Observational studyPLoS pathogens2018
The impact of serotype-specific vaccination on phylodynamic parameters of Streptococcus pneumoniae and the pneumococcal pan-genome.
Observational study in PLoS pathogens, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers, 1 of them a synthesis that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
24 citing papers in PubMed, 1 synthesis or guideline pooled it, 37 citations in OpenAlex.
- Serotype replacement and mobile genetic elements inMicrobial genomics · 2025Pooled it
- A reusable model of pangenome selection informs optimal surveillance strategies over vaccine introductions.Genome medicine · 2026Article
- ZPY-CpG-Ch, a broad coverage vaccine againstScience advances · 2026Article
- Predicting optimal impact interventions in the post-HPV vaccination world.International journal of cancer · 2026Review
- Epidemiological and Genomic Insights into Linezolid-Non-Susceptible Enterococci in Pediatric Patients.Current microbiology · 2026Article
- How does date-rounding affect phylodynamic inference for public health?PLoS computational biology · 2025Article
- Implications of Cross-Reactivity and Cross-Protection for Pneumococcal Vaccine Development.Vaccines · 2024Review
- Biological puzzles solved by usingJournal of bacteriology · 2024Review
- A narrative review of genomic characteristics, serotype, immunogenicity, and vaccine development ofClinical and experimental vaccine research · 2024Review
- Pneumococcal population genomics changes during the early time period of conjugate vaccine uptake in southern India.Microbial genomics · 2024Article
- Prevalence and resistance characteristics of multidrug-resistantFrontiers in cellular and infection microbiology · 2023Article
- Article
- Phylogeography and resistome of pneumococcal meningitis in West Africa before and after vaccine introduction.Microbial genomics · 2021Article
- Pneumococcal Pneumonia and Invasive Pneumococcal Disease in Those 65 and Older: Rates of Detection, Risk Factors, Vaccine Effectiveness, Hospitalisation and Mortality.Geriatrics (Basel, Switzerland) · 2021Review
- Frequency-dependent selection can forecast evolution in Streptococcus pneumoniae.PLoS biology · 2020Article
- Weaving the Strands of Life (Human biology · 2020Review
- TargetingDrug target insights · 2020Article
- Bacterial Factors Required for Transmission of Streptococcus pneumoniae in Mammalian Hosts.Cell host & microbe · 2019Article
- International genomic definition of pneumococcal lineages, to contextualise disease, antibiotic resistance and vaccine impact.EBioMedicine · 2019Article
- Article
Corrections and comments
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Authors and funding
13 authors at 3 institutions in 2 countries.
Funding
Abstract
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.