ArticleEBioMedicine2019
International genomic definition of pneumococcal lineages, to contextualise disease, antibiotic resistance and vaccine impact.
Article in EBioMedicine, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 161 papers, 3 of them syntheses that pooled it.
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Who cites it
161 citing papers in PubMed, 3 syntheses or guidelines pooled it, 262 citations in OpenAlex.
- Serotype distribution of invasive and non-invasive pneumococcal disease in adults ≥65 years of age following the introduction of 10- and 13-valent pneumococcal conjugate vaccines in infant national immunization programs: a systematic literature review.Frontiers in public health · 2025Pooled it
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- Analysing pneumococcal invasiveness using Bayesian models of pathogen progression rates.PLoS computational biology · 2022Pooled it
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- High-throughput antigen discovery using Functional Genomic Vaccinology (FGV) identifies protective Streptococcus pneumoniae vaccine candidates.Nature communications · 2026Article
- Translation Inhibiting Antibiotics Induce an asRNA Regulating Purine Metabolism inbioRxiv : the preprint server for biology · 2026Article
- Strain-level transmission inference across multi-kingdom metagenomic data using TRACS.Nature microbiology · 2026Article
- Genomic surveillance of post-immunization pneumococcal carriage in Ghana.Microbial genomics · 2026Article
- Clonal expansion of global pneumococcal sequence cluster 3 within serotype 8 after 13-valent pneumococcal conjugate vaccine introduction, South Africa.Microbial genomics · 2026Article
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- Pneumococcus uses COMMD2 to alter host cellular immunity.Nature communications · 2026Article
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- Genomic and phenotypic characterization of a multidrug-resistant Streptococcus pneumoniae 19 F ST320 isolate from a pediatric SARS-CoV-2 case in Yogyakarta, Indonesia.Scientific reports · 2026Article
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- Genomic characterization of mobile genetic elements associated with antimicrobial resistance inMicrobial genomics · 2026Article
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- A tiled amplicon protocol for culture-free whole-genome sequencing ofJournal of clinical microbiology · 2026Article
- Genomic characterization of invasive disease-causingMicrobial genomics · 2026Article
101 more citing papers are in PubMed but not listed here.
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Authors and funding
27 authors at 17 institutions in 11 countries.
Funding
Abstract
backgroundPneumococcal conjugate vaccines have reduced the incidence of invasive pneumococcal disease, caused by vaccine serotypes, but non-vaccine-serotypes remain a concern. We used whole genome sequencing to study pneumococcal serotype, antibiotic resistance and invasiveness, in the context of genetic background.
methodsOur dataset of 13,454 genomes, combined with four published genomic datasets, represented Africa (40%), Asia (25%), Europe (19%), North America (12%), and South America (5%). These 20,027 pneumococcal genomes were clustered into lineages using PopPUNK, and named Global Pneumococcal Sequence Clusters (GPSCs). From our dataset, we additionally derived serotype and sequence type, and predicted antibiotic sensitivity. We then measured invasiveness using odds ratios that relating prevalence in invasive pneumococcal disease to carriage.
findingsThe combined collections (n = 20,027) were clustered into 621 GPSCs. Thirty-five GPSCs observed in our dataset were represented by >100 isolates, and subsequently classed as dominant-GPSCs. In 22/35 (63%) of dominant-GPSCs both non-vaccine serotypes and vaccine serotypes were observed in the years up until, and including, the first year of pneumococcal conjugate vaccine introduction. Penicillin and multidrug resistance were higher (p < .05) in a subset dominant-GPSCs (14/35, 9/35 respectively), and resistance to an increasing number of antibiotic classes was associated with increased recombination (R
interpretationWe define GPSCs that can be assigned to any pneumococcal genomic dataset, to aid international comparisons. Existing non-vaccine-serotypes in most GPSCs preclude the removal of these lineages by pneumococcal conjugate vaccines; leaving potential for serotype replacement. A subset of GPSCs have increased resistance, and/or serotype-independent invasiveness.
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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.