Changes in nasal and throat microbiota composition during and after mupirocin and chlorhexidine decolonization treatment in asymptomatic methicillin-resistant Staphylococcus aureus carriers: a longitudinal observational study

OBJECTIVES: Decolonization 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 decolonization 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 decolonization 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 after treatment and analysed by 16S rRNA gene sequencing. A reference group of untreated community-dwelling adults (n = 116) served as comparison. RESULTS: At 1-month follow-up, 21 of 34 participants (62%) were successfully decolonized, whereas 13 (38%) remained MRSA positive at one or more body sites. At baseline, no nasal bacterial taxa were significantly associated with nasal MRSA decolonization 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 decolonization and those who remained colonized with MRSA. Nasal community state types characterized by S. aureus, coagulase-negative staphylococci, Moraxella, and Dolosigranulum became less prevalent during treatment, whereas community state types dominated by Corynebacterium and Cutibacterium increased in prevalence. Among successfully decolonized participants, the nasal microbiota at 3 and 6 months after treatment continued to differ from baseline and from the reference group, mainly because of a sustained depletion of Dolosigranulum and Moraxella. In contrast, the throat microbiota showed only short-term compositional changes. CONCLUSIONS: Decolonization treatment significantly alters the nasal microbiota, with both short-term and persistent effects. Future strategies could consider supplementation with beneficial nasal commensals, such as Dolosigranulum, after treatment to promote microbiome recovery.