Multistate population and whole genome sequence-based strain surveillance of invasive pneumococci recovered in the USA during 2017

Increased Proportions of Invasive Pneumococcal Disease Cases Among Adults Experiencing Homelessness Sets the Stage for New Serotype 4 Capsular-Switch Recombinants

BACKGROUND

The Centers for Disease Control and Prevention's Active Bacterial Core surveillance (ABCs) identified increased serotype 4 invasive pneumococcal disease (IPD), particularly among adults experiencing homelessness (AEH).

METHODS

We quantified increased proportions of IPD cases in AEH during 2016-2022. Employing genomic-based characterization of IPD isolates, we identified serotype-switch variants. Recombinational analyses were used to identify the genetic donor and recipient strain that generated a serotype 4 progeny strain. We performed phylogenetic analyses of the serotype 4 progeny and of the serotype 12F genetic recipient to determine genetic distances.

RESULTS

We identified a cluster of 30 highly related (0-21 nucleotide differences) IPD isolates recovered during 2022-2023, corresponding to a serotype 4 capsular-switch variant. This strain arose through a multifragment recombination event between serotype 4/ST10172 and serotype 12F/ST220 parental strains. Twenty-five of the 30 cases occurred in Oregon. Of 29 cases with known residence status, 16 occurred in AEH. Variant emergence coincided with a 2.6-fold increase (57 to 148) of cases caused by the serotype 4/ST10172 donor lineage in 2022 compared to 2019 and its first appearance in Oregon. Most serotypes showed sequential increases of AEH IPD/all IPD ratios during 2016-2022 (eg, for all serotypes combined, 247/2198, 11.2% during 2022 compared to 405/5317, 7.6% for 2018-2019, P < .001). Serotypes 4 and 12F each caused more IPD than any other serotype in AEH during 2020-2022 (207 combined case isolates accounting for 38% of all IPD in AEH).

CONCLUSIONS

Expansion and increased transmission of serotypes 4 and 12F among adults potentially led to recent genesis of an impactful hybrid serotype-switch variant.

Acute respiratory infections due to antibiotic-nonsusceptible Streptococcus pneumoniae in United States adults

Background

We aimed to estimate the burden of antibiotic-nonsusceptible non-bacteremic pneumonia and sinusitis due to Streptococcus pneumoniae (pneumococcus) in US adults (≥18 years).

Methods

We estimated antibiotic-nonsusceptible pneumococcal sinusitis and non-bacteremic pneumonia incidence as products of non-bacteremic pneumococcal pneumonia and sinusitis incidence rates, serotype distribution, and serotype-specific antimicrobial nonsusceptibility prevalences by antibiotic class and guideline-recommended agents from 2016-2019. We derived pneumonia and sinusitis incidence rates from national healthcare utilization surveys and administrative datasets; pneumococcal-attributable attributable percents and serotype distributions from published data; and serotype-specific nonsusceptibility estimates from Active Bacterial Core surveillance data. We evaluated nonsusceptibility for all serotypes and those targeted by 15-, 20- and 21-valent pneumococcal conjugate vaccines (PCV15/20/21).

Results

An estimated 16.4% (95% confidence interval 12.8-21.4%) of non-bacteremic pneumococcal pneumonia and 19.0% (14.8-24.9%) of sinusitis cases were nonsusceptible to ≥3 antibiotic classes, translating to 243,521 (179,673-333,675) and 1,844,726 (1,070,763-2,904,089) outpatient visits for pneumonia and sinusitis, respectively, and 10,155 (7,542-13,803) pneumonia hospitalizations annually. An estimated 31.2% (26.6-36.3%) of non-bacteremic pneumococcal pneumonia and 10.5% (9.4-12.0%) of pneumococcal sinusitis cases were nonsusceptible to ≥1 outpatient first-line antibiotic agent. Cases attributable to serotypes targeted by PCV15, PCV20, and PCV21 that were nonsusceptible to ≥3 antibiotic classes accounted for 7.4% (4.7-11.1%), 8.5% (5.8-12.1%), and 12.6% (9.2-17.5%) of all non-bacteremic pneumococcal pneumonia cases, and 8.4% (5.3-12.5%), 9.4% (6.2-13.4), and 14.4% (10.4-20.0%) of all pneumococcal sinusitis cases.

Conclusions

We demonstrated high proportions of antibiotic nonsusceptibility in non-bacteremic pneumococcal pneumonia and sinusitis in US adults. PCVs and antibiotic stewardship may mitigate antibiotic nonsusceptibility in pneumococcal disease.

Update on the evolving landscape of pneumococcal capsule types: new discoveries and way forward

SUMMARYStreptococcus pneumoniae (the "pneumococcus") is a significant human pathogen. The key determinant of pneumococcal fitness and virulence is its ability to produce a protective polysaccharide (PS) capsule, and anti-capsule antibodies mediate serotype-specific opsonophagocytic killing of bacteria. Notably, immunization with pneumococcal conjugate vaccines (PCVs) has effectively reduced the burden of disease caused by serotypes included in vaccines but has also spurred a relative upsurge in the prevalence of non-vaccine serotypes. Recent advancements in serotyping and bioinformatics surveillance tools coupled with high-resolution analytical techniques have enabled the discovery of numerous new capsule types, thereby providing a fresh perspective on the dynamic pneumococcal landscape. This review offers insights into the current pneumococcal seroepidemiology highlighting important serotype shifts in different global regions in the PCV era. It also comprehensively summarizes newly discovered serotypes from 2007 to 2024, alongside updates on revised chemical structures and the de-novo determinations of structures for previously known serotypes. Furthermore, we spotlight emerging evidence on non-pneumococcal Mitis-group strains that express capsular PS that are serologically and biochemically related to the pneumococcal capsule types. We further discuss the implications of these recent findings on capsule nomenclature, pneumococcal carriage detection, and future PCV design. The review maps out the current status and also outlines the course for future research and vaccine strategies, ensuring a continued effective response to the evolving pneumococcal challenge.

PNEUMOCOCCAL SEROTYPE DISTRIBUTION AND COVERAGE OF EXISTING AND PIPELINE PNEUMOCOCCAL VACCINES

Background

Streptococcus pneumoniae (pneumococcus) causes invasive pneumococcal disease (IPD) and non-invasive acute respiratory infections (ARIs). Three pneumococcal conjugate vaccines (PCVs) are recommended in the United States with additional products in clinical trials. We aimed to estimate 1) proportions of IPD cases and pneumococcal ARIs caused by serotypes targeted by existing and pipeline PCVs and 2) annual U.S. pneumococcal burdens potentially preventable by PCVs.

Methods

We estimated serotype distribution and proportions of non-invasive pneumococcal ARIs (AOM [children only], sinusitis, non-bacteremic pneumonia) and IPD attributable to serotypes targeted by each PCV using Markov chain Monte Carlo approaches incorporating data from studies of serotype distribution in ARIs and Active Bacterial Core Surveillance (ABCs) data. We then estimated annual numbers of outpatient-managed pneumococcal ARIs, non-bacteremic pneumococcal pneumonia hospitalizations, and IPD cases potentially preventable by PCVs in the United States by multiplying pneumococcal disease incidence rates by PCV-targeted proportions of disease and vaccine effectiveness estimates.

Results

In children, PCV15, PCV20, PCV24, PCV25, and PCV31 serotypes account for 16% (95% confidence interval: 15-17%), 31% (30-32%), 34% (32-35%), 43% (42-44%), and 68% (67-69%) of pneumococcal acute otitis media cases, respectively. In adults, PCV15, PCV20, PCV21, PCV24, PCV25, and PCV31 serotypes account for 43% (38-47%), 52% (47-57%), 69% (64-73%), 65% (61-70%), 62% (57-67%), and 87% (83-90%) of pneumococcal non-bacteremic pneumonia cases. For IPD, 42-85% of pediatric and 42-94% of adult cases were due to PCV-targeted serotypes. PCV-preventable burdens encompassed 270 thousand-3.3 million outpatient-managed ARIs, 2-17 thousand non-bacteremic pneumonia hospitalizations, and 3-14 thousand IPD cases in the United States annually.

Conclusions

Across pneumococcal conditions, coverage and preventable burdens were lowest for PCV15 and highest for PCV31, with PCV21 also targeting sizeable burdens of adult disease. Serotype distribution across syndromes may inform vaccine formulations and policy.

Health-economic burden attributable to novel serotypes in candidate 24- and 31-valent pneumococcal conjugate vaccines

INTRODUCTION

Next-generation pneumococcal vaccines currently in clinical trials include 24- and 31-valent pneumococcal conjugate vaccines (PCV24, PCV31), which aim to prevent upper-respiratory carriage and disease involving the targeted serotypes. We aimed to estimate the comprehensive health-economic burden associated with acute respiratory infections (ARIs) and invasive pneumococcal disease (IPD) attributable to PCV24- and PCV31-additional (non-PCV20) serotypes in the United States.

MATERIAL AND METHODS

We multiplied all-cause incidence rate estimates for acute otitis media (AOM), sinusitis, and non-bacteremic pneumonia by estimates of the proportions of each of these conditions attributable to pneumococci and the proportions of pneumococcal infections involving PCV24- and PCV31-additional serotypes. We estimated serotype-specific IPD incidence rates using US Active Bacterial Core surveillance data. We accounted for direct medical and non-medical costs associated with each condition to estimate resulting health-economic burden. Non-medical costs included missed work and lost quality-adjusted life years due to death and disability.

RESULTS

The health-economic burden of PCV24-additional serotypes totaled $1.3 ($1.1-1.7) billion annually in medical and non-medical costs, comprised of $0.9 ($0.7-1.2) billion due to ARIs and $0.4 ($0.3-0.5) billion due to IPD. For PCV31-additional serotypes, medical and non-medical costs totaled $7.5 ($6.6-8.6) billion annually, with $5.5 ($4.7-6.6) billion due to ARIs and $1.9 ($1.8-2.1) billion due to IPD. The largest single driver of costs was non-bacteremic pneumonia, particularly in adults aged 50-64 and ≥65 years.

CONCLUSIONS

Additional serotypes in PCV24 and PCV31, especially those included in PCV31, account for substantial health-economic burden in the United States.

A phase 2, randomized, blinded, dose-finding, controlled clinical trial to evaluate the safety, tolerability, and immunogenicity of a 24-valent pneumococcal conjugate vaccine (VAX-24) in healthy adults 65 years and older

Despite current polysaccharide and conjugate vaccine use, pneumococcal diseases remain prevalent in older adults. VAX-24 is a 24-valent pneumococcal conjugate vaccine (PCV) containing eCRM, a proprietary carrier protein with non-native amino acids (para-azidomethyl-L-phenylalanine) that undergo site-specific conjugation to pneumococcal polysaccharides that have been activated with a small-molecule linker (dibenzocyclooctyne). Site-specific conjugation utilizing click chemistry enables consistent exposure of T-cell epitopes, reduction in carrier protein to pneumococcal polysaccharide ratio, and enhances manufacturing process consistency to improve PCVs by increasing serotype coverage while minimizing carrier suppression. Healthy adults aged 65 or older were randomized in a 1:1:1:1 ratio to receive a single injection of VAX-24 at 1 of 3 dose levels (1.1, 2.2, or a mixed dose of 2.2 or 4.4 mcg) or Prevnar 20® (PCV20) in a phase 2, blinded study. Primary outcome measures were solicited local and systemic events within 7 days post-vaccination, unsolicited adverse events (AEs) within 1 month, and serious AEs, medically attended AEs, or new onset of chronic disease within 6 months of vaccination. Serotype-specific opsonophagocytic activity (OPA) and immunoglobulin G (IgG) were measured pre-vaccination and at 1 month post-vaccination. Of 207 participants enrolled, 200 completed the trial. Safety profiles were comparable across the three VAX-24 doses and PCV20. Robust OPA and IgG immune responses were seen for all 24 serotypes. On average, immune responses to VAX-24 2.2 mcg dose were similar or higher compared to PCV20. In adults ≥ 65 years, VAX-24 had a safety profile similar to PCV20 through six months post-vaccination and induced robust OPA and IgG responses to all 24 serotypes, supporting prior data showing that site-specific conjugation allows for increased serotype coverage with similar or higher immune response vs other PCVs. The outcome of this phase 2 study further supports use of VAX-24 2.2 mcg dose in phase 3 trials. Clinicaltrials.gov: NCT05297578.

Vaccine-induced strain replacement: theory and real-life implications

The value of preventive medicine is superior to treatment with vaccinations occupying high priority. Nevertheless, heavy pressure has started to form in regard to strains not included in vaccines contributing to the changing epidemiology of pathogen subtypes leading to 'vaccine-induced strain replacement'. Among other mechanisms, increasing fitness of nonvaccine strains and metabolic shifts in the subtypes have been described. Classical examples include pneumococcal infections and viral diseases, such as the human papilloma virus. Recently, it has been described in SARS-CoV-2, leading to the emergence of new subtypes, such as Omicron and Delta variants. The phenomenon has also been reported in Mycobacterium tuberculosis, Neisseria meningitidis and rotavirus. This study addresses the concepts, examples and implications of this phenomenon.

Effectiveness of 13-valent pneumococcal conjugate vaccine for prevention of invasive pneumococcal disease among children in the United States between 2010 and 2019: An indirect cohort study

BACKGROUND

A U.S. case-control study (2010-2014) demonstrated vaccine effectiveness (VE) for ≥ 1 dose of the thirteen-valent pneumococcal conjugate vaccine (PCV13) against vaccine-type (VT) invasive pneumococcal disease (IPD) at 86 %; however, it lacked statistical power to examine VE by number of doses and against individual serotypes.

METHODS

We used the indirect cohort method to estimate PCV13 VE against VT-IPD among children aged < 5 years in the United States from May 1, 2010 through December 31, 2019 using cases from CDC's Active Bacterial Core surveillance, including cases enrolled in a matched case-control study (2010-2014). Cases and controls were defined as individuals with VT-IPD and non-PCV13-type-IPD (NVT-IPD), respectively. We estimated absolute VE using the adjusted odds ratio of prior PCV13 receipt (1-aOR x 100 %).

RESULTS

Among 1,161 IPD cases, 223 (19.2 %) were VT cases and 938 (80.8 %) were NVT controls. Of those, 108 cases (48.4 %; 108/223) and 600 controls (64.0 %; 600/938) had received > 3 PCV13 doses; 23 cases (17.6 %) and 15 controls (2.4 %) had received no PCV doses. VE ≥ 3 PCV13 doses against VT-IPD was 90.2 % (95 % Confidence Interval75.4-96.1 %), respectively. Among the most commonly circulating VT-IPD serotypes, VE of ≥ 3 PCV13 doses was 86.8 % (73.7-93.3 %), 50.2 % (28.4-80.5 %), and 93.8 % (69.8-98.8 %) against serotypes 19A, 3, and 19F, respectively.

CONCLUSIONS

At least three doses of PCV13 continue to be effective in preventing VT-IPD among children aged < 5 years in the US. PCV13 was protective against serotypes 19A and 19F IPD; protection against serotype 3 IPD did not reach statistical significance.

Evaluating the safety, tolerability, and immunogenicity of a 24-valent pneumococcal conjugate vaccine (VAX-24) in healthy adults aged 18 to 64 years: a phase 1/2, double-masked, dose-finding, active-controlled, randomised clinical trial

BACKGROUND

Despite substantial reductions in pneumococcal disease with the availability of pneumococcal conjugate vaccines, a significant burden of pneumococcal disease remains due to the diversity of serotypes combined with serotype replacement. We developed a new vaccine candidate, VAX-24 (24-valent pneumococcal conjugate vaccine), using cell-free protein synthesis to produce a variant of cross-reactive material 197 (eCRM) as the carrier protein, increasing serotype coverage while minimising carrier suppression. The aim of this clinical trial was to assess the safety, tolerability, and immunogenicity of three different doses of VAX-24 compared to pneumococcal 20-valent conjugate vaccine (PCV20).

METHODS

This was a phase 1/2, randomised, double-masked study of VAX-24 versus PCV20 conducted in the USA. Key inclusion criteria included being a male or female aged 18 to 64 years in good health; key exclusion criteria included previous history of pneumococcal disease, receipt of a licensed or investigational pneumococcal vaccine, or immunosuppressive therapy. Participants were randomly allocated in a 1:1:1:1 ratio by permuted block to receive one dose of VAX-24 (1·1 μg of each antigen, 2·2 μg of each antigen, or 2·2 μg of 17 antigens mixed with 4·4 μg of seven antigens), or PCV20. The safety population included all participants with safety data. The immunogenicity population was as per-treatment in phase 2. Primary outcome measures included solicited and unsolicited adverse events. Secondary outcomes included serotype-specific opsonophagocytic activity (OPA) geometric mean titres (GMT), and IgG geometric mean concentrations (GMC) were measured 1 month postvaccination. Traditional non-inferiority criteria included OPA geometric mean ratio (GMR), with a lower bound of the two sided 95% CI of greater than 0·5 for shared serotypes. This completed trial is registered at ClinicalTrials.gov, NCT05266456.

FINDINGS

Safety profiles were comparable among the treatment groups, with 170 of 209 participants (81%, 95% CI 75·2-86·2) to 178 of 207 participants (86%, 80·5-90·4) reporting at least one solicited adverse event among the three VAX-24 groups. 24 of 207 participants (12%, 7·6-16·8) to 32 of 209 of participants (15%, 10·7-20·9) experiened an unsolicited treatment emergent adverse event within 1 month postvaccination. VAX-24 2·2 μg met traditional OPA GMR non-inferiority criteria for all 20 shared serotypes; 16 serotypes elicited GMR point estimates greater than 1·0, and four reached the lower bound of the two-sided 95% CI greater than 1·0.

INTERPRETATION

VAX-24 had a safety profile similar to PCV20 at all doses, with the 2·2 μg dose showing increased serotype coverage with decreased carrier suppression.

FUNDING

Vaxcyte.

Predicted serotype-specific effectiveness of pneumococcal conjugate vaccines V114 and PCV20 against invasive pneumococcal disease in children

BACKGROUND

Next-generation, higher-valency pneumococcal conjugate vaccines (PCVs), 15-valent PCV V114 and 20-valent PCV (PCV20), have been assessed by comparing their immune responses across serotypes shared with the 13-valent PCV (PCV13). Without efficacy or real-world vaccine effectiveness (VE) it becomes important to relate IgG titers to VE to aid in the interpretation of the immune response elicited by V114 and PCV20.

METHODS

We estimated the protective antibody concentrations for each serotype in 7-valent PCV (PCV7) and PCV13 which were then used to predict the serotype-specific VE for each PCV7 and PCV13 non PCV7 serotype present in V114 and PCV20.

RESULTS

The predicted effectiveness of V114 was comparable to PCV7 and PCV13 for 11 of the 13 shared serotypes (1, 4, 5, 6B, 7F, 9 V, 14, 18C, 19A, 19F, and 23F), with improved effectiveness against serotype 3 and decreased effectiveness against serotype 6A. PCV20 had predicted effectiveness comparable to PCV7 and PCV13 for 7 of the 13 shared serotypes (5, 6A, 7F, 9 V, 18C, 19F, and 23F), with decreased effectiveness against the remaining serotypes (1, 3, 4, 6B, 14, and 19A).

CONCLUSIONS

Prediction of serotype-specific VE values suggests that V114 retains greater effectiveness than PCV20 toward most serotypes present in PCV7 and PCV13.

Comparison of next generation technologies and bioinformatics pipelines for capsular typing of Streptococcus pneumoniae

Whole genome sequencing (WGS)-based approaches for pneumococcal capsular typing have become an alternative to serological methods. In silico serotyping from WGS has not yet been applied to long-read sequences produced by third-generation technologies. The objective of the study was to determine the capsular types of pneumococci causing invasive disease in Catalonia (Spain) using serological typing and WGS and to compare the performance of different bioinformatics pipelines using short- and long-read data from WGS. All invasive pneumococcal pediatric isolates collected in Hospital Sant Joan de Déu (Barcelona) from 2013 to 2019 were included. Isolates were assigned a capsular type by serological testing based on anticapsular antisera and by different WGS-based pipelines: Illumina sequencing followed by serotyping with PneumoCaT, SeroBA, and Pathogenwatch vs MinION-ONT sequencing coupled with serotyping by Pathogenwatch from pneumococcal assembled genomes. A total of 119 out of 121 pneumococcal isolates were available for sequencing. Twenty-nine different serotypes were identified by serological typing, with 24F (n = 17; 14.3%), 14 (n = 10; 8.4%), and 15B/C (n = 8; 6.7%) being the most common serotypes. WGS-based pipelines showed initial concordance with serological typing (>91% of accuracy). The main discrepant results were found at the serotype level within a serogroup: 6A/B, 6C/D, 9A/V, 11A/D, and 18B/C. Only one discrepancy at the serogroup level was observed: serotype 29 by serological testing and serotype 35B/D by all WGS-based pipelines. Thus, bioinformatics WGS-based pipelines, including those using third-generation sequencing, are useful for pneumococcal capsular assignment. Possible discrepancies between serological typing and WGS-based approaches should be considered in pneumococcal capsular-type surveillance studies.

A Phase 3, Randomized, Double-Blind, Comparator-Controlled Study to Evaluate Safety, Tolerability, and Immunogenicity of V114, a 15-Valent Pneumococcal Conjugate Vaccine, in Allogeneic Hematopoietic Cell Transplant Recipients (PNEU-STEM)

BACKGROUND

Individuals who receive allogeneic hematopoietic cell transplant (allo-HCT) are immunocompromised and at high risk of pneumococcal infections, especially in the months following transplant. This study evaluated the safety and immunogenicity of V114 (VAXNEUVANCE; Merck, Sharp & Dohme LLC, a subsidiary of Merck & Co., Inc., Rahway, NJ, USA), a 15-valent pneumococcal conjugate vaccine (PCV), when given to allo-HCT recipients.

METHODS

Participants received 3 doses of V114 or PCV13 (Prevnar 13; Wyeth LLC) in 1-month intervals starting 3-6 months after allo-HCT. Twelve months after HCT, participants received either PNEUMOVAX 23 or a fourth dose of PCV (if they experienced chronic graft vs host disease). Safety was evaluated as the proportion of participants with adverse events (AEs). Immunogenicity was evaluated by measuring serotype-specific immunoglobulin G (IgG) geometric mean concentrations (GMCs) and opsonophagocytic activity (OPA) geometric mean titers (GMTs) for all V114 serotypes in each vaccination group.

RESULTS

A total of 274 participants were enrolled and vaccinated in the study. The proportions of participants with AEs and serious AEs were generally comparable between intervention groups, and the majority of AEs in both groups were of short duration and mild-to-moderate intensity. For both IgG GMCs and OPA GMTs, V114 was generally comparable to PCV13 for the 13 shared serotypes, and higher for serotypes 22F and 33F at day 90.

CONCLUSIONS

V114 was well tolerated in allo-HCT recipients, with a generally comparable safety profile to PCV13. V114 induced comparable immune responses to PCV13 for the 13 shared serotypes, and was higher for V114 serotypes 22F and 33F. Study results support the use of V114 in allo-HCT recipients. Clinical Trials Registration. clinicaltrials.gov (NCT03565900) and European Union at EudraCT 2018-000066-11.

A phase 3 study of safety and immunogenicity of V114, a 15-valent pneumococcal conjugate vaccine, followed by 23-valent pneumococcal polysaccharide vaccine, in children with HIV

OBJECTIVES

To evaluate the safety and immunogenicity of V114 [15-valent pneumococcal conjugate vaccine (PCV) containing serotypes 1, 3, 4, 5, 6A, 6B, 7F, 9 V, 14, 18C, 19A, 19F, 22F, 23F, 33F], followed by 23-valent pneumococcal polysaccharide vaccine (PPSV23) 8 weeks later, in children with HIV.

DESIGN

This phase 3 study (NCT03921424) randomized participants 6-17 years of age with HIV (CD4 + T-cell count ≥200 cells/μl, plasma HIV RNA <50 000 copies/ml) to receive V114 or 13-valent PCV (PCV13) in a double-blind manner on Day 1, followed by PPSV23 at Week 8.

METHODS

Adverse events (AEs), pneumococcal serotype-specific immunoglobulin G (IgG), and opsonophagocytic activity (OPA) were evaluated 30 days after each vaccination.

RESULTS

The proportion of participants experiencing at least one AE post-PCV was 78.8% in the V114 group ( n  = 203) and 69.6% in the PCV13 group ( n  = 204); respective proportions post-PPSV23 were 75.4% ( n  = 203) and 77.2% ( n  = 202). There were no vaccine-related serious AEs. IgG geometric mean concentrations (GMCs) and OPA geometric mean titers (GMTs) were generally comparable between V114 and PCV13 for shared serotypes at Day 30, and were higher for V114 compared with PCV13 for the additional V114 serotypes 22F and 33F. Approximately 30 days after PPSV23, IgG GMCs and OPA GMTs were generally comparable between the V114 and PCV13 groups for all 15 serotypes in V114.

CONCLUSIONS

In children with HIV, a sequential administration of V114 followed 8 weeks later with PPSV23 is well tolerated and induces immune responses for all 15 pneumococcal serotypes included in V114.

Pneumococcal Vaccination in Adults: A Narrative Review of Considerations for Individualized Decision-Making

Pneumococcal disease remains one of the major causes of severe disease in both children and adults. Severe disease may be prevented by pneumococcal polysaccharide and conjugate vaccines, which currently cover more than 20 serotypes. However, unlike routine pneumococcal vaccination in children, guidelines promote only limited pneumococcal vaccination in adults, and do not cater for decision-making for individual patients. In this narrative review, considerations for individualized decision-making are identified and discussed. This review identifies and discusses considerations for individualized decision-making, including the risk of severe disease, immunogenicity, clinical efficacy, mucosal immunity, herd immunity, concomitant administration with other vaccines, waning immunity, and replacement strains.

A global genomic perspective on the multidrug-resistant Streptococcus pneumoniae 15A-CC63 sub-lineage following pneumococcal conjugate vaccine introduction

The introduction of pneumococcal conjugate vaccines (PCV7, PCV10, PCV13) around the world has proved successful in preventing invasive pneumococcal disease. However, immunization against Streptococcus pneumoniae has led to serotype replacement by non-vaccine serotypes, including serotype 15A. Clonal complex 63 (CC63) is associated with many serotypes and has been reported in association with 15A after introduction of PCVs. A total of 865 CC63 isolates were included in this study, from the USA (n=391) and a global collection (n=474) from 1998-2019 and 1995-2018, respectively. We analysed the genomic sequences to identify serotypes and penicillin-binding protein (PBP) genes 1A, 2B and 2X, and other resistance determinants, to predict minimum inhibitory concentrations (MICs) against penicillin, erythromycin, clindamycin, co-trimoxazole and tetracycline. We conducted phylogenetic and spatiotemporal analyses to understand the evolutionary history of the 15A-CC63 sub-lineage. Overall, most (89.5 %, n=247) pre-PCV isolates in the CC63 cluster belonged to serotype 14, with 15A representing 6.5 % of isolates. Conversely, serotype 14 isolates represented 28.2 % of post-PCV CC63 isolates (n=618), whilst serotype 15A isolates represented 65.4 %. Dating of the CC63 lineage determined the most recent common ancestor emerged in the 1980s, suggesting the 15A-CC63 sub-lineage emerged from its closest serotype 14 ancestor prior to the development of pneumococcal vaccines. This sub-lineage was predominant in the USA, Israel and China. Multidrug resistance (to three or more drug classes) was widespread among isolates in this sub-lineage. We show that the CC63 lineage is globally distributed and most of the isolates are penicillin non-susceptible, and thus should be monitored.

Cost-Effectiveness Analysis of Routine Use of 15-Valent Pneumococcal Conjugate Vaccine in the US Pediatric Population

This study evaluated the clinical and economic impact of routine pediatric vaccination with the 15-valent pneumococcal conjugate vaccine (PCV15, V114) compared with the 13-valent PCV (PCV13) from a societal perspective in the United States (US). A Markov decision-analytic model was constructed to estimate the outcomes for the entire US population over a 100-year time horizon. The model estimated the impact of V114 versus PCV13 on pneumococcal disease (PD) incidence, post meningitis sequalae, and deaths, taking herd immunity effects into account. V114 effectiveness was extrapolated from the observed PCV13 data and PCV7 clinical trials. Costs (2021$) included vaccine acquisition and administration costs, direct medical costs for PD treatment, direct non-medical costs, and indirect costs, and were discounted at 3% per year. In the base case, V114 prevented 185,711 additional invasive pneumococcal disease, 987,727 all-cause pneumonia, and 11.2 million pneumococcal acute otitis media cases, compared with PCV13. This led to expected gains of 90,026 life years and 96,056 quality-adjusted life years with a total saving of $10.8 billion. Sensitivity analysis showed consistent results over plausible values of key model inputs and assumptions. The findings suggest that V114 is a cost-saving option compared to PCV13 in the routine pediatric vaccination program.

Safety, tolerability, and immunogenicity of V114, a 15-valent pneumococcal conjugate vaccine, administered concomitantly with influenza vaccine in healthy adults aged ≥50 years: a randomized phase 3 trial (PNEU-FLU)

Streptococcus pneumoniae and influenza viruses are associated with significant morbidity and mortality in older adults. Concomitant vaccination against these agents reduces hospitalization and mortality rates. This phase 3 trial evaluated safety, tolerability, and immunogenicity of concomitant and non-concomitant administration of V114, a 15-valent pneumococcal conjugate vaccine containing serotypes 1, 3, 4, 5, 6A, 6B, 7F, 9V, 14, 18C, 19F, 19A, 22F, 23F, 33F, and quadrivalent inactivated influenza vaccine (QIV), in healthy adults aged ≥50 years. Participants (N = 1,200) were randomized 1:1 to receive either V114 administered concomitantly with QIV (concomitant group) or QIV plus placebo (non-concomitant group) on Day 1, followed by placebo (concomitant group) or V114 (non-concomitant group) 30 days later. Randomization was stratified by age and history of pneumococcal polysaccharide vaccine receipt. Overall, 426 (71.0%) and 438 (73.5%) participants in the concomitant and non-concomitant groups experienced solicited injection-site adverse events (AEs); 278 (46.3%) and 300 (50.3%) reported solicited systemic AEs. Most solicited AEs were mild or moderate in severity and of short duration. Non-inferiority for pneumococcal- and influenza-specific antibody responses (lower bound 95% confidence interval of opsonophagocytic activity [OPA] and hemagglutination inhibition geometric mean titers [GMTs] ratios ≥0.5) was demonstrated for concomitant versus non-concomitant administration for all 15 pneumococcal serotypes and all four influenza strains. Consistent with previous studies, a trend was observed toward lower pneumococcal OPA GMTs in the concomitant versus the non-concomitant group. V114 administered concomitantly with QIV is generally well tolerated and immunologically non-inferior to non-concomitant administration, supporting coadministration of both vaccines.

Health and economic burden associated with 15-valent pneumococcal conjugate vaccine serotypes in Korea and Hong Kong

Use of pneumococcal conjugate vaccines (PCVs) has greatly reduced the incidence of invasive pneumococcal disease (IPD). V114 (VAXNEUVANCE™, Merck Sharp & Dohme Corp. a subsidiary of Merck & Co. Inc. Kenilworth, NJ, USA) is a 15-valent PCV currently approved in adults in the United States, containing the 13 serotypes in licensed PCV13 and 2 additional serotypes (22F and 33F) which are important contributors to residual pneumococcal disease. This study quantified the health and economic burden of IPD attributable to V114 serotypes in hypothetical birth cohorts from Korea and Hong Kong. A Markov model was used to estimate the case numbers and costs of IPD in unvaccinated birth cohorts over 20 years. The model was applied to 3 scenarios in Korea (pre-PCV7, pre-PCV13, and post-PCV13) and to 2 scenarios in Hong Kong (pre-PCV7 and post-PCV13). For Korea, the model predicted 62, 26, and 8 IPD cases attributable to V114 serotypes in the pre-PCV7, pre-PCV13, and post-PCV13 scenarios, respectively. Costs of V114-type IPD fell from $1.691 million pre-PCV7 to $.212 million post-PCV13. For Hong Kong, the model estimated 62 V114-associated IPD cases in the pre-PCV7 scenario and 46 in the post-PCV13 scenario. Costs attributed to all V114 serotypes were $2.322 million and $1.726 million in the pre-PCV7 and post-PCV13 periods, respectively. Vaccine-type serotypes are predicted to cause continuing morbidity and cost in Korea (19A) and Hong Kong (3 and 19A). New pediatric pneumococcal vaccines must continue to protect against serotypes in licensed vaccines to maintain disease reduction, while extending coverage to non-vaccine serotypes.

An Overview of Macrolide Resistance in Streptococci: Prevalence, Mobile Elements and Dynamics

Streptococcal infections are usually treated with beta-lactam antibiotics, but, in case of allergic patients or reduced antibiotic susceptibility, macrolides and fluoroquinolones are the main alternatives. This work focuses on studying macrolide resistance rates, genetic associated determinants and antibiotic consumption data in Spain, Europe and also on a global scale. Macrolide resistance (MR) determinants, such as ribosomal methylases (erm(B), erm(TR), erm(T)) or active antibiotic efflux pumps and ribosomal protectors (mef(A/E)-mrs(D)), are differently distributed worldwide and associated with different clonal lineages and mobile genetic elements. MR rates vary together depending on clonal dynamics and on antibiotic consumption applying selective pressure. Among Streptococcus, higher MR rates are found in the viridans group, Streptococcus pneumoniae and Streptococcus agalactiae, and lower MR rates are described in Streptococcus pyogenes. When considering different geographic areas, higher resistance rates are usually found in East-Asian countries and milder or lower in the US and Europe. Unfortunately, the availability of data varies also between countries; it is scarce in low- and middle- income countries from Africa and South America. Thus, surveillance studies of macrolide resistance rates and the resistance determinants involved should be promoted to complete global knowledge among macrolide resistance dynamics.

Multi-valent pneumococcal conjugate vaccine for global health: From problem to platform to production

Childhood bacterial meningitis and pneumonia represent leading causes of mortality, with the latter persisting as one of the top causes of mortality for children under 5 y of age. The prohibitive costs of developing and producing broader spectrum conjugate vaccines impact availability and affordability, resulting in a barrier to health equity and access to disease preventing vaccines, which restrict global health disease prevention efforts. Inventprise was founded in response to the need for innovation that can help reduce disease burden with improved coverage and more affordable vaccines. Inventprise 25-valent pneumococcal conjugate vaccine candidate with the patented Hz-PEG-Hz linker technology platform is expected to provide the broadest coverage against pathogenic pneumococcal serotypes encountered by populations regardless of where they live. The innovative automation technology and tightly controlled manufacturing requirements were implemented to mitigate the high capital cost for constructing a manufacturing facility in the United States, in addition to the prohibitive cost for the workforce required for running a complex plant.

A Multicenter Evaluation of Trends in Antimicrobial Resistance Among Streptococcus pneumoniae Isolates From Adults in the United States

Background

Management of pneumococcal disease is complicated by high rates of antimicrobial resistance (AMR). This study assessed AMR trends for Streptococcus pneumoniae isolates from adults with pneumococcal disease.

Methods

From January 2011 to February 2020, we evaluated 30-day nonduplicate S. pneumoniae isolates from 290 US hospitals (BD Insights Research Database) from adults (≥18 years) in inpatient and outpatient settings. Isolates were required to have ≥1 AMR result for invasive (blood, cerebrospinal fluid/neurologic) or noninvasive (respiratory or ear/nose/throat) pneumococcal disease samples. Determination of AMR was based on facility reports of intermediate or resistant. Descriptive statistics and generalized estimated equations were used to assess variations over time.

Results

Over the study period, 34 039 S. pneumoniae isolates were analyzed (20 749 [61%] from noninvasive sources and 13 290 [39%] from invasive sources). Almost half (46.6%) of the isolates were resistant to ≥1 drug, and noninvasive isolates had higher rates of AMR than invasive isolates. Total S. pneumoniae isolates had high rates of resistance to macrolides (37.7%), penicillin (22.1%), and tetracyclines (16.1%). Multivariate modeling identified a significant increasing trend in resistance to macrolides (+1.8%/year; P < .001). Significant decreasing trends were observed for penicillin (-1.6%/year; P < .001), extended-spectrum cephalosporins (ESCs; -0.35%/year; P < .001), and ≥3 drugs (-0.5%/year; P < .001).

Conclusions

Despite decreasing trends for penicillin, ESCs, and resistance to ≥3 drugs, AMR rates are persistently high in S. pneumoniae isolates among US adults. Increasing macrolide resistance suggests that efforts to address AMR in S. pneumoniae may require antimicrobial stewardship efforts and higher-valent pneumococcal conjugate vaccines.

Predicting effectiveness of the V114 vaccine against invasive pneumococcal disease in children

BACKGROUND

The potential impact of new pneumococcal conjugate vaccines (PCVs) is assessed by using immune responses to predict their effectiveness against invasive pneumococcal disease (IPD). This analysis predicted the serotype-specific effectiveness against IPD of a new 15-valent PCV (V114) for the serotypes shared with a 13-valent PCV (PCV13), in a US pediatric population given a 3 + 1 dosing regimen.

METHODS

Beginning with the known serotype-specific antibody concentrations after vaccination with placebo, 7-valent PCV (PCV7) and PCV13, reverse cumulative distribution curves were used, along with published serotype-specific vaccine effectiveness of PCV7 and PCV13, to derive a protective antibody concentration (C_p) for each PCV13 serotype in V114. Serotype-specific effectiveness was predicted using the C_p estimates and the respective serotype-specific antibody concentrations of placebo and V114 recipients in recent pediatric clinical trials.

RESULTS

Predicted serotype-specific V114 effectiveness values ranged from 86% to 99% for PCV7 serotypes and from 59% to 97% for (non-PCV7) PCV13 serotypes.

CONCLUSIONS

V114 serotype-specific effectiveness against IPD in a US pediatric population was predicted to be largely comparable to that of PCV7 and PCV13 for shared serotypes, with models suggesting likelihood of high overall benefit gained from increased serotype 3 effectiveness, and additional protection against serotypes 22 F and 33 F.

Invasive Pneumococcal Disease Clusters Disproportionally Impact Persons Experiencing Homelessness, Injecting Drug Users, and the Western United States

BACKGROUND

Invasive pneumococcal disease (IPD) isolates forming genomic clusters can reflect rapid disease transmission between vulnerable individuals.

METHODS

We performed whole genome sequencing of 2820 IPD isolates recovered during 2019 through Centers for Disease Control and Prevention's Active Bacterial Core surveillance to provide strain information (serotypes, resistance, genotypes), and 2778 of these genomes were analyzed to detect highly related genomic clusters.

RESULTS

Isolates from persons experiencing homelessness (PEH) were more often within genomic clusters than those from persons not experiencing homelessness (PNEH) (105/198 [53.0%] vs 592/2551 [23.2%]; P < .001). The 4 western sites accounted for 33.4% (929/2778) of isolates subjected to cluster analysis yet accounted for 48.7% (343/705) of clustering isolates (P < .001) and 75.8% (150/198) of isolates recovered from PEH (P < .001). Serotypes most frequent among PEH were (in rank order) 12F, 4, 3, 9N, 8, 20, and 22F, all of which were among the 10 serotypes exhibiting the highest proportions of clustering isolates among all cases. These serotypes accounted for 44.9% (1265/2820) of all IPD cases and are included within available vaccines.

CONCLUSIONS

We identified serotype-specific and geographic differences in IPD transmission. We show the vulnerability of PEH within different regions to rapidly spreading IPD transmission networks representing several pneumococcal serotypes included in available vaccines.

Safety and Immunogenicity of V114, a 15-valent Pneumococcal Conjugate Vaccine, Compared With 13- valent Pneumococcal Vaccine in Japanese Adults Aged ≥65 Years: Subgroup Analysis of a Randomized Phase III Trial (PNEU-AGE)

The safety and immunogenicity of V114, a 15-valent pneumococcal conjugate vaccine (PCV), was assessed in a pivotal Phase III trial in healthy adults ≥50 years of age (NCT03950622, Japic-CTI 194845). We report a subgroup analysis of 245 Japanese participants (all ≥65 years of age). Participants were randomized 1:1 to receive a single dose of V114 or 13-valent PCV (PCV13). Immune responses were evaluated at baseline and 30 days post-vaccination. Non-serious and serious adverse events (AEs) were evaluated post-vaccination through 14 days and 6 months, respectively. Proportions of participants experiencing solicited and serious AEs were comparable for both vaccines; all solicited AEs were mild or moderate in severity. Serotype-specific opsonophagocytic activity (OPA) geometric mean titers at 30 days post-vaccination were comparable between groups for all 13 shared serotypes and higher with V114 for the unique serotypes 22F and 33F. Proportions of participants with a ≥4-fold rise in serotype-specific OPA responses from pre-vaccination to 30 days post-vaccination were higher with V114 than PCV13 for serotypes 3, 22F, and 33F. V114 was well tolerated and immunogenic in Japanese adults ≥65 years of age, with safety and immunogenicity profiles consistent with that seen in the overall study population.

Pneumococcal serotypes in adults hospitalized with community-acquired pneumonia in Greece using urinary antigen detection tests: the EGNATIA study, November 2017 - April 2019

Greece introduced a 13-valent pneumococcal conjugate vaccine (PCV13) into the infant national immunization program in 2010 (3 + 1 schedule until June 2019). Since 2015, PCV13 has been recommended for adults aged 19-64 years with comorbidities and adults ≥65 years sequentially with 23-valent pneumococcal polysaccharide vaccine (PPSV23). We examined pneumococcal serotype distribution among Greek adults aged ≥19 years hospitalized with community-acquired pneumonia (CAP) during November 2017-April 2019. This was an interim analysis of EGNATIA, a prospective study of adult hospitalized CAP in the cities of Ioannina and Kavala. Pneumococcus was identified using cultures, BinaxNow®, serotype-specific urinary antigen detection assays (UAD-1/2). Our analysis included overall 482 hospitalized CAP patients (mean age: 70.5 years; 56.4% male). 53.53% of patients belonged to the highest pneumonia severity index (PSI) classes (IV-V). Pneumococcus was detected in 65 (13.5%) patients, with more than half (57%) of cases detected only by UAD. Approximately two-thirds of pneumococcal CAP occurred in those aged ≥65 years (n = 40, 8.3% of CAP). More than half of pneumococcal CAP (n = 35, 53.8%) was caused by PCV13 serotypes. Most frequently detected PCV13 serotypes were 3, 19A, 23F, collectively accounting for 83% of PCV13 vaccine-type (VT) CAP and 6% of all-cause CAP. Overall, 82.9% of PCV13 VT CAP occurred among persons with an indication (age/risk-based) for PCV13 vaccination. Even with a mature PCV13 childhood immunization program, a persistent burden of PCV13 VT CAP exists in Greek adults. Strategies to increase PCV13 (and higher-valency PCVs, when licensed) coverage in adults should be implemented to reduce the disease burden.

Safety and immunogenicity of V114, a 15-valent pneumococcal conjugate vaccine, in adults living with HIV

OBJECTIVES

To evaluate safety and immunogenicity of V114 [15-valent pneumococcal conjugate vaccine (PCV) containing serotypes 1, 3, 4, 5, 6A, 6B, 7F, 9V, 14, 18C, 19A, 19F, 22F, 23F, and 33F], followed by 23-valent pneumococcal polysaccharide vaccine (PPSV23) 8 weeks later, in adults living with HIV.

DESIGN

In this phase 3 study (V114-018; NCT03480802), pneumococcal vaccine-naive adults with HIV (CD4+ cell count ≥50 cells/μl, plasma HIV RNA <50 000 copies/ml, receiving antiretroviral therapy) were randomized 1 : 1 to receive one dose of V114 or licensed 13-valent PCV (PCV13) on day 1; participants received PPSV23 at week 8.

METHODS

Adverse events and serotype-specific opsonophagocytic activity (OPA) and immunoglobulin G (IgG) antibodies were evaluated after each vaccination.

RESULTS

Of 302 participants enrolled, 292 (96.7%) completed the study. Proportions of participants experiencing at least one adverse event were 73.0 and 62.7% in the V114 and PCV13 groups following PCV and 60.7 and 71.6% following PPSV23. Most solicited adverse events were of mild or moderate severity and short duration. OPA geometric mean titers (GMTs) and IgG geometric mean concentrations (GMCs) were generally comparable between groups for shared serotypes at day 30 and maintained at week 12. OPA and IgG responses for additional serotypes in V114 (22F, 33F) were higher following V114 than PCV13 at day 30 but comparable at week 12, 30 days post-PPSV23.

CONCLUSION

In pneumococcal vaccine-naive adults living with HIV, V114 was well tolerated and induced immune responses for all 15 pneumococcal serotypes. V114 can be followed by PPSV23 8 weeks later to broaden serotype coverage.

Estimates of the Health and Economic Burden of Pneumococcal Infections Attributable to the 15-Valent Pneumococcal Conjugate Vaccine Serotypes in the USA

Introduction

Despite the availability of vaccines, pneumococcal disease (PD) is associated with high clinical and economic burden, mainly caused by non-vaccine serotypes and certain vaccine-type serotypes. V114 is a 15-valent pneumococcal conjugate vaccine (PCV) that contains two epidemiologically important serotypes, 22F and 33F, in addition to the 13 serotypes in 13-valent PCV (PCV13). This study quantified the epidemiologic and economic burden of PD attributable to V114 serotypes among adults in the USA.

Methods

A Markov model was used to estimate the burden of V114 serotypes in a hypothetical, non-vaccinated cohort of US adults ≥ 19 years of age who were tracked from 2019 until death. The model calculated all the invasive pneumococcal disease (IPD) and non-bacteremic pneumococcal pneumonia (NBPP) cases, deaths, and costs. Economic burden was estimated from a healthcare payer perspective (2019 US dollars) and discounted at 3%.

Results

The model estimated 415,229 and 10.3 million lifetime cases of V114-type IPD and NBPP, respectively. Serotypes 22F and 33F caused approximately 33% of IPD cases and 20% of NBPP cases, while serotype 3 accounted for approximately 36% of IPD cases and 13% of NBPP cases. V114 serotypes caused 472,063 total lifetime deaths. Total discounted lifetime costs attributable to V114 serotypes were $44.8 billion US dollars.

Conclusions

In this hypothetical model of a non-vaccinated cohort of US adults, V114 serotypes were associated with a substantial health and economic burden, the majority of which was attributable to serotypes 3, 22F, and 33F. The addition of V114 to the national vaccination recommendations may help to reduce the epidemiologic and economic burden associated with PD in adults ≥ 19 years of age in the USA by providing increased coverage of these serotypes.

Supplementary Information

The online version contains supplementary material available at 10.1007/s40121-022-00588-x.

Lot-to-lot consistency, safety, tolerability, and immunogenicity of V114, a 15-valent pneumococcal conjugate vaccine, in healthy adults aged ≥50 years: A randomized phase 3 trial (PNEU-TRUE)

BACKGROUND

Older adults are at risk of pneumococcal disease and associated morbidity and mortality. This phase 3 study (V114-020) assessed lot-to-lot consistency across safety and immunogenicity outcomes for V114, a 15-valent pneumococcal conjugate vaccine (PCV), in healthy adults aged ≥ 50 years.

METHODS

Adults were randomized in a 3:3:3:1 ratio to receive a single dose of one of three lots of V114 or 13-valent PCV (PCV13), stratified by age (50-64 years, 65-74 years, and ≥ 75 years). Serotype-specific opsonophagocytic activity (OPA) and immunoglobulin G (IgG) antibodies were evaluated at baseline (Day 1) and 30 days post-vaccination. Non-serious and serious adverse events (AEs) were evaluated post-vaccination through 14 days and Month 6, respectively.

RESULTS

Of 2340 participants enrolled, 2282 (97.5%) completed the study. Proportions of participants experiencing ≥ 1 AE were 81.0%, 77.4%, and 78.0% for V114 lots 1, 2, and 3, respectively. Comparison of V114 combined lots with PCV13 showed that proportions of participants experiencing AEs, solicited AEs, and serious AEs were comparable for both vaccines, with the exception of injection-site pain (more frequently reported with V114). OPA geometric mean titers (GMTs) and IgG geometric mean concentrations (GMCs) at 30 days post-vaccination were comparable across V114 lots, and all lots met predefined equivalence criteria for all 15 vaccine serotypes (lower and upper limits of the 95% confidence intervals of serotype-specific OPA GMT ratios for all possible pairwise comparisons across the three lots were within the equivalence margin of 0.5-2.0). Serotype-specific OPA GMTs and IgG GMCs were comparable in the V114 combined lots and PCV13 groups for the 13 shared serotypes and higher in the V114 group for serotypes unique to V114 (22F and 33F).

CONCLUSIONS

V114 is well tolerated with a consistent safety profile and immune response across manufacturing lots.

CLINICAL TRIALS REGISTRATION

NCT03950856 (www.clinicaltrials.gov); 2018-004266-33 (EudraCT).

Ambient NO2 is associated with Streptococcus pneumoniae-induced pneumonia in children and increases the minimum inhibitory concentration of penicillin

The present study aimed to assess the correlation between ambient air pollutants and Streptococcus pneumoniae (S. pneumoniae)-induced pneumonia in children and retrospectively reviewed the daily data regarding S. pneumoniae from children with pneumonia in a tertiary hospital of Hangzhou City, between January 1st, 2018, and December 31st, 2018. The excess risk (ER) of NO₂ with regard to the daily number of S. pneumoniae isolates obtained from the respiratory tract specimens of children with pneumonia was 13.31% (95% confidence interval [CI]: 3.12-24.51%, P = 0.010) in the single-pollutant model. An increase of 10 μg/m³ in NO₂ exposure was associated with a 23.30% increased risk for the acquisition of S. pneumoniae-induced pneumonia in children (95% CI: 2.02-49.02%; P = 0.031) according to the multi-pollutant model. The ER of NO₂ with regard to the daily number of S. pneumoniae isolates (1 μg/ml ≤ minimum inhibitory concentration (MIC) to penicillin ≤ 2 μg/ml) obtained from the respiratory tract specimens of children with pneumonia was 15.80% (95% CI: 2.02-31.45%; P = 0.024) in the single-pollutant model. According to the multi-pollutant model, the ER of NO₂ with regard to the daily number of S. pneumoniae isolates (1 μg/ml ≤ MIC to penicillin ≤ 2 μg/ml) obtained from the respiratory tract specimens of children with pneumonia was 37.09% (95% CI: 5.70-77.81%; P = 0.018). In conclusion, ambient NO₂ is associated with S. pneumoniae-induced pneumonia in children. More importantly, NO₂ exposure is associated with the increased MICs of penicillin against S. pneumoniae from children with pneumonia.

Transition of Serotype 35B Pneumococci From Commensal to Prevalent Virulent Strain in Children

In our community-based prospective cohort study in young children, we observed a significant increase in pneumococcal serotype 35B nasopharyngeal (NP) commensal colonization during the 2011–2014 timeframe, but these strains were not associated with disease. Beginning in 2015 and continuing through to the present, the serotype 35B virulence changed, and it became the dominant bacteria isolated and associated with pneumococcal acute otitis-media (AOM) in our cohort. We performed comparative analyses of 250 35B isolates obtained from 140 children collected between 2006 and 2019. Changes in prevalence, clonal-complex composition, and antibiotic resistance were analyzed. Seventy-two (29%) of 35B isolates underwent whole-genome sequencing to investigate genomic changes associated with the shift in virulence that resulted in increased rates of 35B-associated AOM disease. 35B strains that were commensals and AOM disease-causing were mainly associated with sequence type (ST) 558. Antibiotic concentrations of β-lactams and ofloxacin necessary to inhibit growth of 35B strains rose significantly (2006–2019) (p<0.005). However, only isolates from the 35B/ST558 showed significant increases in MIC₅₀ of penicillin and ofloxacin between the years 2006–2014 and 2015–2019 (p=0.007 and p<0.0001). One hundred thirty-eight SNPs located in 34 different genes were significantly associated with post-2015 strains. SNPs were found in nrdG (metal binding, 10%); metP and metN (ABC transporter, 9%); corA (Mg²⁺ transporter, 6%); priA (DNA replication, 5%); and on the enzymic gene ldcB (LD-carboxypeptidase, 3%). Pneumococcal serotype 35B strains was a common NP commensal during 2010–2014. In 2015, a shift in increasing number of AOM cases occurred in young children caused by 35B, that was associated with changes in genetic composition and antibiotic susceptibility.

Matching-adjusted indirect comparison of pneumococcal vaccines V114 and PCV20

BACKGROUND

V114 (15-valent pneumococcal conjugate vaccine [PCV15]) and a 20-valent PCV (PCV20) are approved for adults (≥18 years) in the United States. We present methodologies to indirectly compare immune responses to V114 versus PCV20.

RESEARCH DESIGN AND METHODS

Indirect treatment comparison and matching-adjusted indirect comparison (MAIC) were performed to estimate opsonophagocytic activity (OPA) geometric mean titer (GMT) ratios of V114/PCV20 at 30 days post-vaccination with PCV13 as common comparator for 13 serotypes (STs) shared with a 13-valent PCV (PCV13) among pneumococcal vaccine-naïve adults aged ≥60 years. Data from three V114 studies were pooled (V114, N = 2,196; PCV13, N = 843). In the MAIC analysis, data were reweighted, matching participant age and sex in NCT03760146 (PCV20, N = 1,507; PCV13, N = 1,490).

RESULTS

The lower bound of V114/PCV20 OPA GMT ratio for all PCV13 STs is greater than the prespecified  0.5 non-inferiority margin and those for five PCV13 STs (3, 6A, 6B, 18C, and 23F) are greater than the prespecified 1.2 superiority margin. V114 was associated with 77% greater OPA GMT for ST3 versus PCV20.

CONCLUSION

V114 was non-inferior to PCV20 for all PCV13 STs and statistically superior for five PCV13 STs.

Large-scale genomic analysis of antimicrobial resistance in the zoonotic pathogen Streptococcus suis

BACKGROUND

Antimicrobial resistance (AMR) is among the gravest threats to human health and food security worldwide. The use of antimicrobials in livestock production can lead to emergence of AMR, which can have direct effects on humans through spread of zoonotic disease. Pigs pose a particular risk as they are a source of zoonotic diseases and receive more antimicrobials than most other livestock. Here we use a large-scale genomic approach to characterise AMR in Streptococcus suis, a commensal found in most pigs, but which can also cause serious disease in both pigs and humans.

RESULTS

We obtained replicated measures of Minimum Inhibitory Concentration (MIC) for 16 antibiotics, across a panel of 678 isolates, from the major pig-producing regions of the world. For several drugs, there was no natural separation into 'resistant' and 'susceptible', highlighting the need to treat MIC as a quantitative trait. We found differences in MICs between countries, consistent with their patterns of antimicrobial usage. AMR levels were high even for drugs not used to treat S. suis, with many multidrug-resistant isolates. Similar levels of resistance were found in pigs and humans from regions associated with zoonotic transmission. We next used whole genome sequences for each isolate to identify 43 candidate resistance determinants, 22 of which were novel in S. suis. The presence of these determinants explained most of the variation in MIC. But there were also interesting complications, including epistatic interactions, where known resistance alleles had no effect in some genetic backgrounds. Beta-lactam resistance involved many core genome variants of small effect, appearing in a characteristic order.

CONCLUSIONS

We present a large dataset allowing the analysis of the multiple contributing factors to AMR in S. suis. The high levels of AMR in S. suis that we observe are reflected by antibiotic usage patterns but our results confirm the potential for genomic data to aid in the fight against AMR.

Structural, Genetic, and Serological Elucidation of Streptococcus pneumoniae Serogroup 24 Serotypes: Discovery of a New Serotype, 24C, with a Variable Capsule Structure

Pneumococcal capsules are important in pneumococcal pathogenesis and vaccine development. Although conjugate vaccines have brought about a significant reduction in invasive pneumococcal disease (IPD) caused by vaccine serotypes, the relative serotype prevalence has shifted with the dramatic emergence of serotype 24F in some countries. Here, we describe 14 isolates (13 IPD and 1 non-IPD) expressing a new capsule type, 24C, which resembles 24F but has a novel serological profile. We also describe the antigenic, biochemical, and genetic basis of 24F and 24C and the related serotypes 24A and 24B. Structural studies show that 24B, 24C, and 24F have identical polysaccharide backbones [β-Ribf-(1→4)-α-Rhap-(1→3)-β-GlcpNAc-(1→4)-β-Rhap-(1→4)-β-Glcp] but with different side chains, as follows: 24F has arabinitol-phosphate and 24B has ribitol-phosphate. 24C has a mixture of 24F and 24B repeating units, with the ratio of ribitol to arabinitol being strain dependent. In contrast, the 24A capsule has a backbone without β-Ribf but with arabinitol-phosphate and phosphocholine side chains. These structures indicate that factor-sera 24d and 24e recognize arabinitol and ribitol, respectively, which explains the serology of serogroup 24, including those of 24C. The structures can be genetically described by the bispecificity of wcxG, which is capable of transferring arabinitol or ribitol when arabinitol is limiting. Arabinitol is likely not produced in 24B but is produced in reduced amounts in 24C due to various mutations in abpA or abpB genes. Our findings demonstrate how pneumococci modulate their capsule structure and immunologic properties with small genetic changes, thereby evading host immune responses. Our findings also suggest a potential for new capsule types within serogroup 24.

Invasive Pneumococcal Strain Distributions and Isolate Clusters Associated With Persons Experiencing Homelessness During 2018

BACKGROUND

We aimed to characterize invasive pneumococcal disease (IPD) isolates collected from multistate surveillance in the United States during 2018 and examine within-serotype propensities of isolates to form related clusters.

METHODS

We predicted strain features using whole genome sequencing obtained from 2885 IPD isolates obtained through the Center for Disease Control and Prevention's Active Bacterial Core surveillance (ABCs), which has a surveillance population of approximately 34.5 million individuals distributed among 10 states. Phylogenetic analysis was provided for serotypes accounting for ≥27 isolates.

RESULTS

Thirteen-valent pneumococcal conjugate vaccine (PCV13) serotypes together with 6C accounted for 23 of 105 (21.9%) of isolates from children aged <5 years and 820 of 2780 (29.5%) isolates from those aged ≥5 years. The most common serotypes from adult IPD isolates were serotypes 3 (413/2780 [14.9%]), 22F (291/2780 [10.5%]), and 9N (191/2780 [6.9%]). Among child IPD isolates, serotypes 15BC (18/105 [17.1%]), 3 (11/105 [10.5%]), and 33F (10/105 [9.5%]) were most common. Serotypes 4, 12F, 20, and 7F had the highest proportions of isolates that formed related clusters together with the highest proportions of isolates from persons experiencing homelessness (PEH). Among 84 isolates from long-term care facilities, 2 instances of highly related isolate pairs from co-residents were identified.

CONCLUSIONS

Non-PCV13 serotypes accounted for >70% of IPD in ABCs; however, PCV13 serotype 3 is the most common IPD serotype overall. Serotypes most common among PEH were more often associated with temporally related clusters identified both among PEH and among persons not reportedly experiencing homelessness.

Non-clinical immunological comparison of a Next-Generation 24-valent pneumococcal conjugate vaccine (VAX-24) using site-specific carrier protein conjugation to the current standard of care (PCV13 and PPV23)

Despite widespread utilization of pneumococcal conjugate vaccines (PCVs) and the resultant disease reduction, the development of PCVs containing additional serotypes remains a public health priority due to serotype replacement and the resultant shift to non-vaccine containing serotypes. However, incorporating additional serotypes to existing PCVs using conventional technologies has proven problematic. Immune responses to individual serotypes have consistently decreased as more polysaccharide-conjugates are added due to carrier suppression. Using our proprietary cell-free protein synthesis (CFPS) platform, we have successfully produced eCRM® based on the CRM₁₉₇ sequence for use as an enhanced carrier protein to develop a 24-valent PCV. The eCRM carrier protein contains multiple non-native amino acids (nnAAs) located outside of the primary T-cell epitope regions, thereby enabling site-specific covalent conjugation of the pneumococcal polysaccharides to the nnAAs to consistently expose the critical T-cell epitopes. eCRM also serves to reduce structural heterogeneity associated with classic reductive-amination conjugation while promoting formation of the conjugate matrix structures, the hallmark of PCVs. This process serves to increase the overall polysaccharide:protein ratio, enabling the inclusion of more serotypes while minimizing carrier-mediated immunological interference. The aim of this non-clinical study was to construct a 24-valent PCV and evaluate its immunogenicity. Using the XPressCF® CFPS platform, the eCRM carrier protein was separately conjugated through nnAAs to each of the 24 pneumococcal polysaccharides through click chemistry and mixed with aluminum phosphate to produce VAX-24, Vaxcyte's proprietary PCV preclinical candidate. VAX-24, Prevnar13® and Pneumovax®23 were administered to New Zealand White rabbits to compare the resulting opsonophagocytic activity (OPA) and anti-capsular IgG antibodies. VAX-24 showed conjugate-like immune responses to all 24 serotypes based on comparable OPA and IgG responses to Prevnar13 and higher responses than Pneumovax 23. This study demonstrates the utility of site-specific conjugation technology in a preclinical setting and the potential for a PCV with improved serotype coverage.

Comprehensive value assessments for new pediatric pneumococcal conjugate vaccines

Although the incidence of invasive pneumococcal disease (IPD) and acute otitis media (AOM) in young children has decreased since the introduction of pneumococcal conjugate vaccines (PCVs), the subsequent emergence of non-vaccine Streptococcus pneumoniae serotypes and the persistence of certain vaccine serotypes both contribute to substantial residual pneumococcal disease. There is a need for the development of new pneumococcal vaccines to address the clinical and economic burden presented by emerging non-vaccine serotypes, while maintaining suppression of serotypes in existing vaccines. To assess the full value of next-generation vaccines, public health evaluations must consider epidemiological and economic data across all vaccine serotypes, including those included in existing vaccines and those unique to the new product. This is supported by two recent analyses that estimated the health and economic burden of IPD (in the United States and Europe) and AOM (in the United States only) associated with the serotypes in V114, a 15-valent pneumococcal conjugate vaccine (PCV15), which contains all serotypes in the licensed 13-valent pneumococcal conjugate vaccine (PCV13) as well as the unique serotypes 22 F and 33 F and was recently approved for use in adults in the US. The analyses demonstrated considerable health and economic burden associated with PCV13 serotypes, as well as increasing burden associated with serotypes 22 F and 33 F. In addition to addressing the burden of non-vaccine serotypes, ability to maintain or improve protection against disease caused by serotypes in existing vaccines will be an important consideration for decision makers.

Health and economic burden associated with 15-valent pneumococcal conjugate vaccine serotypes in children in the United States

AIMS

V114 is an investigational 15-valent pneumococcal conjugate vaccine (PCV) containing the 13 Streptococcus pneumoniae serotypes in 13-valent PCV (PCV13) plus two additional serotypes. This study quantified the health and economic burden of invasive pneumococcal disease (IPD) and acute otitis media (AOM) caused by V114 types among children in the United States.

MATERIALS AND METHODS

A Markov model estimated the number of V114-type IPD and AOM cases and costs in a hypothetical, unvaccinated US birth cohort over 20 years. Three time periods were analyzed using time-specific epidemiological data to determine the number of IPD and AOM cases associated with all 15 serotypes in V114. The time periods were: (1) pre-PCV7 (1999); (2) pre-PCV13 (2009); (3) post-PCV13 (2017). Costs were estimated from a societal perspective (2018 US dollars) and discounted at 3%.

RESULTS

The model estimated 18,983 IPD cases and 5.4 million AOM cases associated with V114 serotypes pre-PCV7, 4,697 IPD cases and 3.0 million AOM cases pre-PCV13, and 948 IPD cases and 0.2 million AOM cases post-PCV13. Total discounted costs associated with V114 serotypes were $1.7 billion pre-PCV7, $730 million pre-PCV13, and $75 million US dollars post-PCV13.

LIMITATIONS

Post-meningitis sequelae, cases of non-bacteremic pneumonia, and direct non-medical costs were not included.

CONCLUSIONS

IPD and AOM cases and costs were estimated in a hypothetical US birth cohort followed for 20 years at three time periods. In all three periods, the serotypes targeted by V114 contributed to significant morbidity and costs. New pediatric pneumococcal vaccines must continue to retain serotypes in licensed vaccines to maintain disease reduction while extending coverage to non-vaccine serotypes.

A Nationwide Outbreak of Invasive Pneumococcal Disease in Israel Caused by Streptococcus Pneumoniae Serotype 2

BACKGROUND

Invasive pneumococcal disease (IPD) caused by Streptococcus pneumoniae serotype 2 (Sp2) is infrequent. Large scale outbreaks have not been reported following pneumococcal conjugate vaccine (PCV) implementation. We describe a Sp2 IPD outbreak in Israel, in the 13-valent PCV (PCV13) era, with focus on Sp2 population structure and evolutionary dynamics.

METHODS

The data derived from a population-based, nationwide active surveillance of IPD since 2009. 7-valent PCV (PCV7)/PCV13 vaccines were introduced in July 2009 and November 2010, respectively. Sp2 isolates were tested for antimicrobial susceptibility, Multilocus Sequence Typing (MLST) and Whole Genome Sequencing (WGS) analysis.

RESULTS

Overall, 170 Sp2 IPD cases were identified during 2009-2019; Sp2 increased in 2015 and caused 6% of IPD during 2015-2019, a 7-fold increase compared with 2009-2014.The outbreak was caused by a previously unreported molecular type (ST-13578), initially observed in Israel in 2014. This clone caused 88% of Sp2 during 2015-2019. ST-13578 is a single-locus variant of ST-1504, previously reported globally, including in Israel. WGS analysis confirmed clonality among the ST-13578 population. Single-nucleotide polymorphisms-dense regions support a hypothesis that the ST-13578 outbreak clone evolved from ST-1504 by recombination.All tested strains were penicillin-susceptible (MIC <0.06 μg/mL). The ST-13578 clone was identified almost exclusively (99%) in the Jewish population and was mainly distributed in 3/7 Israeli districts. The outbreak is still ongoing, although declining since 2017.Conclusions: To the best of our knowledge, this is the first widespread Sp2 outbreak since PCV13 introduction worldwide, caused by the emerging ST-13578 clone.

Cost-effectiveness analysis of replacing the 10-valent pneumococcal conjugate vaccine (PCV10) with the 13-valent pneumococcal conjugate vaccine (PCV13) in Brazil infants

Brazil currently has a 10-valent pneumococcal conjugate vaccine (PCV10) pediatric national immunization program (NIP). However, in recent years, there has been significant progressive increases in pneumococcal disease attributed to serotypes 3, 6A, and 19A, which are covered by the 13-valent PCV (PCV13). We sought to evaluate the cost-effectiveness and budget impact of switching from PCV10 to PCV13 for Brazilian infants from a payer perspective. A decision-analytic model was adapted to evaluate the clinical and economic outcomes of continuing PCV10 or switching to PCV13. The analysis estimated future costs ($BRL), quality-adjusted life-years (QALYs), and health outcomes for PCV10 and PCV13 over 5 y. Input parameters were from published sources. Future serotype dynamics were predicted using Brazilian and global historical trends. Over 5 y, PCV13 could prevent 12,342 bacteremia, 15,330 meningitis, 170,191 hospitalized pneumonia, and 25,872 otitis media cases, avert 13,709 pneumococcal disease deaths, gain 20,317 QALYs, and save 172 million direct costs compared with PCV10. The use of PCV13 in the Brazilian NIP could reduce pneumococcal disease, improve population health, and save substantial health-care costs. Results are reliable even when considering uncertainty for possible serotype dynamics with different underlying assumptions.

Upsurge of Conjugate Vaccine Serotype 4 Invasive Pneumococcal Disease Clusters Among Adults Experiencing Homelessness in California, Colorado, and New Mexico

After 7-valent pneumococcal conjugate vaccine introduction in the United States in 2000, invasive pneumococcal disease (IPD) due to serotype 4 greatly decreased in children and adults. Starting in 2013, serotype 4 IPD incidence increased among adults within 3 of 10 Active Bacterial Core surveillance sites. Of 325 serotype 4 cases among adults in 2010-2018, 36% were persons experiencing homelessness (PEH); incidence of serotype 4 IPD among PEH was 100-300 times higher than in the general population within these 3 areas. Genome sequencing for isolates recovered 2015-2018 (n = 246), revealed that increases in serotype 4 IPD were driven by lineages ST10172, ST244, and ST695. Within each lineage, clusters of near-identical isolates indicated close temporal relatedness. Increases in serotype 4 IPD were limited to Colorado, California, and New Mexico, with highest increases among PEH, who were at increased risk for exposure to and infections caused by these strains.

Expanded sequential quadriplex real-time polymerase chain reaction (PCR) for identifying pneumococcal serotypes, penicillin susceptibility, and resistance markers

We expanded our current Centers for Disease Control and Prevention triplexed real-time polymerase chain reaction scheme identifying 11 individual serotypes and 10 serogroups to a quadriplex format identifying 34 individual serotypes and 13 small serogroups, 4 antibiotic resistance determinants, pilus targets, and penicillin susceptibility. Newly developed assays are specific for serotypes/serogroups, are sensitive (10 copies/reaction), and further discriminate larger serogroups into individual serotypes or smaller serogroups.