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Concept: Pneumococcal vaccine

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The pneumococcus is a diverse pathogen whose primary niche is the nasopharynx. Over 90 different serotypes exist, and nasopharyngeal carriage of multiple serotypes is common. Understanding pneumococcal carriage is essential for evaluating the impact of pneumococcal vaccines. Traditional serotyping methods are cumbersome and insufficient for detecting multiple serotype carriage, and there are few data comparing the new methods that have been developed over the past decade. We established the PneuCarriage project, a large, international multi-centre study dedicated to the identification of the best pneumococcal serotyping methods for carriage studies.

Concepts: Microbiology, Pneumonia, Streptococcus pneumoniae, Vaccination, Pneumococcal conjugate vaccine, Pneumococcal vaccine, Serotype

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On September 19, 2014, CDC published the Advisory Committee on Immunization Practices (ACIP) recommendation for the routine use of 13-valent pneumococcal conjugate vaccine (PCV13) among adults aged ≥65 years, to be used in series with 23-valent pneumococcal polysaccharide vaccine (PPSV23) (1). This replaced the previous recommendation that adults aged ≥65 years should be vaccinated with a single dose of PPSV23. As a proxy for estimating PCV13 and PPSV23 vaccination coverage among adults aged ≥65 years before and after implementation of these revised recommendations, CDC analyzed claims for vaccination submitted for reimbursement to the Centers for Medicare & Medicaid Services (CMS). Claims from any time during a beneficiary’s enrollment in Medicare Parts A (hospital insurance) and B (medical insurance) since reaching age 65 years were assessed among beneficiaries continuously enrolled in Medicare Parts A and B during annual periods from September 19, 2009, through September 18, 2016. By September 18, 2016, 43.2% of Medicare beneficiaries aged ≥65 years had claims for at least 1 dose of PPSV23 (regardless of PCV13 status), 31.5% had claims for at least 1 dose of PCV13 (regardless of PPSV23 status), and 18.3% had claims for at least 1 dose each of PCV13 and PPSV23. Claims for either type of pneumococcal vaccine were highest among beneficiaries who were older, white, or with chronic and immunocompromising medical conditions than among healthy adults. Implementation of the National Vaccine Advisory Committee’s standards for adult immunization practice to assess vaccination status at every patient encounter, recommend needed vaccines, and administer vaccination or refer to a vaccinating provider might help increase pneumococcal vaccination coverage and reduce the risk for pneumonia and invasive pneumococcal disease among older adults (2).

Concepts: Pneumonia, Streptococcus pneumoniae, Vaccine, Vaccination, Vaccination schedule, Pneumococcal conjugate vaccine, Pneumococcal vaccine, Pneumococcal polysaccharide vaccine

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In the United States, the introduction of the heptavalent pneumococcal conjugate vaccine (PCV) largely eliminated vaccine serotypes (VT); non-vaccine serotypes (NVT) subsequently increased in carriage and disease. Vaccination also disrupts the composition of the pneumococcal pangenome, which includes mobile genetic elements and polymorphic non-capsular antigens important for virulence, transmission, and pneumococcal ecology. Antigenic proteins are of interest for future vaccines; yet, little is known about how the they are affected by PCV use. To investigate the evolutionary impact of vaccination, we assessed recombination, evolution, and pathogen demographic history of 937 pneumococci collected from 1998-2012 among Navajo and White Mountain Apache Native American communities. We analyzed changes in the pneumococcal pangenome, focusing on metabolic loci and 19 polymorphic protein antigens. We found the impact of PCV on the pneumococcal population could be observed in reduced diversity, a smaller pangenome, and changing frequencies of accessory clusters of orthologous groups (COGs). Post-PCV7, diversity rebounded through clonal expansion of NVT lineages and inferred in-migration of two previously unobserved lineages. Accessory COGs frequencies trended toward pre-PCV7 values with increasing time since vaccine introduction. Contemporary frequencies of protein antigen variants are better predicted by pre-PCV7 values (1998-2000) than the preceding period (2006-2008), suggesting balancing selection may have acted in maintaining variant frequencies in this population. Overall, we present the largest genomic analysis of pneumococcal carriage in the United States to date, which includes a snapshot of a true vaccine-naïve community prior to the introduction of PCV7. These data improve our understanding of pneumococcal evolution and emphasize the need to consider pangenome composition when inferring the impact of vaccination and developing future protein-based pneumococcal vaccines.

Concepts: Immune system, Pneumonia, Streptococcus pneumoniae, Vaccine, Vaccination schedule, Antigen, Pneumococcal conjugate vaccine, Pneumococcal vaccine

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S. pneumoniae can cause a wide spectrum of diseases, including invasive pneumococcal disease and pneumonia. Two types of pneumococcal vaccines are indicated for use in adults: 23-valent pneumococcal polysaccharide vaccines (PPV23) and a 13-valent pneumococcal conjugate vaccine (PCV13).

Concepts: Pneumonia, Streptococcus pneumoniae, Vaccine, Pneumococcal conjugate vaccine, Pneumococcal vaccine, Pneumococcal polysaccharide vaccine, Haemophilus influenzae, Polysaccharide encapsulated bacteria

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While significant protection from pneumococcal disease has been achieved by the use of polysaccharide and polysaccharide-protein conjugate vaccines, capsule-independent protection has been limited by serotype replacement along with disease caused by nonencapsulatedStreptococcus pneumoniae(NESp). NESp strains compose approximately 3% to 19% of asymptomatic carriage isolates and harbor multiple antibiotic resistance genes. Surface proteins unique to NESp enhance colonization and virulence despite the lack of a capsule even though the capsule has been thought to be required for pneumococcal pathogenesis. Genes for pneumococcal surface proteins replace the capsular polysaccharide (cps) locus in some NESp isolates, and these proteins aid in pneumococcal colonization and otitis media (OM). NESp strains have been isolated from patients with invasive and noninvasive pneumococcal disease, but noninvasive diseases, specifically, conjunctivitis (85%) and OM (8%), are of higher prevalence. Conjunctival strains are commonly of the so-called classical NESp lineages defined by multilocus sequence types (STs) ST344 and ST448, while sporadic NESp lineages such as ST1106 are more commonly isolated from patients with other diseases. Interestingly, sporadic lineages have significantly higher rates of recombination than classical lineages. Higher rates of recombination can lead to increased acquisition of antibiotic resistance and virulence factors, increasing the risk of disease and hindering treatment. NESp strains are a significant proportion of the pneumococcal population, can cause disease, and may be increasing in prevalence in the population due to effects on the pneumococcal niche caused by pneumococcal vaccines. Current vaccines are ineffective against NESp, and further research is necessary to develop vaccines effective against both encapsulated and nonencapsulated pneumococci.

Concepts: Bacteria, Microbiology, Pneumonia, Streptococcus pneumoniae, Streptococcus, Pneumococcal conjugate vaccine, Pneumococcal vaccine, Otitis media

4

With the global efforts of reducing pneumococcal disease through widespread introduction of pneumococcal vaccines, concerns have emerged on the potential increase of morbidity and mortality from S. aureus disease. Little is known however, of the carriage rates of S. aureus or of its' relationship with carriage of S. pneumoniae in rural Africa, and West Africa in particular where very high rates of carriage of S. pneumoniae have been reported. This study aims to evaluate the prevalence, antibiotic susceptibility patterns and genotypes of S. aureus isolated from the nasopharynx of healthy individuals in rural Gambia before the introduction of routine use of pneumococcal conjugate vaccines in the country.

Concepts: Microbiology, Pneumonia, Staphylococcus aureus, Streptococcus pneumoniae, Streptococcus, Pneumococcal conjugate vaccine, Pneumococcal vaccine, Gram positive bacteria

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Introduction of 13-valent pneumococcal conjugate vaccine in the United States was not associated with a significant change in prevalence of penicillin resistance in nonvaccine type serotypes because of the variable success of highly resistant serotypes. Differences in regional serotype distribution and serotype-specific resistance contributed to geographic heterogeneity of penicillin resistance.

Concepts: Microbiology, Pneumonia, Streptococcus pneumoniae, United States, Antibiotic resistance, Pneumococcal conjugate vaccine, Pneumococcal vaccine, Pneumococcal polysaccharide vaccine

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We used whole-genome sequencing to characterize 199 nonvaccine serotype 35B pneumococcal strains that caused invasive pneumococcal disease (IPD) in the United States during 2015-2016 and related these findings to previous serotype 35B IPD data obtained by Active Bacterial Core surveillance. Penicillin-nonsusceptible 35B IPD increased during post-pneumococcal 7-valent conjugate vaccine years (2001-2009) and increased further after implementation of pneumococcal 13-valent conjugate vaccine in 2010. This increase was caused primarily by the 35B/sequence type (ST) 558 lineage. 35B/ST558 and vaccine serotype 9V/ST156 lineages were implicated as cps35B donor and recipient, respectively, for a single capsular switch event that generated emergent 35B/ST156 progeny in 6 states during 2015-2016. Three additional capsular switch 35B variants were identified, 2 of which also involved 35B/ST558 as cps35B donor. Spread of 35B/ST156 is of concern in view of past global predominance of pathogenic ST156 vaccine serotype strains. Protection against serotype 35B should be considered in next-generation pneumococcal vaccines.

Concepts: Microbiology, Pneumonia, Streptococcus pneumoniae, Streptococcus, Pneumococcal infection, Pneumococcal conjugate vaccine, Pneumococcal vaccine, Meningitis

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We assessed known risk factors, clinical presentation, and outcome of invasive pneumococcal disease (IPD) in children 3-59 months of age after introduction of the 7-valent pneumococcal conjugate vaccine (PCV7) in England and Wales. During September 2006-March 2010, a total of 1,342 IPD episodes occurred in 1,332 children; 14.9% (198/1,332) had comorbidities. Compared with IPD caused by PCV7 serotypes (44/248; 17.7%), comorbidities were less common for the extra 3 serotypes in the 10-valent vaccine (15/299; 5.0%) but similar to the 3 additional PCV13 serotypes (45/336; 13.4%) and increased for the 11 extra serotypes in 23-valent polysaccharide vaccine (PPV23) (39/186; 21.0%) and non-PPV23 serotypes (38/138; 27.5%). Fifty-two (3.9%) cases resulted from PCV7 failure; 9 (0.7%) case-patients had recurrent IPD. Case-fatality rate was 4.4% (58/1,332) but higher for meningitis (11.0%) and children with comorbidities (9.1%). Thus, comorbidities were more prevalent in children with IPD caused by non-PCV13 serotypes and were associated with increased case fatality.

Concepts: Pneumonia, Streptococcus pneumoniae, Vaccine, Vaccination schedule, Pneumococcal conjugate vaccine, Pneumococcal vaccine, Pneumococcal polysaccharide vaccine, Meningitis

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Uniquely among high income countries, Australia uses a 3+0 schedule (3 primary doses; no booster) for infant pneumococcal conjugate vaccine since January 2005, initially 7-valent (PCV7) then 13-valent (PCV13) from July 2011. We measured vaccine effectiveness (VE) of both PCVs against invasive pneumococcal disease (IPD) by two methods.

Concepts: Pneumonia, Streptococcus pneumoniae, Vaccine, Vaccination, Vaccination schedule, Pneumococcal conjugate vaccine, Pneumococcal vaccine, Pneumococcal polysaccharide vaccine