Does the organic status impact air quality, microbial communities, and antimicrobial resistance genes in egg farms?

By 2036, Canadian egg farmers will have replaced conventional cage systems with alternative housing. Alternative housing, such as aviaries, provides hens with more room to roam and enrichments, enabling natural behaviours and improving welfare. Organic egg production is also increasing, limiting the use of antibiotics and providing added enrichments. However, added litter, increased movement and flock size in aviary systems generate more bioaerosols and particulate matter (PM) compared to caged housing. Despite this, microbiological risks associated with organic systems remain poorly documented in contrast to other alternative systems.

This study compares PM concentrations, microbial communities, bacterial diversity, and antimicrobial resistance genes (ARG) in organic and non-organic farm environments. Four aviary-style egg farms (two organic, two free run/non-organic), were sampled three times within a year (winter and summer 2024; winter 2025). Air, litter, and egg wash samples were collected, and PM concentrations were measured. Indicator and pathogenic taxa were assessed with quantitative PCR (qPCR), while high-throughput qPCR assessed ARG profiles. Amplicon sequencing evaluated bacterial diversity.

Overall, results do not indicate trends driven by farm status (organic vs. non-organic), but rather by farm-specific factors such as hen age, density, and litter presence. For example, Enterococcus spp. quantified by qPCR was detected at significantly higher levels on egg surfaces in organic farms, while concentrations were higher in non-organic farms for air and litter samples. Different patterns emerged in ARG profiles, with certain genes found exclusively in non-organic farms. Patterns also varied across substrate, with several ARG absent in litter samples yet present in air and egg washes. Bacterial diversity analyses are ongoing, but preliminary ordination analysis shows that samples cluster according to farm, suggesting a strong farm-level effect on bacterial community composition.

Ultimately, these findings will help fill critical knowledge gaps in our understanding of microbial communities in organic egg production.