ArticleNature communications2025
GPS Pipeline: portable, scalable genomic pipeline for Streptococcus pneumoniae surveillance from Global Pneumococcal Sequencing Project.
Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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.
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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
9 citing papers in PubMed.
- A reusable model of pangenome selection informs optimal surveillance strategies over vaccine introductions.Genome medicine · 2026Article
- A WGS workflow for identifying genetically modified and foodborne-pathogenicFood chemistry. Molecular sciences · 2026Article
- Genomic characterization of mobile genetic elements associated with antimicrobial resistance inMicrobial genomics · 2026Article
- Genomic characterization of invasive disease-causingMicrobial genomics · 2026Article
- Genomic features of pneumococcal strains isolated from paediatric patients with invasive disease during pneumococcal conjugate vaccine introduction in Lima, Peru.Microbial genomics · 2026Article
- A mini review of genome-predicted β-lactam susceptibility inFrontiers in cellular and infection microbiology · 2026Review
- GPS Pipeline: portable, scalable genomic pipeline for Streptococcus pneumoniae surveillance from Global Pneumococcal Sequencing Project.Nature communications · 2025Article
- Comparison of Illumina and Oxford Nanopore Technology systems for the genomic characterization ofMicrobiology spectrum · 2025Article
- Estimating between-country migration in pneumococcal populations.G3 (Bethesda, Md.) · 2024Article
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
Streptococcus pneumoniae (pneumococcus) is a major pathogen globally, responsible for an estimated one million deaths annually and contributing significantly to the global burden of antimicrobial resistance. Ongoing surveillance of its vaccine antigen (i.e. serotypes), antimicrobial resistance, and pneumococcal lineages is crucial for assessing the impact of vaccination programs and guiding future vaccine design. However, current bioinformatics tools have several limitations that prevent them from enabling comprehensive analysis that allows simultaneous, large-scale, and independent generation of these crucial data. Here, we present the GPS Pipeline that enables reliable extraction of public health information from pneumococcal genomes using in silico methods. It can accurately identify 102 of 107 known serotypes, recognise 1053 pneumococcal lineages, and predict susceptibilities to 19 common antibiotics. Built on Nextflow and utilising containerisation technology, the GPS Pipeline minimises software setup requirements and bioinformatics expertise while facilitating large-scale analysis of genomic data. The GPS Pipeline was applied and validated on 20,924 pneumococcal genomes worldwide, demonstrating its effectiveness in enhancing responsiveness in pneumococcal genomic surveillance.
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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.