role of Pneumococcal Conjugate Vaccine in the Era of Multi-Drug Resistance

Streptococcus pneumoniae related diseases are a leading cause of morbidity and mortality, especially in children and in the elderly population. It is transmitted to other individuals through droplets and it can spread to other parts of the human host, causing a wide spectrum of clinical syndromes, affecting between 10 and 100 cases per 100,000 people in Europe and the USA. In order to reduce morbidity and mortality caused by this agent, pneumococcal vaccines have been developed over the years and have shown incredible effectiveness in reducing the spread of this bacterium and the development of related diseases, obtaining a significant reduction in mortality, especially in developing countries. However, considerable problems are emerging mainly due to the replacement phenomenon, multi-drug resistance, and the high production costs of conjugated vaccines. There is still a debate about the indications given by various countries to different age groups; this is one of the reasons for the diffusion of different serotypes. To cope with these problems, significant efforts have been made in the research field to further improve vaccination serotypes coverage. On the other hand, an equally important commitment by health care systems to all age group populations is needed to improve vaccination coverage.

Nasopharyngeal carriage of Streptococcus pneumoniae in healthy children aged less than five years

PURPOSE

In Turkey, pneumococcal conjugate vaccine (PCV) was introduced to the national immunization program as PCV7 in 2008, and was replaced with PCV13 in 2011. The aim of the study was to demonstrate the pneumococcal carriage rate and the serotype distribution in healthy children under 5 years in Turkey who were vaccinated with PCV13.

METHODS

We conducted a cross-sectional study including the collection of questionnaire data and nasopharyngeal (NP) specimens among children aged <5 years from five centers from March 2019 to March 2020. Pneumococcal isolates were identified using optochin sensitivity and bile solubility. Serotyping was performed using a latex agglutination kit and Quellung reaction.

RESULTS

NP swab samples were collected from 580 healthy children. The observed overall carriage rate was 17.8%. None of the hypothesised predictors of S. pneumoniae carriage, except maternal education level was statistically significant (p = 0.017). High maternal education level appeared to decrease the risk (lower vs. higher maternal education OR: 1.992 [95% CI; 1.089-3.643], p = 0.025). The overall NP S. pneumoniae carriage prevalence for the PCV13-vaccinated children was 17.8% (103/580). The most common serotypes detected were serotype 15B (n = 10, 9.7%), serotype 23F (n = 9, 8.7%), serotype 23A (n = 9, 8.7%), serotype 11A (n = 7, 6.7%), serotype 19F (n = 5, 4.8%) and serotype 15F (n = 5, 4.8%). Of the isolates, 28 (27.2%) were in PCV13 vaccine strains (VSs), and 75 (72.8%) strains were non-VS. The serotype coverage rate was 27.2% for PCV13.

CONCLUSION

The overall S. pneumoniae carriage rate was higher than in earlier studies from Turkey. Post-vaccine era studies from around the world have reported a decrease in VS serotypes and a 'serotype replacement' to non-VS serotypes, as we determined in our study.

Persistent Circulation of Vaccine Serotypes and Serotype Replacement After 5 Years of Infant Immunization With 13-Valent Pneumococcal Conjugate Vaccine in the United Kingdom

BACKGROUND

Following programmatic introduction of the 13-valent pneumococcal conjugate vaccine (PCV13), there is residual carriage and disease due to PCV13-covered serotypes.

METHODS

PCV13-immunized children aged 13-48 months, N = 988, were enrolled between February 2014 and August 2015 ("late PCV13"), and had nasopharyngeal pneumococcal carriage compared with 7-valent pneumococcal conjugate vaccine (PCV7) immunized children, N = 567, enrolled between November 2010 and September 2011 ("early PCV13"). Nasopharyngeal pneumococci were molecular-serotyped by microarray. Invasive pneumococcal disease (IPD) cases were identified through enhanced national surveillance.

RESULTS

Compared with PCV7-immunized children, carriage among PCV13-immunized children was significantly lower for serotypes 19A (odds ratio [OR], 0.08 [95% confidence interval {CI}, .02-.25]), 6C (OR, 0.11 [95% CI, .03-.32]), and 7F (8 vs 0 cases). IPD incidence in children <5 years was significantly lower for serotypes 1 (incidence rate ratio [IRR], 0.03 [95% CI, 0-.19]) and 7F (IRR, 0.13 [95% CI, .05-.36]) but not 19A (IRR, 0.6 [95% CI, .3-1.12]) or serotype 3 (IRR, 2.3 [95% CI, .86-6.15]) in the late PCV13 period than in the early PCV13 period. The most significant rises in IPD incidence were for serotypes 8, 12F, and 24F.

CONCLUSIONS

PCV13 has reduced serotype 19A carriage among vaccinated children. We found no impact of PCV13 on serotype 3 carriage or disease, and emergence of non-PCV13-serotype disease.

Pneumococcal carriage in children with COVID-19

Background: SARS-CoV-2 is the new virus, and Streptococcus pneumoniae is one of the most important pathogens affecting humans. However, we do not yet know whether these microorganisms interact. Thus, we aimed to evaluate the relationship between Streptococcus pneumoniae and SARS-CoV-2 in pediatric patients.Methods: This study was conducted retrospectively by means of medical records of pediatric patients who were tested for SARS-CoV-2 between March 11 and June 04, 2020, in the University of Health Sciences, Ankara Educating and Training Hospital and Hacettepe University Faculty of Medicine.Results: We evaluated 829 pediatric patients for S. pneumoniae and SARS-CoV-2 from their nasopharyngeal specimen. Of 115 children positive for SARS-CoV-2, 32.2% had a positive S. pneumoniae test, whereas of 714 children negative for SARS-CoV-2, 14.1% had a positive S. pneumoniae test (p < .01). We compared patients with positive vs. negative SARS-CoV-2 tests according to S. pneumoniae positivity There were no statistically significant differences in terms of gender, underlying disease, fever, cough, leukocytosis, lymphopenia, increased CRP, increased procalcitonin, findings of chest x-ray, severity of disease, and treatment.Conclusion: The nasopharyngeal S. pneumoniae carriage rate in patients with COVID-19 was higher than in non-infected children, while S. pneumoniae carriage did not affect the course of COVID-19 disease. Pneumococcal vaccination is significant, such that we do not know the outcomes of increased pneumococcal carriage for the upcoming months of pandemic.

Early Signals of Vaccine-driven Perturbation Seen in Pneumococcal Carriage Population Genomic Data

Background

Pneumococcal conjugate vaccines (PCVs) have reduced pneumococcal diseases globally. Pneumococcal genomic surveys elucidate PCV effects on population structure but are rarely conducted in low-income settings despite the high disease burden.

Methods

We undertook whole-genome sequencing (WGS) of 660 pneumococcal isolates collected through surveys from healthy carriers 2 years from 13-valent PCV (PCV13) introduction and 1 year after rollout in northern Malawi. We investigated changes in population structure, within-lineage serotype dynamics, serotype diversity, and frequency of antibiotic resistance (ABR) and accessory genes.

Results

In children <5 years of age, frequency and diversity of vaccine serotypes (VTs) decreased significantly post-PCV, but no significant changes occurred in persons ≥5 years of age. Clearance of VT serotypes was consistent across different genetic backgrounds (lineages). There was an increase of nonvaccine serotypes (NVTs)—namely 7C, 15B/C, and 23A—in children <5 years of age, but 28F increased in both age groups. While carriage rates have been recently shown to remain stable post-PCV due to replacement serotypes, there was no change in diversity of NVTs. Additionally, frequency of intermediate-penicillin-resistant lineages decreased post-PCV. Although frequency of ABR genes remained stable, other accessory genes, especially those associated with mobile genetic element and bacteriocins, showed changes in frequency post-PCV.

Conclusions

We demonstrate evidence of significant population restructuring post-PCV driven by decreasing frequency of vaccine serotypes and increasing frequency of few NVTs mainly in children under 5. Continued surveillance with WGS remains crucial to fully understand dynamics of the residual VTs and replacement NVT serotypes post-PCV.

Summary of evidence to reduce the two-dose infant priming schedule to a single dose of the 13-valent pneumococcal conjugate vaccine in the national immunisation programme in the UK

Pneumococcal conjugate vaccines (PCVs) are highly effective in preventing invasive and non-invasive pneumococcal infections in all age groups through a combination of direct and indirect protection. In many industrialised countries with established PCV programmes, the maximum benefit of the PCV programme has already been achieved, with most cases now due to non-PCV serotypes. On Jan 1, 2020, the UK changed its childhood pneumococcal immunisation programme from a two-dose infant priming schedule with the 13-valent PCV at 8 and 16 weeks after birth, to a single priming dose at 12 weeks after birth, while retaining the 12-month booster. This decision was made after reviewing the evidence from surveillance data, clinical trials, epidemiological analyses, vaccine effectiveness estimates, and modelling studies to support the reduced schedule. In this Review, we summarise the epidemiology of pneumococcal disease in the UK, the evidence supporting the decision to implement a reduced schedule, and the national and global implications of the proposed schedule.

Upper airways colonisation of Streptococcus pneumoniae in adults aged 60 years and older: A systematic review of prevalence and individual participant data meta-analysis of risk factors

•

Systematic review and meta-analysis of 18 studies and more than 6000 participants.

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Adults over the age of 60 had a pooled prevalence of pneumococcal carriage of 9%.

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Risk factors: contact with children, smoking and residing in a nursing home.

Background

Colonisation with Streptococcus pneumoniae can lead to invasive pneumococcal disease and pneumonia. Pneumococcal acquisition and prevalence of colonisation are high in children. In older adults, a population susceptible to pneumococcal disease, colonisation prevalence is reported to be lower, but studies are heterogeneous.

Methods

This is a systematic review and meta-analysis of prevalence of, and risk factors for, pneumococcal colonisation in adults ≥ 60 years of age (PROSPERO #42016036891). We identified peer-reviewed studies reporting the prevalence of S. pneumoniae colonisation using MEDLINE and EMBASE (until April 2016), excluding studies of acute disease. Participant-level data on risk factors were sought from each study.

Findings

Of 2202 studies screened, 29 were analysable: 18 provided participant-level data (representing 6290 participants). Prevalence of detected pneumococcal colonisation was 0–39% by conventional culture methods and 3–23% by molecular methods. In a multivariate analysis, colonisation was higher in persons from nursing facilities compared with the community (odds ratio (OR) 2•30, 95% CI 1•26–4•21 and OR 7•72, 95% CI 1•15–51•85, respectively), in those who were currently smoking (OR 1•69, 95% CI 1•12–2•53) or those who had regular contact with children (OR 1•93, 95%CI 1•27–2•93). Persons living in urban areas had significantly lower carriage prevalence (OR 0•43, 95%CI 0•27–0•70).

Interpretation

Overall prevalence of pneumococcal colonisation in older adults was higher than expected but varied by risk factors. Future studies should further explore risk factors for colonisation, to highlight targets for focussed intervention such as pneumococcal vaccination of high-risk groups.

Funding

No funding was required.

Factors associated with pneumococcal carriage and density in children and adults in Fiji, using four cross-sectional surveys

This study describes predictors of pneumococcal nasopharyngeal carriage and density in Fiji. We used data from four annual (2012-2015) cross-sectional surveys, pre- and post-introduction of ten-valent pneumococcal conjugate vaccine (PCV10) in October 2012. Infants (5-8 weeks), toddlers (12-23 months), children (2-6 years), and their caregivers participated. Pneumococci were detected and quantified using lytA qPCR, with molecular serotyping by microarray. Logistic and quantile regression were used to determine predictors of pneumococcal carriage and density, respectively. There were 8,109 participants. Pneumococcal carriage was negatively associated with years post-PCV10 introduction (global P<0.001), and positively associated with indigenous iTaukei ethnicity (aOR 2.74 [95% CI 2.17-3.45] P<0.001); young age (infant, toddler, and child compared with caregiver participant groups) (global P<0.001); urban residence (aOR 1.45 [95% CI 1.30-2.57] P<0.001); living with ≥2 children <5 years of age (aOR 1.42 [95% CI 1.27-1.59] P<0.001); low family income (aOR 1.44 [95% CI 1.28-1.62] P<0.001); and upper respiratory tract infection (URTI) symptoms (aOR 1.77 [95% CI 1.57-2.01] P<0.001). Predictors were similar for PCV10 and non-PCV10 carriage, except PCV10 carriage was negatively associated with PCV10 vaccination (0.58 [95% CI 0.41-0.82] P = 0.002) and positively associated with exposure to household cigarette smoke (aOR 1.21 [95% CI 1.02-1.43] P = 0.031), while there was no association between years post-PCV10 introduction and non-PCV10 carriage. Pneumococcal density was positively associated with URTI symptoms (adjusted median difference 0.28 [95% CI 0.16, 0.40] P<0.001) and toddler and child, compared with caregiver, participant groups (global P = 0.008). Predictors were similar for PCV10 and non-PCV10 density, except infant, toddler, and child participant groups were not associated with PCV10 density. PCV10 introduction was associated with reduced the odds of overall and PCV10 pneumococcal carriage in Fiji. However, after adjustment iTaukei ethnicity was positively associated with pneumococcal carriage compared with Fijians of Indian Descent, despite similar PCV10 coverage rates.

Decreasing case fatality rate following invasive pneumococcal disease, North East England, 2006-2016

Declining mortality following invasive pneumococcal disease (IPD) has been observed concurrent with a reduced incidence due to effective pneumococcal conjugate vaccines. However, with IPD now increasing due to serotype replacement, we undertook a statistical analysis to estimate the trend in all-cause 30-day case fatality rate (CFR) in the North East of England (NEE) following IPD. Clinical, microbiological and demographic data were obtained for all laboratory-confirmed IPD cases (April 2006–March 2016) and the adjusted association between CFR and epidemiological year estimated using logistic regression. Of the 2510 episodes of IPD included in the analysis, 486 died within 30 days of IPD (CFR 19%). Increasing age, male sex, a diagnosis of septicaemia, being in ⩾1 clinical risk groups, alcohol abuse and individual serotypes were independently associated with increased CFR. A significant decline in CFR over time was observed following adjustment for these significant predictors (adjusted odds ratio 0.93, 95% confidence interval 0.89–0.98; P = 0.003). A small but significant decline in 30-day all-cause CFR following IPD has been observed in the NEE. Nonetheless, certain population groups remain at increased risk of dying following IPD. Despite the introduction of effective vaccines, further strategies to reduce the ongoing burden of mortality from IPD are needed.

Changes in pneumococcal carriage prevalence and factors associated with carriage in Norwegian children, four years after introduction of PCV13

Background

Streptococcus pneumoniae carriage is often asymptomatic but can cause invasive pneumococcal disease. Pneumococcal carriage is a prerequisite for disease, with children as main reservoir and transmitters. Childhood carriage can therefore be used to determine which serotypes circulate in the population and which may cause disease in the non-vaccinated population. In 2006, a pneumococcal conjugate vaccine (PCV7) was introduced into the Norwegian Childhood Immunisation Programme, which was replaced by the more valent PCV13 in 2011. We investigated changes in pneumococcal carriage prevalence 4 years after switching to PCV13 compared to three previous surveys, and analysed factors associated with carriage in children.

Methods

We conducted a cross-sectional study in Norway, autumn 2015, among children attending day-care centres. We collected questionnaire data and nasopharyngeal swabs to identify pneumococcal serotypes. We compared the carriage prevalence in 2015 with surveys conducted in the same setting performed before widespread vaccination (2006; n = 610), 2 years after PCV7 introduction (2008; n = 600), and 2 years after switching to PCV13 (2013; n = 874). Using multilevel logistic regression we determined the association between pneumococcal carriage and previously associated factors.

Results

In 2015, 896 children participated, with age ranging from 8 to 80 months. The overall carriage prevalence was 48/100 children [95%CI 44–53] in 2015, 38% [29–46] lower than in 2006 pre-PCV7, and 23% [12–32] lower than in 2013, 2 years after switching to PCV13. The PCV13 carriage prevalence was 2.8/100 children [1.9–4.2] in 2015. Increasing age (p < 0.001), recent antimicrobial use (odds ratio = 0.42 [0.21–0.57]) and being vaccinated (odds ratio = 0.37 [0.29–0.47]) were negatively associated with carriage.

Conclusions

Our study showed a continued decrease in overall pneumococcal carriage, mainly fuelled by the decline in vaccine serotypes after vaccine introduction. Childhood vaccination with PCV13 should be continued to keep low PCV13 carriage, transmission and disease. Furthermore, the low prevalence of PCV13-type carriage in children endorse the choice of not recommending PCV13 in addition to the 23-valent pneumococcal polysaccharide vaccine to most medical risk groups in Norway, as little disease caused by these serotypes can be expected.

Changing Epidemiology and Predisposing Factors for Invasive Pneumococcal Disease at Two Australian Tertiary Hospitals

BACKGROUND

Invasive pneumococcal disease (IPD) is associated with significant morbidity and mortality in children. Universal pneumococcal conjugate vaccination has changed the epidemiology of IPD. In vaccinated children, IPD can be a marker of an underlying immunodeficiency.

METHODS

This is a retrospective audit of children younger than 18 years with IPD admitted to 2 tertiary pediatric hospitals in Australia between 2011 and 2017. Data on predisposing conditions, immunologic evaluation, pneumococcal serotype, antibiotic susceptibility and treatment were collected.

RESULTS

During the 7-year period, there were 131 presentations with IPD in 127 children; 3 children had recurrent IPD. Patients presented with sepsis (41%), empyema (29%), meningitis (18%), mastoiditis (12%), pneumonia (10%) and septic arthritis (4%). In 19 (15%) presentations, risk factors for IPD were present, including malignancy, hematologic disorder, chronic liver disease, chronic kidney disease and cochlear implant. Pneumococcal serotypes were determined in 78/131 (60%) of presentations: the most frequent serotypes were 19A (19%), 3 (13%), 7F (10%) and 19F (8%) and non-vaccine serotypes 22F (8%), 35B (6%), 15A (4%) and 38 (4%). Overall, 11% of isolates were non-susceptible to ceftriaxone. Only 36 patients (32%) had an immunologic evaluation, and 4 patients had proven or probable immunodeficiency.

CONCLUSION

Although pneumococcal conjugate vaccine serotypes 19A, 3, 19F and 7F remain frequent causes of IPD, non-vaccine serotypes are emerging. Our data support vancomycin treatment for children with pneumococcal meningitis given 11% of our isolates were not susceptible to ceftriaxone. It is important to consider underlying conditions predisposing to IPD in a population with high rates of pneumococcal vaccination.

Nasopharyngeal pneumococcal carriage in healthy Turkish children after 13-valent conjugated pneumococcal vaccine implementation in the national immunization program

BACKGROUND

In Turkey, pneumococcal conjugated vaccine (PCV) was introduced to the national immunization program as PCV7 in 2008, and was replaced with PCV13 in 2011. The aims of this study were to investigate the effects of PCV13 on nasopharyngeal pneumococcal carriage (NPC) by determining the serotype distribution, and to identify risk factors for carriage, in healthy Turkish children.

METHODS

This prospective study was conducted on 500 healthy children aged 0-13 years between April and November 2014. Nasopharyngeal swab samples were taken, and molecular method for capsular serotyping was performed by multiplex PCR.

RESULTS

Of 500 children, 43.4% were unvaccinated with a PCV (7- or 13-valent), 56.6% were vaccinated and The NPC rate was found to be 9.8%. Of 49 positive Streptococcus pneumoniae isolates, 26 (53%) were PCV13 vaccine strains (VSs), and 17 (34.7%) were non-VS. Six isolates (12.2%) were not typeable by the method applied. The most common serotypes detected were serotype 3 (18.3%), serotype 19F (14.2%), serotype 6A/B (8.1%), serotype 11A (8.1%), and serotype 15B (8.1%). The total coverage rate of the PCV13 serotypes was 60.4%.

CONCLUSION

A significant decrease in carriage rate was detected within three years after the introduction of PCV13 in Turkey. However, the nasopharyngeal carriage of PCV13 strains was found to be interestingly high.

Determinants of high residual post-PCV13 pneumococcal vaccine-type carriage in Blantyre, Malawi: a modelling study

BACKGROUND

In November 2011, Malawi introduced the 13-valent pneumococcal conjugate vaccine (PCV13) into the routine infant schedule. Four to 7 years after introduction (2015-2018), rolling prospective nasopharyngeal carriage surveys were performed in the city of Blantyre. Carriage of Streptococcus pneumoniae vaccine serotypes (VT) remained higher than reported in high-income countries, and impact was asymmetric across age groups.

METHODS

A dynamic transmission model was fit to survey data using a Bayesian Markov-chain Monte Carlo approach, to obtain insights into the determinants of post-PCV13 age-specific VT carriage.

RESULTS

Accumulation of naturally acquired immunity with age and age-specific transmission potential were both key to reproducing the observed data. VT carriage reduction peaked sequentially over time, earlier in younger and later in older age groups. Estimated vaccine efficacy (protection against carriage) was 66.87% (95% CI 50.49-82.26%), similar to previous estimates. Ten-year projected vaccine impact (VT carriage reduction) among 0-9 years old was lower than observed in other settings, at 76.23% (CI 95% 68.02-81.96%), with sensitivity analyses demonstrating this to be mainly driven by a high local force of infection.

CONCLUSIONS

There are both vaccine-related and host-related determinants of post-PCV13 pneumococcal VT transmission in Blantyre with vaccine impact determined by an age-specific, local force of infection. These findings are likely to be generalisable to other Sub-Saharan African countries in which PCV impact on carriage (and therefore herd protection) has been lower than desired, and have implications for the interpretation of post-PCV carriage studies and future vaccination programs.

Multicenter study of serotype distribution of Streptococcus pneumoniae nasopharyngeal isolates from healthy children in the Russian Federation after introduction of PCV13 into the National Vaccination Calendar

Russia introduced PCV13 in 2014. We studied the serotype composition of S. pneumoniae isolated from the nasopharynx of healthy children younger than 6 years in St. Petersburg, Smolensk, Perm, Krasnoyarsk, Khanty-Mansiysk and Khabarovsk, between 2016 and 2018. 2.4% of children had completed a 3-dose course of PCV13, while 25.6% had received 1 or 2 doses. Pneumococcal DNA detection by PCR demonstrated S. pneumoniae in 37.2% of samples with regional variation between sites (27.3 to 56.9%). There was little difference between vaccinated, partially vaccinated and un-vaccinated children. Children who had received at least 1 dose of PCV13 had lower carriage rates of vaccine serotypes than their unvaccinated peers (49.9 vs. 61.4%; p < 0.001). Children who had received at least 1 dose of PCV13 showed increased carriage rates of non-vaccine serotypes (50 vs 38.6%; P < 0.001). Especially serogroup 15AF was more prevalent among fully immunized children than among their peers (12.5 vs 2.7%; P < 0.05).

Serotype evolution in Western Europe: perspectives on invasive pneumococcal diseases (IPD)

Introduction: Epidemiologic trends for IPD have evolved with the introduction of pneumococcal conjugate vaccines into childhood immunization programs. We document the ongoing impact of PCV programs in 15 Western European countries.Areas covered: Data were collected from relevant published observational studies and national surveillance websites from January 2010 through January 2018. In countries using PCV13, the proportion of IPD due to PCV13 serotypes declined significantly (from 60-78% to 8-26%) in children <5 years of age within 5-8 years following vaccine introduction. In countries using PCV10, a marked decrease in PCV10-serotype IPD was reported; however, the proportion of IPD due to PCV13 serotypes remained high at 58-64%, predominantly due to serotypes 19A and 3.Expert opinion: The prevalence of vaccine-type IPD in adults remained high; emerging non-vaccine serotypes such as 8, 12F, 22F, 33F, and 15B/C should be a focus of future vaccine development.

Evolution of Streptococcus pneumoniae Serotype 3 in England and Wales: A Major Vaccine Evader

Despite its inclusion in pneumococcal conjugate vaccine 13 (PCV13), Streptococcus pneumoniae serotype 3 remains a major cause of invasive pneumococcal disease in England and Wales. Previous studies have indicated that there are distinct lineages within serotype 3 clonal complex 180 and the clade distributions have shifted in recent years with the emergence of clade II. We undertook whole genome sequencing and genomic analysis of 616 serotype 3 isolates from England and Wales between 2003 and 2018, including invasive and carriage isolates. Our investigations showed that clade II has expanded since 2014 and now represents 50% of serotype 3 invasive pneumococcal disease (IPD) isolates in England and Wales. Genomic analysis of antibiotic resistance and protein antigen genes showed that distinct profiles are present within the clades which could account for the recent emergence of this clade. This investigation highlights the importance and utility of routine whole genome sequencing and its ability to identify new and emerging variation at the single nucleotide level which informs surveillance and will impact future vaccine development.

Clinical Effectiveness of Conjugate Pneumococcal Vaccination in Hematopoietic Stem Cell Transplantation Recipients

Hematopoietic stem cell transplantation (HSCT) recipients are vulnerable to invasive pneumococcal disease (IPD), with reported IPD rates ranging from 3.81 to 22.5/1000 HSCT. This IPD risk could relate to immunodeficiency, low vaccination uptake, and poor immunogenicity of pneumococcal polysaccharide vaccine (PPV). Literature comparing the clinical effectiveness of pneumococcal conjugate vaccination (PCV) and PPV after HSCT is limited. In this retrospective analysis of HSCT recipients at our center from 2004 to 2015, we evaluated vaccination uptake and compared IPD rates in patients receiving PPV (pre-2010 group) and PCV (post-2010 group). IPD was determined from microbiological results for all HSCT recipients from January 2004 to June 30, 2019. Eight hundred patients had a total of 842 HSCT events, including autologous HSCT (auto-HSCT; n = 562) and allogeneic HSCT (allo-HSCT; n = 280). More than 90% of the HSCT recipients were enrolled, and >93% of surviving HSCT recipients completed the vaccination protocol. Fifteen IPD episodes occurred in 13 patients between 2004 and June 30, 2019. Thirteen episodes occurred in the pre-2010 group, even though 9 of 13 (69%) serotyped isolates were covered by PPV. Two episodes occurred in the post-2010 group; neither serotype was covered by PCV. Thus, with PCV introduction, IPD rate was significantly reduced from 38.5/1000 unique HSCTs pre-2010 to 4.0/1000 unique HSCTs post-2010 (P < .001). A significant reduction was seen in both auto-HSCTs (from 29.4 to 3.1 /1000 unique auto-HSCTs; P = .011) and allo-HSCTs (from 58.3 to 5.6/1000 unique allo-HSCTs; P = .011). PCV demonstrated superior clinical effectiveness over PPV, highlighting its importance in preventing infectious complications after HSCT. Robust vaccination programs at transplantation centers are needed to optimize vaccination uptake and completion.

The Genomics of Streptococcus Pneumoniae Carriage Isolates from UK Children and Their Household Contacts, Pre-PCV7 to Post-PCV13

We used whole genome sequencing (WGS) analysis to investigate the population structure of 877 Streptococcus pneumoniae isolates from five carriage studies from 2002 (N = 346), 2010 (N = 127), 2013 (N = 153), 2016 (N = 187) and 2018 (N = 64) in UK households which covers the period pre-PCV7 to post-PCV13 implementation. The genomic lineages seen in the population were determined using multi-locus sequence typing (MLST) and PopPUNK (Population Partitioning Using Nucleotide K-mers) which was used for local and global comparisons. A Roary core genome alignment of all the carriage genomes was used to investigate phylogenetic relationships between the lineages. The results showed an influx of previously undetected sequence types after vaccination associated with non-vaccine serotypes. A small number of lineages persisted throughout, associated with both non-vaccine and vaccine types (such as ST199), or that could be an example of serotype switching from vaccine to non-vaccine types (ST177). Serotype 3 persisted throughout the study years, represented by ST180 and Global Pneumococcal Sequencing Cluster (GPSC) 12; the local PopPUNK analysis and core genome maximum likelihood phylogeny separated them into two clades, one of which is only seen in later study years. The genomic data showed that serotype replacement in the carriage studies was mostly due to a change in genotype as well as serotype, but that some important genetic lineages, previously associated with vaccine types, persisted.

Pneumococcal carriage among children under five in Accra, Ghana, five years after the introduction of pneumococcal conjugate vaccine

Background

The study objective was to determine the carriage and serotype distribution of Streptococcus pneumoniae among children in Accra, Ghana, five years after the introduction of the pneumococcal conjugate vaccine (PCV-13) in 2012.

Methods

Nasopharyngeal swab samples were collected from 410 children below 5 years of age in Accra, Ghana, from September to December, 2016. Pneumococcal isolates were identified by optochin sensitivity and bile solubility. Serotyping was performed using the latex agglutination kit and Quellung reaction. The isolates were furthermore tested for antimicrobial susceptibility for different antimicrobials, including penicillin (PEN). Twelve isolates including seven non-typeable (NT) isolates were characterized using whole-genome sequencing analysis (WGS).

Results

The overall carriage prevalence was found to be 54% (95% CI, 49–59%), and 20% (95% CI, 49–59%) of the children were carrying PCV-13 included serotypes, while 37% (95% CI, 33–42%) of the children were carrying non-PCV-13 serotypes. Based on the serotype distribution, 33% of all observed serotypes were included in PCV-13 while 66% were non-PCV-13 serotypes. The dominating non-PCV-13 serotypes were 23B, 16F, and 11A followed by PCV-13 serotypes 23F and 19F. The PCV-13 covers the majority of resistant isolates in Accra. A proportion of 22.3% of the isolates showed intermediate resistance to penicillin G, while only one isolate showed full resistance. Forty-five isolates (20.5%) were defined as multidrug-resistant (MDR) as they were intermediate/resistant to three or more classes of antimicrobials. Of the seven NT isolates characterized by WGS, four showed highest match to genotype 38, while the remaining three showed highest match to genotype 14. Four MDR serotype 19A isolates were found to be MLST 320.

Conclusion

PCV-13 introduced in Ghana did not eliminate PCV-13 covered serotypes, and the carriage rate of 54% in this study is similar to carriage studies from pre PCV-13 period. However, the penicillin non-susceptible isolates have been reduced from 45% of carriage isolates before PCV-13 introduction to 22.3% of the isolates in this study. Continuous monitoring of serotype distribution is important, and in addition, an evaluation of an alternative vaccination schedule from 3 + 0 to 2 + 1 will be important to consider.

Electronic supplementary material

The online version of this article (10.1186/s12887-019-1690-5) contains supplementary material, which is available to authorized users.

Effectiveness of the seven-valent and thirteen-valent pneumococcal conjugate vaccines in England: The indirect cohort design, 2006-2018

BACKGROUND

The 7-valent pneumococcal conjugate vaccine (PCV7) was introduced into the UK childhood immunisation programme in 2006 and replaced with a 13-valent vaccine (PCV13) in 2010. Both vaccines led to rapid declines in vaccine-serotype invasive pneumococcal disease (IPD). Here, we assessed the long-term vaccine-effectiveness (VE) of both vaccines in England.

METHODS

Public Health England conducts enhanced national surveillance of IPD in England. VE against IPD was estimated using vaccine-serotype IPD cases and non-vaccine serotype IPD controls among vaccine-eligible children from September 2006 to June 2018 (the Broome method).

RESULTS

Vaccine history was available for 3421 IPD cases, including 1299 due to the additional PCV13 serotypes and the PCV13-related serotype 6C, 274 PCV7 serotypes and 1848 non-PCV13 serotypes. For the complete 2 + 1 schedule, both PCV7 and PCV13 showed high effectiveness against PCV7 serotypes with a combined VE of 92.0% (95%CI, 81.7-96.7). For the 2 + 1 schedule, PCV13 VE against the additional PCV13 serotypes plus 6C was 73.7% (31.1-89.9) compared to 90.0% (75.3 - 96.0) for PCV7 against PCV7 serotypes, although PCV13 VE increased to 84.8% (58.7-94.4) if serotype 3 was excluded; all 36 eligible serotype 3 IPD cases were fully-vaccinated with PCV13. Case numbers were low in older ages but there was evidence of waning, which was significant for serotype 19A for which there were sufficient numbers of cases for analysis.

CONCLUSIONS

PCVs are highly effective in preventing vaccine-serotype IPD except for serotype 3 which has been increasing in incidence. Serotype 19A IPD has also persisted, likely due to a slightly lower VE and/or more rapid waning of protection.

Relationship between immune response to pneumococcal conjugate vaccines in infants and indirect protection after vaccine implementation

Introduction: Streptococcus pneumoniae is a leading cause of morbidity and mortality worldwide. Widespread infant vaccination with pneumococcal conjugate vaccines (PCVs) substantially reduced vaccine-serotype pneumococcal disease by direct protection of immunized children and indirect protection of the community via decreased nasopharyngeal carriage and transmission. Essential to grasping the public health implications of pediatric PCV immunization is an understanding of how PCV formulations impact carriage. Areas covered: Using clinical evidence, this review examines how the immune response to PCVs is associated with subsequent nasopharyngeal carriage reduction in vaccinated infants and toddlers. By combining direct and indirect protection, carriage reduction results in a reduced spread of vaccine serotypes, and eventually, a decrease in vaccine serotype disease incidence in community members of all ages. Expert opinion: The current review presents some of the aspects that influence the overall impact of PCVs on vaccine-serotype carriage, and thus, spread. The link between reduction of vaccine-serotype carriage and the eventual reduction of vaccine-serotype disease in the wider community is described by comparing data from current PCVs, specifically with respect to their ability to reduce carriage of some cross-reacting serotypes (i.e. 6A versus 6B and 19A versus 19F).

Risk of transmission of vaccine-preventable diseases in healthcare settings

The transmission of infectious agents within healthcare settings is a priority public health problem. Although the main burden of healthcare-associated infections is commonly caused by Gram-negative bacteria and fungi, vaccine-preventable diseases represent an additional infectious risk for patients attending healthcare facilities. Hepatitis B, rotavirus gastroenteritis, influenza, measles, pertussis and pneumococcal and meningococcal invasive bacterial infections still represent a threat, notwithstanding the presence of universal vaccination programs. For this reason, healthcare worker immunization is an important strategy to limit the risk of vaccine-preventable diseases in such a fragile population.

Effect of ten-valent pneumococcal conjugate vaccine on invasive pneumococcal disease and nasopharyngeal carriage in Kenya: a longitudinal surveillance study

BACKGROUND

Ten-valent pneumococcal conjugate vaccine (PCV10), delivered at 6, 10, and 14 weeks of age was introduced in Kenya in January, 2011, accompanied by a catch-up campaign in Kilifi County for children aged younger than 5 years. Coverage with at least two PCV10 doses in children aged 2-11 months was 80% in 2011 and 84% in 2016; coverage with at least one dose in children aged 12-59 months was 66% in 2011 and 87% in 2016. We aimed to assess PCV10 effect against nasopharyngeal carriage and invasive pneumococcal disease (IPD) in children and adults in Kilifi County.

METHODS

This study was done at the KEMRI-Wellcome Trust Research Programme among residents of the Kilifi Health and Demographic Surveillance System, a rural community on the Kenyan coast covering an area of 891 km2. We linked clinical and microbiological surveillance for IPD among admissions of all ages at Kilifi County Hospital, Kenya, which serves the community, to the Kilifi Health and Demographic Surveillance System from 1999 to 2016. We calculated the incidence rate ratio (IRR) comparing the prevaccine (Jan 1, 1999-Dec 31, 2010) and postvaccine (Jan 1, 2012-Dec 31, 2016) eras, adjusted for confounding, and reported percentage reduction in IPD as 1 minus IRR. Annual cross-sectional surveys of nasopharyngeal carriage were done from 2009 to 2016.

FINDINGS

Surveillance identified 667 cases of IPD in 3 211 403 person-years of observation. Yearly IPD incidence in children younger than 5 years reduced sharply in 2011 following vaccine introduction and remained low (PCV10-type IPD: 60·8 cases per 100 000 in the prevaccine era vs 3·2 per 100 000 in the postvaccine era [adjusted IRR 0·08, 95% CI 0·03-0·22]; IPD caused by any serotype: 81·6 per 100 000 vs 15·3 per 100 000 [0·32, 0·17-0·60]). PCV10-type IPD also declined in the post-vaccination era in unvaccinated age groups (<2 months [no cases in the postvaccine era], 5-14 years [adjusted IRR 0·26, 95% CI 0·11-0·59], and ≥15 years [0·19, 0·07-0·51]). Incidence of non-PCV10-type IPD did not differ between eras. In children younger than 5 years, PCV10-type carriage declined between eras (age-standardised adjusted prevalence ratio 0·26, 95% CI 0·19-0·35) and non-PCV10-type carriage increased (1·71, 1·47-1·99).

INTERPRETATION

Introduction of PCV10 in Kenya, accompanied by a catch-up campaign, resulted in a substantial reduction in PCV10-type IPD in children and adults without significant replacement disease. Although the catch-up campaign is likely to have brought forward the benefits by several years, the study suggests that routine infant PCV10 immunisation programmes will provide substantial direct and indirect protection in low-income settings in tropical Africa.

FUNDING

Gavi, The Vaccine Alliance and The Wellcome Trust of Great Britain.

Environmental factors which can affect the burden of pneumococcal disease and the immune response to pneumococcal vaccines: the need for more precisely delineated vaccine recommendations

Introduction: Precision medicine describes the customization of healthcare tailored to the individual patient. Generally, vaccines are considered as public health tools rather than from the individual patient perspective. However, adult vaccination programs in particular should consider many different factors, at the individual level and also from societal, cultural and country-specific perspectives. Currently, most immunization programs, including those for pneumococcal vaccines, have only been adopted on the basis of age or medical risk. Areas covered: Based on a broad literature search, this review addresses possible environmental factors which can affect the burden of pneumococcal disease and the immune response to pneumococcal vaccines. Expert opinion: Factors which influence the incidence of pneumococcal disease and the reaction against pneumococcal vaccination, including personal conditions, geographic/ethnic factors and social risks, are diverse. To maximize the effects of pneumococcal vaccination, not only for public health but also to induce optimal effects at the individual level, vaccines need to be verified under diverse situations and with collaboration among relevant medical societies, governments, and the pharmaceutical industry. Whereas vaccines are generally considered only from the public health perspective, flexible, comprehensive and tailored pneumococcal immunization programs, with appropriate policy support, can generate a greater positive impact on public health.

Persistence of Nasopharyngeal Pneumococcal Vaccine Serotypes and Increase of Nonvaccine Serotypes Among Vaccinated Infants and Their Mothers 5 Years After Introduction of Pneumococcal Conjugate Vaccine 13 in The Gambia

BACKGROUND

The widespread use of pneumococcal conjugate vaccine (PCV) has brought about a dramatic decrease in pneumococci of vaccine serotypes (VTs) but nonvaccine serotypes (NVTs) have emerged.

METHODS

We conducted a cross-sectional survey (CSS) among infants who received 3 doses of 13-valent PCV (PCV13) and their mothers 5 years (CSS3) after PCV13 introduction. Nasopharyngeal swab samples were collected and cultured for isolation of Streptococcus pneumoniae. Whole-genome sequencing of the nontypeable strains was performed. Data were compared with those from 2 previous surveys conducted before PCV13 introduction (CSS1) and 1 year later (CSS2).

RESULTS

Among infants, VT carriage decreased from 33.3% (113/339) in CSS1 to 11.4% (40/351) in CSS3 (P = .001) while NVTs increased from 53.1% (180/339) in CSS1 to 74.4% (261/351) in CSS3 (P < .001). Among mothers, there was a significant decrease in VTs between CSS2 8.4% (29/347) and CSS3 5.6% (19/342) (P = .006). NVTs increased from 16.6% (55/331) in CSS1 to 32.2% (110/342) in CSS3 (P < .001). In CSS3, the most prevalent VTs were 7F in infants and 3 in mothers, and the most prevalent NVTs were serogroup 16 and nontypeables, respectively. Genomic analysis showed that VTs were more likely than NVTs to lose their ability to express the capsule.

CONCLUSIONS

Five years after PCV13 introduction, we show both direct (infants) and indirect effects (mothers) of the vaccine, while NVT replacement has occurred in both groups. Ongoing circulation of VTs warrants further study of their relevance in any consideration of a reduced dose schedule.