Characterization and Functional Analysis of the Oropharyngeal Microbiome in ICU staff via Metagenomic Sequencing

Abstract Background ICU staff face an elevated risk of colonization by drug-resistant bacteria, potentially associated with persistent occupational exposure to hospital environments. The oropharynx, as a key ecological niche at the interface of the respiratory and digestive tracts, serves as an important reservoir for opportunistic pathogens. This study employed shotgun metagenomic sequencing to systematically characterize the composition and functional profiles of the oropharyngeal microbiota in ICU staff. Methods A cross-sectional study was conducted, enrolling 10 full-time ICU staff (with ≥ 5 years of clinical experience) and 10 healthy non-medical controls with no history of medical-related employment. Oropharyngeal swabs were collected for metagenomic sequencing. Multi-dimensional comparative analyses were conducted between the two groups, covering community structure, taxonomic composition, KEGG metabolic pathways, virulence factor profiles, and antibiotic resistance gene (ARG) profiles. Results Compared with the control group, ICU staff exhibited significantly reduced genus-level richness (Chao1 index) but elevated community evenness, resulting in higher Shannon and Simpson indices, with a clearly distinct overall microbial community structure. The abundances of potential pathogenic genera including Pseudomonas, Streptococcus, Escherichia, Mycobacteroides, and Helicobacter were significantly enriched, whereas core oral commensal genera such as Prevotella were depleted. Functionally, ICU staff exhibited significant enrichment in bacterial biofilm formation, drug metabolism–cytochrome P450, and ABC transporter pathways; marked upregulation of virulence factors associated with adhesion, immune evasion, and endotoxin biosynthesis; and elevated abundances of five resistance genes primarily derived from Streptococcus and Haemophilus species (mel, patB, mdtG, hmrM, and rlmA(II)). Conclusion ICU occupational exposure is associated with systematic remodeling of the oropharyngeal microbiota, characterized by depletion of core oral commensals and enrichment of opportunistic pathogens. Functionally, this remodeling supports the formation of a potential synergistic resistance system of "biofilm barrier–P450 metabolic inactivation–ABC active efflux," providing novel metagenomic evidence for microbiome-based surveillance and occupational health protection of healthcare workers.