ArticleNature communications2020
Within-host microevolution of Streptococcus pneumoniae is rapid and adaptive during natural colonisation.
Article in Nature communications, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Who cites it
43 citing papers in PubMed.
- Simulating the host niche: balancing complexity and control in the experimental evolution of antibiotic resistance and pathoadaptation.Microbiology (Reading, England) · 2026Review
- ZPY-CpG-Ch, a broad coverage vaccine againstScience advances · 2026Article
- Low-Abundance and FragmentaryBiomolecules · 2026Article
- Modelling impacts of paediatric amoxicillin shortage management on pneumococcal resistance and invasive disease in Europe.Nature communications · 2026Article
- Emergence of multidrug-resistant ST876 serotype 14Frontiers in cellular and infection microbiology · 2026Article
- Genetic diversity ofGut microbes · 2025Article
- Within-host genetic diversity of pneumococcal serotype 3 during one-year prolonged carriage in a healthy adult.Nature communications · 2025Article
- The Global, Regional, and National Burden of Lower Respiratory Infections Caused byHealthcare (Basel, Switzerland) · 2025Article
- Within-host bacterial evolution and the emergence of pathogenicity.Nature microbiology · 2025Review
- Population sequencing for phylogenetic diversity and transmission analyses.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Colonization dynamics ofInfection and immunity · 2025Article
- Phenotypic and genetic heterogeneity ofMicrobial genomics · 2025Article
- Insights into Within-Host Evolution and Dynamics of Oral and Intestinal Streptococci Unveil Niche Adaptation.International journal of molecular sciences · 2024Article
- Ultrastructural, metabolic and genetic characteristics of determinants facilitating the acquisition of macrolide resistance by Streptococcus pneumoniae.Drug resistance updates : reviews and commentaries in antimicrobial and anticancer chemotherapy · 2024Article
- Deep longitudinal lower respiratory tract microbiome profiling reveals genome-resolved functional and evolutionary dynamics in critical illness.Nature communications · 2024Article
- Development of the Pneumococcal Genome Library, a core genome multilocus sequence typing scheme, and a taxonomic life identification number barcoding system to investigate and define pneumococcal population structure.Microbial genomics · 2024Article
- Biological puzzles solved by usingJournal of bacteriology · 2024Review
- Estimating geographical spread ofMicrobial genomics · 2024Article
- Long-term evolution of Streptococcus mitis and Streptococcus pneumoniae leads to higher genetic diversity within rather than between human populations.PLoS genetics · 2024Article
- Spontaneous mutations and mutational responses to penicillin treatment in the bacterial pathogenMarine life science & technology · 2024Article
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Authors and funding
19 authors.
Funding
Abstract
Genomic evolution, transmission and pathogenesis of Streptococcus pneumoniae, an opportunistic human-adapted pathogen, is driven principally by nasopharyngeal carriage. However, little is known about genomic changes during natural colonisation. Here, we use whole-genome sequencing to investigate within-host microevolution of naturally carried pneumococci in ninety-eight infants intensively sampled sequentially from birth until twelve months in a high-carriage African setting. We show that neutral evolution and nucleotide substitution rates up to forty-fold faster than observed over longer timescales in S. pneumoniae and other bacteria drives high within-host pneumococcal genetic diversity. Highly divergent co-existing strain variants emerge during colonisation episodes through real-time intra-host homologous recombination while the rest are co-transmitted or acquired independently during multiple colonisation episodes. Genic and intergenic parallel evolution occur particularly in antibiotic resistance, immune evasion and epithelial adhesion genes. Our findings suggest that within-host microevolution is rapid and adaptive during natural colonisation.
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