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<p><i>Streptococcus pneumoniae</i> adapts within hosts through genetic variation and genome plasticity, facilitating persistence under antibiotic and immune pressures. Here, we investigated a prolonged pneumococcal carriage episode (&gt;337 days) in a healthy, HIV-uninfected adult in Malawi. Whole-genome sequencing of single-colony isolates and plate sweep samples confirmed persistent colonisation by a multidrug-resistant serotype 3 strain with a distinct sequence type (GPSC10-ST18362), which maintained stable predominance despite transient acquisition of other serotypes. The sequentially sampled isolates showed 2 to 11 single-nucleotide polymorphism differences, no evidence of recombination, and modest gene loss involving mobile genetic elements. The total genome size decreased from 2.06 Mb to 2.03 Mb across isolates. Intrahost single-nucleotide variants were identified in genes related to metabolism, stress response, and DNA repair, but showed no consistent signatures of positive selection. Capsular locus analysis revealed deletions consistent with GPSC10-related vaccine-escape profiles. These findings highlight the capacity of GPSC10-ST18362 to persist asymptomatically for months with limited within-host genomic diversity.</p>

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

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年10月7日

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  • Lusako L. Sibale,
  • Stephanie W. Lo,
  • Newton Kalata,
  • Tinashe K. Nyazika,
  • Ndaona Mitole,
  • Victoria Dyster,
  • Alice Kusakala,
  • Mercy Khwiya,
  • Gift Sagawa,
  • Joseph A. Phiri,
  • Akuzike Kalizang’oma,
  • Todd D. Swarthout,
  • Ken Malisita,
  • Arox W. Kamng’ona,
  • Robert S. Heyderman,
  • Stephen D. Bentley,
  • Brenda A. Kwambana-Adams,
  • Chrispin Chaguza,
  • Kondwani C. Jambo

摘要

Streptococcus pneumoniae adapts within hosts through genetic variation and genome plasticity, facilitating persistence under antibiotic and immune pressures. Here, we investigated a prolonged pneumococcal carriage episode (>337 days) in a healthy, HIV-uninfected adult in Malawi. Whole-genome sequencing of single-colony isolates and plate sweep samples confirmed persistent colonisation by a multidrug-resistant serotype 3 strain with a distinct sequence type (GPSC10-ST18362), which maintained stable predominance despite transient acquisition of other serotypes. The sequentially sampled isolates showed 2 to 11 single-nucleotide polymorphism differences, no evidence of recombination, and modest gene loss involving mobile genetic elements. The total genome size decreased from 2.06 Mb to 2.03 Mb across isolates. Intrahost single-nucleotide variants were identified in genes related to metabolism, stress response, and DNA repair, but showed no consistent signatures of positive selection. Capsular locus analysis revealed deletions consistent with GPSC10-related vaccine-escape profiles. These findings highlight the capacity of GPSC10-ST18362 to persist asymptomatically for months with limited within-host genomic diversity.