ArticleMicrobial genomics2018
SeroBA: rapid high-throughput serotyping of Streptococcus pneumoniae from whole genome sequence data.
Article in Microbial genomics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 112 papers, 1 of them a synthesis that pooled it.
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
112 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Analysing pneumococcal invasiveness using Bayesian models of pathogen progression rates.PLoS computational biology · 2022Pooled it
- Pneumococcal population structure influences the effects of air pollution on invasive disease risk in South Africa.Nature microbiology · 2026Article
- Characteristics of Streptococcus pneumoniae colonising Cypriot children during a period of high PCV10 and PCV13 vaccine coverage: serotypes and antimicrobial resistance.BMC infectious diseases · 2026Article
- Phylogenetic analysis of serotype 19A-sequence type (ST)2331Microbial 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
- Genomic surveillance of post-immunization pneumococcal carriage in Ghana.Microbial genomics · 2026Article
- Genomic epidemiology ofMicrobial genomics · 2026Article
- Fourteen-year genomic surveillance of pediatric invasive Streptococcus pneumoniae: genomic and pan-genomic characterization.BMC microbiology · 2026Article
- Genomic characterization of mobile genetic elements associated with antimicrobial resistance inMicrobial genomics · 2026Article
- High-resolution genomics uncovers region-specific evolution and virulence of ocularMicrobiology spectrum · 2026Article
- Preliminary genomic assessment of invasive Streptococcus pneumoniae serotype 3 isolates in Malaysia.BMC genomic data · 2026Article
- Article
- Lineage structure and penicillin-binding protein variability in clinicalFrontiers in public health · 2026Article
- Emergence of multidrug-resistant ST876 serotype 14Frontiers in cellular and infection microbiology · 2026Article
- Serotypes, antibiotic susceptibility and whole-genome characterization ofJournal of medical microbiology · 2025Article
- Population snapshot ofMicrobial genomics · 2025Article
- Article
- SeroBA(v2.0) and SeroBAnk: a robust genome-based serotyping scheme and comprehensive atlas of capsular diversity inMicrobial genomics · 2025Article
- Tracking the evolution of emerging serotypes and antibiotic resistance patterns in Streptococcus pneumoniae among Indian adults using high-throughput genome sequencing.BMC infectious diseases · 2025Article
- GPS Pipeline: portable, scalable genomic pipeline for Streptococcus pneumoniae surveillance from Global Pneumococcal Sequencing Project.Nature communications · 2025Article
52 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
7 authors.
Funding
Abstract
Streptococcus pneumoniae is responsible for 240 000-460 000 deaths in children under 5 years of age each year. Accurate identification of pneumococcal serotypes is important for tracking the distribution and evolution of serotypes following the introduction of effective vaccines. Recent efforts have been made to infer serotypes directly from genomic data but current software approaches are limited and do not scale well. Here, we introduce a novel method, SeroBA, which uses a k-mer approach. We compare SeroBA against real and simulated data and present results on the concordance and computational performance against a validation dataset, the robustness and scalability when analysing a large dataset, and the impact of varying the depth of coverage on sequence-based serotyping. SeroBA can predict serotypes, by identifying the cps locus, directly from raw whole genome sequencing read data with 98 % concordance using a k-mer-based method, can process 10 000 samples in just over 1 day using a standard server and can call serotypes at a coverage as low as 15-21×. SeroBA is implemented in Python3 and is freely available under an open source GPLv3 licence from: https://github.com/sanger-pathogens/seroba.
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.