Metagenomic Detection of Viruses in Aerosol Samples from Workers in Animal Slaughterhouses

<div><p>Published studies have shown that workers in animal slaughterhouses are at a higher risk of lung cancers as compared to the general population. No specific causal agents have been identified, and exposures to several chemicals have been examined and found to be unrelated. Evidence suggests a biological aetiology as the risk is highest for workers who are exposed to live animals or to biological material containing animal faeces, urine or blood. To investigate possible biological exposures in animal slaughterhouses, we used a metagenomic approach to characterise the profile of organisms present within an aerosol sample. An assessment of aerosol exposures for individual workers was achieved by the collection of personal samples that represent the inhalable fraction of dust/bioaerosol in workplace air in both cattle and sheep slaughterhouses. Two sets of nine personal aerosol samples were pooled for the cattle processing and sheep processing areas respectively, with a total of 332,677,346 sequence reads and 250,144,492 sequence reads of 85 bp in length produced for each. Eukaryotic genome sequence was found in both sampling locations, and bovine, ovine and human sequences were common. Sequences from WU polyomavirus and human papillomavirus 120 were detected in the metagenomic dataset from the cattle processing area, and these sequences were confirmed as being present in the original personal aerosol samples. This study presents the first metagenomic description of personal aerosol exposure and this methodology could be applied to a variety of environments. Also, the detection of two candidate viruses warrants further investigation in the setting of occupational exposures in animal slaughterhouses.</p></div

Summary of mapping statistics for WU polyomavirus and human papillomavirus 120 sequences identified in the cattle processing area aerosol sample, when mapped to reference genomes GU296398.1 for WUPyV, and JQ963485.1 for HPV120, using the Bowtie 2 software [28].

<p>Summary of mapping statistics for WU polyomavirus and human papillomavirus 120 sequences identified in the cattle processing area aerosol sample, when mapped to reference genomes GU296398.1 for WUPyV, and JQ963485.1 for HPV120, using the Bowtie 2 software <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0072226#pone.0072226-Langmead1" target="_blank">[28]</a>.</p

Similarity plot comparing NZ2284 with all available prototype EV B strains and PV1.

<p>Schematic above the graph indicates the position of each gene within the EV genome.</p

Phylogenetic trees for each region of all available prototype EV B strains.

<p>Trees were rooted with PV1. Bootstrap values below 50 were removed. Bars indicate nucleotide substitution distance.</p

Identity of virus contigs as reported by BLASTN search against the non-redundant genbank nucleotide database, and subsequent taxonomic assignment by MEGAN.

<p>Identity of virus contigs as reported by BLASTN search against the non-redundant genbank nucleotide database, and subsequent taxonomic assignment by MEGAN.</p

Phylogenetic trees for each genome fragment of all available prototype EV B strains.

<p>Trees were rooted with PV1. Bootstrap values below 50 were removed. Bars indicate nucleotide substitution distance.</p