Air microbiomes reveal presence of Shiga toxin-producing Escherichia coli in airborne cattle pen soil adjacent to large feedlot

Cattle are a reservoir for the zoonotic human foodborne pathogen Shiga toxin-producing Escherichia coli (STEC), the causative agent of many disease outbreaks associated with contaminated fresh leafy greens. Concentrated animal feeding operations (CAFOs) housing cattle generate fugitive dust, however the potential risk of STEC movement by means of the aerosolized dust is not well known. In this investigation, we used metagenome sequencing of air samples collected in an agricultural setting to investigate airborne transfer of STEC from a large CAFO to the surrounding area. Shiga toxin genes and other E. coli virulence genes were observed in air metagenomes, and their presence was positively correlated with abundance of cattle mitochondrial DNA (mtDNA). Air bacterial community composition differed based on STEC presence, and source tracking utilizing the air metagenomes indicated that cattle feedlot soil contributed to the air bacterial communities. Moreover, a novel biomarker for cattle pen soil, Corynebacterium maris, was identified that correlated with both E. coli virulence gene presence and cattle mtDNA abundance. Overall, our results demonstrate a definitive link between aerosolized cattle feedlot dust and airborne STEC transfer to adjacent and nearby agricultural fields. This work highlights the importance of including the potential for airborne transmission of pathogens in risk assessments for contamination by human foodborne pathogens of fresh produce grown in proximity to CAFOs.