Staphylococci in high resolution: Capturing diversity within the human nasal microbiota
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 sequenci...
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| Vydané v: | Cell reports (Cambridge) Ročník 44; číslo 6; s. 115854 |
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| Hlavní autori: | , , , , , , , , , , , , , , , , , , , , , |
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| Jazyk: | English |
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United States
Elsevier Inc
24.06.2025
Elsevier |
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| ISSN: | 2211-1247, 2211-1247 |
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| 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.
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•The human nose harbors two major staphylococcal community state types (sCSTs)•S. aureus and S. epidermidis dominate the two sCSTs alongside various co-colonizers•Predominance of either S. aureus or S. epidermidis is highly persistent over time•sCSTs are comparable across two cohorts from Denmark and Germany
Nasal staphylococci cluster into two stable community state types, dominated by either S. aureus or S. epidermidis, in a Danish and a German cohort. Each type included distinct subclusters defined by co-colonizing staphylococci. S. aureus was reduced when co-occurring with Dolosigranulum and Corynebacterium, highlighting microbial interactions relevant to infection prevention. |
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| AbstractList | 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. 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.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. 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. [Display omitted] •The human nose harbors two major staphylococcal community state types (sCSTs)•S. aureus and S. epidermidis dominate the two sCSTs alongside various co-colonizers•Predominance of either S. aureus or S. epidermidis is highly persistent over time•sCSTs are comparable across two cohorts from Denmark and Germany Nasal staphylococci cluster into two stable community state types, dominated by either S. aureus or S. epidermidis, in a Danish and a German cohort. Each type included distinct subclusters defined by co-colonizing staphylococci. S. aureus was reduced when co-occurring with Dolosigranulum and Corynebacterium, highlighting microbial interactions relevant to infection prevention. 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. Nasal staphylococci cluster into two stable community state types, dominated by either S. aureus or S. epidermidis, in a Danish and a German cohort. Each type included distinct subclusters defined by co-colonizing staphylococci. S. aureus was reduced when co-occurring with Dolosigranulum and Corynebacterium, highlighting microbial interactions relevant to infection prevention. |
| ArticleNumber | 115854 |
| Author | Iversen, Søren Ng, Duncan Y.K. Radke, Dörte Erikstrup, Lise Tornvig Johannesen, Thor Bech Stegger, Marc Holtfreter, Silva Weiss, Stefan Erikstrup, Christian Christiansen, Mette Theilgaard Samietz, Stefanie Liu, Cindy M. Dinh, Khoa Manh Skov, Robert Rendboe, Amalie Katrine Price, Lance B. Ingham, Anna Cäcilia Andersen, Paal Skytt Edslev, Sofie Marie Ng, Kim Lee Völker, Uwe Bröker, Barbara M. |
| AuthorAffiliation | 8 Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany 11 Department of Clinical Medicine, Aarhus University, Aarhus, Denmark 7 Department of Prosthetic Dentistry, Gerodontology and Biomaterials, University Medicine Greifswald, Greifswald, Germany 6 Division of Epidemiological Infectious Disease Preparedness, Statens Serum Institut, Copenhagen, Denmark 3 Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark 1 Department of Sequencing and Bioinformatics, Statens Serum Institut, Copenhagen, Denmark 4 Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark 10 Department of Clinical Microbiology, Aarhus University Hospital, Aarhus, Denmark 15 Senior author 9 Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany 12 Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark 2 Department of Environmental an |
| AuthorAffiliation_xml | – name: 8 Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany – name: 6 Division of Epidemiological Infectious Disease Preparedness, Statens Serum Institut, Copenhagen, Denmark – name: 4 Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark – name: 11 Department of Clinical Medicine, Aarhus University, Aarhus, Denmark – name: 2 Department of Environmental and Occupational Health, George Washington University Milken Institute School of Public Health, Washington, DC, USA – name: 14 These author contributed equally – name: 13 Antimicrobial Resistance and Infectious Diseases Laboratory, Harry Butler Institute, Murdoch University, Perth, WA, Australia – name: 5 Institute for Immunology, University Medicine Greifswald, Greifswald, Germany – name: 12 Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark – name: 1 Department of Sequencing and Bioinformatics, Statens Serum Institut, Copenhagen, Denmark – name: 3 Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark – name: 10 Department of Clinical Microbiology, Aarhus University Hospital, Aarhus, Denmark – name: 16 Lead contact – name: 7 Department of Prosthetic Dentistry, Gerodontology and Biomaterials, University Medicine Greifswald, Greifswald, Germany – name: 9 Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany – name: 15 Senior author |
| Author_xml | – sequence: 1 givenname: Anna Cäcilia surname: Ingham fullname: Ingham, Anna Cäcilia email: anmc@ssi.dk organization: Department of Sequencing and Bioinformatics, Statens Serum Institut, Copenhagen, Denmark – sequence: 2 givenname: Duncan Y.K. surname: Ng fullname: Ng, Duncan Y.K. organization: Department of Sequencing and Bioinformatics, Statens Serum Institut, Copenhagen, Denmark – sequence: 3 givenname: Søren surname: Iversen fullname: Iversen, Søren organization: Department of Sequencing and Bioinformatics, Statens Serum Institut, Copenhagen, Denmark – sequence: 4 givenname: Cindy M. surname: Liu fullname: Liu, Cindy M. organization: Department of Sequencing and Bioinformatics, Statens Serum Institut, Copenhagen, Denmark – sequence: 5 givenname: Khoa Manh surname: Dinh fullname: Dinh, Khoa Manh organization: Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark – sequence: 6 givenname: Silva surname: Holtfreter fullname: Holtfreter, Silva organization: Institute for Immunology, University Medicine Greifswald, Greifswald, Germany – sequence: 7 givenname: Sofie Marie surname: Edslev fullname: Edslev, Sofie Marie organization: Department of Sequencing and Bioinformatics, Statens Serum Institut, Copenhagen, Denmark – sequence: 8 givenname: Thor Bech surname: Johannesen fullname: Johannesen, Thor Bech organization: Department of Sequencing and Bioinformatics, Statens Serum Institut, Copenhagen, Denmark – sequence: 9 givenname: Amalie Katrine surname: Rendboe fullname: Rendboe, Amalie Katrine organization: Department of Sequencing and Bioinformatics, Statens Serum Institut, Copenhagen, Denmark – sequence: 10 givenname: Mette Theilgaard surname: Christiansen fullname: Christiansen, Mette Theilgaard organization: Department of Sequencing and Bioinformatics, Statens Serum Institut, Copenhagen, Denmark – sequence: 11 givenname: Kim Lee surname: Ng fullname: Ng, Kim Lee organization: Department of Sequencing and Bioinformatics, Statens Serum Institut, Copenhagen, Denmark – sequence: 12 givenname: Robert surname: Skov fullname: Skov, Robert organization: Division of Epidemiological Infectious Disease Preparedness, Statens Serum Institut, Copenhagen, Denmark – sequence: 13 givenname: Stefanie surname: Samietz fullname: Samietz, Stefanie organization: Department of Prosthetic Dentistry, Gerodontology and Biomaterials, University Medicine Greifswald, Greifswald, Germany – sequence: 14 givenname: Dörte surname: Radke fullname: Radke, Dörte organization: Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany – sequence: 15 givenname: Stefan surname: Weiss fullname: Weiss, Stefan organization: Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany – sequence: 16 givenname: Uwe surname: Völker fullname: Völker, Uwe organization: Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany – sequence: 17 givenname: Barbara M. surname: Bröker fullname: Bröker, Barbara M. organization: Institute for Immunology, University Medicine Greifswald, Greifswald, Germany – sequence: 18 givenname: Lise Tornvig surname: Erikstrup fullname: Erikstrup, Lise Tornvig organization: Department of Clinical Microbiology, Aarhus University Hospital, Aarhus, Denmark – sequence: 19 givenname: Christian surname: Erikstrup fullname: Erikstrup, Christian organization: Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark – sequence: 20 givenname: Lance B. surname: Price fullname: Price, Lance B. organization: Department of Sequencing and Bioinformatics, Statens Serum Institut, Copenhagen, Denmark – sequence: 21 givenname: Paal Skytt surname: Andersen fullname: Andersen, Paal Skytt organization: Department of Sequencing and Bioinformatics, Statens Serum Institut, Copenhagen, Denmark – sequence: 22 givenname: Marc surname: Stegger fullname: Stegger, Marc organization: Department of Sequencing and Bioinformatics, Statens Serum Institut, Copenhagen, Denmark |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/40517386$$D View this record in MEDLINE/PubMed |
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| Keywords | Staphylococcus epidermidis carriage community state type nasal microbiota CP: Microbiology staphylococci microbial abundance microbiome antagonist Staphylococcus aureus |
| Language | English |
| License | This is an open access article under the CC BY-NC-ND license. Copyright © 2025 The Authors. Published by Elsevier Inc. All rights reserved. This is an open access article under the CC BY-NC-ND license (https://creativecommons.org/licenses/by-nc-nd/4.0/). |
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| Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 AUTHOR CONTRIBUTIONS Conceptualization, A.C.I., S.M.E., M.S., K.M.D., L.T.E., C.E., B.M.B., U.V., S. H., D.Y.K.N., L.B.P., R.S., P.S.A., and S.I.; data curation, A.C.I., K.M.D., L.T. E., C.E., C.M.L., D.Y.K.N., T.B.J., S.H., S.W., D.R., and S.I.; formal analysis, A.C.I. and D.Y.K.N.; funding acquisition, M.S., K.M.D., L.T.E., C.E., L.B.P., B.M.B., and P.S.A.; investigation, M.S., K.M.D., L.T.E., C.E., S.H., D.R., S.S., S.W., M.T.C., A.K.R., and S.I.; methodology, M.S., A.C.I., D.Y.K.N., M.T.C., T.B.J., and S.I.; project administration, A.C.I., S.M.E., D.Y.K.N., P.S.A., and M.S.; resources, M.S., K.M.D., L.T.E., C.E., and P.S.A.; software, K.L.N.; supervision, A.C.I., M.S., D.Y.K.N., and P.S.A.; validation, A.C.I. and D.Y.K.N.; visualization, A.C.I. and D.Y.K.N.; writing – original draft, A.C.I. and D.Y.K.N.; writing – review & editing, A.C.I., S.M.E., M.S., K.M.D., L.T.E., C.E., L.B.P., C.M.L., B.M.B., U.V., S.H., D.Y.K.N., P.S.A., S.I., and R.S. All authors read and approved the final manuscript. |
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| Title | Staphylococci in high resolution: Capturing diversity within the human nasal microbiota |
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