Within-species phenotypic resistance rather than community turnover tracks antimicrobial usage in Staphylococcus aureus on swine farms.

Bioaerosol-mediated transfer of antimicrobial-resistant bacteria from swine farms to workers represents a poorly quantified occupational hazard. Whether farm-level antimicrobial usage track resistance through community-level taxonomic turnover or through within-species phenotypic differences remains unclear. Existing occupational risk assessments also lack phenotypic resistance resolution and corrections for microbial viability. Here, we performed antimicrobial susceptibility testing of 962 isolates across six species from six Korean swine farms stratified by defined daily dose for animals (DDDvet), four compartments (fecal, aerosol, pig nasal, worker nasal), and two seasons. Flow cytometric viability and quantitative polymerase chain reaction (qPCR)-corrected abundance data were integrated into a Monte Carlo quantitative microbial risk assessment (QMRA) for occupational Staphylococcus aureus nasal colonization. Isolate-level resistance was higher on high-usage farms for S. aureus but not for the other four species, a species-selective pattern that six farms could not resolve at the farm level, and community composition showed no detectable association with usage. Escherichia abundance declined by approximately four orders of magnitude during aerosolization, whereas Staphylococcus persisted and was highest in worker nasal samples. QMRA estimated median daily colonization probabilities of 1.98 × 10-4 to 8.63 × 10-4, exceeding the per-working-day equivalent of the U.S. EPA infection risk benchmark by 2.7 to 3.3 orders of magnitude, although colonization and infection are distinct outcomes. Annualized colonization probability reached 19.4% in the highest-risk scenario under the reference dose-response parameter, and the daily probability ratio between the highest-risk and lowest-risk scenarios was 4.4 and insensitive to that parameter. The model was most sensitive to aerosol genus composition rather than to total bioaerosol load. These findings shift airborne AMR research from gene abundance and total exposure load toward species-resolved phenotypic ecology and composition-driven occupational risk assessment in intensive livestock systems.