Staphylococci in high resolution: Capturing diversity within the human nasal microbiota

Anna Cäcilia Ingham, Department of Sequencing and Bioinformatics, Statens Serum Institut, Copenhagen, Denmark. Electronic address: anmc@ssi.dk.
Duncan Y. Ng, Department of Sequencing and Bioinformatics, Statens Serum Institut, Copenhagen, Denmark.
Søren Iversen, Department of Sequencing and Bioinformatics, Statens Serum Institut, Copenhagen, Denmark.
Cindy M. Liu, Department of Sequencing and Bioinformatics, Statens Serum Institut, Copenhagen, Denmark; Department of Environmental and Occupational Health, George Washington University Milken Institute School of Public Health, Washington, DC, USA.
Khoa Manh Dinh, Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark; Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark.
Silva Holtfreter, Institute for Immunology, University Medicine Greifswald, Greifswald, Germany.
Sofie Marie Edslev, Department of Sequencing and Bioinformatics, Statens Serum Institut, Copenhagen, Denmark.
Thor Bech Johannesen, Department of Sequencing and Bioinformatics, Statens Serum Institut, Copenhagen, Denmark.
Amalie Katrine Rendboe, Department of Sequencing and Bioinformatics, Statens Serum Institut, Copenhagen, Denmark.
Mette Theilgaard Christiansen, Department of Sequencing and Bioinformatics, Statens Serum Institut, Copenhagen, Denmark.
Kim Lee Ng, Department of Sequencing and Bioinformatics, Statens Serum Institut, Copenhagen, Denmark.
Robert Skov, Division of Epidemiological Infectious Disease Preparedness, Statens Serum Institut, Copenhagen, Denmark.
Stefanie Samietz, Department of Prosthetic Dentistry, Gerodontology and Biomaterials, University Medicine Greifswald, Greifswald, Germany.
Dörte Radke, Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany.
Stefan Weiss, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany.
Uwe Völker, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany.
Barbara M. Bröker, Institute for Immunology, University Medicine Greifswald, Greifswald, Germany.
Lise Tornvig Erikstrup, Department of Clinical Microbiology, Aarhus University Hospital, Aarhus, Denmark.
Christian Erikstrup, Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark; Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.
Lance B. Price, Department of Sequencing and Bioinformatics, Statens Serum Institut, Copenhagen, Denmark; Department of Environmental and Occupational Health, George Washington University Milken Institute School of Public Health, Washington, DC, USA.
Paal Skytt Andersen, Department of Sequencing and Bioinformatics, Statens Serum Institut, Copenhagen, Denmark; Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark.
Marc Stegger, Department of Sequencing and Bioinformatics, Statens Serum Institut, Copenhagen, Denmark; Antimicrobial Resistance and Infectious Diseases Laboratory, Harry Butler Institute, Murdoch University, Perth, WA, Australia.

Document Type

Journal Article

Publication Date

6-24-2025

Journal

Cell reports

Volume

44

Issue

6

DOI

10.1016/j.celrep.2025.115854

Keywords

CP: Microbiology; Staphylococcus aureus; Staphylococcus epidermidis; antagonist; carriage; community state type; microbial abundance; microbiome; nasal microbiota; staphylococci

Abstract

Staphylococci include both nasal commensals and opportunistic pathogens, globally responsible for a large proportion of infection-related deaths, especially in S. aureus carriers. To understand staphylococcal temporal dynamics within the nasal microbiota, we employed Staphylococcus-targeted sequencing in two cohorts from Denmark and Germany. We identified two major staphylococcal community state types (sCSTs)-one dominated by S. aureus and one dominated by S. epidermidis-and eight subgroups defined by co-colonizing coagulase-negative staphylococci. The distribution of sCSTs was similar between the two cohorts. Predominance of either S. aureus or S. epidermidis was highly persistent over time, whereas co-colonizing staphylococcal species were transient with varying stability among the sCST subgroups. Detection of S. aureus by culture was positively associated with absolute abundance by qPCR. S. aureus domination was diminished when Dolosigranulum and Corynebacterium co-occurred. Our findings could inform efforts to reduce S. aureus nasal colonization and infection.

Department

Environmental and Occupational Health

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