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<p><i>Staphylococcus aureus</i> colonises the nose in humans, with individuals defined as persistent, intermittent or non-carriers. Unlike the gut microbiome, the nasal microbiome has not been studied in large numbers of people. Here, we define the nasal microbiome in ~1100 individuals from the CARRIAGE study (ISRCTN: ISRCTN10474633) and combine with <i>S. aureus</i> culture data. We identify seven community state types (CST), including two CSTs more common in females. Approximately 70% of those who are persistently colonised with <i>S. aureus</i> have a CST dominated by <i>S. aureus</i>, while non-carriers are distributed across the other six CSTs. Intermittent carriers are not a unique state but have microbiomes that resemble non- or persistent carriers. Persistent carriage is positively associated with <i>S. aureus</i> abundance, and negatively associated with three <i>Corynebacterium</i> species, <i>Dolosigranulum pigrum</i>, <i>Staphylococcus epidermidis</i>, and <i>Moraxella catarrhalis</i>; the microbiome can be exploited with machine learning to accurately predict the persistence of <i>S. aureus</i> colonisation. Finally, we find that certain <i>S. aureus</i> lineages are better adapted to colonisation than others. Our data provides a comprehensive view of the nasal microbiome with respect to <i>S. aureus</i> colonisation, describing two key states: a <i>S. aureus</i> dominated CST in which <i>S. aureus</i> shapes the microbiome, and CSTs in which <i>S. aureus</i> is rare or absent.</p>

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Large-scale characterisation of the nasal microbiome redefines Staphylococcus aureus colonisation status

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年12月2日

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  • Dinesh Aggarwal,
  • Katherine L. Bellis,
  • Beth Blane,
  • Marcus C. de Goffau,
  • Josef Wagner,
  • Duncan Y. K. Ng,
  • Kathy E. Raven,
  • Plamena Naydenova,
  • Stephen Kaptoge,
  • Susan Burton,
  • Rachel Henry,
  • Catherine Perry,
  • Matthew R. Walker,
  • Carmel Moore,
  • Carol Churcher,
  • Sophia T. Girgis,
  • Catarina Ribeiro de Sousa,
  • Lauma Sarkane,
  • Joe Brennan,
  • Asha Akram,
  • Shannon Duthie,
  • Elisha Johnson,
  • Mercedesz Juhasz,
  • David Anderson,
  • Susan Irvine,
  • Amy McMahon,
  • Liz Lay,
  • Susannah J. Salter,
  • Claire Raisen,
  • Xiaoliang Ba,
  • Mark Holmes,
  • Andries J. van Tonder,
  • Emanuele Di Angelantonio,
  • Adam S. Butterworth,
  • Joan A. Geoghegan,
  • John Danesh,
  • Julian Parkhill,
  • Sharon J. Peacock,
  • Ewan M. Harrison

摘要

Staphylococcus aureus colonises the nose in humans, with individuals defined as persistent, intermittent or non-carriers. Unlike the gut microbiome, the nasal microbiome has not been studied in large numbers of people. Here, we define the nasal microbiome in ~1100 individuals from the CARRIAGE study (ISRCTN: ISRCTN10474633) and combine with S. aureus culture data. We identify seven community state types (CST), including two CSTs more common in females. Approximately 70% of those who are persistently colonised with S. aureus have a CST dominated by S. aureus, while non-carriers are distributed across the other six CSTs. Intermittent carriers are not a unique state but have microbiomes that resemble non- or persistent carriers. Persistent carriage is positively associated with S. aureus abundance, and negatively associated with three Corynebacterium species, Dolosigranulum pigrum, Staphylococcus epidermidis, and Moraxella catarrhalis; the microbiome can be exploited with machine learning to accurately predict the persistence of S. aureus colonisation. Finally, we find that certain S. aureus lineages are better adapted to colonisation than others. Our data provides a comprehensive view of the nasal microbiome with respect to S. aureus colonisation, describing two key states: a S. aureus dominated CST in which S. aureus shapes the microbiome, and CSTs in which S. aureus is rare or absent.