ArticleMicrobial genomics2020
Visualizing variation within Global Pneumococcal Sequence Clusters (GPSCs) and country population snapshots to contextualize pneumococcal isolates.
Article in Microbial genomics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers, 2 of them syntheses that pooled it.
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47 citing papers in PubMed, 2 syntheses or guidelines pooled it, 66 citations in OpenAlex.
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- Preliminary genomic assessment of invasive Streptococcus pneumoniae serotype 3 isolates in Malaysia.BMC genomic data · 2026Article
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- The rise and global spread of IMP carbapenemases (1996-2023): a genomic epidemiology study.Nature communications · 2025Article
- Global pneumococcal sequence cluster lineage for invasive pneumococcal isolates in Denmark from summer 2019 to 2023.Scientific reports · 2025Article
- Genomic analysis and pneumococcal population dynamics across PCV implementation in South Korea, 1997-2023.Microbial genomics · 2025Article
- The rise and global spread of IMP carbapenemases (1996-2023): a genomic epidemiology study.medRxiv : the preprint server for health sciences · 2025Article
- Integrated population clustering and genomic epidemiology with PopPIPE.Microbial genomics · 2025Article
- Re-evaluation of boundaries ofInternational journal of systematic and evolutionary microbiology · 2025Article
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- Prediction of antimicrobial susceptibility of pneumococci based on whole-genome sequencing data: a direct comparison of two genomic tools to conventional antimicrobial susceptibility testing.Journal of clinical microbiology · 2025Article
- A decade of 10-valent pneumococcal conjugate vaccine use in Lithuania: trends in invasive pneumococcal serotype dynamics.Frontiers in public health · 2025Article
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Authors and funding
43 authors at 20 institutions in 13 countries.
Funding
Abstract
Knowledge of pneumococcal lineages, their geographic distribution and antibiotic resistance patterns, can give insights into global pneumococcal disease. We provide interactive bioinformatic outputs to explore such topics, aiming to increase dissemination of genomic insights to the wider community, without the need for specialist training. We prepared 12 country-specific phylogenetic snapshots, and international phylogenetic snapshots of 73 common Global Pneumococcal Sequence Clusters (GPSCs) previously defined using PopPUNK, and present them in Microreact. Gene presence and absence defined using Roary, and recombination profiles derived from Gubbins are presented in Phandango for each GPSC. Temporal phylogenetic signal was assessed for each GPSC using BactDating. We provide examples of how such resources can be used. In our example use of a country-specific phylogenetic snapshot we determined that serotype 14 was observed in nine unrelated genetic backgrounds in South Africa. The international phylogenetic snapshot of GPSC9, in which most serotype 14 isolates from South Africa were observed, highlights that there were three independent sub-clusters represented by South African serotype 14 isolates. We estimated from the GPSC9-dated tree that the sub-clusters were each established in South Africa during the 1980s. We show how recombination plots allowed the identification of a 20 kb recombination spanning the capsular polysaccharide locus within GPSC97. This was consistent with a switch from serotype 6A to 19A estimated to have occured in the 1990s from the GPSC97-dated tree. Plots of gene presence/absence of resistance genes (
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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.