Efficiency of Airborne Sample Analysis Platform (ASAP) bioaerosol sampler for pathogen detection

Potential airborne human pathogens: A relevant inhabitant in built environments but not considered in indoor air quality standards

Potential airborne human pathogens (PAHPs) may be a relevant component of the air microbiome in built environments. Despite that PAHPs can cause infections, particularly in immunosuppressed patients at medical centers, they are scarcely considered in standards of indoor air quality (IAQ) worldwide. Here, we reviewed the current information on microbial aerosols (bacteria, fungal and viruses) and PAHPs in different types of built environments (e.g., medical center, industrial and non-industrial), including the main factors involved in their dispersion, the methodologies used in their study and their associated biological risks. Our analysis identified the human occupancy and ventilation systems as the primary sources of dispersal of microbial aerosols indoors. We also observed temperature and relative humidity as relevant physicochemical factors regulating the dispersion and viability of some PAHPs. Our analysis revealed that some PAHPs can survive and coexist in different environments while other PAHPs are limited or specific for an environment. In relation to the methodologies (conventional or molecular) the nature of PAHPs and sampling type are pivotal. In this context, indoors air-borne viruses are the less studies because their small size, environmental lability, and absence of efficient sampling techniques and universal molecular markers for their study. Finally, it is noteworthy that PAHPs are not commonly considered and included in IAQ standards worldwide, and when they are included, the total abundance is the single parameter considered and biological risks is excluded. Therefore, we propose a revision, design and establishment of public health policies, regulations and IAQ standards, considering the interactions of diverse factors, such as nature of PAHPs, human occupancy and type of built environments where they develop.

Detection of hospital environmental contamination during SARS-CoV-2 Omicron predominance using a highly sensitive air sampling device

Background and objectives

The high transmissibility of SARS-CoV-2 has exposed weaknesses in our infection control and detection measures, particularly in healthcare settings. Aerial sampling has evolved from passive impact filters to active sampling using negative pressure to expose culture substrate for virus detection. We evaluated the effectiveness of an active air sampling device as a potential surveillance system in detecting hospital pathogens, for augmenting containment measures to prevent nosocomial transmission, using SARS-CoV-2 as a surrogate.

Methods

We conducted air sampling in a hospital environment using the AerosolSense^TM air sampling device and compared it with surface swabs for their capacity to detect SARS-CoV-2.

Results

When combined with RT-qPCR detection, we found the device provided consistent SARS-CoV-2 detection, compared to surface sampling, in as little as 2 h of sampling time. The device also showed that it can identify minute quantities of SARS-CoV-2 in designated "clean areas" and through a N95 mask, indicating good surveillance capacity and sensitivity of the device in hospital settings.

Conclusion

Active air sampling was shown to be a sensitive surveillance system in healthcare settings. Findings from this study can also be applied in an organism agnostic manner for surveillance in the hospital, improving our ability to contain and prevent nosocomial outbreaks.

Environmental DNA reveals diversity and abundance of Alternaria species in neighbouring heterogeneous landscapes in Worcester, UK

Alternaria is a pathogenic and allergenic fungus affecting 400 plant species and 334 million people globally. This study aimed at assessing the diversity of Alternaria species in airborne samples collected from closely located (7 km apart) and heterogeneous sites (rural, urban and unmanaged grassland) in Worcester and Lakeside, the UK. A secondary objective was to examine how the ITS1 subregion varies from ITS2 in Alternaria species diversity and composition. Airborne spores were collected using Burkard 7-day and multi-vial Cyclone samplers for the period 5 July 2016-9 October 2019. Air samples from the Cyclone were amplified using the ITS1and ITS2 subregions and sequenced using Illumina MiSeq platform whereas those from the Burkard sampler were identified and quantified using optical microscopy. Optical microscopy and eDNA revealed a high abundance of Alternaria in the rural, urban and unmanaged sites. ITS1 and ITS2 detected five and seven different Alternaria species at the three sampling sites, respectively. A. dactylidicola, A. metachromatica and A. infectoria were the most abundant. The rural, urban and unmanaged grassland sites had similar diversity (PERMANOVA) of the species due to similarity in land use and proximity of the sites. Overall, the study showed that heterogeneous and neighbouring sites with similar land uses can have similar Alternaria species. It also demonstrated that an eDNA approach can complement the classical optical microscopy method in providing more precise information on fungal species diversity in an environment for targeted management. Similar studies can be replicated for other allergenic and pathogenic fungi.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s10453-022-09760-9.

Evaluation of a bioaerosol sampler for indoor environmental surveillance of Severe Acute Respiratory Syndrome Coronavirus 2

The worldwide spread of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has ubiquitously impacted many aspects of life. As vaccines continue to be manufactured and administered, limiting the spread of SARS-CoV-2 will rely more heavily on the early identification of contagious individuals occupying reopened and increasingly populated indoor environments. In this study, we investigated the utility of an impaction-based bioaerosol sampling system with multiple nucleic acid collection media. Heat-inactivated SARS-CoV-2 was utilized to perform bench-scale, short-range aerosol, and room-scale aerosol experiments. Through bench-scale experiments, AerosolSense Capture Media (ACM) and nylon flocked swabs were identified as the highest utility media. In room-scale aerosol experiments, consistent detection of aerosol SARS-CoV-2 was achieved at an estimated aerosol concentration equal to or greater than 0.089 genome copies per liter of room air (gc/L) when air was sampled for eight hours or more at less than one air change per hour (ACH). Shorter sampling periods (75 minutes) yielded consistent detection at ~31.8 gc/L of room air and intermittent detection down to ~0.318 gc/L at (at both 1 and 6 ACH). These results support further exploration in real-world testing scenarios and suggest the utility of indoor aerosol surveillance as an effective risk mitigation strategy in occupied buildings.

A potential approach for assessing the quality of human and nonhuman adenoviral vector preparations

Various types of human and nonhuman adenoviral (AdV) vectors are being used as gene delivery vectors in preclinical and clinical investigations. The objective of this study was to determine the ratio between the 2 best assays that would effectively address the variability in the titration of various AdV vectors in different cell lines and help obtain consistent results in preclinical and clinical studies using different AdV vectors. Here, we compared plaque-forming units, tissue culture infectious dose 50, focus-forming units (FFU), virus particle (VP) count, and genome copy number (GCN) of purified preparations of human AdV type C5, bovine AdV type 3, and porcine AdV type 3 to determine a correlation between infectious and noninfectious virus particles. Our results suggest that a VP:FFU or a VP:GCN ratio could accurately reflect the quality of an AdV preparation and could serve as an indicator to control batch-to-batch variability.

Bioaerosol Sampling: Classical Approaches, Advances, and Perspectives

Bioaerosol sampling is an essential and integral part of any bioaerosol investigation. Since bioaerosols are very diverse in terms of their sizes, species, biological properties, and requirements for their detection and quantification, bioaerosol sampling is an active, yet challenging research area. This paper was inspired by the discussions during the 2018 International Aerosol Conference (IAC) (St. Louis, MO) regarding the need to summarize the current state of the art in bioaerosol research, including bioaerosol sampling, and the need to develop a more standardized set of guidelines for protocols used in bioaerosol research. The manuscript is a combination of literature review and perspectives: it discusses the main bioaerosol sampling techniques and then overviews the latest technical developments in each area; the overview is followed by the discussion of the emerging trends and developments in the field, including personal sampling, application of passive samplers, and advances toward improving bioaerosol detection limits as well as the emerging challenges such as collection of viruses and collection of unbiased samples for bioaerosol sequencing. The paper also discusses some of the practical aspects of bioaerosol sampling with particular focus on sampling aspects that could lead to bioaerosol determination bias. The manuscript concludes by suggesting several goals for bioaerosol sampling and development community to work towards and describes some of the grand bioaerosol challenges discussed at the IAC 2018.

DNA metabarcoding uncovers fungal diversity of mixed airborne samples in Italy

Fungal spores and mycelium fragments are particles which become and remain airborne and have been subjects of aerobiological studies. The presence and the abundance of taxa in aerobiological samples can be very variable and impaired by changeable climatic conditions. Because many fungi produce mycotoxins and both their mycelium fragments and spores are potential allergens, monitoring the presence of these taxa is of key importance. So far data on exposure and sensitization to fungal allergens are mainly based on the assessment of few, easily identifiable taxa and focused only on certain environments. The microscopic method used to analyze aerobiological samples and the inconspicuous fungal characters do not allow a in depth taxonomical identification. Here, we present a first assessment of fungal diversity from airborne samples using a DNA metabarcoding analysis. The nuclear ITS2 region was selected as barcode to catch fungal diversity in mixed airborne samples gathered during two weeks in four sites of North-Eastern and Central Italy. We assessed the taxonomic composition and diversity within and among the sampled sites and compared the molecular data with those obtained by traditional microscopy. The molecular analyses provide a tenfold more comprehensive determination of the taxa than the traditional morphological inspections. Our results prove that the metabarcoding analysis is a promising approach to increases quality and sensitivity of the aerobiological monitoring. The laboratory and bioinformatic workflow implemented here is now suitable for routine, high-throughput, regional analyses of airborne fungi.