Impact of seasonal variations on microbiome diversity and antibiotic resistance in aerosolized bacteria in a dairy facility

Abstract

The development and spread of antibiotic resistant bacteria (ARB) pose a serious threat to animal and human health. This is especially relevant to open-stall dairy farms where environmental factors play a significant role. This study identified the presence of ARB and their dissemination within a dairy farm over three seasons. The effect of environmental factors – temperature, relative humidity, and wind – on bacterial microbiome diversity and antibiotic resistance in aerosol and manure samples were investigated. Manure and aerosol samples were collected at two different visits. QIIME2 analysis showed that Firmicutes was the most abundant phylum (49%) followed by Proteobacteria (29%), Actinobacteriota (17%), and Bacteroidota (4%) in all samples. Kirby-Bauer disk diffusion tests revealed that all manure samples were resistant to eight different antibiotics even though the dairy cows were not fed antibiotics. The strongest antibiotic resistance in aerosol samples was found during winter compared to other seasons. Winter aerosol samples had the lowest microbiome diversity, but the strongest antibiotic resistance. Antibiotic resistance mapping indicates that ARB were transported with the wind generated from axial fans and natural ventilation. It was shown that low temperatures and wind correspond with increased antibiotic resistance and spread of ARB in the environment.