Microbial diversity in bioaerosol samples causing ODTS compared to reference bioaerosol samples as measured using Illumina sequencing and MALDI-TOF

Characterization of bioaerosol exposures in wastewater treatment plant workers and serum levels of lung and inflammatory markers

Wastewater treatment plant (WWTP) workers are exposed to bioaerosols containing bacteria, fungi, and endotoxin, potentially posing health risks to workers. This study quantified personal exposure levels to airborne bacteria and fungi, endotoxin, and dust among 44 workers during two seasons at four WWTPs. Associations between the exposure measurements and serum levels of biomarkers CRP, SAA, and CC16 were also assessed. The potential deposition of viable microorganisms in workers' airways were explored using stationary fractionating samplers. Microbial communities were characterized using long-read nanopore amplicon sequencing and MALDI-TOF mass spectrometry to identify species, including pathogenic or allergenic microorganisms. We found that bacterial and fungal exposure levels were significantly associated with work task (p < 0.001 and p = 0.00041, respectively), with high exposure variability within and between tasks. Workshop, sewer system inspection, and sewer cleaning were associated with the highest exposure levels. A significant positive correlation was found between CRP and bacterial exposure (p = 0.013), while significant negative correlations were found between CRP and endotoxin and dust exposures (p = 0.012 and p = 0.018, respectively). No significant associations were found between SAA or CC16 and the exposure measures. Microbial community composition in bioaerosols differed significantly between some work tasks while others showed similar compositions. Viable hazardous microorganisms such as Clostridium perfringens and Aspergillus fumigatus were found in workers' exposures and in respiratory fractions of stationary air samples, indicating potential lung deposition. Further research is needed to assess possible long-term health risks from bioaerosol exposure at WWTPs.

Selective transmission of airborne bacterial communities from the ocean to the atmosphere over the Northern Pacific Ocean

This study simultaneously measured the taxonomic diversity of bacterial communities in both seawater and PM2.5 aerosol samples collected from the Northern Pacific Ocean during a cruise covering 7724 km between 37°N 126°E and 58°N 179°E. The relative abundance of Proteobacteria, Cyanobacteria, and Firmicutes were found to be more prevalent in aerosol samples (39 ± 16 %, 5.1 ± 1.9 %, and 3.2 ± 1.7 %, respectively) than in seawater samples (26 ± 9 %, 3.8 ± 1.7 %, and 0.02 ± 0.09 %, respectively). The preferential aerosolization of bacterial communities such as Proteobacteria and Firmicutes was likely to be accompanied by a terrestrial origin and high hydrophobicity. Cyanobacteria could undergo increased aerosolization, possibly because of their smaller size in the significantly higher salinity open ocean (32.8 ± 0.14 PSU) compared to those in lower salinity coastal areas (31.3 ± 1.4 PSU). The results of this study indicated that bacterial properties substantially affect their transfer from the ocean to the atmosphere, possibly influencing climate change and public health.

Fungal and bacterial species on biowaste workers' hands and inhalation zone, and potential airway deposition

This study aims to investigate the microbiological working environment of biowaste workers, focusing on airborne fungal and bacterial species exposure, size distribution, and species on workers' hands. The research, conducted across six plants with 45 personal exposure assessments, revealed a total of 150 bacterial species and 47 fungal species on workers' hands, including 19 and 9 species classified in risk class 2 (RC2), respectively. Workers' exposure analysis identified 172 bacterial and 32 fungal species, with several in RC2. In work areas, 55 anaerobic bacterial species belonging to RC2 were found. Different species compositions were observed in various particle size fractions, with the highest species richness for anaerobic bacteria in the fraction potentially depositing in the secondary bronchi and for fungi in the pharynx fraction. The geometric mean aerodynamic diameter (DG) of RC2 anaerobic bacteria was 3.9 µm, <1.6 µm for Streptomyces, 3.4 µm for Aspergillus, and 2.0 µm for Penicillium. Overlapping species were identified on workers' hands, in their exposure, and in work areas, with Bacillus amyloliquefaciens, Leuconostoc mesenteroides, Bacillus cereus, Enterococcus casseliflavus, and Aspergillus niger consistently present. While the majority of RC2 bacterial species lacked documented associations with occupational health problems, certain bacteria and fungi, including Bacillus cereus, Escherichia coli, Enterobacter, Klebsiella pneumonia, Aspergillus fumigatus, Aspergillus niger, Aspergillus flavus, Lichtheimia corymbifera, Lichtheimia ramosa, and Paecilomyces variotii, have previously been linked to occupational health issues. In conclusion, biowaste workers were exposed to a wide range of microorganisms including RC2 species which would deposit in different parts of the airways.

Exposure to resistant fungi across working environments and time

Antifungal resistance has emerged as a significant health concern with increasing reports of resistant variants in previously susceptible species. At present, little is known about occupational exposure to antifungal-resistant fungi. This study aimed to investigate Danish workers' occupational exposure to airborne fungi resistant to first-line treatment drugs. A retrospective study was performed on a unique collection of personal exposure samples gathered over a twenty-year period from Danish working environments, in sectors including agriculture, animal handling, waste management, and healthcare. A total of 669 samples were cultivated at 37 °C and fungal colonies were identified using MALDI-TOF MS. Subsequently, identification was confirmed by amplicon sequencing the genes of calmodulin and beta-tubulin to unveil potential cryptic species. Infectious fungi (495 isolates from 23 species) were tested for resistance against Itraconazole, Voriconazole, Posaconazole, and Amphotericin B. Working environments were highly variable in the overall fungal exposure, and showed vastly different species compositions. Resistance was found in 30 isolates of the species Aspergillus fumigatus (4 of 251 isolates), A. nidulans (2 of 13), A. niger complex (19 of 131), A. versicolor (3 of 18), and A. lentulus (2 of 2). Sequence analysis revealed several cryptic species within the A. niger complex including A. tubingensis, A. luchuensis, and A. phoenicis. Among the resistant A. fumigatus isolates, two contained the well-described TR34/L98H mutation in the cyp51A gene and promoter region, while the remainder harbored silent mutations. The results indicate that the working environment significantly contributes to exposure to resistant fungi, with particularly biofuel plant workers experiencing high exposure. Differences in the prevalence of resistance across working environments may be linked to the underlying species composition.

A comprehensive review of microbial contamination in the indoor environment: sources, sampling, health risks, and mitigation strategies

The quality of the indoor environment significantly impacts human health and productivity, especially given the amount of time individuals spend indoors globally. While chemical pollutants have been a focus of indoor air quality research, microbial contaminants also have a significant bearing on indoor air quality. This review provides a comprehensive overview of microbial contamination in built environments, covering sources, sampling strategies, and analysis methods. Microbial contamination has various origins, including human occupants, pets, and the outdoor environment. Sampling strategies for indoor microbial contamination include air, surface, and dust sampling, and various analysis methods are used to assess microbial diversity and complexity in indoor environments. The review also discusses the health risks associated with microbial contaminants, including bacteria, fungi, and viruses, and their products in indoor air, highlighting the need for evidence-based studies that can relate to specific health conditions. The importance of indoor air quality is emphasized from the perspective of the COVID-19 pandemic. A section of the review highlights the knowledge gap related to microbiological burden in indoor environments in developing countries, using India as a representative example. Finally, potential mitigation strategies to improve microbiological indoor air quality are briefly reviewed.

Occupational exposure to inhalable pathogenic microorganisms in waste sorting

This study assessed microorganisms in personal inhalable work air samples aiming to identify potential human pathogens, and correlate exposure to adverse health outcomes in waste workers. Full-shift personal exposure was measured in six different waste sorting plants. Microbial concentrations in inhalable air samples were analysed using MALDI-TOF MS for cultivable, and next generation sequencing (NGS) for non-cultivable microorganisms. Concentrations of bacterial and fungal CFUs varied substantially within and between waste sorting plants, ranging from no identifiable organisms to a maximum concentration in the order of 105 CFU/m3. Bacillus and Staphylococcus were among the most abundant bacterial genera, whilst fungal genera were dominated by Aspergillus and Penicillium. Approximately 15% of all identified species were human pathogens classified in risk group 2, whereas 7% belonged to risk group 1. Furthermore, significant correlations between concentrations of fungi in risk group 1 and self-reported adverse symptoms, such as wheezing were identified in exposed workers. The combination of culture-based methods and NGS facilitated the investigation of infectious microbial species with potential pathophysiological properties as well as non-infectious biological agents in inhalable work air samples and thereby contributed to the risk assessment of occupational exposure in waste sorting.

Airborne transmission of biological agents within the indoor built environment: a multidisciplinary review

The nature and airborne dispersion of the underestimated biological agents, monitoring, analysis and transmission among the human occupants into building environment is a major challenge of today. Those agents play a crucial role in ensuring comfortable, healthy and risk-free conditions into indoor working and leaving spaces. It is known that ventilation systems influence strongly the transmission of indoor air pollutants, with scarce information although to have been reported for biological agents until 2019. The biological agents' source release and the trajectory of airborne transmission are both important in terms of optimising the design of the heating, ventilation and air conditioning systems of the future. In addition, modelling via computational fluid dynamics (CFD) will become a more valuable tool in foreseeing risks and tackle hazards when pollutants and biological agents released into closed spaces. Promising results on the prediction of their dispersion routes and concentration levels, as well as the selection of the appropriate ventilation strategy, provide crucial information on risk minimisation of the airborne transmission among humans. Under this context, the present multidisciplinary review considers four interrelated aspects of the dispersion of biological agents in closed spaces, (a) the nature and airborne transmission route of the examined agents, (b) the biological origin and health effects of the major microbial pathogens on the human respiratory system, (c) the role of heating, ventilation and air-conditioning systems in the airborne transmission and (d) the associated computer modelling approaches. This adopted methodology allows the discussion of the existing findings, on-going research, identification of the main research gaps and future directions from a multidisciplinary point of view which will be helpful for substantial innovations in the field.

A cross sectional study on airborne inhalable microorganisms, endotoxin, and particles in pigeon coops - Risk assessment of exposure

Pigeon breeding is associated with symptoms of the airways. The aim of this study is to illuminate the bacteriological and toxicological characteristics of airborne dust in pigeon coops. Airborne dust was sampled in 31 urban pigeon coops with homing and fancy pigeons, and following the dust was characterized. In total 141 different bacterial species were identified using MALDI-TOF MS, and of these 11 species are classified in risk group 2. Of the cultivable bacteria, Staphylococcus equorum was present in the highest concentration. Microorganisms in the dust were able to form biofilm, and the amount correlated positively with the number of bacteria. Next generation sequencing showed 180 genera with Acinetobacter in highest reads. On average 999 ± 225 ZOTUs were observed per sample with a Shannon-Wiener biodiversity index of 6.17 ± 0.24. Of the identified species the following have previously been suggested as causative agents of extrinsic allergic alveolitis: Alcaligenes faecalis, Bacillus subtilis, Pantoea agglomerans, Sphingobacterium spiritivorum, Thermoactinomyces sp., and Streptomyces albus. Staphylococcus was present on particles with sizes between 1.1 and > 7.0 μm with a geometric mean diameter of particles on 4.7 ± 1.1 μm. Concentrations of airborne endotoxin and dust were elevated compared to references, and the geometric mean concentrations were 102 EU/m³ and 1.07 mg dust/m³, respectively. Upon exposure to the airborne dust human granulocytes produced Reactive Oxidative Species during the first 5 min, and then no further reaction was observed. The concentrations of bacteria in general, Staphylococcus spp., and endotoxin and biodiversity were associated significantly with season, temperature and/or relative humidity, but not with type or density of pigeons. The bacterial composition and biodiversity indices were not affected by type of pigeon. In conclusion, the exposure to bacteria and endotoxin in pigeon houses should not be neglected in the evaluation of causative agents of airways symptoms among pigeon breeders.

Work clothes as a vector for microorganisms: Accumulation, transport, and resuspension of microorganisms as demonstrated for waste collection workers

Work clothes may act as a vector for the transport of microorganisms leading to second-hand exposure; however, this has not been studied in work environments. We investigated whether microorganisms accumulate on workers' clothes in environments with elevated microbial exposures, and whether they are transported with the clothes and subsequently resuspended to the air. To study this, we selected waste collection workers and potential transport of bacteria and fungi to waste truck cabs via clothes, and compared the microbial communities within truck cabs, in waste collection workers' personal exposure, and on clean T-shirts worn by the workers. Microbial communities were also investigated for the presence of potentially harmful microorganisms. Results showed that microorganisms accumulated in large quantities (GM = 3.69 × 10⁵ CFU/m²/h for bacteria, GM = 8.29 × 10⁴ CFU/m²/h for fungi) on workers' clothes. The concentrations and species composition of airborne fungi in the truck cabs correlated significantly with the accumulation and composition of fungi on clothes and correlated to concentrations (a trend) and species composition of their personal exposures. The same patterns were not found for bacteria, indicating that work clothes to a lesser degree act as a vector for bacteria under waste collection workers' working conditions compared to fungi. Several pathogenic or allergenic microorganisms were present, e.g.: Klebsiella oxytoca, K. pneumoniae, Proteus mirabilis, Providencia rettgeri, Pseudomonas aeruginosa, and Aspergillus fumigatus, A. glaucus, A. nidulans, A. niger, and various Penicillium species. The potential 'take-home' exposure to these microorganisms are of most concern for immunocompromised or atopic individuals or people with open wounds or cuts. In conclusion, the large accumulation of microorganisms on workers' clothes combined with the overlap between fungal species for the different sample types, and the presence of pathogenic and allergenic microorganisms forms the basis for encouragement of good clothing hygiene during and post working hours.

Sex-Specific Differences in Resolution of Airway Inflammation in Fat-1 Transgenic Mice Following Repetitive Agricultural Dust Exposure

In agriculture industries, workers are at increased risk for developing pulmonary diseases due to inhalation of agricultural dusts, particularly when working in enclosed confinement facilities. Agricultural dusts inhalation leads to unresolved airway inflammation that precedes the development and progression of lung disease. We have previously shown beneficial effects of the omega-3 polyunsaturated fatty acid (ω-3 PUFA) DHA in protecting against the negative inflammatory effects of repetitive dust exposure in the lung. Dietary manipulation of pulmonary disease risk is an attractive and timely approach given the contribution of an increased ω-6 to ω-3 PUFA ratio to low grade inflammation and chronic disease in the Western diet. To prevent any confounding factors that comes with dietary supplementation of ω-3 PUFA (different sources, purity, dose, and duration), we employed a Fat-1 transgenic mouse model that convert ω-6 PUFA to ω-3 PUFA, leading to a tissue ω-6 to ω-3 PUFA ratio of approximately 1:1. Building on our initial findings, we hypothesized that attaining elevated tissue levels of ω-3 PUFA would attenuate agricultural dust-induced lung inflammation and its resolution. To test this hypothesis, we compared wild-type (WT) and Fat-1 transgenic mice in their response to aqueous extracts of agricultural dust (DE). We also used a soluble epoxide hydrolase inhibitor (sEH) to potentiate the effects of ω-3 PUFA, since sEH inhibitors have been shown to stabilize the anti-inflammatory P450 metabolites derived from both ω-3 and ω-6 PUFA and promote generation of specialized pro-resolving lipid mediators from ω-3 PUFA. Over a three-week period, mice were exposed to a total of 15 intranasal instillations of DE obtained from swine confinement buildings in the Midwest. We observed genotype and sex-specific differences between the WT vs. Fat-1 transgenic mice in response to repetitive dust exposure, where three-way ANOVA revealed significant main effects of treatment, genotype, and sex. Also, Fat-1 transgenic mice displayed reduced lymphoid aggregates in the lung following DE exposure as compared to WT animals exposed to DE, suggesting improved resilience to the DE-induced inflammatory effects. Overall, our data implicate a protective role of ω-3 FA in the lung following repetitive dust exposure.

Review of biological risks associated with the collection of municipal wastes

In many countries, the management of household waste has recently changed with an increased focus upon waste sorting resulting in lower collection frequency for some waste fractions. A consequence of this is the potential for increased growth of microorganisms in the waste before collection, which can lead to an increased exposure via inhalation for waste collection workers. Through a review of the literature, we aimed to evaluate risks caused by waste collecting workers' exposure to bioaerosols and to illuminate potential measures to reduce the exposure. Across countries and waste types, median exposure to fungi, bacteria, and endotoxin were typically around 10⁴ colony forming units (cfu)/m³, 10⁴ cfu/m³, and 10 EU/m³, respectively. However, some studies found 10-20+ times higher or lower median exposure levels. It was not clear how different types of waste influence the occupational exposure levels. Factors such as high loading, ventilation in and cleaning of drivers' cabs, increased collection frequency, waste in sealed sacks, and use of hand sanitizer reduce exposure. Incidences of gastrointestinal problems, irritation of the eye and skin and symptoms of organic dust toxic syndrome have been reported in workers engaged in waste collection. Several studies reported a correlation between bioaerosol exposure level and reduced lung function as either a short or a long term effect; exposure to fungi and endotoxin is often associated with an inflammatory response in exposed workers. However, a better understanding of the effect of specific microbial species on health outcomes is needed to proceed to more reliable risk assessments. Due to the increasing recycling effort and to the effects of global warming, exposure to biological agents in this working sector is expected to increase. Therefore, it is important to look ahead and plan future measures as well as improve methods to prevent long and short-term health effects.

Occupational exposure to fungi on recyclable paper pots and growing media and associated health effects - A review of the literature

Different types of pots and growing and casing media, including biodegradable materials, are used for plant and mushroom production. The fungus Peziza ostracoderma has gained attention for its visible growth on growing media for plants and casing media for mushrooms. Through a review of the literature we aim to evaluate whether exposure to fungi from recyclable pots and different growing and casing media occurs and causes occupational health effects. Based on the published papers, specific fungal species were not related to a specific medium. Thus P. ostracoderma has been found on paper pots, peat, sterilized soil, vermiculite, and rockwool with plants, and on peat, pumice, and paper casing for mushrooms. It has been found in high concentrations in the air in mushroom farms. Also Acremonium spp., Aspergillus niger, A. fumigatus, Athelia turficola, Aureobasidium pullulans, Chaetomium globosum, Chrysonilia sitophila, Cladosporium spp., Cryptostroma corticale, Lecanicillium aphanocladii, Sporothrix schenckii, Stachybotrys chartarum, and Trichoderma spp. have been found on different types of growing or casing media. Most of the fungi have also been found in the air in greenhouses, but the knowledge about airborne fungal species in mushroom farms is very limited. Eight publications describe cases of health effects associated directly with exposure to fungi from pots or growing or casing media. These include cases of hypersensitivity pneumonitis caused by exposure to: A. fumigatus, A. niger, Au. pullulans, Cr. corticale, P. ostracoderma, and a mixture of fungi growing on different media. Different approaches have been used to avoid growth of saprophytes including: chemical fungicides, the formulation of biodegradable pots and growing media and types of peat. To increase the sustainability of growing media different types of media are tested for their use and with the present study we highlight the importance of also considering the occupational health of the growers who may be exposed to fungi from the media and pots.

A characterization of bioaerosols in biowaste pretreatment plants in relation to occupational health

Occupational exposure to microorganisms can be associated with adverse health outcomes. In this study, we assessed exposure to bioaerosols in two biowaste pretreatment plants in Denmark, which differed in location (city or countryside) and how they were built ('closed-off processes' or 'open processes'). Bioaerosol exposures were characterized by microbial concentrations in personal, stationary, sedimented dust, and hand samples, and their size distribution was assessed. Furthermore, species were identified by matrix-assisted laser desorption-ionisation time-of-flight mass spectrometry (MALDI-TOF MS), and inhalable dust, endotoxin, biofilm production, the total inflammatory potential, and fungicide resistance to four fungicides (amphotericin B, caspofungin acetate, itraconazole, voriconazole) were determined. Bacterial and fungal concentrations were on average (GM) in the order of 10⁴ cfu/m³, but ranged from 10² to 10⁸ cfu/m³. Several species which may cause health problems were identified. Personal endotoxin exposures were on average 28 EU/m³, but both personal and stationary samples ranged from 0.6 to 2035 EU/m³. Bioaerosols had the potential to form biofilms and to induce inflammation as measured in a human cell line. Exposures were higher in the plants that outdoor reference values. Higher exposures were found in the 'open process' plant, such as in microbial concentrations, species richness, endotoxin, biofilm production, and the total inflammatory potential. Six out of 28 tested Aspergillus fumigatus isolates were resistant to fungicides (amphotericin B and voriconazole). In conclusion, there is a high exposure to bioaerosols during work in biowaste pretreatment plants, however, results also suggests that how the plant is built and functions may affect the exposures.

Toxicity studies of Aspergillus fumigatus administered by inhalation to B6C3F1/N mice (revised)

Aspergillus fumigatus is a thermotolerant, soil-borne fungal species that is ubiquitous in the environment. Mold was nominated to the National Toxicology Program (NTP) by a private individual due to suspected adverse health effects associated with personal exposure in indoor and occupational settings. A. fumigatus is of particular concern in the biowaste industry as the species can contaminate self-heating compost piles. Because of this potential for personal and occupational exposure and the lack of available toxicity data, toxicity studies were conducted in which male and female B6C3F1/N mice were exposed to A. fumigatus conidia (spores) two times a week for 3 months. All in-life procedures, including inhalation exposure, test article preparation, and hematology analysis, were completed by the National Institute for Occupational Safety and Health (NIOSH, Morgantown, WV). Battelle (Columbus, OH) conducted terminal necropsies, measured terminal body and organ weights, and evaluated gross lesions on-site at NIOSH. Tissue processing and histopathology were completed at Battelle. Grocott's methenamine silver (GMS) staining was performed at NIOSH. Genetic toxicology studies on mouse peripheral blood erythrocytes were conducted by Integrated Laboratory Systems, LLC (Research Triangle Park, NC). (Abstract Abridged).

A cohort study of cucumber greenhouse workers' exposure to microorganisms as measured using NGS and MALDI-TOF MS and biomarkers of systemic inflammation

Work in greenhouses entails exposure to airborne fungi and bacteria. The aims of this study are to obtain knowledge about whether exposure to fungal and bacterial genera and species during work in a cucumber greenhouse is affected by work tasks, and whether a cohort of greenhouse workers' serum levels of serum amyloid A (SAA) and C-reactive protein (CRP), biomarkers of systemic inflammation, are associated with this. Data on personal exposure to airborne fungal and bacterial species measured over 4 years as well as serum levels of SAA and CRP sampled over two years were analyzed. For data analysis, the main work tasks were grouped into three different groups, called 'grouped work task'. Microorganisms were identified using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF MS) and next-generation sequencing (NGS). The 'daily exposure' of greenhouse workers' were as follows: 4.8 × 10⁴ CFU bacteria/m³, 1.4 × 10⁶ CFU fungi/m³, and 392 EU/m³ of endotoxin. Workers were exposed to many different microbial species including several species within the genera Acinetobacter, Bacillus, Microbacterium, Pseudomonas, Staphylococcus, and Streptomyces. The genera Ralstonia and Cladosporium were found in most samples. The exposure levels as well as the microbial composition were associated significantly with grouped work task and season with high exposures during tasks in close contact with mature and old plants and in the autumn. CRP and SAA levels were also associated with exposure level and grouped work tasks. The Shannon-Wiener indices were not different in the 3 'grouped work tasks'. Several specific species including e.g. Halomonas elongata, Stenotrophomonas maltophilia, Podosphaera fusca, and Wallemia spp. were found frequently or in high concentrations in the exposures associated with the highest levels of CRP and SAA. The microorganisms S. maltophilia, P. fusca, and Wallemia spp. were also found on the cucumber plant leaves. In conclusion, both exposure level and the species composition seem to have an effect on the serum levels of CRP and SAA of exposed workers. The greenhouse workers were exposed to only a few species characterized as human pathogens.

Wastewater treatment plant workers' exposure and methods for risk evaluation of their exposure

Work in wastewater treatment plants (WWTPs) can be associated with respiratory symptoms and diarrhea. The aim of this study was to obtain knowledge about WWTP workers' exposure to airborne bacteria and endotoxin, and the inflammatory potential (TIP) of their exposure, and to evaluate the risk posed by the exposure by 1) calculating a hazard index and relating the exposure to suggested occupational exposure limits (OELs), 2) estimating the potential deposition of bacteria in the airways, 3) relating it to the risk group classification of bacteria by the European Union, and 4) estimating the TIP of the personal exposure. A cohort of 14 workers were followed over one year. Bioaerosols were collected using personal and stationary samplers in a grid chamber house and an aeration tank area. Airborne bacteria were identified using (MALDI-TOF MS), and TIP of exposure was measured using HL-60 cells. A significant effect of season, work task, and person was found on the personal exposure. A hazard index based on exposure levels indicates that the risk caused by inhalation is low. In relation to suggested OELs, 14% and 34% of the personal exposure were exceeded for endotoxin (≥50 EU/m³) and bacteria (≥500 CFU/m³). At least 70% of the airborne bacteria in the grid chamber house and the aeration tank area could potentially deposit in the lower respiratory tract. From the personal samples, three of 131 bacterial species, Enterobacter cloacae, Staphylococcus aureus, and Yersinia enterocolitica are classified within Risk Group 2. Seven additional bacteria from the stationary samples belong to Risk Group 2. The bacterial species composition was affected significantly by season (p = 0.014) and by sampling type/area (p = 0.001). The TIP of WWTP workers' exposure was higher than of a reference sample, and the highest TIP was measured in autumn. TIP of personal exposure correlated with bacterial exposure. Based on the geometric average exposures to endotoxin (9.2 EU/m³) and bacteria (299 CFU/m³) and based on the calculated hazard index, the risk associated with exposure is low. However, since 43 of 106 exposure levels exceed suggested OELs, the TIP of exposure was elevated and associated with bacterial exposure, and WWTP workers were exposed to pathogenic bacteria, a continued focus on preventive measures is important. The identification of bacteria to species level in personal samples was necessary in the risk assessment, and measurement of the microbial composition made the source tracking possible.

An Overview of Bioinformatics Tools for DNA Meta-Barcoding Analysis of Microbial Communities of Bioaerosols: Digest for Microbiologists

High-throughput DNA sequencing (HTS) has changed our understanding of the microbial composition present in a wide range of environments. Applying HTS methods to air samples from different environments allows the identification and quantification (relative abundance) of the microorganisms present and gives a better understanding of human exposure to indoor and outdoor bioaerosols. To make full use of the avalanche of information made available by these sequences, repeated measurements must be taken, community composition described, error estimates made, correlations of microbiota with covariates (variables) must be examined, and increasingly sophisticated statistical tests must be conducted, all by using bioinformatics tools. Knowing which analysis to conduct and which tools to apply remains confusing for bioaerosol scientists, as a litany of tools and data resources are now available for characterizing microbial communities. The goal of this review paper is to offer a guided tour through the bioinformatics tools that are useful in studying the microbial ecology of bioaerosols. This work explains microbial ecology features like alpha and beta diversity, multivariate analyses, differential abundances, taxonomic analyses, visualization tools and statistical tests using bioinformatics tools for bioaerosol scientists new to the field. It illustrates and promotes the use of selected bioinformatic tools in the study of bioaerosols and serves as a good source for learning the “dos and don’ts” involved in conducting a precise microbial ecology study.

A Review on Airborne Microbes: The Characteristics of Sources, Pathogenicity and Geography

Microbes are widespread and have been much more studied in recent years. In this review, we describe detailed information on airborne microbes that commonly originate from soil and water through liquid–air and soil–air interface. The common bacteria and fungi in the atmosphere are the phyla of Firmicutes, Proteobacteria, Bacteroides, Actinobacteria, Cyanobacteria and Ascomycota, Basidiomycota, Chytridiomycota, Rozellomycota that include most pathogens leading to several health problems. In addition, the stability of microbial community structure in bioaerosols could be affected by many factors and some special weather conditions like dust events even can transport foreign pathogens to other regions, affecting human health. Such environments are common for a particular place and affect the nature and interaction of airborne microbes with them. For instance, meteorological factors, haze and foggy days greatly influence the concentration and abundance of airborne microbes. However, as microorganisms in the atmosphere are attached on particulate matters (PM), the high concentration of chemical pollutants in PM tends to restrain the growth of microbes, especially gathering atmospheric pollutants in heavy haze days. Moreover, moderate haze concentration and/or common chemical components could provide suitable microenvironments and nutrition for airborne microorganism survival. In summary, the study reviews much information and characteristics of airborne microbes for further study.

Potential Respiratory Deposition and Species Composition of Airborne Culturable, Viable, and Non-Viable Fungi during Occupancy in a Pig Farm

Fungal species composition and site of deposition within the airways affects whether diseases develop and where they may arise. The aim of this study is to obtain knowledge regarding the potential deposition of airborne culturable, viable, and non-viable fungi in the airways of pig farm workers, and how this composition changes over multiple sampling days. Airborne fungi were sampled using impactors and subsequently analyzed using amplicon sequencing and matrix assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS) fingerprinting. The geometric mean aerodynamic diameter (Dg) of airborne particles with culturable airborne fungi were not affected by sampling days and ranged in size between 3.7 and 4.6 µm. Amplicon sequencing of the internal transcribed spacer region of the rRNA gene operon, in combination with DNA interchelating agents, revealed a large presence of non-viable fungi, but several pathogenic and toxic fungal species were detected in the viable portion. The diversity was found to be significantly associated with the sampling day but did not change significantly over multiple sampling rounds during the same day. The non-viable fraction contained genera typically associated with the pig gastrointestinal tract, such as Kazachstania and Vishniacozyma. In conclusion, the Dg of culturable fungi was between 3.7 and 4.6 µm, and the Dg of the viable and total fungi was 1.5 and 2.1 µm, respectively. The species composition changed over the multiple sampling days.

Recent Advances in Monitoring, Sampling, and Sensing Techniques for Bioaerosols in the Atmosphere

Bioaerosols in the form of microscopic airborne particles pose pervasive risks to humans and livestock. As either fully active components (e.g., viruses, bacteria, and fungi) or as whole or part of inactive fragments, they are among the least investigated pollutants in nature. Their identification and quantification are essential to addressing related dangers and to establishing proper exposure thresholds. However, difficulties in the development (and selection) of detection techniques and an associated lack of standardized procedures make the sensing of bioaerosols challenging. Through a comprehensive literature search, this review examines the mechanisms of conventional and advanced bioaerosol detection methods. It also provides a roadmap for future research and development in the selection of suitable methodologies for bioaerosol detection. The development of sample collection and sensing technology make it possible for continuous and automated operation. However, intensive efforts should be put to overcome the limitations of current technology as most of the currently available options tend to suffer from lengthy sample acquisition times and/or nonspecificity of probe material.

Microbial Community Composition Analysis in Spring Aerosols at Urban and Remote Sites over the Tibetan Plateau

This study presents features of airborne culturable bacteria and fungi from three different sites (Lanzhou; LZ; 1520 m ASL, Lhasa; LS; 3640 m ASL and Qomolangma; ZF; 4276 m ASL) representing urban (LZ and LS) and remote sites (ZF) over the Tibetan Plateau (TP). Total suspended particle (TSP) samples were collected with an air sampler (Laoying 2030, China) on a quartz filter. Community structures of bacteria and fungi were studied and compared among three different locations. The average levels of bacterial load in the outdoor air ranged from approximately 8.03 × 101 to 3.25 × 102 CFU m–3 (Colony forming unit per m3). However, the average levels of fungal loads ranged from approximately 3.88 × 100 to 1.55 × 101 CFU m−3. Bacterial load was one magnitude higher at urban sites LZ (2.06 × 102–3.25 × 102 CFU m−3) and LS (1.96 × 102–3.23 × 102 CFU m−3) compared to remote sites ZF (8.03 × 101–9.54 × 101 CFU m−3). Similarly, the maximum fungal load was observed in LZ (1.02 × 101–1.55 × 101 CFU m−3) followed by LS (1.03 × 101–1.49 × 101 CFU m−3) and ZF (3.88 × 100–6.26 × 100 CFU m−3). However, the maximum microbial concentration was observed on the same day of the month, corresponding to a high dust storm in Lanzhou during the sampling period. The reported isolates were identified by phylogenetic analysis of 16S rRNA genes for bacteria and ITS sequences for fungi amplified from directly extracted DNA. Bacterial isolates were mostly associated with Proteobacteria, Eurotiomycetes and Bacillus, whereas fungal isolates were mostly Aspergillus and Alternaria. Overall, this is a pioneer study that provides information about the airborne microbial concentration and composition of three sites over the TP region depending on environmental parameters. This study provided preliminary insight to carry out more advanced and targeted analyses of bioaerosol in the sites presented in the study.

Methods for Bioaerosol Characterization: Limits and Perspectives for Human Health Risk Assessment in Organic Waste Treatment

Bioaerosol characterization represents a major challenge for the risk assessment and management of exposed people. One of the most important bioaerosol sources is the organic waste collection and treatment. This work analyzed and discussed the literature with the purpose of investigating the main techniques used nowadays for bioaerosol monitoring during organic waste treatment. The discussion includes an overview on the most efficient sampling, DNA extraction, and analysis methods, including both the cultural and the bio-molecular approach. Generally, an exhaustive biological risk assessment is not applied due to the organic waste heterogeneity, treatment complexity, and unknown aerosolized emission rate. However, the application of bio-molecular methods allows a better bioaerosol characterization, and it is desirable to be associated with standardized cultural methods. Risk assessment for organic waste workers generally includes the evaluation of the potential exposition to pathogens and opportunistic pathogens or to other microorganisms as biomarkers. In most cases, Saccharopolyspora rectivirgula, Legionella spp., Aspergillus spp., and Mycobacterium spp. are included. Future perspectives are focused on identifying common composting biomarkers, on investigating the causality process between chronic bioaerosol exposure and disease onset, and finally, on defining common exposure limits.

Towards a risk evaluation of workers' exposure to handborne and airborne microbial species as exemplified with waste collection workers

Bioaerosol exposure is associated with health problems. The aim of this study is to evaluate whether it is possible to assess the risks posed by waste collection workers' exposure through identification and characterization of bacterial and fungal species, to which the workers are exposed. Using MALDI-TOF MS, microorganisms in waste collection workers' exposure through air, hand, and contact with the steering wheel were identified. Fungi found in high concentrations from the workers' exposure were characterized for the total inflammatory potential (TIP), cytotoxicity, and biofilm-forming capacity. In total, 180 different bacterial and 37 different fungal species in the workers' exposure samples were identified. Some of them belong to Risk Group 2, e.g. Escherichia coli, Klebsiella oxytoca, Staphylococcus aureus, and Aspergillus fumigatus, some have been associated with occupational health problems e.g. Penicillium citrinum and P. glabrum and some are described as emerging pathogens e.g. Aureobasidium pullulans. The TIP of fungal species was dose-dependent. High TIP values were found for Penicillium italicum, P. brevicompactum, P. citrinum, and P. glabrum. Several species were cytotoxic, e.g. A. niger and P. expansum, while some, e.g. P. chrysogenum, did not affect the cell viability. Based on waste workers' average inhalation rate, they inhaled up to 2.3 × 10⁴ cfu of A. niger, 7.4 × 10⁴ cfu of P. expansum, and 4.0 × 10⁶ cfu of P. italicum per work day. Some species e.g. A. niger and P. citrinum were able to form biofilm. In conclusion, the workers were exposed to several species of microorganisms of which some to varying degrees can be evaluated concerning risk. Thus, some microorganisms belong to Risk Group 2, and some are described as causing agents of occupational health problems, emerging pathogens, or intrinsically antibiotic resistant. For some other species very little is known. The TIP, cytotoxicity, and ability to form biofilm of the dominating fungi support and expand previous findings. These parameters depended on the species and the dose, thus highlighting the importance of species identification and exposure level in the risk assessment of exposure.

Genomics of Aerobic Photoheterotrophs in Wheat Phyllosphere Reveals Divergent Evolutionary Patterns of Photosynthetic Genes in Methylobacterium spp

Phyllosphere is a habitat to a variety of viruses, bacteria, fungi, and other microorganisms, which play a fundamental role in maintaining the health of plants and mediating the interaction between plants and ambient environments. A recent addition to this catalogue of microbial diversity was the aerobic anoxygenic phototrophs (AAPs), a group of widespread bacteria that absorb light through bacteriochlorophyll α (BChl a) to produce energy without fixing carbon or producing molecular oxygen. However, culture representatives of AAPs from phyllosphere and their genome information are lacking, limiting our capability to assess their potential ecological roles in this unique niche. In this study, we investigated the presence of AAPs in the phyllosphere of a winter wheat (Triticum aestivum L.) in Denmark by employing bacterial colony based infrared imaging and MALDI-TOF mass spectrometry (MS) techniques. A total of ∼4,480 colonies were screened for the presence of cellular BChl a, resulting in 129 AAP isolates that were further clustered into 21 groups based on MALDI-TOF MS profiling, representatives of which were sequenced using the Illumina NextSeq and Oxford Nanopore MinION platforms. Seventeen draft and four complete genomes of AAPs were assembled belonging in Methylobacterium, Rhizobium, Roseomonas, and a novel Alsobacter. We observed a diverging pattern in the evolutionary rates of photosynthesis genes among the highly homogenous AAP strains of Methylobacterium (Alphaproteobacteria), highlighting an ongoing genomic innovation at the gene cluster level.

Continuous Surveillance of Bioaerosols On-Site Using an Automated Bioaerosol-Monitoring System

Real-time on-site monitoring of bioaerosols in an air environment is important for preventing various adverse health effects including respiratory diseases and allergies caused by bioaerosols. Here, we report the development of an on-site automated bioaerosol-monitoring system (ABMS) using integrated units including a wet-cyclone bioaerosol sampler, a thermal-lysis unit for extracting adenosine triphosphate (ATP), an ATP-detection unit based on the immobilization of luciferase/luciferin for bioluminescence reactions, and a photomultiplier tube-based detector. The performance of the bioaerosol detection system was verified using Escherichia coli (E. coli) as a model source. Each unit was optimized to process ∼9.6 × 10⁵ times the concentrated ratio of collected bioaerosol samples, using a 3 min lysis time to extract ATP, and has a detection limit of ∼375 colony-forming units (CFUs)/mL with more than 30 days of stability for the immobilized-luciferase/luciferin detection unit supported by a glass-fiber conjugation pad. After the integration of all units, the ABMS achieved E. coli bioaerosol monitoring with continuous detection at 5 min intervals and a minimum detection limit of ∼130 CFU/m_air³. Furthermore, the rapid responsivity and stable operation performance of the ABMS under test-bed conditions and during a field test demonstrated that the ABMS is capable of continuously monitoring bioaerosols in real-time with high sensitivity. The monitoring system developed here with immobilization strategies for bioluminescence reactions triggered by ATP extracted from collected bioaerosol samples using a simple heat-lysis method may help establish sustainable platforms to obtain stable signals for the real-time detection of bioaerosols on-site.

The Inhalable Mycobiome of Sawmill Workers: Exposure Characterization and Diversity

Exposure to fungal spores has been associated with respiratory symptoms and allergic alveolitis among sawmill workers, but the complexity of sawmill workers' fungal exposure has been poorly studied. We characterized the fungal diversity in air samples from sawmill workers' breathing zones and identified differences in the richness, diversity, and taxonomic composition between companies, departments, wood types, and seasons. Full-shift personal inhalable dust samples (n = 86) collected from 11 industrial sawmill, sorting mill, and planer mill companies processing spruce and/or pine were subjected to DNA metabarcoding using the fungal internal transcribed spacer (ITS) region 2. The workers were exposed to a higher total number of operational taxonomic units (OTUs) in summer than in winter and when processing spruce than when processing pine. Workers in the saw department had the richest fungal exposure, followed by workers in the planing department and sorting of dry timber department. Sawmills explained 11% of the variation in the fungal community composition of the exposure, followed by season (5%) and department (3%). The fungal compositions of the exposures also differed between seasons, sawmills, wood types, and departments at the taxonomic level, ranging from the phylum to the species level. The differences in exposure diversity suggest that the potential health effects of fungal inhalation may also be different; hence, a risk assessment based on the fungal diversity differences should be performed. This study may serve as a basis for establishing a fungal profile of signature species that are specific for sawmills and that can be measured quantitatively in future risk assessments of sawmill workers.IMPORTANCE To gain more knowledge about exposure-response relationships, it is important to improve exposure characterization by comprehensively identifying the temporal and spatial fungal composition and diversity of inhalable dust at workplaces. The variation in the diverse fungal communities to which individuals are exposed in different seasons and sawmills suggests that variations in exposure-related health effects between seasons and companies can be expected. More importantly, the distinct fungal profiles between departments across companies indicate that workers in different job groups are differently exposed and that health risks can be department specific. DNA metabarcoding provides insight into a broad spectrum of airborne fungi that may serve as a basis for obtaining important knowledge about the fungi to which workers are exposed.

Occupational exposure during treatment of offshore drilling waste and characterization of microbiological diversity

The exposure for workers handling and recycling offshore drilling waste are previously not described, and given the potential for exposure to hazardous components, there is a need for characterizing this occupational exposure. In this study five plants recycling offshore drilling waste with different techniques were included. Measurements were conducted in both winter and summer to include seasonal exposure variations. Altogether >200 personal air-exposure measurements for oil mist, oil vapor, volatile organic compounds (VOC), hydrogen sulfide (H₂S) and solvents were carried out respectively. Microorganisms related to drilling waste were identified in bulk samples and in stationary air measurements from two of the plants. The exposure to oil mist and oil vapor were below 10% of the current Norwegian occupational exposure limits (OEL) for all measured components. The plants using the Resoil or TCC method had a statistically significant higher exposure to oil vapor than the plant using complete combustion (p-value <0.05). No statistically significant difference was found between the different treatment methods for oil mist. The exposure to solvents was generally low (additive factor < 0.03). Endotoxin measurements done during winter showed a median concentration of 5.4 endotoxin units (EU)/m³. Levels of H₂S above the odor threshold of 0.1 ppm were measured at four plants. Both drill mud and slop water contained a high number and diversity of bacteria (2-4 × 10⁴ colony forming unit (CFU)/mL), where a large fraction was Gram-negative species. Some of the identified microorganisms are classified as potentially infectious pathogens for humans and thus might be a hazard to workers.

Biological Particles in the Indoor Environment

Airborne microorganisms are very difficult to assess accurately under field conditions owing to differences in the sample collection efficiency of the selected sampler and variations in DNA extraction efficiencies. Consequently, bioaerosol abundance and biodiversity can be underestimated, making it more difficult to link specific bioaerosol components to diseases and human health risk. Owing to the low biomass in air samples, it remains a challenge to obtain a representative microbiological sample to recover sufficient DNA for downstream analyses. Improved sampling methods are particularly crucial, especially for investigating viral communities, owing to the extremely low biomass of viral particles in the air compared with other environments. Without detailed information about sampling, characterization and enumeration techniques, interpretation of exposure level is very difficult. Despite this, bioaerosol research has been enhanced by molecular tools, especially next-generation sequencing approaches that have allowed faster and more detailed characterization of air samples.

Source specific exposure and risk assessment for indoor aerosols

Poor air quality is a leading contributor to the global disease burden and total number of deaths worldwide. Humans spend most of their time in built environments where the majority of the inhalation exposure occurs. Indoor Air Quality (IAQ) is challenged by outdoor air pollution entering indoors through ventilation and infiltration and by indoor emission sources. The aim of this study was to understand the current knowledge level and gaps regarding effective approaches to improve IAQ. Emission regulations currently focus on outdoor emissions, whereas quantitative understanding of emissions from indoor sources is generally lacking. Therefore, specific indoor sources need to be identified, characterized, and quantified according to their environmental and human health impact. The emission sources should be stored in terms of relevant metrics and statistics in an easily accessible format that is applicable for source specific exposure assessment by using mathematical mass balance modelings. This forms a foundation for comprehensive risk assessment and efficient interventions. For such a general exposure assessment model we need 1) systematic methods for indoor aerosol emission source assessment, 2) source emission documentation in terms of relevant a) aerosol metrics and b) biological metrics, 3) default model parameterization for predictive exposure modeling, 4) other needs related to aerosol characterization techniques and modeling methods. Such a general exposure assessment model can be applicable for private, public, and occupational indoor exposure assessment, making it a valuable tool for public health professionals, product safety designers, industrial hygienists, building scientists, and environmental consultants working in the field of IAQ and health.

Bioaerosol biomonitoring: Sampling optimization for molecular microbial ecology

Bioaerosols (or biogenic aerosols) have largely been overlooked by molecular ecologists. However, this is rapidly changing as bioaerosols play key roles in public health, environmental chemistry and the dispersal ecology of microbes. Due to the low environmental concentrations of bioaerosols, collecting sufficient biomass for molecular methods is challenging. Currently, no standardized methods for bioaerosol collection for molecular ecology research exist. Each study requires a process of optimization, which greatly slows the advance of bioaerosol science. Here, we evaluated air filtration and liquid impingement for bioaerosol sampling across a range of environmental conditions. We also investigated the effect of sampling matrices, sample concentration strategies and sampling duration on DNA yield. Air filtration using polycarbonate filters gave the highest recovery, but due to the faster sampling rates possible with impingement, we recommend this method for fine -scale temporal/spatial ecological studies. To prevent bias for the recovery of Gram-positive bacteria, we found that the matrix for impingement should be phosphate-buffered saline. The optimal method for bioaerosol concentration from the liquid matrix was centrifugation. However, we also present a method using syringe filters for rapid in-field recovery of bioaerosols from impingement samples, without compromising microbial diversity for high -throughput sequencing approaches. Finally, we provide a resource that enables molecular ecologists to select the most appropriate sampling strategy for their specific research question.

Recovery of Fungal Cells from Air Samples: a Tale of Loss and Gain

There are limitations in establishing a direct link between fungal exposure and health effects due to the methodology used, among other reasons. Culture methods ignore the nonviable/uncultivable fraction of airborne fungi. Molecular methods allow for a better understanding of the environmental health impacts of microbial communities. However, there are challenges when applying these techniques to bioaerosols, particularly to fungal cells. This study reveals that there is a loss of fungal cells when samples are recovered from air using wet samplers and aimed to create and test an improved protocol for concentrating mold spores via filtration prior to DNA extraction. Results obtained using the new technique showed that up to 3 orders of magnitude more fungal DNA was retrieved from the samples using quantitative PCR. A sequencing approach with MiSeq revealed a different diversity profile depending on the methodology used. Specifically, 8 fungal families out of 19 families tested were highlighted to be differentially abundant in centrifuged and filtered samples. An experiment using laboratory settings showed the same spore loss during centrifugation for Aspergillus niger and Penicillium roquefortii strains. We believe that this work helped identify and address fungal cell loss during processing of air samples, including centrifugation steps, and propose an alternative method for a more accurate evaluation of fungal exposure and diversity.IMPORTANCE This work shed light on a significant issue regarding the loss of fungal spores when recovered from air samples using liquid medium and centrifugation to concentrate air particles before DNA extraction. We provide proof that the loss affects the overall fungal diversity of aerosols and that some taxa are differentially more affected than others. Furthermore, a laboratory experiment confirmed the environmental results obtained during field sampling. The filtration protocol described in this work offers a better description of the fungal diversity of aerosols and should be used in fungal aerosol studies.

Microbial species and biodiversity in settling dust within and between pig farms

The airborne fungal and bacterial species present in pig farm dust have not been well characterised even though these bioaerosols are known to cause inflammation and other airway maladies. In this study, the microbial species and composition in airborne dust within and between pig farms were investigated. Passively sedimenting dust from six pig farms were collected using electrostatic dust collectors. The bacterial and fungal species were identified using matrix-assisted laser desorption-ionisation time-of-flight mass spectrometry (MALDI-TOF MS) and next generation sequencing (NGS). Dust samples taken within the same stable section revealed high resemblance and stability. Constrained statistical analysis of the microbial community compositions indicated that the types of stable did not appear to have a great effect on the bacterial and fungal β-diversity. In contrast to this, the farm from which samples were taken appeared to have the greatest effect on the bacterial β-diversity, but this trend was not observed for the fungal β-diversity. The most common bacteria and fungi according to NGS data were anaerobes typically associated with the pig intestinal tract and yeasts respectively. Bacterial sedimentation varied at a rate between 10³ and 10⁹ CFU/m²/day, with the most common species after aerobic incubation being Aerococcus viridans and Staphylococcus equorum, while Clostridium perfringens and Staphylococcus simulans were the most common species after anaerobic incubation. A total of 28 different species of bacteria and fungi were classifiable as pathogens. In conclusion, the biodiversity in pig farm dust shows a high diversity of bacterial species. However, samples from the same stable section resembled each other, but also different sections within the same farm also resembled each other, thus indicating a high degree of community stability in the dust source. In regards to fungal identification, the biodiversity was observed to be similar between samples from different stable sections and farms, indicating a higher degree of similarities in the mycobiomes found across pig farms studied.

Expanded cardboard waste sorting and occupational exposure to microbial species

Member states of the European Union have to maximize recycling. The current, Danish cardboard recycling system can be improved by increasing the kinds of cardboard products that can be recycled to include e.g. used beverage cartons and pizza boxes (i.e. an expanded cardboard fraction (ECF)). This study aims to obtain knowledge about exposure to airborne endotoxin and microorganisms at species level at different collection frequencies of ECF, and whether an increase in waste sorted fractions means that each waste fraction is collected less frequently. Bacterial and endotoxin concentrations were associated significantly with temperature inside the waste containers and endotoxin and fungal exposures with collection frequency. The concentration of fungi was highest at the truck back and for reduced collection frequencies. The geometric mean diameters of particles with bacteria were between 3.0 and 5.2 μm and with fungi between 3.8 μm and 6.0 μm. In total, 81 and 25 different bacterial and fungal species were found at the waste receiving plant, respectively. Work with ECF caused exposures to food-related microorganisms (e.g. Arthrobacter arilaitensis and Penicillium camemberti), potential pathogens (e.g. Bacillus cereus, Salmonella sp. and P. expansum), and commensal bacteria. Bacillus cereus and Salmonella were found in the particle size fraction often being swallowed. Workers collecting EFC will be at risk of being exposed to microbial species that normally are related to residual waste. It seems to be advisable with an EFC collection frequency shorter than eight weeks. However, introduction of new waste fractions has generally been associated with reduced collection frequencies.

Bioaerosol Sampler Choice Should Consider Efficiency and Ability of Samplers To Cover Microbial Diversity

Bioaerosol studies aim to describe the microbial content and increase understanding of the aerosolization processes linked to diseases. Air samplers are used to collect, identify, and quantify bioaerosols. Studies comparing the performances of air samplers have typically used a culture approach or have targeted a specific microorganism in laboratory settings. The objective of this study was to use environmental field samples to compare the efficiencies of 3 high-airflow-rate samplers for describing bioaerosol diversity using a next-generation sequencing approach. Two liquid cyclonic impactors and one electrostatic filter dry sampler were used in four wastewater treatment plants to target bacterial diversity and in five dairy farms to target fungal diversity. The dry electrostatic sampler was consistently more powerful in collecting more fungal and bacterial operational taxonomic units (OTUs). Substantial differences in OTU abundances between liquid and dry sampling were revealed. The majority of the diversity revealed by dry electrostatic sampling was not identified using the cyclonic liquid impactors. The findings from this work suggest that the choice of a bioaerosol sampler should include information about the efficiency and ability of samplers to cover microbial diversity. Although these results suggest that electrostatic filters result in better coverage of the microbial diversity among the tested air samplers, further studies are needed to confirm this hypothesis. While it is difficult to determine a single universally optimal air sampler, this work provides an in-depth look at some of the considerations that are essential when choosing an air sampler for studying the microbial ecology of bioaerosols.IMPORTANCE Associating bioaerosol exposure and health problems is challenging, and adequate exposure monitoring is a priority for scientists in the field. Conclusions that can be drawn from bioaerosol exposure studies are highly dependent on the design of the study and the methodologies used. The air sampling strategy is the first methodological step leading to an accurate interpretation of what is present in the air. Applying new molecular approaches to evaluate the efficiencies of the different types of samplers used in the field is necessary in order to circumvent traditional approaches and the biases they introduce to such studies. The results and conclusions provided in this paper should be taken in consideration when conducting a bioaerosol study.

Validation of a quantitative PCR based detection system for indoor mold exposure assessment in bioaerosols

Determination and assessment of airborne fungal particles is complex and results of different sampling and analytical strategies are hard to compare due to limitations of each of the techniques. Here, an indoor mold detection system based on quantitative polymerase chain reaction (qPCR) is described and validated for its reliability and stability to identify airborne fungal particles collected. Data obtained from testing the system with fungal DNA, spore suspensions and bioaerosols indicated a need for spiking and normalization of measurements due to material loss and assay specific bias. Considering the loss of material during sample processing, detection limits defined for suspensions of Tritirachium oryzae spores were roughly 18 spores per sample. Detection of fungal spore mixtures nebulized under controlled conditions in a bioaerosol chamber showed generally 2-3 times higher normalized values measured with the molecular system compared to cultivation. Data obtained from a mold infested indoor sampling site and its corresponding outdoor reference measurement showed good correlations between qPCR and high-throughput sequencing (rho = 0.83, p < 0.01), if Cladosporium species were excluded. Taking necessary data normalization into account, the described qPCR detection system shows great potential to complement commonly used culture based approaches with the aim to improve the precision of indoor mold assessments. In contrast to already available qPCR assays that detect certain molds on a species level, this system covers a broad range of relevant fungal communities, serving as a promising alternative to high-throughput sequencing to identify indoor molds.

Emerging Insights into the Occupational Mycobiome

PURPOSE OF REVIEW

The evolution of molecular-based methods over the last two decades has provided new approaches to identify and characterize fungal communities or "mycobiomes" at resolutions previously not possible using traditional hazard identification methods. The recent focus on fungal community assemblages within indoor environments has provided renewed insight into overlooked sources of fungal exposure. In occupational studies, internal transcribed spacer (ITS) region sequencing has recently been utilized in a variety of environments ranging from indoor office buildings to agricultural commodity and harvesting operations.

RECENT FINDINGS

Fungal communities identified in occupational environments have been primarily placed in the phylum Ascomycota and included classes typically identified using traditional fungal exposure methods such as the Eurotiomycetes, Dothideomycetes, Sordariomycetes, and Saccharomycetes. The phylum Basidiomycota has also been reported to be more prevalent than previously estimated and ITS region sequences have been primarily derived from the classes Agaricomycetes and Ustilaginomycetes. These studies have also resolved sequences placed in the Basidiomycota classes Tremellomycetes and Exobasidiomycetes that include environmental and endogenous yeast species. These collective datasets have shown that occupational fungal exposures include a much broader diversity of fungi than once thought. Although the clinical implications for occupational allergy are an emerging field of research, establishing the mycobiome in occupational environments will be critical for future studies to determine the complete spectrum of worker exposures to fungal bioaerosols and their impact on worker health.

Exposure to field vs. storage wheat dust: different consequences on respiratory symptoms and immune response among grain workers

PURPOSE

The aim of this study was to understand the differential acute effects of two distinct wheat-related dusts, such as field or stored wheat dust handling, on workers' health and how those effects evolved at 6 month intervals.

METHODS

Exposure, work-related symptoms, changes in lung function, and blood samples of 81 workers handling wheat and 61 controls were collected during the high exposure season and 6 months after. Specific IgG, IgE, and precipitins against 12 fungi isolated from wheat dust were titrated by enzyme-linked immunosorbent assay, dissociation-enhanced lanthanide fluorescence immunoassay, and electrosyneresis. The level of fungi was determined in the workers' environment. Levels of exhaled fraction of nitrogen monoxide (F_ENO) and total IgE were obtained. Exposure response associations were investigated by mixed logistic and linear regression models.

RESULTS

The recent exposure to field wheat dust was associated with a higher prevalence for five of six self-reported airway symptoms and with a lower F_ENO than those in the control population. Exposure to stored wheat dust was only associated with cough. No acute impact of exposure on respiratory function was observed. Exposure to field wheat dust led to workers' sensitization against the three field fungi Aureobasidum, Cryptococcus, and Phoma, although exposure to storage wheat dust was associated with tolerance. The level of Ig remained stable 6 months after exposure.

CONCLUSION

The clinical picture of workers exposed to field or storage wheat dust differed. The systematic characterization of the aerosol microbial profile may help to understand the reasons for those differences.

Microbial hazards during harvesting and processing at an outdoor United States cannabis farm

Cannabis cultivation is an emerging industry within the United States. Organic dust derived in part from naturally occurring microorganisms is known to cause byssinosis in the hemp industry. In this pilot study, bacteria and fungi encountered by workers at an outdoor cannabis farm that utilized organic practices were elucidated by 16 S ribosomal RNA (rRNA) and Internal Transcribed Spacer (ITS) region sequencing, respectively. Area (n = 14) and personal air samples (n = 12) were collected during harvesting and processing activities. 16 S rRNA and ITS regions of extracted bacterial and fungal genomic DNA were amplified and sequenced using Sanger sequencing. Bacterial sequencing resolved 1,077 sequences that were clustered into 639 operational taxonomic units (OTUs) and predominantly placed in the phylum, Actinobacteria (46%). Personal air samples revealed higher bacterial and Actinobacteria diversity compared to outdoor area samples collected within the facility (p < 0.05). A high degree of dissimilarity between bacteria was identified within and between samples. Fungal sequences (n = 985) were identified and predominantly clustered in the phylum Ascomycota (53%). Of the 216 fungal OTUs elucidated, the cannabis plant pathogenic species, Botrytis cinerea, was the most prevalent and accounted for 34% of all fungal sequences. The relative abundance of B. cinerea was highest in personal air samples (59%) compared to area samples collected in the drying room (19%), greenhouse (18%), and outdoor environment (6%). There was 49% sample similarity between fungi identified within personal air samples, but higher dissimilarity coefficients were observed within and between greenhouse, drying room, and outdoor area air samples. The results of this pilot study suggest that the cannabis farm workers are potentially exposed to Actinobacteria as well as the cannabis plant pathogen, B. cinerea during harvesting, bud-stripping, and hand-trimming processes.

Mold and Human Health: a Reality Check

There are possibly millions of mold species on earth. The vast majority of these mold spores live in harmony with humans, rarely causing disease. The rare species that does cause disease does so by triggering allergies or asthma, or may be involved in hypersensitivity diseases such as allergic bronchopulmonary aspergillosis or allergic fungal sinusitis. Other hypersensitivity diseases include those related to occupational or domiciliary exposures to certain mold species, as in the case of Pigeon Breeder's disease, Farmer's lung, or humidifier fever. The final proven category of fungal diseases is through infection, as in the case of onchomycosis or coccidiomycosis. These diseases can be treated using anti-fungal agents. Molds and fungi can also be particularly important in infections that occur in immunocompromised patients. Systemic candidiasis does not occur unless the individual is immunodeficient. Previous reports of "toxic mold syndrome" or "toxic black mold" have been shown to be no more than media hype and mass hysteria, partly stemming from the misinterpreted concept of the "sick building syndrome." There is no scientific evidence that exposure to visible black mold in apartments and buildings can lead to the vague and subjective symptoms of memory loss, inability to focus, fatigue, and headaches that were reported by people who erroneously believed that they were suffering from "mycotoxicosis." Similarly, a causal relationship between cases of infant pulmonary hemorrhage and exposure to "black mold" has never been proven. Finally, there is no evidence of a link between autoimmune disease and mold exposure.

Concentrations of Staphylococcus species in indoor air as associated with other bacteria, season, relative humidity, air change rate, and S. aureus-positive occupants

The aim of this study was to obtain knowledge about concentrations of Staphylococcus aureus, MRSA (methicillin-resistant S. aureus), and other Staphylococcus species in indoor air in Greater Copenhagen and about factors affecting the concentrations. The effects of season, temperature, relative humidity, air change rate (ACR), other bacterial genera, area per occupant, and presence of S. aureus-positive occupants were studied. In samples from 67 living rooms, S. hominis, S. warneri, S. epidermidis, and S. capitis were found in 13-25%; S. saprophyticus, S. cohnii, and S. pasteuri in 5-10%; and S. lugdunensis, S. haemolyticus, S. caprae, S. equorum, S. kloosii, S. pettenkoferi, S. simulans, and S. xylosus in less than 3%. Staphylococcus aureus were found in two of 67 living rooms: spa type t034 (an MRSA) was recovered from a farmhouse, while spa type t509 was found in an urban home. Two species, S. equorum and S. kloosii, were found only in the farmhouse. Staphylococcus was significantly associated with season with lowest concentration and richness in winter. Genera composition was associated with ACR with smaller fractions of Staphylococcus at higher ACR, while richness was significantly and negatively associated with area per occupant. Concentration of Staphylococcus correlated positively with the total concentration of bacteria, but negatively with the total concentration of other bacteria. The concentration of Staphylococcus was not significantly associated with concentrations of the other abundant genera Bacillus, Kocuria, and Micrococcus. In offices with S. aureus-positive occupants, airborne S. aureus was not found. In conclusion, Staphylococcus species constitute a considerable proportion of the airborne bacteria in the studied homes and offices. However, both S. aureus and MRSA had very low prevalence during all seasons. Thus, transmission of S. aureus and MRSA through the air in living rooms in Copenhagen is expected to be limited. The negative associations between ACR and the fraction Staphylococcus constituted out of total bacteria, and between area per occupant and Staphylococcus richness indicate that it might be possible to affect the presence of airborne Staphylococcus in homes.

Characterisation of Arctic Bacterial Communities in the Air above Svalbard

Atmospheric dispersal of bacteria is increasingly acknowledged as an important factor influencing bacterial community biodiversity, biogeography and bacteria–human interactions, including those linked to human health. However, knowledge about patterns in microbial aerobiology is still relatively scarce, and this can be attributed, in part, to a lack of consensus on appropriate sampling and analytical methodology. In this study, three different methods were used to investigate aerial biodiversity over Svalbard: impaction, membrane filtration and drop plates. Sites around Svalbard were selected due to their relatively remote location, low human population, geographical location with respect to air movement and the tradition and history of scientific investigation on the archipelago, ensuring the presence of existing research infrastructure. The aerial bacterial biodiversity found was similar to that described in other aerobiological studies from both polar and non-polar environments, with Proteobacteria, Actinobacteria, and Firmicutes being the predominant groups. Twelve different phyla were detected in the air collected above Svalbard, although the diversity was considerably lower than in urban environments elsewhere. However, only 58 of 196 bacterial genera detected were consistently present, suggesting potentially higher levels of heterogeneity. Viable bacteria were present at all sampling locations, showing that living bacteria are ubiquitous in the air around Svalbard. Sampling location influenced the results obtained, as did sampling method. Specifically, impaction with a Sartorius MD8 produced a significantly higher number of viable colony forming units (CFUs) than drop plates alone.

Assessment of fungal diversity in a water-damaged office building

Recent studies have described fungal communities in indoor environments using gene sequencing-based approaches. In this study, dust-borne fungal communities were elucidated from a water-damaged office building located in the northeastern region of the United States using internal transcribed spacer (ITS) rRNA gene sequencing. Genomic DNA was extracted from 5 mg of floor dust derived from 22 samples collected from either the lower floors (n = 8) or a top floor (n = 14) of the office building. ITS gene sequencing resolved a total of 933 ITS sequences and was clustered into 216 fungal operational taxonomic units (OTUs). Analysis of fungal OTUs at the 97% similarity threshold showed a difference between the lower and top floors that was marginally significant (p = 0.049). Species richness and diversity indices were reduced in the lower floor samples compared to the top floor samples and there was a high degree of compositional dissimilarity within and between the two different areas within the building. Fungal OTUs were placed in the phyla Ascomycota (55%), Basidiomycota (41%), Zygomycota (3%), Glomeromycota (0.4%), Chytridiomycota (0.3%), and unassigned fungi (0.5%). The Ascomycota classes with the highest relative abundances included the Dothideomycetes (30%) and Eurotiomycetes (16%). The Basidiomycota consisted of the classes Ustilaginomycetes (14%), Tremellomycetes (11%), and Agaricomycetes (8%). Sequence reads derived from the plant pathogen Ustilago syntherismae were the most abundant in the analysis as were obligate Basidiomycota yeast species that accounted for 12% and 11% of fungal ITS sequences, respectively. ITS gene sequencing provides additional insight into the diversity of fungal OTUs. These data further highlight the contribution of fungi placed in the phylum Basidiomycota, obligate yeasts, as well as xerophilic species that are typically not resolved using traditional culture methods.

Microbiota Composition and Pulmonary Surfactant Protein Expression as Markers of Death by Drowning

Pathological diagnosis of drowning remains a challenge for forensic science, because of a lack of pathognomonic findings. We analyzed microbiota and surfactant protein in the lungs for a novel diagnosis of drowning. All rats were divided into drowning, postmortem submersion, and control groups. The water, lungs, closed organs (kidney and liver), and cardiac blood in rats were assayed by targeting 16S ribosomal RNA of Miseq sequencing. Lung samples were analyzed by immunohistochemical staining for surfactant protein A. The closed organs and cardiac blood of drowned group have a lot of aquatic microbes, which have not been detected in postmortem submersion group. Furthermore, intra-alveolar granular staining of surfactant protein A (SP-A) was severely observed in the drowned group than the postmortem submersion and control groups. The findings suggested that the presence of aquatic microbiota in the closed organs and increased expression of SP-A could be markers for a diagnosis of drowning.