Clinical Predictors of Nose/Throat Bacteriome and Fungal Colonization in Skilled Nursing Facility Residents

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 subacute care in a skilled nursing facility (SNF).

We collected combined nose/throat swab samples from 301 adults every 3 days for up to 5 visits. Bacteriome composition was detected via 16S ribosomal RNA amplicon sequencing and C. albicans colonization by quantitative polymerase chain reaction. Functional potential was inferred using PICRUSt2 software. We used ADAPT (Analysis of Microbiome Differential Abundance by Pooling Tobit Models) software to evaluate bacteriome compositional and functional differences based on C. albicans colonization, adjusting for age, sex, antibiotic exposure, and medical device presence.

C. albicans colonization was more common among participants with devices and antibiotic use, but this difference was not statistically significant. Participants had mean age of 77 years, 63.8% were female, 48.5% received antibiotics, and 20.3% had a medical device at entry. Nose/throat bacteriome was significantly less diverse and rich in the presence of C. albicans, antibiotic exposure, and device use (P < .05), but composition varied little during follow-up. With C. albicans, predicted bacteriome function favored acid-tolerant, biofilm-forming species (Scardovia wiggsiae and Lactobacillus fermentum; P < .01), and depleted glycolate degradation (log10 fold change, -0.45; adjusted P = .01).

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.