J Infect Dis. 2026 Mar 16:jiag166. doi: 10.1093/infdis/jiag166. Online ahead of print.
ABSTRACT
BACKGROUND: Microbiomes resist or facilitate pathogen invasion and modulate host immune responses and infection susceptibility. We describe nose/throat bacteriome composition and predicted functional changes associated with Candida albicans colonization, antibiotic use, and medical devices among adults receiving short-term sub-acute care in a skilled nursing facility (SNF).
METHODS: We collected combined nose/throat swabs from 301 adults every three days for up to five visits. Bacteriome composition was detected via 16S rRNA amplicon sequencing and C. albicans colonization by qPCR. Functional potential was inferred using PICRUSt2. We used ADAPT software to evaluate bacteriome compositional and functional differences by C. albicans colonization adjusting for age, sex, antibiotic exposure, and medical device presence.
RESULTS: C. albicans colonization was more common among participants with devices and antibiotic use, but not statistically significantly. Participants had mean age 77 years, 63.8% female, 48.5% received antibiotics, and 20.3% had device at entry. Nose/throat bacteriome was significantly less diverse and rich in the presence of C. albicans, antibiotic exposure, and device use (p<0.05), but composition varied little during follow-up. With C. albicans, predicted bacteriome function favored acid-tolerant, biofilm-forming species (S. wiggsiae, L. fermentum; p<0.01), and depleted glycolate degradation (log10fold change -0.45; adjusted p=0.01).
CONCLUSION: Nose/throat bacteriome composition and function were significantly associated with C. albicans colonization and C. albicans colonization was strongly associated with antibiotic exposure and medical device use. These findings underline the importance of integrating fungal colonization assessment and clinical factors into microbiome studies aimed at preserving bacteriome resilience and reducing infection risk in vulnerable populations.
PMID:41839646 | DOI:10.1093/infdis/jiag166
