ArticleScientific reports2019
Identifying genes associated with invasive disease in S. pneumoniae by applying a machine learning approach to whole genome sequence typing data.
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
16 citing papers in PubMed.
- Genomic and statistical models to characterizeMicrobial genomics · 2026Article
- Pan-Genome-Wide Association Study Identifies Genetic Factors Associated with the Pathogenicity of Invasive Serotype 19F Streptococcus Pneumoniae.Infection and drug resistance · 2025Article
- Non-invasiveEuro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin · 2024Article
- Disease-Associated Streptococcus pneumoniae Genetic Variation.Emerging infectious diseases · 2024Article
- The metabolic, virulence and antimicrobial resistance profiles of colonising Streptococcus pneumoniae shift after PCV13 introduction in urban Malawi.Nature communications · 2023Article
- Pan-Genome-Wide Association Study of Serotype 19A Pneumococci Identifies Disease-Associated Genes.Microbiology spectrum · 2023Article
- Polymorphisms predicting phylogeny in hepatitis B virus.Virus evolution · 2023Article
- Differences in genetic flux in invasiveHeliyon · 2022Article
- Forest and Trees: Exploring Bacterial Virulence with Genome-wide Association Studies and Machine Learning.Trends in microbiology · 2021Review
- A Narrative Review of the Molecular Epidemiology and Laboratory Surveillance of Vaccine Preventable Bacterial Meningitis Agents:Microorganisms · 2021Review
- Identification of Nitrogen Fixation Genes inMicroorganisms · 2020Article
- Bacterial genome-wide association study of hyper-virulent pneumococcal serotype 1 identifies genetic variation associated with neurotropism.Communications biology · 2020Article
- Article
- Coinfinder: detecting significant associations and dissociations in pangenomes.Microbial genomics · 2020Article
- Detection, forecasting and control of infectious disease epidemics: modelling outbreaks in humans, animals and plants.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2019Article
- Gene Tags Assessment by Comparative Genomics (GTACG): A User-Friendly Framework for Bacterial Comparative Genomics.Frontiers in genetics · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors.
Funding
Abstract
Streptococcus pneumoniae, a normal commensal of the upper respiratory tract, is a major public health concern, responsible for substantial global morbidity and mortality due to pneumonia, meningitis and sepsis. Why some pneumococci invade the bloodstream or CSF (so-called invasive pneumococcal disease; IPD) is uncertain. In this study we identify genes associated with IPD. We transform whole genome sequence (WGS) data into a sequence typing scheme, while avoiding the caveat of using an arbitrary genome as a reference by substituting it with a constructed pangenome. We then employ a random forest machine-learning algorithm on the transformed data, and find 43 genes consistently associated with IPD across three geographically distinct WGS data sets of pneumococcal carriage isolates. Of the genes we identified as associated with IPD, we find 23 genes previously shown to be directly relevant to IPD, as well as 18 uncharacterized genes. We suggest that these uncharacterized genes identified by us are also likely to be relevant for IPD.
Indexed as
Identifiers
What OpenQuestion holds
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.