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Rapid but Transient Microevolution with Minimal Recombination During High-Transmission Streptococcus pneumoniae

Tiago Touret1, Hermínia de Lencastre2,3, Raquel Sá-Leão1

  • 1Laboratory of Molecular Microbiology of Human Pathogens, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.

Microbial Drug Resistance (Larchmont, N.Y.)
|April 2, 2026
PubMed

Insights

Pneumococcal evolution in children with asymptomatic carriage is rapid and transient, driven by short-term adaptations rather than recombination. Most mutations were unique, indicating limited long-term evolutionary impact during this study.

Area of Science:

  • Microbiology
  • Evolutionary Biology
  • Genomics

Background:

  • Asymptomatic carriage of Streptococcus pneumoniae (pneumococcus) is common, especially in high-transmission settings like day-care centers.
  • Understanding within-host pneumococcal evolution during carriage is crucial for controlling transmission and disease.

Purpose of the Study:

  • To investigate pneumococcal clonal dynamics, mutation accumulation, and the role of recombination during asymptomatic carriage in a high-transmission environment.
  • To characterize the rate and patterns of microevolution in pneumococcal isolates from children over a 1-year period.

Main Methods:

  • Whole-genome sequencing of 259 pneumococcal isolates collected monthly from 47 children over 1 year.
  • Analysis of clonal lineages, single-nucleotide polymorphisms (SNPs), mutation rates, and evidence of recombination.
  • Comparison of observed mutations with regional collections and assessment of antimicrobial exposure impact.

Main Results:

  • 22 distinct pneumococcal lineages were identified, with most genomic changes being nonsynonymous SNPs.
  • The mean mutation rate was 4.85 × 10-6 substitutions/site/year, with variations across clones.
  • Recombination played a limited detectable role (≈4%), and most mutations were transient, with few persisting long-term or associated with antimicrobial use.

Conclusions:

  • Pneumococcal microevolution during asymptomatic carriage in high-transmission settings is rapid but largely transient.
  • Short-term adaptive responses to host or niche pressures dominate, with limited opportunity for long-term evolutionary change or significant recombination.
  • Findings highlight the dynamic nature of pneumococcal populations during carriage and its implications for transmission dynamics.

Keywords:
Streptococcus pneumoniaecarriageday-care centersevolutionwhole-genome sequencing

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