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

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.

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Publication Details

Journal
Nature Communications
Published
2025-12-02
DOI
https://doi.org/10.1038/s41467-025-66564-4
Citations
3
Primary Topic
Oral microbiology and periodontitis research
Type
article
Field-Weighted Citation Impact
4.40

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article

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

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3 citations
Nature Communications
Oral microbiology and periodontitis research
4.40
article

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

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

Abstract

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.

Nature CommunicationsVol. 16(1)
University of Cambridge (GB), Wellcome Sanger Institute (GB), British Heart Foundation (GB), National Institute for Health and Care Research (GB), Human Technopole (IT), Health Data Research UK (GB), Imperial College London (GB), University of Birmingham (GB)
Scottish Government, UK Research and Innovation, National Institute for Health and Care Research, British Heart Foundation, Department of Health and Social Care, Public Health Agency, Isaac Newton Trust, Chief Scientist Office, Scottish Government Health and Social Care Directorate, Medical Research Council, Engineering and Physical Sciences Research Council, Economic and Social Research Council, Health and Social Care Research and Development Division, NIHR Cambridge Biomedical Research Centre
Openalex Percentile: Top 5%
Oral microbiology and periodontitis research
4.40
DOIOpen Access PDFOpenAlex
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