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

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 and Ewan M. Harrison ()
Additional contact information
Dinesh Aggarwal: University of Cambridge, Department of Medicine
Katherine L. Bellis: University of Cambridge, Department of Medicine
Beth Blane: University of Cambridge, Department of Medicine
Marcus C. de Goffau: Wellcome Sanger Institute, Parasites and Microbes Programme
Josef Wagner: Wellcome Sanger Institute, Parasites and Microbes Programme
Duncan Y. K. Ng: Wellcome Sanger Institute, Parasites and Microbes Programme
Kathy E. Raven: University of Cambridge, Department of Medicine
Plamena Naydenova: University of Cambridge, Department of Medicine
Stephen Kaptoge: University of Cambridge, British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care
Susan Burton: University of Cambridge, British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care
Rachel Henry: University of Cambridge, British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care
Catherine Perry: University of Cambridge, British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care
Matthew R. Walker: University of Cambridge, British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care
Carmel Moore: University of Cambridge, British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care
Carol Churcher: University of Cambridge, Department of Medicine
Sophia T. Girgis: University of Cambridge, Department of Medicine
Catarina Ribeiro de Sousa: University of Cambridge, Department of Medicine
Lauma Sarkane: University of Cambridge, Department of Medicine
Joe Brennan: University of Cambridge, Department of Medicine
Asha Akram: University of Cambridge, Department of Medicine
Shannon Duthie: University of Cambridge, British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care
Elisha Johnson: University of Cambridge, British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care
Mercedesz Juhasz: University of Cambridge, British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care
David Anderson: University of Cambridge, British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care
Susan Irvine: University of Cambridge, British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care
Amy McMahon: University of Cambridge, British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care
Liz Lay: University of Cambridge, Department of Veterinary Medicine
Susannah J. Salter: University of Cambridge, Department of Veterinary Medicine
Claire Raisen: University of Cambridge, Department of Veterinary Medicine
Xiaoliang Ba: University of Cambridge, Department of Veterinary Medicine
Mark Holmes: University of Cambridge, Department of Veterinary Medicine
Andries J. van Tonder: University of Cambridge, Department of Veterinary Medicine
Emanuele Di Angelantonio: University of Cambridge, British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care
Adam S. Butterworth: University of Cambridge, British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care
Joan A. Geoghegan: University of Birmingham, Institute of Microbiology and Infection
John Danesh: University of Cambridge, British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care
Julian Parkhill: University of Cambridge, Department of Veterinary Medicine
Sharon J. Peacock: University of Cambridge, Department of Medicine
Ewan M. Harrison: University of Cambridge, Department of Medicine

Nature Communications, 2025, vol. 16, issue 1, 1-17

Abstract: 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.

Date: 2025
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DOI: 10.1038/s41467-025-66564-4

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