Fungal aerosols at dairy farms using molecular and culture techniques

Occupational exposure to harmful bioaerosols in industrial environments is a real threat to the workers. In particular, dairy-farm workers are exposed to high levels of fungal bioaerosols on a daily basis. Associating bioaerosol exposure and health problems is challenging and adequate exposure monitoring is a top priority for aerosol scientists. Using only culture-based tools does not express the overall microbial diversity and underestimate the large spectrum of microbes in bioaerosols and therefore the extended fungal profile that farmers are exposed to. The aim of this study was to provide an in-depth characterization of fungal exposure at Eastern Canadian dairy farms using qPCR and high-throughput sequencing methods. Specific primers were used for the quantification of Penicillium/Aspergillus and Aspergillus fumigatus in dairy farms air samples. Illumina Miseq sequencing of the ITS1 region provided sequences for the diversity analyses. The minimum and maximum concentration of Penicillium/Aspergillus ranged from 4.6 × 106 to 9.4 × 106 gene copies/m3 and from 1 × 104 gene copies/m3 to 4.8 × 105 gene copies/m3 for Aspergillus fumigatus, respectively. Differences in the diversity profiles of the five dairy farms support the idea that the novel approach identifies a large number of fungal taxa. The most striking differences include Microascus, Piptoporus, Parastagonospora, Dissoconium, Microdochium, Tubilicrinis, Ganoderma, Ustilago, Phlebia and Wickerhamomyces. The presence of a diverse portrait of fungi in air may represent a health risk for workers who are exposed on a daily basis. The broad spectrum of fungi detected in this study includes many known pathogens like Aspergillus, Acremonium, Alternaria and Fusarium. Adequate monitoring of bioaerosol exposure is necessary to evaluate and minimize risks. [Display omitted] •Molecular and culture techniques enable the study of fungal diversity in aerosols from dairy farms•A practical bioinformatics workflow is described for the treatment of raw sequencing reads and diversity analyses•The type of cattle feed and animal confinement influence fungal composition of aerosols•Culture techniques underestimate fungal diversity compared to high-throughput sequencing•Molecular techniques allow the description of fungal diversity in aerosols for a better assessment of occupational exposure