First Metagenomic Survey of the Microbial Diversity in Bioaerosols Emitted in Waste Sorting Plants

Abstract

Waste sorting activities are source of occupational bioaerosol exposures that are associated with several health disorders. New analytical tools, based on next-generation sequencing (NGS) technologies, provide powerful methods to assess the microbial composition of bioaerosols. The objectives of the study were (i) to assess the feasibility and the repeatability of NGS-based biodiversity measurements and (ii) to study the microbial biodiversity using NGS in bioaerosols emitted in a waste sorting plant (WSP). Three stationary parallel samples were collected in a sorting cabin using closed-face cassettes equipped with polycarbonate membranes. Bacterial and fungal diversity was assessed by sequencing 16S and 18S rDNA genes using either Illumina sequencing or 454 pyrosequencing methods. At sampling point, airborne bacteria were dominated by Proteobacteria, Firmicutes, and Actinobacteria with prevailing genera assigned to unclassified Enterobacteriaceae, Staphylococcus, Acinetobacter, Leuconostoc, Pseudomonas, and Lactobacillus. Airborne fungi were dominated by Ascomycota with prevailing genera assigned to Penicillium, Aspergillus, Rhizopus, Wallemia, and Hemicarpenteles. The NGS biodiversity measurements revealed a higher biodiversity bioaerosols that previously reported for WSP in studies carried out using culture methods followed by identification of microorganisms. These results provide the first survey about taxonomic biodiversity in bioaerosols from WSPs using high-throughput sequencing.

Emerging Insights into the Occupational Mycobiome

“…Table 1 lists a collection of occupational studies that have employed ITS region sequencing and the fungal taxa most frequently identified. Working environments assessed using this methodological approach have included indoor office buildings [15–17], biomethanization plants [18], and biowaste sorting facilities [19, 20••], as well as agricultural commodity and harvesting operations [21–23] (Table 1). These studies have utilized either ITS clone library approaches or more recent high-throughput sequencing platforms such as Illumina MiSeq.…”

“…Clinically relevant fungal taxa placed in the order Pleosporales that expresses homologous Alt a 1 allergen [58] were identified in a wheat grain production facility and included Epicoccum nigrum , Alternaria ethzedia , and Didymella exitialis (Table 1) [22]. Sequences placed in the Basidiomycota were also resolved in these occupational environments and included the Agaricomycetes in biomethanization facilities [18], as well as Wallemia species and Cryptococcus victoriae in a waste sorting plant [19] and wheat production facility [22], respectively. Studies of outdoor biowaste and agricultural commodity processing demonstrate the ubiquity of pre-established fungal contaminants such as A. fumigatus but additionally highlight overlooked fungal sources placed in the Ascomycota and Basidiomycota to be more prevalent than previously estimated and contribute to worker exposures.…”

“…Further, the significance of these datasets has been highlighted in a recent consensus report titled “Microbes of the Built Environment” published in 2017 by the National Academies of Sciences, Engineering, and Medicine [14••]. In contrast, ITS region sequencing has only recently been employed in a limited number of occupational environments that have included indoor office buildings [15–17], biomethanization plants [18], and biowaste sorting facilities [19, 20••], as well as agricultural commodity and harvesting operations [21–23]. Although these initial studies have provided preliminary insights into occupational fungal exposures, the concordance between fungal communities across different occupational sectors currently remains unknown.…”

Aspergillus collected in specific indoor settings: their molecular identification and susceptibility pattern

“…There are some limitations in this study, including the use of screening media for passive sampling, wherein the number of obtained azole-resistant isolates belonging to the genus Aspergillus may be underestimated due to the dominance of other genera with faster growth rates (Degois et al 2017), such as the isolates belonging to Mucorales order (especially in the waste industry). As Mucorales are, in general, less susceptible to voriconazole, the growth of these species in voriconazole-screening media, may hinder the presence of Aspergillus (Springer et al 2016;Caetano et al 2018).…”

Bioaerosols and Transmission, a Diverse and Growing Community of Practice

“…Progress in the field has been stimulated by advances in other areas which have been applied to the study of infectious bioaerosols. These include: (a) enhanced detection by molecular methods, principally real-time and quantitative PCR, nextgeneration sequencing, metagenomics, and biosensors (25)(26)(27)(28)(29)(30), and (b) establishment of both conventional and novel infrastructure, such as small and large-scale wind tunnels, biocontained rotating drums for aging aerosols, and field-ready aerosol samplers (31)(32)(33). Ongoing research has also facilitated the development and dissemination of procedures and protocols for experimental work, including artificial aerosols, as well as animal models of transmission including the ferret model for influenza virus transmission and macaque model for Ebola virus transmission (34,35).…”