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<p>Madagascar is the most plague-affected country globally, yet the phylogenetic diversity of <i>Yersinia pestis</i> in this country remains insufficiently characterized. In this study, we analyzed whole-genome sequences of 614 <i>Y. pestis</i> strains, with 141 strains newly sequenced, collected over 96 years across Madagascar. All isolates emerged in 1898 and belong to the phylogroup 1.ORI3, supporting a single introduction event to Madagascar, followed by local diversification. We identified 23 distinct subgroups, including eight previously undescribed. Although most novel subgroups were rarely detected or rapidly extinguished, the ɣ subgroup circulated between 2016 and 2019 in southeastern Madagascar—an area historically plague-free for 64 years. Our analysis revealed extensive strain diversity and subgroup persistence, with some subgroups, such as α and β, persisting silently for decades before reemerging during the 2017 pneumonic plague epidemic. These findings uncover deep, previously underestimated phylogenetic diversity and long-term dynamics of <i>Y. pestis</i> in Madagascar, providing critical insights for understanding transmission patterns and informing future plague surveillance and control efforts.</p>

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Evaluating the early diversification of Yersinia pestis and its phylogeographic expansion over 96 years of evolution in Madagascar

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年11月26日

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  • Lovasoa Nomena Randriantseheno,
  • Jason W. Sahl,
  • Adrien Rieux,
  • Guillem Mas Fiol,
  • Dawn Birdsell,
  • Olivier Gorgé,
  • Eric Valade,
  • Javier Pizarro-Cerdà,
  • Voahangy Andrianaivoarimanana,
  • David M. Wagner,
  • Minoarisoa Rajerison

摘要

Madagascar is the most plague-affected country globally, yet the phylogenetic diversity of Yersinia pestis in this country remains insufficiently characterized. In this study, we analyzed whole-genome sequences of 614 Y. pestis strains, with 141 strains newly sequenced, collected over 96 years across Madagascar. All isolates emerged in 1898 and belong to the phylogroup 1.ORI3, supporting a single introduction event to Madagascar, followed by local diversification. We identified 23 distinct subgroups, including eight previously undescribed. Although most novel subgroups were rarely detected or rapidly extinguished, the ɣ subgroup circulated between 2016 and 2019 in southeastern Madagascar—an area historically plague-free for 64 years. Our analysis revealed extensive strain diversity and subgroup persistence, with some subgroups, such as α and β, persisting silently for decades before reemerging during the 2017 pneumonic plague epidemic. These findings uncover deep, previously underestimated phylogenetic diversity and long-term dynamics of Y. pestis in Madagascar, providing critical insights for understanding transmission patterns and informing future plague surveillance and control efforts.