Storage effects on bacterial concentration: determination of impinger and filter samples

Filter forensics: microbiota recovery from residential HVAC filters

BACKGROUND

Establishing reliable methods for assessing the microbiome within the built environment is critical for understanding the impact of biological exposures on human health. High-throughput DNA sequencing of dust samples provides valuable insights into the microbiome present in human-occupied spaces. However, the effect that different sampling methods have on the microbial community recovered from dust samples is not well understood across sample types. Heating, ventilation, and air conditioning (HVAC) filters hold promise as long-term, spatially integrated, high volume samplers to characterize the airborne microbiome in homes and other climate-controlled spaces. In this study, the effect that dust recovery method (i.e., cut and elution, swabbing, or vacuuming) has on the microbial community structure, membership, and repeatability inferred by Illumina sequencing was evaluated.

RESULTS

The results indicate that vacuum samples captured higher quantities of total, bacterial, and fungal DNA than swab or cut samples. Repeated swab and vacuum samples collected from the same filter were less variable than cut samples with respect to both quantitative DNA recovery and bacterial community structure. Vacuum samples captured substantially greater bacterial diversity than the other methods, whereas fungal diversity was similar across all three methods. Vacuum and swab samples of HVAC filter dust were repeatable and generally superior to cut samples. Nevertheless, the contribution of environmental and human sources to the bacterial and fungal communities recovered via each sampling method was generally consistent across the methods investigated.

CONCLUSIONS

Dust recovery methodologies have been shown to affect the recovery, repeatability, structure, and membership of microbial communities recovered from dust samples in the built environment. The results of this study are directly applicable to indoor microbiota studies utilizing the filter forensics approach. More broadly, this study provides a better understanding of the microbial community variability attributable to sampling methodology and helps inform interpretation of data collected from other types of dust samples collected from indoor environments.

Aerobiology: Experimental Considerations, Observations, and Future Tools

Understanding airborne survival and decay of microorganisms is important for a range of public health and biodefense applications, including epidemiological and risk analysis modeling. Techniques for experimental aerosol generation, retention in the aerosol phase, and sampling require careful consideration and understanding so that they are representative of the conditions the bioaerosol would experience in the environment. This review explores the current understanding of atmospheric transport in relation to advances and limitations of aerosol generation, maintenance in the aerosol phase, and sampling techniques. Potential tools for the future are examined at the interface between atmospheric chemistry, aerosol physics, and molecular microbiology where the heterogeneity and variability of aerosols can be explored at the single-droplet and single-microorganism levels within a bioaerosol. The review highlights the importance of method comparison and validation in bioaerosol research and the benefits that the application of novel techniques could bring to increasing the understanding of aerobiological phenomena in diverse research fields, particularly during the progression of atmospheric transport, where complex interdependent physicochemical and biological processes occur within bioaerosol particles.

Characterizing the bacterial communities in retail stores in the United States

The microorganisms present in retail environments have not been studied in detail despite the fact that these environments represent a potentially important location for exposure. In this study, HVAC filter dust samples in 13 US retail stores were collected and analyzed via pyrosequencing to characterize the indoor bacterial communities and to explore potential relationships between these communities and building and environmental parameters. Although retail stores contained a diverse bacterial community of 788 unique genera, over half of the nearly 118K sequences were attributed to the Proteobacteria phylum. Streptophyta, Bacillus, Corynebacterium, Pseudomonas, and Acinetobacter were the most prevalent genera detected. The recovered indoor airborne microbial community was statistically associated with both human oral and skin microbiota, indicating occupants are important contributors, despite a relatively low occupant density per unit volume in retail stores. Bacteria generally associated with outdoor environments were present in the indoor communities with no obvious association with air exchange rate, even when considering relative abundance. No significant association was observed between the indoor bacterial community recovered and store location, store type, or season. However, predictive functional gene profiling showed significant associations between the indoor community and season. The microbiome recovered from multiple samples collected months apart from the same building varied significantly indicating that caution is warranted when trying to characterize the bacterial community with a single sampling event.

Detection of viable antibiotic-resistant/sensitive Acinetobacter baumannii in indoor air by propidium monoazide quantitative polymerase chain reaction

Acinetobacter baumannii represents a significant cause of nosocomial infections. Therefore, we combined real-time quantitative polymerase chain reaction (PCR) with the propidium monoazide (PMA-qPCR) to assess the feasibility of detecting viable, airborne A. baumannii. The biological collection efficiencies of three samplers for collecting airborne A. baumannii were evaluated by PMA-qPCR in a chamber study. After sampling, the effects of storage in collection fluid on A. baumannii were evaluated. The results showed that the culturable ratio of A. baumannii measured using the culture method was significantly correlated with the viable ratio measured using PMA-qPCR, but was not significantly correlated with the qPCR results. It was indicated that the AGI-30 impinger and the BioSampler were much more effective than the Nuclepore filter sampler for collecting airborne A. baumannii. The storage temperature was critical for aerosol samples, as the loss of viable A. baumannii was minimized when the PMA-bound DNA was stored at -20°C or if the collected cells were stored at 4°C and subsequently processed by PMA-qPCR within 1 month. The PMA-qPCR method was also to distinguish between colistin-sensitive and colistin-resistant A. baumannii, and no colistin-sensitive A. baumannii was detected by PMA-qPCR upon treatment of the BioSampler collection medium with 2 μg/ml colistin for 5 min.

Methods for quantifying Staphylococcus aureus in indoor air

Staphylococcus aureus has been detected in indoor air and linked to human infection. Quantifying S. aureus by efficient sampling methods followed by appropriate sample storage treatments is essential to characterize the exposure risk of humans. This laboratory study evaluated the effects of sampler type (all-glass impinger (AGI-30), BioSampler, and Andersen one-stage sampler (Andersen 1-STG)), collection fluid (deionized water (DW), phosphate-buffered saline (PBS), and Tween mixture (TM)), and sampling time (3-60 min) on cell recovery. Effects of storage settings on bacterial concentration were also assessed over 48 h. Results showed BioSampler performed better than Andersen 1-STG and AGI-30 (P < 0.05) and TM was superior to PBS and DW (P < 0.05). An increase in sampling time negatively affected the recoveries of cells in PBS of BioSampler and AGI-30 (P < 0.05), whereas cell recoveries in TM were increased at sampling of 6-15 min compared with 3 min. Concentrations of cells collected in PBS were decreased with storage time at 4 and 23 °C (P < 0.05), while cells stored in TM showed stable concentrations at 4 °C (P > 0.05) and increased cell counts at 23 °C (P < 0.05). Overall, sampling by BioSampler with TM followed by sample transportation and storage at 4 °C is recommended.

Comparison of antibiotic resistance, biofilm formation and conjugative transfer of Staphylococcus and Enterococcus isolates from International Space Station and Antarctic Research Station Concordia

The International Space Station (ISS) and the Antarctic Research Station Concordia are confined and isolated habitats in extreme and hostile environments. The human and habitat microflora can alter due to the special environmental conditions resulting in microbial contamination and health risk for the crew. In this study, 29 isolates from the ISS and 55 from the Antarctic Research Station Concordia belonging to the genera Staphylococcus and Enterococcus were investigated. Resistance to one or more antibiotics was detected in 75.8 % of the ISS and in 43.6 % of the Concordia strains. The corresponding resistance genes were identified by polymerase chain reaction in 86 % of the resistant ISS strains and in 18.2 % of the resistant Concordia strains. Plasmids are present in 86.2 % of the ISS and in 78.2 % of the Concordia strains. Eight Enterococcus faecalis strains (ISS) harbor plasmids of about 130 kb. Relaxase and/or transfer genes encoded on plasmids from gram-positive bacteria like pIP501, pRE25, pSK41, pGO1 and pT181 were detected in 86.2 % of the ISS and in 52.7 % of the Concordia strains. Most pSK41-homologous transfer genes were detected in ISS isolates belonging to coagulase-negative staphylococci. We demonstrated through mating experiments that Staphylococcus haemolyticus F2 (ISS) and the Concordia strain Staphylococcus hominis subsp. hominis G2 can transfer resistance genes to E. faecalis and Staphylococcus aureus, respectively. Biofilm formation was observed in 83 % of the ISS and in 92.7 % of the Concordia strains. In conclusion, the ISS isolates were shown to encode more resistance genes and possess a higher gene transfer capacity due to the presence of three vir signature genes, virB1, virB4 and virD4 than the Concordia isolates.

Comparison of sampling methods for the assessment of indoor microbial exposure

Indoor microbial exposure has been related to allergy and respiratory disorders. However, the lack of standardized sampling methodology is problematic when investigating dose-response relationships between exposure and health effects. In this study, different sampling methods were compared regarding their assessment of microbial exposures, including culturable fungi and bacteria, endotoxin, as well as the total inflammatory potential (TIP) of dust samples from Danish homes. The Gesamtstaubprobenahme (GSP) filter sampler and BioSampler were used for sampling of airborne dust, whereas the dust fall collector (DFC), the electrostatic dust fall collector (EDC), and vacuum cleaner were used for sampling of settled dust. The GSP assessed significantly higher microbial levels than the BioSampler, yet measurements from both samplers correlated significantly. Considerably higher levels of fungi, endotoxin, and TIP were found in the EDC compared with the DFC, and regarding fungi, the EDC correlated more strongly and significantly with vacuumed dust than the DFC. Fungi in EDC and vacuum dust correlated most strongly with airborne dust, and in particular, the measurements from the EDC associated well with those from GSP. Settled dust from the EDC was most representative of airborne dust and may thus be considered as a surrogate for the assessment of indoor airborne microbial exposure.

PRACTICAL IMPLICATIONS

Significant discrepancies between sampling methods regarding indoor microbial exposures have been revealed. This study thus facilitates comparison between methods and may therefore be used as a frame of reference when studying the literature or when conducting further studies on indoor microbial exposure. Results also imply that the relatively simple EDC method for the collection of settled dust may be used as an alternative to otherwise tedious and time-consuming airborne dust sampling.

Evaluation of the airborne bacterial population in the periodically confined Antarctic base Concordia

The environmental airborne bacterial population in relation to human confinement was investigated over a period of 1 year in the Concordia Research Station, which is located on the Eastern Antarctic plateau. The unique location of the station makes it suitable for different research domains such as glaciology, atmospheric sciences, astronomy, etc. Furthermore, it is used as a test bed for long-duration spaceflights to study the physiologic and psychological adaptation to isolated environments. A total of 96 samples were collected at eight different locations in the station at regular intervals. The airborne bacterial contamination was for 90% of the samples lower than 10.0 x 10(2) colony-forming units per cubic meter of air (CFU/m(3)) and the total bacterial contamination increased over time during confinement but diminished after re-opening of the base. Viable airborne bacteria with different morphology were identified by biochemical analyses. The predominant microflora was identified as Staphylococcus sp. (24.9% of total) and Bacillus sp. (11.6% of total) and was associated with human activity, but also environmental species such as Sphingomonas paucimobilis (belonging to the alpha-Proteobacteria) could establish themselves in the airborne population. A few opportunistic pathogens (6%) were also identified.

Development of a method for bacteria and virus recovery from heating, ventilation, and air conditioning (HVAC) filters

The aim of the work presented here is to study the effectiveness of building air handling units (AHUs) in serving as high volume sampling devices for airborne bacteria and viruses. An HVAC test facility constructed according to ASHRAE Standard 52.2-1999 was used for the controlled loading of HVAC filter media with aerosolized bacteria and virus. Nonpathogenic Bacillus subtilis var. niger was chosen as a surrogate for Bacillus anthracis. Three animal viruses; transmissible gastroenteritis virus (TGEV), avian pneumovirus (APV), and fowlpox virus were chosen as surrogates for three human viruses; SARS coronavirus, respiratory syncytial virus, and smallpox virus; respectively. These bacteria and viruses were nebulized in separate tests and injected into the test duct of the test facility upstream of a MERV 14 filter. SKC Biosamplers upstream and downstream of the test filter served as reference samplers. The collection efficiency of the filter media was calculated to be 96.5 +/- 1.5% for B. subtilis, however no collection efficiency was measured for the viruses as no live virus was ever recovered from the downstream samplers. Filter samples were cut from the test filter and eluted by hand-shaking. An extraction efficiency of 105 +/- 19% was calculated for B. subtilis. The viruses were extracted at much lower efficiencies (0.7-20%). Our results indicate that the airborne concentration of spore-forming bacteria in building AHUs may be determined by analyzing the material collected on HVAC filter media, however culture-based analytical techniques are impractical for virus recovery. Molecular-based identification techniques such as PCR could be used.

Collection efficiencies of aerosol samplers for virus-containing aerosols

Collection efficiencies of four bioaerosol samplers (Andersen impactor, AGI-30 impinger, gelatin filter, and nuclepore filter) were evaluated for virus-containing aerosols. Four different bacteriophages were used as surrogates for the mammalian viruses. Results showed that the collection efficiency was significantly affected by the morphology of the virus particles. For hydrophilic viruses, the collection efficiencies of the Andersen impactor, impinger, and gelatin filter were 10 times higher than that of the nuclepore filter. For hydrophilic viruses, the collection efficiencies of all four samplers were 10-100 times higher than hydrophobic viruses. The infectivity of the virus in collected samples was also evaluated for an AGI-30 impinger. Results showed that the viruses retained more infectivity when the samples were refrigerated (up to 1 day) during storage than when stored at room temperature (up to 8 h). Therefore, even when refrigerated, airborne virus samples collected using an impinger should be processed as soon as possible to avoid loss of virus infectivity.

Source bioaerosol concentration and rRNA gene-based identification of microorganisms aerosolized at a flood irrigation wastewater reuse site

Reuse of partially treated domestic wastewater for agricultural irrigation is a growing practice in arid regions throughout the world. A field sampling campaign to determine bioaerosol concentration, culturability, and identity at various wind speeds was conducted at a flooded wastewater irrigation site in Mexicali, Baja California, Mexico. Direct fluorescent microscopy measurements for total microorganisms, culture-based assays for heterotrophs and gram-negative enteric bacteria, and small-subunit rRNA gene-based cloning were used for microbial characterizations of aerosols and effluent wastewater samples. Bioaerosol results were divided into two wind speed regimens: (i) below 1.9 m/s, average speed 0.5 m/s, and (ii) above 1.9 m/s, average speed 4.5 m/s. Average air-borne concentration of total microorganisms, culturable heterotrophs, and gram-negative enteric bacteria were, respectively, 1.1, 4.2, and 6.2 orders of magnitude greater during the high-wind-speed regimen. Small-subunit rRNA gene clone libraries processed from samples from air and the irrigation effluent wastewater during a high-wind sampling event indicate that the majority of air clone sequences were more than 98% similar to clone sequences retrieved from the effluent wastewater sample. Overall results indicate that wind is a potential aerosolization mechanism of viable wastewater microorganisms at flood irrigation sites.