Fan Exhaust Air Sampling of Livestock Operations as a Proxy for Indoor Bioaerosol Monitoring

Fan exhaust air sampling is a reliable monitoring proxy for indoor bioaerosols from livestock operations. Air samples collected indoors and at fan exhaust have highly similar bacterial diversity. At low indoor concentrations, specific microbial markers are still detectable in the air collected at the fan exhaust.

The incidence of animal and zoonotic diseases is expected to increase in the coming years, imposing the reinforcement of biosecurity measures for livestock operations. Airborne transmission of certain infectious agents underscores the importance of surveilling bioaerosols. However, having access to livestock operations for monitoring purposes is now challenging. Hence, it has become imperative to explore alternative strategies to assess indoor bioaerosols. This study aimed to compare bacterial diversity and quantify microbial markers found in bioaerosols indoors and at the fan exhausts of pig-finishing buildings (PFBs) and broiler chicken barns (BCBs). Bioaerosols were collected using a filter-based, high-flow rate air sampler in 12 facilities (10 PFBs and 2 BCBs) during the warm season in Eastern Canada, corresponding to maximal ventilation rate operations. Four farms-PFB-1, PFB-2, BCB-1, and BCB-2-were visited multiple times, while the other eight PFBs (PFB-3 to PFB-10) were visited once. At each farm, indoor air samples were paired with samples from the corresponding sidewall extraction fans. Amplicon-based sequencing and quantitative PCR (qPCR) were performed to describe bacterial diversity and quantify specific microbial (bacterial and archaeal 16S rRNA genes, Enterococcus spp., and a phage of Aerococcus viridans) and animal (swine and poultry DNA) markers. No significant differences in OTUs abundance and diversity between indoor bioaerosols and their corresponding fan exhaust samples were observed. There were also no significant differences between an indoor and its corresponding fan exhaust air sample when comparing OTUs relative abundance and their presence-absence. Similarly, concentrations of bacterial 16S rRNA genes in indoor samples (10⁶-10⁸) did not significantly differ from those found in samples collected at the fan exhaust (10⁵-10⁸) for both PFBs and BCBs. Strong correlations were observed between sampling sites for Archaea, Enterococcus, and A. viridans phage concentrations while poultry and swine DNA concentrations at fan exhausts did not correlate with indoor levels. All investigated markers were detectable at fan exhausts, even at low indoor concentrations (10²-10³). Our study suggests that air sampling at the fan exhaust of barns provides a representative picture of the indoor bioaerosols both for bacterial diversity and barn-specific indicators when the fans are in use. This method appears promising for characterizing indoor air quality based on emissions and could be highly valuable in cases where biosecurity measures or outbreaks restrict access to barns.