Changes in nasal and throat microbiota composition during and after mupirocin and chlorhexidine decolonisation treatment in asymptomatic MRSA carriers: a longitudinal observational study

Authors

• Sofie Marie Edslev, Department of Sequencing and Bioinformatics, Statens Serum Institut, Copenhagen, Denmark; European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Staphylococci and Staphylococcal Diseases (ESGS), Basel, Switzerland. Electronic address: smed@ssi.dk.
• Cindy M. Liu, European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Staphylococci and Staphylococcal Diseases (ESGS), Basel, Switzerland; Antibiotic Resistance Action Center, Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, Washington, DC, USA.
• Bobby Zhao Lo, Department of Clinical Microbiology and MRSA Knowledge Center, Copenhagen University Hospital - Amager and Hvidovre, Hvidovre, Denmark.
• Heidi Meiniche, Department of Clinical Microbiology and MRSA Knowledge Center, Copenhagen University Hospital - Amager and Hvidovre, Hvidovre, Denmark.
• Berit Lilje, Department of Sequencing and Bioinformatics, Statens Serum Institut, Copenhagen, Denmark.
• Daniel E. Park, Antibiotic Resistance Action Center, Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, Washington, DC, USA.
• Amalie Rendboe, Department of Sequencing and Bioinformatics, Statens Serum Institut, Copenhagen, Denmark.
• Tony Pham, Antibiotic Resistance Action Center, Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, Washington, DC, USA.
• Juan E. Salazar, Antibiotic Resistance Action Center, Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, Washington, DC, USA.
• Tor Toudahl, Department of Sequencing and Bioinformatics, Statens Serum Institut, Copenhagen, Denmark.
• Anna Cäcilia Ingham, Department of Sequencing and Bioinformatics, Statens Serum Institut, Copenhagen, Denmark; European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Staphylococci and Staphylococcal Diseases (ESGS), Basel, Switzerland.
• Maliha Aziz, Antibiotic Resistance Action Center, Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, Washington, DC, USA.
• Mette Damkjær Bartels, European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Staphylococci and Staphylococcal Diseases (ESGS), Basel, Switzerland; Department of Clinical Microbiology and MRSA Knowledge Center, Copenhagen University Hospital - Amager and Hvidovre, Hvidovre, Denmark; Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark.
• Paal Skytt Andersen, Department of Sequencing and Bioinformatics, Statens Serum Institut, Copenhagen, Denmark.
• Robert Leo Skov, Department of Sequencing and Bioinformatics, Statens Serum Institut, Copenhagen, Denmark; European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Staphylococci and Staphylococcal Diseases (ESGS), Basel, Switzerland.
• Lance B. Price, Department of Sequencing and Bioinformatics, Statens Serum Institut, Copenhagen, Denmark; European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Staphylococci and Staphylococcal Diseases (ESGS), Basel, Switzerland; Antibiotic Resistance Action Center, Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, Washington, DC, USA.
• Marc Stegger, Department of Sequencing and Bioinformatics, Statens Serum Institut, Copenhagen, Denmark; European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Staphylococci and Staphylococcal Diseases (ESGS), Basel, Switzerland; Antibiotic Resistance Action Center, Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, Washington, DC, USA; Antimicrobial Resistance and Infectious Diseases Laboratory, Harry Butler Institute, Murdoch University, Murdoch, WA, Australia.

Document Type

Journal Article

Publication Date

2-24-2026

Journal

Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases

DOI

10.1016/j.cmi.2026.02.020

Abstract

OBJECTIVES: Decolonisation treatment of asymptomatic methicillin-resistant Staphylococcus aureus (MRSA) carriage is recommended as a preventive measure in several countries, including Denmark. This study aimed to investigate the temporal dynamics of the nasal and throat microbiota in MRSA carriers undergoing decolonisation treatment and to assess bacterial changes associated with treatment success. METHODS: Adults with asymptomatic nasal MRSA carriage (n=34) were included in this prospective observational study. Participants underwent a 5-day decolonisation regimen consisting of 2% mupirocin nasal ointment and daily skin cleansing with 4% chlorhexidine soap. Nasal and throat samples were collected at multiple time points from baseline to 6 months post-treatment and analysed by 16S rRNA gene sequencing. A reference group of untreated community-dwelling adults (n=116) served as comparison. RESULTS: At one-month follow-up, 21 of 34 participants (62%) were successfully decolonized, while 13 (38%) remained MRSA-positive at one or more body sites. At baseline, no nasal bacterial taxa were significantly associated with nasal MRSA decolonisation outcome. The nasal bacterial community changed significantly within the first 2 days of treatment and remained distinct from the baseline composition for 30 days, both among those with successful decolonisation and those who remained colonized with MRSA. Nasal community state types (CSTs) characterized by S. aureus, coagulase-negative staphylococci, Moraxella, and Dolosigranulum became less prevalent during treatment, whereas CSTs dominated by Corynebacterium and Cutibacterium increased in prevalence. Among successfully decolonised participants, the nasal microbiota at 3 and 6 months post-treatment continued to differ from baseline and from the reference group, mainly due to a sustained depletion of Dolosigranulum and Moraxella. In contrast, the throat microbiota showed only short-term compositional changes. CONCLUSIONS: Decolonisation treatment significantly alters the nasal microbiota, with both short-term and persistent effects. Future strategies could consider supplementation with beneficial nasal commensals, like Dolosigranulum, after treatment to promote microbiome recovery.

APA Citation

Edslev, Sofie Marie; Liu, Cindy M.; Lo, Bobby Zhao; Meiniche, Heidi; Lilje, Berit; Park, Daniel E.; Rendboe, Amalie; Pham, Tony; Salazar, Juan E.; Toudahl, Tor; Ingham, Anna Cäcilia; Aziz, Maliha; Bartels, Mette Damkjær; Andersen, Paal Skytt; Skov, Robert Leo; Price, Lance B.; and Stegger, Marc, "Changes in nasal and throat microbiota composition during and after mupirocin and chlorhexidine decolonisation treatment in asymptomatic MRSA carriers: a longitudinal observational study" (2026). GW Authored Works. Paper 8673.
https://hsrc.himmelfarb.gwu.edu/gwhpubs/8673

Department

Environmental and Occupational Health