Potential Roles of the Nasal Microbiome in Pathogen Exposures in Dairy Workers

Objective: Livestock workers are exposed to bioaerosols comprising pathogens including influenza D virus (IDV), influenza A (IAV), and methicillin-resistant Staphylococcus aureus (MRSA), all of which can colonize the upper airways (e.g., anterior nares) and pose public health risks. The role of the nasal microbiome in occupational exposure is not well understood. Methods: Here, we characterized the nasal microbiomes of US dairy workers to investigate the microbiome’s effects on pathogen carriage. We collected 237 lavages from 31 dairy workers to determine the presence of influenzas A, C, and D; methicillin-susceptible Staphylococcus aureus (MSSA); and MRSA. Nasal lavages were analyzed via PCR to quantify workers’ nasal microbiomes, and differences in microbiome characteristics were analyzed according to pathogen presence. Results: Overall, 32.1% of lavages tested positive for MSSA, 11.4% tested positive for MRSA, 17.3% tested positive for IDV, 2.5% tested positive for IAV, and 1.3% tested positive for ICV. Nasal samples positive for IAV and those positive for MSSA clustered separately with robust Aitchison PCA, but no significant differences in alpha diversity were observed. Differential abundance analysis revealed significant differences in genera among lavages testing positive for MRSA, MSSA, IDV, and IAV (e.g., Staphylococcus , Streptococcus , and Bacillus ). Conclusions: Future work is needed to ascertain whether the microbiome might protect against pathogen exposures among livestock workers.