Within-host pneumococcal evolution during asymptomatic carriage remains poorly characterized in high-transmission settings. We performed whole-genome sequencing of 259 isolates sampled monthly for 1 year from 47 children attending a single day-care to assess clonal dynamics, mutation accumulation, and the role of recombination. Isolates were resolved into 22 lineages based on serotype and multilocus sequence type. Most genomic changes were nonsynonymous single-nucleotide polymorphism, with only 30% of 357 mutations observed in more than 1 isolate. The mean mutation rate was 4.85 × 10-6 substitutions/site/year, with elevated rates in specific clones (notably 6B-176, 23F-81, and 19F-177). Outlier strains revealed co-circulating sublineages and room-structured divergence in a nontypeable lineage. Putative recombination accounted for ≈4% of mutations, indicating a limited detectable role during the study period. Parallel mutations occurred in genes linked to metabolism, regulation, and immune evasion (e.g., piaA, prtA, pspA, and ciaH). Antimicrobial exposure was not associated with increased mutational burden, and only a handful of mutations persisted when compared with a 2018-2019 regional collection. Overall, pneumococcal microevolution in this high-transmission setting was rapid but largely transient, with little contribution from recombination. These findings indicate that the dynamics captured over this 1-year period reflect rapid, short-term adaptive responses to host or niche pressures, with limited opportunity for longer-term evolutionary change.
Touret et al. (Thu,) studied this question.