Within-host pneumococcal serotype 3 genetic diversity and evolution during a one-year prolonged carriage episode in a healthy adult

Streptococcus pneumoniae can rapidly evolve within hosts through genetic mutations, recombination, and mobile genetic elements, enabling adaptation to antibiotics and immune pressures. Here, we detail a longitudinal phenotypic and genomic analysis of a pneumococcal serotype 3 prolonged carriage episode (> 335 days) in a healthy HIV-uninfected adult in Malawi. Whole Genome Sequencing (WGS) of single-colony culture isolates confirmed persistent carriage of a novel multidrug-resistant serotype 3 strain (GPSC10-ST18362), outcompeting other transiently acquired serotypes during the study period. Sequentially sampled isolates showed between 2 to 11 single nucleotide polymorphism (SNP) differences randomly distributed across the genome with no evidence of recombination, but high mutation rates were observed in genes associated with antimicrobial resistance. Further analysis of the sequenced plate sweep samples revealed intrahost single nucleotide variants in several genes associated with survival, including bacterial metabolism, virulence, DNA synthesis and repair, and oxidative stress defence. The study has demonstrated the prolonged carriage of a novel pneumococcal serotype 3 (GPSC10-ST18362) in a healthy adult, revealing its association with multidrug resistance and potential within-host adaptive mechanisms.