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ABSTRACT: Conventional cages for laying hens will be banned in Canada as of 2036, and the egg industry is transitioning toward enriched colony housing and aviaries. While higher concentrations of particulate matter have been previously reported in aviaries and other cage-free housing systems, concentrations of total bacteria and archaea suspended in the air are still uncharacterized in Canadian enriched colonies and aviaries. The aim of the present study was to conduct a longitudinal survey of airborne total bacteria and of airborne total archaea in twelve enriched colonies and twelve aviaries in Eastern Canada during a whole laying period. High-throughput sequencing of 16S rRNA gene amplicons was used to reveal and compare bacterial diversity at the start and the end of the production cycle, and during the cold and the warm seasons. Total bacterial and archaeal concentrations were significantly higher in aviaries (p < 0.05) versus enriched colonies, and in the cold season for both housing types (p < 0.05). While flock age did not have a significant effect on total bacterial and archaeal concentrations, it did on bacterial diversity in both enriched colony houses and aviaries (p < 0.05). The 2 housing systems were significantly different in their diversity of bacteria.

Background/Objectives: Antibiotic resistance gene (ARG) spread is driven by horizontal gene transfer (HGT). Ciliated protozoa may contribute to this process, as their predation has been shown to facilitate HGT in certain bacteria. Here, this phenomenon was further investigated using A. salmonicida subsp. salmonicida. This fish pathogen bears an extensive and dynamic plasmidome, suggesting a high potential for HGT. Methods: A. salmonicida strains carrying one of three conjugative plasmids bearing ARGs (pSN254b, pRAS1b or pAsa4b) were cocultured with a recipient, either A. salmonicida, E. coli or A. hydrophila. Conjugation rates were assessed in the presence and absence of the ciliate Tetrahymena borealis. PCR genotyping confirmed the acquisition of the conjugative plasmids and was used to verify the mobilization of other plasmids. Results: The basal rate of conjugation observed was high. Under the conditions studied, ciliate predation did not appear to influence the conjugation rate, except at higher proportions of ciliates, which typically hampered conjugation. Microscopy revealed that most bacteria were digested in these conditions. PCR screening demonstrated that small mobilizable plasmids from A. salmonicida (pAsa1, pAsa2, pAsa3, and pAsal1) were acquired by the recipients along with the conjugative plasmids, with a slight effect of the ciliates in some donor/recipient cell combination. Conclusions: These results highlight how A. salmonicida can conjugate efficiently with different species and how complex its relationship with ciliates is.

Objectives To adapt the content and functionalities of Brain Health PRO, a web-based multidomain program designed to increase dementia literacy, to the context and needs of users, providers and community organisations across Québec, Canada.Design Five consecutive qualitative co-creation focus group sessions 30–90 min in duration each, exploring potential barriers and facilitators to usability, accessibility, comprehensibility, participant recruitment and retention.Setting Virtual meetings.Participants A 15-member team based in Québec and Ontario, Canada, consisting of 9 researchers (including a graduate student and the project coordinator), representing occupational therapy, sensory rehabilitation, neuropsychology, psychology, health science and research methods, 3 informal caregivers of older adults living with cognitive decline and 3 members of the Federation of Quebec Alzheimer Societies.Data analysis Session recordings were summarised through both qualitative description and thematic analysis.Results The synthesised recommendations included adjustments around diversity, the complexity and presentation styles of the materials, suggestions on refining the web interface and the measurement approaches; it influenced aspects of participant recruitment, retention efforts and engagement with the content of Brain Health PRO.Conclusions Co-creation in dementia prevention research is important because it involves collaboration between researchers, community support and service providers, and persons with lived experience as care providers, in the design and implementation of clinical studies. This approach helps to ensure that the content and presentation of educational material is relevant and meaningful to the target population and those involved in its delivery, and it leads to a greater understanding of their needs and perspectives.

Introduction: A thorough understanding of the microbial ecology within the swine value chain is essential to develop new strategies to optimize the microbiological quality of pork products. To our knowledge, no study to date has followed the microbiota through the value chain from live farm animals to the cuts of meat obtained for market. The objective of this study is to evaluate how the microbiota of pigs and their environment influence the microbial composition of samples collected throughout the value chain, including the meat plant and meat cuts.Method and results: Results from 16S rDNA sequencing, short-chain fatty acid concentrations and metabolomic analysis of pig feces revealed that the microbiota from two farms with differing sanitary statuses were distinctive. The total aerobic mesophilic bacteria and Enterobacteriaceae counts from samples collected at the meat plant after the pre-operation cleaning and disinfection steps were at or around the detection limit and the pigs from the selected farms were the first to be slaughtered on each shipment days. The bacterial counts of individual samples collected at the meat plant did not vary significantly between the farms. Alpha diversity results indicate that as we move through the steps in the value chain, there is a clear reduction in the diversity of the microbiota. A beta diversity analysis revealed a more distinct microbiota at the farms compared to the meat plant which change and became more uniform as samples were taken towards the end of the value chain. The source tracker analysis showed that only 12.92% of the microbiota in shoulder samples originated from the farms and 81% of the bacteria detected on the dressed carcasses were of unknown origin.Discussion: Overall, the results suggest that with the current level of microbial control at farms, it is possible to obtain pork products with similar microbiological quality from different farms. However, broader studies are required to determine the impact of the sanitary status of the herd on the final products.

Background Poor air quality is associated with poor health. Little attention is given to the complex array of environmental exposures and air pollutants that affect mental health during the life course. Aims We gather interdisciplinary expertise and knowledge across the air pollution and mental health fields. We seek to propose future research priorities and how to address them. Method Through a rapid narrative review, we summarise the key scientific findings, knowledge gaps and methodological challenges. Results There is emerging evidence of associations between poor air quality, both indoors and outdoors, and poor mental health more generally, as well as specific mental disorders. Furthermore, pre-existing long-term conditions appear to deteriorate, requiring more healthcare. Evidence of critical periods for exposure among children and adolescents highlights the need for more longitudinal data as the basis of early preventive actions and policies. Particulate matter, including bioaerosols, are implicated, but form part of a complex exposome influenced by geography, deprivation, socioeconomic conditions and biological and individual vulnerabilities. Critical knowledge gaps need to be addressed to design interventions for mitigation and prevention, reflecting ever-changing sources of air pollution. The evidence base can inform and motivate multi-sector and interdisciplinary efforts of researchers, practitioners, policy makers, industry, community groups and campaigners to take informed action. Conclusions There are knowledge gaps and a need for more research, for example, around bioaerosols exposure, indoor and outdoor pollution, urban design and impact on mental health over the life course.

Abstract Background The different clinical manifestations, from none to severe, and the variability in efficacy of SARS-CoV-2 diagnosis by upper respiratory tract testing, make diagnosis of COVID-19 and prevention of transmission especially challenging. In addition, the ways by which the virus can most efficiently transmit still remain unclear. Case Presentation We report the case a 48-year-old man who presents primary COVID-19 pneumonia. He was initially admitted for cholecystitis but, upon review of his abdominal CT scan, a segmental zone of ground glass opacity was identified in the right lower lobe. A bronchoalveolar lavage proved positive to SARS-CoV-2 by RT-qPCR, even if he tested negative by oro-nasopharyngeal swab at admission and the day after he underwent bronchoscopy. The near absence of the virus in his saliva 2 days after, combined with a very sharp increase in salivary viral load on the third day, also rule out the possibility of prior viral replication in the upper airway and clearance. In addition, rapidly increasing bilateral alveolar lung infiltrates appeared as the upper respiratory tests begin to detect the virus. Conclusions For this patient to have developed primary COVID-19 pneumonia, a contagious aerosol must have traveled to the lower respiratory system. This case gives indirect but compelling evidence that aerosol may spread the virus. It also highlights the limitations of oral and nasal testing methods and the importance of anatomical considerations when studying infections by SARS-CoV-2.

ObjectiveWhile facing personal protective equipment (PPE) shortages during the COVID-19 pandemic, several institutions looked to PPE decontamination and reuse options. This study documents the effect of two hydrogen peroxide treatments on filtration efficiency and fit tests as well as the side effects for volunteers after the decontamination of N95 filtering facepiece respirators (FFRs). We also propose an efficient and large-scale treatment protocol that allows for the traceability of this protective equipment in hospitals during PPE shortages.MethodsThe effects of low-temperature hydrogen peroxide sterilization and hydrogen peroxide vapor (HPV) on two FFR models (filtration, decontamination level, residual emanation) were evaluated. Ten volunteers reported comfort issues and side effects after wearing 1h FFRs worn and decontaminated up to five times.ResultsThe decontamination process does not negatively affect FFR efficiency, but repeated use and handling tend to lead to damage, limiting the number of times FFRs can be reused. Moreover, the recommended 24-h post-treatment aeration does not sufficiently eliminate residual hydrogen peroxide. Prolonged aeration time increased user comfort when using decontaminated FFRs.ConclusionsHPV and low-temperature hydrogen peroxide sterilization seem to be appropriate treatments for FFR decontamination when the PPE is reused by the same user. PPE decontamination and reuse methods should be carefully considered as they are critical for the comfort and safety of healthcare workers.

Moral injuries can occur when perpetrating, failing to prevent, or bearing witness to acts that transgress deeply held moral beliefs and expectations. The COVID-19 crisis highlighted the fact that psychosocial stressors at work, such as high emotional demands, are placing Canadian healthcare workers at risk of moral injuries. Evidence linking psychosocial stressors at work to moral injuries are needed to better predict, prevent and manage moral injuries, as these stressors are frequent and modifiable occupational risk factors. This protocol presents a study aiming to: 1) understand workplace events having the potential to either cause or reduce moral injuries, 2) predict the risk and severity of moral injuries using a disease prevention model, 3) identify biological signatures (biomarkers) associated with psychosocial stressors at work and moral injuries and 4) elaborate preliminary guidelines of organizational practices for frontline healthcare workers to reduce and manage moral injuries. This study is a mixed methods research with three components: qualitative, quantitative and biological. The data collection has been completed and because of the COVID-19 pandemic, it was adjusted to allow for gathering qualitative and quantitative data remotely. Frontline healthcare workers and leaders were included. Through focus groups and individual interviews, and an online questionnaire, events and psychosocial working conditions that may increase the risk of moral injuries will be documented. In addition, blood samples which were collected from a sub-sample of volunteer participants will measure an innovative set of biomarkers associated with vulnerability to stress and mental health. Data analyses are ongoing. We anticipate to identify workplace events that may trigger moral injuries. We expect that potential predictors of moral injury risk occurrence and severity will be identified from psychosocial stressors at work that can be improved by implementing organizational practices. We also expect to observe a different mental health state and biological inflammation signature across workers exposed compared to workers not exposed to psychosocial stressors at work. Based on these future findings, we intend to develop preliminary recommendations of organizational practices for managers. This research will contribute to expand our knowledge of the events in the workplace likely to generate or lessen the impact moral injuries, to build a model for predicting the risk of moral injuries at work, all in the specific context of the COVID-19 health crisis among healthcare workers.

Manure spreading from farm animals can release antibiotic-resistant bacteria (ARB) carrying antimicrobial resistance genes (ARGs) into the air, posing a potential threat to human and animal health due to the intensive use of antibiotics in the livestock industry. This study analyzed the effect of different manure types and spreading methods on airborne bacterial emissions and antibiotic resistance genes in a controlled setting. Cow, poultry manure, and pig slurry were spread in a confined environment using two types of spreaders (splash plate and dribble bar), and the resulting emissions were collected before, during, and after spreading using high-volume air samplers coupled to a particle counter. Total bacteria, fecal indicators, and a total of 38 different subtypes of ARGs were further quantified by qPCR. Spreading poultry manure resulted in the highest emission rates of total bacteria (1011 16S gene copies/kg manure spread), Archaea (106 16S gene copies/kg manure), Enterococcus (105 16S gene copies/kg manure), and E. coli (104 16S gene copies/kg manure), followed by cow manure and pig slurry with splash plates and the dribble bar. Manure spreading was associated with the highest rates of airborne aminoglycoside genes for cow and poultry (106 gene copies/kg manure), followed by pig slurry (104 gene copies/kg manure). This study shows that the type of manure and spreading equipment can affect the emission rates of airborne bacteria, and ARGs.

Nathan Dumont-Leblond et al. present a protocol for lung microbiota analysis, including all steps from patient recruitment to bioinformatics. The data show how methodological variation, such as use of different DNA extraction kits, can impact the results and represent an important step toward methods standardization in the pulmonary microbiome field.

There is currently an ongoing worldwide pandemic of a novel virus belonging to the family of Coronaviruses (CoVs) which are large, enveloped, plus-stranded RNA viruses. Coronaviruses belong to the order of Nidovirales, family of Coronavirinae and are divided into four genera: alphacoronavirus, betacoronavirus, gammacoronavirus and deltacoronavirus. CoVs cause diseases in a wide variety of birds and mammals and have been found in humans since 1960. To date, seven human CoVs were identified including the alpha-CoVs HCoVs-NL63 and HCoVs-229E and the beta-CoVs HCoVs-OC43, HCoVs-HKU1, the severe acute respiratory syndrome-CoV (SARS-CoV), the Middle East respiratory syndrome-CoV (MERS-CoV) and the novel virus that first appeared in December 2019 in Wuhan, China, and rapidly spread to 213 countries as of the writing this paper. It was officially named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by the international committee on taxonomy of viruses (ICTV) and the disease’s name is COVID-19 for coronavirus disease 2019. SARS-CoV-2 is very contagious and is capable of spreading from human to human. Infection routes include droplet and contact, and aerosol transmission is currently under investigation. It is associated with a respiratory illness that may cause severe pneumonia and acute respiratory distress syndrome (ARDS). SARS-CoV-2 became an emergency of international concern. As of July 12, 2020, the virus has been responsible for 12,698,995 confirmed cases and 564,924 deaths worldwide and the number is still increasing. Up until now, no specific treatment has yet been proven effective against SARS-CoV-2. Since the beginning of this outbreak, several interesting papers on SARS-CoV-2 and COVID-19 have been published to report on the phylogenetic evolution, epidemiology, pathogenesis, transmission as well as clinical characteristics of COVID-19 and possible treatments agents.This paper is a systematic review of the available literature on SARS-CoV-2. It was performed in accordance with PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) and aims to help readers access the latest knowledge surrounding this new infectious disease and to provide a reference for future studies.

ABSTRACTThe worldwide repercussions of COVID-19 sparked important research efforts, yet the detailed contribution of aerosols in the transmission of SARS-CoV-2 has not been elucidated. In an attempt to quantify viral aerosols in the environment of infected patients, we collected 100 air samples in acute care hospital rooms hosting 22 patients over the course of nearly two months using three different air sampling protocols. Quantification by RT-qPCR (ORF1b) led to 11 positive samples from 6 patient rooms (Ct < 40). Viral cultures were negative. No correlation was observed between particular symptoms, length of hospital stay, clinical parameters, and time since symptom onset and the detection of airborne viral RNA. Low detection rates in the hospital rooms may be attributable to the appropriate application of mitigation methods according to the risk control hierarchy, such as increased ventilation to 4.85 air changes per hour to create negative pressure rooms. Our work estimates the mean emission rate of patients and potential airborne concentration in the absence of ventilation. Additional research is needed understand aerosolization events occur, contributing factors, and how best to prevent them.

Wastewater treatment plants (WWTPs) are confirmed sources of bioaerosols and can be a hotspot for both antibiotic-resistant bacteria and antibiotic-resistant genes (ARGs). Bioaerosols can be a source of dispersion for bacteria and ARGs into the environment. Biofiltration is one of the most effective technologies to mitigate odors from WWTPs. The objective of this study was to evaluate the capacity of an odor biofiltration system designed to remove volatile compounds, to influence the airborne bacterial diversity and to reduce the aerosolized microbial and ARG concentrations. In total, 28 air samples were collected before and after treatment of an interior WWTP. Overall, air samples collected upstream had higher total bacterial concentrations, and a shift in bacterial diversity was observed. Legionella and Mycobacterium were detected in low abundance upstream and downstream, whereas Legionella pneumophila was detected but not quantifiable in two samples. Of the 31 ARGs and mobile genetic elements detected by quantitative polymerase chain reaction, 15 exhibited a significant reduction in their relative abundance after biofiltration, and none were significantly higher in the effluent. Overall, these results show the benefits of odor biofiltration systems to reduce bacterial and antimicrobial resistance in treated air, a promising application to limit environmental dispersion.

The use of axenic animal models in experimental research has exponentially grown in the past few years and the most reliable way for confirming their axenic status remains unclear. It is especially the case when using individual ventilated positive-pressure cages such as the Isocage. This type of cage are at a greater risk of contamination and expose animals to a longer handling process leading to more potential stress when opened compared to isolators. The aim of this study was to propose simple ways to detect microbial contaminants with Isocages type isolator resulting by developing, validating and optimizing three different methods (culture, microscopy, and molecular). These three approaches were also tested in situ by spiking 21 axenic mice with different microorganisms. Our results suggest that the culture method can be used for feces and surface station (IBS) swabs exclusively (in Brain Heart Infusion for 7 days at 25°C and 37°C in aerobic conditions, and at 30°C in anaerobic conditions), while microscopy (wet mounts) and molecular method (quantitative PCR) were only suitable for fecal matter analyses. In situ results suggests that the culture and molecular methods can detect up to 100% of bacterial contamination events while the microscopy approach generates many erroneous results when not performed by a skilled microscopist. In situ results also suggest that when an axenic mouse is contaminated by a microbial agent, the microorganism will colonize the mouse to such an extent that detection is obvious in 4 days, in average. This report validates simple but complimentary tests that can be used for optimal detection of contaminants in axenic animal facilities using Isocage type isolators.

Lung dendritic cells (DCs) are divided into two major populations, which include CD103+XCR1+ cDC1s and CD11b+Sirpα+ cDC2s. The maintenance of their relative proportions is dynamic and lung inflammation, such as caused by exposure to lipopolysaccharide (LPS), a component of the outer membrane of Gram-negative bacteria, can have a significant impact on the local cDC signature. Alterations in the lung cDC signature could modify the capacity of the immune system to respond to various pathogens. We consequently aimed to assess the impact of the Gram-negative bacteria Pseudomonas aeruginosa on lung cDC1 and cDC2 populations, and to identify the mechanisms leading to alterations in cDC populations. We observed that exposure to P. aeruginosa decreased the proportions of CD103+XCR1+ cDC1s, while increasing that of CD11b+ DCs. We identified two potential mechanisms involved in this modulation of lung cDC populations. First, we observed an increase in bone marrow pre-DC IRF4 expression suggesting a higher propensity of pre-DCs to differentiate towards the cDC2 lineage. This observation was combined with a reduced capacity of lung XCR1+ DC1s to express CD103. In vitro, we demonstrated that GM-CSF-induced CD103 expression on cDCs depends on GM-CSF receptor internalization and RUNX1 activity. Furthermore, we observed that cDCs stimulation with LPS or P. aeruginosa reduced the proportions of intracellular GM-CSF receptor and decreased RUNX1 mRNA expression. Altogether, these results suggest that alterations in GM-CSF receptor intracellular localization and RUNX1 signaling could be involved in the reduced CD103 expression on cDC1 in response to P. aeruginosa. To verify whether the capacity of cDCs to express CD103 following P. aeruginosa exposure impacts the immune response, WT and Cd103-/- mice were exposed to P. aeruginosa. Lack of CD103 expression led to an increase in the number of neutrophils in the airways, suggesting that lack of CD103 expression on cDC1s could favor the innate immune response to this bacterium.

Monitoring antibiotic resistance genes (ARGs) is vital to the One Health approach to tackling the antibiotic resistance crisis. It has been suggested that conifer needles can be used as passive bioaerosol samplers. Here, the use of conifer needles as biomonitors of ARGs in bioaerosols was assessed as a proof-of-concept. Needles were collected from trees surrounding pig farms, villages, and forest sites in Québec, Canada. Needles were homogenised and DNA was extracted. Results of qPCR analyses showed biomass estimates were consistent across samples. Number and quantity of ARGs was significantly lower in forest sites when compared to the farm and village, comprising a distinct resistome. Consistent with previous findings, the most common ARGs were tetracyclines and sulfonamides, which were found close to agricultural activities. Although results were limited, there is great potential for using the conifer phyllosphere as a passive bioaerosol sampler. This method represents an accessible way to promote ARG surveillance over long distances from point sources.

Antimicrobial resistance (AMR) is continuing to grow across the world. Though often thought of as a mostly public health issue, AMR is also a major agricultural and environmental problem. As such, many researchers refer to it as the preeminent One Health issue. Aerial transport of antimicrobial-resistant bacteria via bioaerosols is still poorly understood. Recent work has highlighted the presence of antibiotic resistance genes in bioaerosols. Emissions of AMR bacteria and genes have been detected from various sources, including wastewater treatment plants, hospitals, and agricultural practices; however, their impacts on the broader environment are poorly understood. Contextualizing the roles of bioaerosols in the dissemination of AMR necessitates a multidisciplinary approach. Environmental factors, industrial and medical practices, as well as ecological principles influence the aerial dissemination of resistant bacteria. This article introduces an ongoing project assessing the presence and fate of AMR in bioaerosols across Canada. Its various sub-studies include the assessment of the emissions of antibiotic resistance genes from many agricultural practices, their long-distance transport, new integrative methods of assessment, and the creation of dissemination models over short and long distances. Results from sub-studies are beginning to be published. Consequently, this paper explains the background behind the development of the various sub-studies and highlight their shared aspects.

The SARS-CoV-2 pandemic has created a troublesome issue for employees in biochemistry clinical laboratories due to fears of aerosol generation during sample treatment. This study was designed to assess aerosol production during the pre-analytical procedures for blood and urine samples using a model bacterium. Air sampling and surface swabbing were conducted during four typical procedures. Bacteria were not recovered in any air or surface samples. Other studies have reported low and undetectable SARS-CoV-2 RNA in blood and urine samples, respectively. Therefore, the occupational risk for employees appears to be low in terms of aerosol exposure from processing SARS-CoV-2 patient samples.

Following recent findings linking the human gut microbiota to gastrointestinal cancer and its treatment, the plausible relationship between lung microbiota and pulmonary cancer is explored. This study aims at characterizing the intratumoral and adjacent healthy tissue microbiota by applying a 16S rRNA gene amplicon sequencing protocol to tissue samples of 29 non-small cancer patients. Emphasis was put on contaminant management and a comprehensive comparison of bacterial composition between cancerous and healthy adjacent tissues of lung adenocarcinoma and squamous cell carcinoma is provided. A variable degree of similarity between the two tissues of a same patient was observed. Each patient seems to possess its own bacterial signature. The two types of cancer tissue do not have a distinct bacterial profile that is shared by every patient. In addition, enteric, potentially pathogenic and pro-inflammatory bacteria were more frequently found in cancer than healthy tissue. This work brings insights into the dynamic of bacterial communities in lung cancer and provides prospective data for more targeted studies.

Influenza and RSV are human viruses responsible for outbreaks in hospitals, long-term care facilities and nursing homes. The present study assessed an air treatment using ozone at two relative humidity conditions (RHs) in order to reduce the infectivity of airborne influenza. Bovine pulmonary surfactant (BPS) and synthetic tracheal mucus (STM) were used as aerosols protectants to better reflect the human aerosol composition. Residual ozone concentration inside the aerosol chamber was also measured. RSV's sensitivity resulted in testing its resistance to aerosolization and sampling processes instead of ozone exposure. The results showed that without supplement and with STM, a reduction in influenza A infectivity of four orders of magnitude was obtained with an exposure to 1.70 ± 0.19 ppm of ozone at 76% RH for 80 min. Consequently, ozone could be considered as a virucidal disinfectant for airborne influenza A. RSV did not withstand the aerosolization and sampling processes required for the use of the experimental setup. Therefore, ozone exposure could not be performed for this virus. Nonetheless, this study provides great insight for the efficacy of ozone as an air treatment for the control of nosocomial influenza A outbreaks.

Reported indoor air quality (IAQ) complaints are common even in relatively new or renovated school buildings in Finland. However, detecting the causes for complaints with commonly used indoor air measurements is difficult. This study presents data on perceived and measured IAQ in six comprehensive school buildings in Finland. The aim of this study was to discover the possible differences of perceived and measured IAQ between schools with reported IAQ complaints and schools without reported IAQ complaints. The initial categorisation of schools with (‘problematic schools’) and without (‘comparison schools’) complaints was ensured via a validated indoor climate survey and a recently developed online questionnaire, which were completed by 186 teachers and 1268 students from the six schools. IAQ measurements of physical parameters, gaseous pollutants, particulate matter and bioaerosols were conducted in four problematic school buildings (26 classrooms) and two comparison school buildings (12 classrooms). Using air sampling as well as exhaust air filters and classroom settled dust to detect the presence of elevated concentrations of airborne cultivable microbes and pathogenic, toxigenic and mycoparasitic Trichoderma strains were the most indicative methods in distinguishing problematic schools from comparison schools. Other IAQ-related measurements did not detect clear differences between problematic and comparison schools, as the concentration levels were very low. The results indicate that the complaints reported by occupants could have been related to excess moisture or mould problems that had not been found or repaired. Ventilation pressure condition investigations and simultaneous exhaust and supply air filter dust culture should be addressed precisely in future studies.

This paper presents the performance of two eukaryotic genomic ribosomal regions, ITS1 and ITS2, in describing fungal diversity in aerosol samples using amplicon-based High-Throughput Sequencing (HTS). Composting sites, biomethanization facilities, and dairy farms, all affected by the presence of fungi, were visited to collect air samples. The amplicon-based HTS approach is a target enrichment method that relies on the amplification of a specific target using particular primers before sequencing. Thus, the results are highly dependent on the quality of amplification. For this reason, the authors of this paper used a shotgun metagenomic approach to compare its outcome with the amplicon-based method. Indeed, shotgun metagenomic does not rely on any amplification prior to sequencing, because all genes are sequenced without a specific target. In addition, culture methods were added to the analyses in biomethanization and dairy farms samples to validate their contribution to fungal diversity of aerosols. The results obtained are unequivocal towards ITS1 outperformance to ITS2 in terms of richness, and taxonomic coverage. The differential abundance analysis did demonstrate that some taxa were exclusively detected only by ITS2, and vice-versa for ITS1. However, the shotgun metagenomic approach showed a taxonomic profile more resembling to ITS1 than ITS2. Based on these results, neither of the barcodes evaluated is perfect in terms of distinguishing all species. Using both barcodes offers a broader view of the fungal aerosol population. However, with the actual knowledge, the authors strongly recommend using ITS1 as a universal fungal barcode for quick general analyses of diversity and when limited financial resources are available, primarily due its ability to capture taxonomic profiles similar to those obtained using the shotgun metagenomic. The culture comparison with amplicon-based sequencing showed the complementarity of both approaches in describing the most abundant taxa.

This study was designed to test the efficacy of an air treatment using ozone and relative humidity (RH) for the inactivation of airborne viruses. Four phages (φX174, PR772, MS2 and φ6) and one eukaryotic virus (murine norovirus MNV-1) were exposed to low ozone concentrations (1.23 ppm for phages and 0.23 ppm for MNV-1) and various levels of RH for 10 to 70 minutes. The inactivation of these viruses was then assessed to determine which of the tested conditions provided the greatest reduction in virus infectivity. An inactivation of at least two orders of magnitude for φX174, MS2 and MNV-1 was achieved with an ozone exposure of 40 minutes at 85% RH. For PR772 and φ6, exposure to the reference condition at 20% RH for 10 minutes yielded the same results. These findings suggest that ozone used at a low concentration is a powerful disinfectant for airborne viruses when combined with a high RH. Air treatment could therefore be implemented inside hospital rooms ventilated naturally.

Abstract Electronic cigarette uses propylene glycol and glycerol to deliver nicotine and flavors to the lungs. Given the hundreds of different brands, the thousands of flavors available and the variations in nicotine concentrations, it is likely that electronic cigarette settings and e‐liquid composition affect the size distribution of particles emitted and ultimately pulmonary deposition. We used the inExpose e‐cigarette extension to study two separate modes of operation of electronic cigarettes, namely power‐controlled and the temperature‐controlled. We also assessed several e‐liquids based on propylene glycol and glycerol concentrations, nicotine content, and selected monomolecular flavoring agents (menthol, vanillin, and maltol). Particle size distribution was measured using a Condensation Particle Counter and a Scanning Mobility Particle Sizer spectrometer. Lung deposition was predicted using the International Commission on Radiological Protection model. For all resistance coils, increase in power delivery generated larger particles while maintaining a higher coil temperature generated smaller particles. Increase in glycerol concentration led to the generation of larger particles. With regard to flavors, we showed that despite minor effect of menthol and maltol, vanillin dramatically increased particle size. Presence of nicotine also increased particle size. Finally, particles emitted by the electronic cigarette were predicted to mainly deposit in the alveoli and conditions generating larger particle sizes led to a reduction in predicted lung deposition. This study shows that coil temperature, propylene glycol and glycerol concentrations, presence of nicotine, and flavors affect the size of particles emitted by an electronic cigarette, directly affecting predicted lung deposition of these particles.

The transmission of infectious microbes via bioaerosols is of significant concern for both human and animal health. However, gaps in our understanding of respiratory pathogen transmission and methodological heterogeneity persist. New developments have enabled progress in this domain, and one of the major turning points has been the recognition that cross-disciplinary collaborations across spheres of human and animal health, microbiology, biophysics, engineering, aerobiology, infection control, public health, occupational health, and industrial hygiene are essential. Collaborative initiatives support advances in topics such as bioaerosol behavior, dispersion models, risk assessment, risk/exposure effects, and mitigation strategies in clinical, experimental, agricultural, and other field settings. There is a need to enhance the knowledge translation for researchers, stakeholders, and private partners to support a growing network of individuals and agencies to achieve common goals to mitigate inter- and intra-species pathogen transmission via bioaerosols.

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.

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Little is known about the microbiota shift induced by exacerbation in chronic obstructive pulmonary disease (COPD) patients. The sputa microbiota of COPD patients was evaluated when clinically stable and during acute exacerbations of the disease. Sputa microbiota was analyzed using 16S ribosomal RNA gene pyrosequencing and quantitative polymerase chain reaction-based pathogen detection. Nine COPD patients were enrolled. Pyrosequencing of 16S rRNA genes identified 2,267 unique bacterial operational taxonomic units. Principal microbiota shifts during exacerbation were in either Proteobacteria, Firmicutes or Bacteroidetes. Streptococcus and Moraxella levels were detected during exacerbation in severe (Global Initiative for Chronic Obstructive Lung Disease 3) COPD patients. Most of the clinically-important genera found in the sputum with the pyrosequencing of 16S rRNA gene correlated with specific quantitative polymerase chain reactions for bacteria while respiratory viruses were nearly absent. Sputum microbiotas of exacerbated COPD patients are complex. This pilot study shows a clear shift in the microbiota of patients during exacerbation. The nature of this shift varies from patient to patient in such a way that the treatment should be patient-specific. Further studies are needed to establish the impact of microbial exacerbations on the pulmonary microbiota.

The release of pathogens into the air from swine confinement buildings are mitigated through preventative measures, such as outgoing air filtration, to reduce the risk of spread to nearby barns and communities. The present study aims to characterize the effectiveness of a percolating biofilter developed by the Research and Development Institute for the Agri-environment (IRDA) to capture airborne contaminants, such as bacteria and viruses emitted from a swine finishing room. Over a 10-month period (summer, fall, and winter), air was sampled upwind and downwind of the biofilter using two wet walled cyclonic samplers. Culture-dependent and molecular biology analyses were used to track changes in microbial concentrations and populations both captured and emitted by the percolating biofilter. Results revealed a minor reduction (median reduction efficiency 14.4%) in culturable bacteria. There was a decrease in total bacteria (qPCR) (75.0%) and other qPCR targeted organisms: archaea (42.1%), coliphages (25.6%), Enterococcus (76.1%), and Escherichia coli (40.9%). The community analyses showed similar bacterial diversity in the air upwind and downwind of the biofilter although more Proteobacteria were present downwind of the unit, likely attributable to the Proteobacteria-rich nutritive solution. Evidence is provided for bioaerosols reduction by a percolating biofilter treating air from a swine fattening-finishing room.

Viral diseases can spread through a variety of routes including aerosols. Yet, limited data are available on the efficacy of aerosolized chemicals to reduce viral loads in the air. Bacteriophages (phages) are often used as surrogates for hazardous viruses in aerosol studies because they are inexpensive, easy to handle, and safe for laboratory workers. Moreover, several of these bacterial viruses display physical characteristics similar to pathogenic human and animal viruses, like morphological size, type of nucleic acids, capsid morphology, and the presence of an envelope. In this study, the efficacy of four chemicals was evaluated on four airborne phages at two different relative humidity levels. Non-tailed bacteriophages MS2 (single-stranded RNA), ϕ6 (double-stranded RNA, enveloped), PR772 (double-stranded DNA), and ϕX174 (single-stranded DNA) were first aerosolized in a 55L rotative environmental chamber at 19°C with 25% and 50% relative humidity. Then, hydrogen peroxide, Eugenol (phenylpropene used in commercial perfumes and flavorings), Mist® (automobile disinfectant containing Triethylene glycol), and Pledge® (multisurface disinfectant containing Isopropanol, n-Alkyl Dimethyl Benzyl Amonium Chlorides, and n-Alkyl Dimethyl Ethylbenzyl Ammonium Chloride) were nebulized with the phages using a separate nebulizer. Aerosols were maintained in suspension during 10 minutes, 1 hour, and 2 hours. Viral aerosols were sampled using an SKC BioSampler and samples were analyzed using qPCR and plaque assays. The resistance levels of the four phages varied depending on the relative humidity (RH) and germicidal products tested. Phage MS2 was the most stable airborne virus under the environmental conditions tested while phage PR772 was the least stable. Pledge® and Eugenol reduced the infectivity of all airborne phages tested. At 25% RH, Pledge® and Eugenol were more effective at reducing infectivity of RNA phages ϕ6 and MS2. At 50% RH, Pledge® was the most effective agent against phage MS2. These findings illustrate that various airborne viruses should be tested to demonstrate the effectiveness of germicidal treatments. This research also provides a set of parameters for testing germicidal products in large-scale settings to reduce the risk of virus transmission.

The gut microbiota is associated with the modulation of mucosal immunity and the etiology of inflammatory bowel diseases (IBD). Previous studies focused on the impact of bacterial species on IBD but seldom suspected archaea, which can be a major constituent of intestinal microbiota, to be implicated in the diseases. Recent evidence supports that two main archaeal species found in the digestive system of humans, Methanobrevibacter smithii (MBS) and Methanosphaera stadtmanae (MSS) can have differential immunogenic properties in lungs of mice; with MSS but not MBS being a strong inducer of the inflammatory response. We thus aimed at documenting the immunogenic potential of MBS and MSS in humans and to explore their association with IBD.To validate the immunogenicity of MBS and MSS in humans, peripheral blood mononuclear cells from healthy subjects were stimulated with these two microorganisms and the production of inflammatory cytokine TNF was measured by ELISA. To verify MBS and MSS prevalence in IBD, stool samples from 29 healthy control subjects and 29 patients suffering from IBD were collected for DNA extraction. Plasma was also collected from these subjects to measure antigen-specific IgGs by ELISA. Quantitative PCR was used for bacteria, methanogens, MBS and MSS quantification.Mononuclear cells stimulated with MSS produced higher concentrations of TNF (39.5 ng/ml) compared to MBS stimulation (9.1 ng/ml). Bacterial concentrations and frequency of MBS-containing stools were similar in both groups. However, the number of stool samples positive for the inflammatory archaea MSS was higher in patients than in controls (47% vs 20%). Importantly, only IBD patients developed a significant anti-MSS IgG response.The prevalence of MSS is increased in IBD patients and is associated with an antigen-specific IgG response.

The etiology of bioaerosol-related pulmonary diseases remains poorly understood. Recently, archaea emerged as prominent airborne components of agricultural environments, but the consequences of airway exposure to archaea remain unknown. Since subcomponents of archaea can be immunogenic, we used a murine model to study the pulmonary immune responses to two archaeal species found in agricultural facilities: Methanobrevibacter smithii (MBS) and Methanosphaera stadtmanae (MSS). Mice were administered intranasally with 6.25, 25 or 100 µg of MBS or MSS, once daily, 3 days a week, for 3 weeks. MSS induced more severe histopathological alterations than MBS with perivascular accumulation of granulocytes, pronounced thickening of the alveolar septa, alveolar macrophages accumulation and increased perivascular mononucleated cell accumulation. Analyses of bronchoalveolar lavage fluids revealed up to 3 times greater leukocyte accumulation with MSS compared to MBS. Instillation of 100 µg of MBS or MSS caused predominant accumulation of monocyte/macrophages (4.5×10(5) and 4.8×10(5) cells/ml respectively) followed by CD4(+) T cells (1.38×10(5) and 1.94×10(5) cells/ml respectively), B cells (0.73×10(5) and 1.28×10(5) cells/ml respectively), and CD8(+) T cells (0.20×10(5) and 0.31×10(5) cells/ml respectively) in the airways. Both archaeal species induced similar titers of antigen-specific IgGs in plasma. MSS but not MBS caused an accumulation of eosinophils and neutrophils in the lungs, which surprisingly, correlated inversely with the size of the inoculum. Stronger immunogenicity of MSS was confirmed by a 3 fold higher accumulation of myeloid dendritic cells in the airways, compared to MBS. Thus, the dose and species of archaea determine the magnitude and nature of the pulmonary immune response. This is the first report of an immunomodulatory role of archaeal species found in bioaerosols.