ArticleScientific data2015
Population genomic datasets describing the post-vaccine evolutionary epidemiology of Streptococcus pneumoniae.
Article in Scientific data, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed.
- Trial
- A reusable model of pangenome selection informs optimal surveillance strategies over vaccine introductions.Genome medicine · 2026Article
- Genomic analysis ofMicrobial genomics · 2026Article
- BaGPipe: an automated, reproducible, and flexible pipeline for bacterial genome-wide association studies.BMC microbiology · 2026Article
- FroM Superstring to Indexing: a space-efficient index for unconstrainedBioinformatics advances · 2026Article
- Integrated population clustering and genomic epidemiology with PopPIPE.Microbial genomics · 2025Article
- AliC and AliD of nonencapsulatedFrontiers in cellular and infection microbiology · 2025Article
- Pneumococcal population dynamics: Investigating vaccine-induced changes through multiscale modelling.PLoS computational biology · 2023Article
- The metabolic, virulence and antimicrobial resistance profiles of colonising Streptococcus pneumoniae shift after PCV13 introduction in urban Malawi.Nature communications · 2023Article
- Accurate and fast graph-based pangenome annotation and clustering with ggCaller.Genome research · 2023Article
- Matchtigs: minimum plain text representation of k-mer sets.Genome biology · 2023Article
- Frequent Transmission of Streptococcus pneumoniae Serotype 35B and 35D, Clonal Complex 558 Lineage, across Continents and the Formation of Multiple Clades in Japan.Antimicrobial agents and chemotherapy · 2023Article
- A comparison of various feature extraction and machine learning methods for antimicrobial resistance prediction inFrontiers in antibiotics · 2023Article
- Inferring the heritability of bacterial traits in the era of machine learning.Bioinformatics advances · 2023Review
- Comparative genomics of Campylobacter jejuni from clinical campylobacteriosis stool specimens.Gut pathogens · 2022Article
- The Outer Surface Protease, SepM, Is Required forJournal of bacteriology · 2022Article
- Pneumococcal capsule blocks protection by immunization with conserved surface proteins.NPJ vaccines · 2021Article
- Simplitigs as an efficient and scalable representation of de Bruijn graphs.Genome biology · 2021Article
- Boosting heritability: estimating the genetic component of phenotypic variation with multiple sample splitting.BMC bioinformatics · 2021Article
- Article
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Authors and funding
7 authors.
Funding
Abstract
Streptococcus pneumoniae is common nasopharyngeal commensal bacterium and important human pathogen. Vaccines against a subset of pneumococcal antigenic diversity have reduced rates of disease, without changing the frequency of asymptomatic carriage, through altering the bacterial population structure. These changes can be studied in detail through using genome sequencing to characterise systematically-sampled collections of carried S. pneumoniae. This dataset consists of 616 annotated draft genomes of isolates collected from children during routine visits to primary care physicians in Massachusetts between 2001, shortly after the seven valent polysaccharide conjugate vaccine was introduced, and 2007. Also made available are a core genome alignment and phylogeny describing the overall population structure, clusters of orthologous protein sequences, software for inferring serotype from Illumina reads, and whole genome alignments for the analysis of closely-related sets of pneumococci. These data can be used to study both bacterial evolution and the epidemiology of a pathogen population under selection from vaccine-induced immunity.
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