Internally controlled PCR system for detection of airborne microorganisms

Recently, we reported the outcomes of feasibility studies of a technological approach allowing rapid detection of a wide range of bioaerosols by combining a personal bioaerosol sampler with a real-time PCR technology. The protocol was found suitable for detection of targeted microorganisms within relatively short time periods. Considering the crucial importance of the PCR procedure quality control, the current paper reports the results of the development of an internally controlled PCR system for utilization by the above technology. The suggested strategy is based on utilization of only two fluorescent dyes, which are used respectively for target and internal amplification control (IAC) DNA amplification. A bacteriophage T4 and recombinant phage fd (M13) were used in this research as target and IAC, respectively. The constructed IAC was added directly to the collection liquid of the personal bioaerosol sampler enabling quality control to be present throughout the entire sampling-analysis procedures. For performance evaluation, serial ten-fold dilutions of T4 phage were aerosolized and sampled over a 10 minutes time period. The results showed that T4 phage could be reliably detected at the concentration of around 200 PFU per litre of air over the 10 minutes sampling period. The developed PCR assay demonstrated high specificity and no cross reaction. It is concluded that the recombinant phage fd is suitable for utilization as an internal control enabling to significantly minimize false negative results for bioaerosol detection procedures.     

Evaluation of PCR primers and PCR conditions for specific detection of common airborne fungi

We examined the selectivity of 53 sets of primers for environmental monitoring of indoor air quality. Thirty-six fungal strains, representing 26 species from 14 genera of commonly occurring fungi, and 16 different bacterial strains, representing both gram-negative and gram-positive species, were included in the experiment. We verified the specificity of 28 of the 53 sets of primers, which were classified as universal fungal, universal bacterial, group or species specific. The PCR conditions required for optimal specificity were also determined. These results can serve as a guide for the step-wise PCR-based detection and identification of airborne fungi commonly found in indoor environments.     

Assessment of airborne fungal spores in different industrial working environments and their importance as health hazards to workers

A survey to assess the occurrence of airborne fungal spores in three different industries, dairies, carpentries and greenhouses, was carried out. The results revealed considerable fungal pollution in the environments of the industries sampled. Noteworthy was the occurrence of fungal genera frequently implicated in allergic and non-allergic diseases, or well known for the production of mycotoxins in foods or characterized by a marked degradative activity on different substrata. Penicillium, Candida, Mucor and Geotrichum were the most common genera identified in the dairies; Penicillium, Cladosporium, yeasts, Trichoderma and Rhizopus occurred more frequently in the carpentries; Cladosporium, Alternaria, Penicillium and Stemphilium were prevailing in the greenhouse.The results of our survey support the idea that, due to their high incidence and variety, fungal spores may represent a potential health hazard in working environments, where their concentration can be affected by many operations and handling.     

Utilizing pyrosequencing and quantitative PCR to characterize fungal populations among house dust samples

Molecular techniques are an alternative to culturing and counting methods in quantifying indoor fungal contamination. Pyrosequencing offers the possibility of identifying unexpected indoor fungi. In this study, 50 house dust samples were collected from homes in the Yakima Valley, WA. Each sample was analyzed by quantitative PCR (QPCR) for 36 common fungi and by fungal tag-encoded flexible (FLX) amplicon pyrosequencing (fTEFAP) for these and additional fungi. Only 24 of the samples yielded amplified results using fTEFAP but QPCR successfully amplified all 50 samples. Over 450 fungal species were detected by fTEFAP but most were rare. Twenty-two fungi were found by fTEFAP to occur with at least an average of ≥0.5% relative occurrence. Many of these fungi seem to be associated with plants, soil or human skin. Combining fTEFAP and QPCR can enhance studies of fungal contamination in homes.     

Real-time PCR detection of toxigenic Fusarium in airborne and settled grain dust and associations with trichothecene mycotoxins

Inhalation of immunomodulating mycotoxins produced by Fusarium spp. that are commonly found in grain dust may imply health risks for grain farmers. Airborne Fusarium and mycotoxin exposure levels are mainly unknown due to difficulties in identifying Fusarium and mycotoxins in personal aerosol samples. We used a novel real-time PCR method to quantify the fungal trichodiene synthase gene (tri5) and DNA specific to F. langsethiae and F. avenaceum in airborne and settled grain dust, determined the personal inhalant exposure level to toxigenic Fusarium during various activities, and evaluated whether quantitative measurements of Fusarium-DNA could predict trichothecene levels in grain dust. Airborne Fusarium-DNA was detected in personal samples even from short tasks (10-60 min). The median Fusarium-DNA level was significantly higher in settled than in airborne grain dust (p < 0.001), and only the F. langsethiae-DNA levels correlated significantly in settled and airborne dust (r(s) = 0.20, p = 0.003). Both F. langsethiae-DNA and tri5-DNA were associated with HT-2 and T-2 toxins (r(s) = 0.24-0.71, p < 0.05 to p < 00.01) in settled dust, and could thus be suitable as indicators for HT-2 and T-2. The median personal inhalant exposure to specific toxigenic Fusarium spp. was less than 1 genome m(-3), but the exposure ranged from 0-10(5) genomes m(-3). This study is the first to apply real-time PCR on personal samples of inhalable grain dust for the quantification of tri5 and species-specific Fusarium-DNA, which may have potential for risk assessments of inhaled trichothecenes.     

Recovery of Francisella tularensis from soil samples by filtration and detection by real-time PCR and cELISA

The aim of this study was to develop a specific and highly sensitive method able to detect very low concentrations of Francisella tularensis in soil samples by real-time PCR (qPCR) with SYBR Green I. tul4 gene, which encodes the 17-kDa protein (TUL4) in F. tularensis strains, was amplified using a LightCycler (LC) device. We achieved a detection limit of 0.69 fg of genomic DNA from F. tularensis subp. holarctica live vaccine strain (LVS), corresponding to a value less than 3.4 genome equivalents per reaction. The qPCR was shown to be specific, highly sensitive and reproducible. In addition, we evaluated 2 new methods for recovering bacteria from soil based on 1-step filtration using glass fiber filters and PVDF filters. These filtration methods enabled us to recover F. tularensis efficiently from soil samples. As few as 50 CFU per 0.5 g of soil were detected by qPCR. Capture enzyme-linked immunosorbent assay (cELISA) allowed us to detect and quantify the amount of bacteria recovered from soil by an immunological method. Although qPCR was more sensitive than cELISA, we did not observe substantial differences in the amount of bacteria quantified by both methods.     

环境样品中 PCBs 的测定

通过碱解、酸洗、萃取、净化、浓缩、脱硫等步骤处理实际样品,利用毛细管柱GC/ECD进行PCBs的定性和定量.方法定性准确,定量良好,具有较高的回收率.各同系物的方法检出限,水样为0.01～0.08ng/L;土壤样为0.003～0.03μg/kg,可以应用于土壤、沉积物、水样、油样等环境样品中PCBs的测定     

Relationship between airborne fungal allergens and meteorological factors in Manisa City, Turkey

In this study, the effect of relative humidity, temperature, and wind on airborne fungal allergens in the 11 different districts of Manisa City was investigated from January 2004 to December 2005. The aim of this study was to conduct a survey to get to know the relation between wind, temperature, and relative humidity and population of allergenic fungal spores in the atmosphere. A total of 792 samples were observed by using the Merck MAS100 air sampler and 12,988 fungal colonies were counted. Fourteen fungal genera could be determined; Cladosporium that was generally found as the predominant genus followed by Penicillium, Aspergillus, and Alternaria. During the entire study, seasonal variation was found to be related to atmospheric conditions especially. The optimal conditions of meteorological factors for the fungi growth resulted in the increased number of mycoflora, qualitatively and quantitatively.     

Airborne and allergenic fungal spores of the Karachi environment and their correlation with meteorological factors

Airborne fungal spores are well known to cause respiratory allergic diseases particularly bronchial asthma, allergic rhinitis, rhino-conjunctivitis and allergic broncho-pulmonary aspergillosis in both adults and children. In order to monitor and analyze airborne fungal flora of the Karachi environment, an aeromycological study was conducted using a Burkard 7-Day Recording Volumetric Spore Trap from January to December 2010. The data recorded from the Spore Trap was further analyzed for percent catch determination, total spores concentration, seasonal periodicities and diurnal variations. Cladosporium spp (44.8%), Alternaria spp. (15.5%), Periconia spp (6.1%), Curvularia spp (2.1%), Stemphylium spp (1.3%) and Aspergillus/Penicillium type (1%) emerged to be major components constituting more than 70% of the airborne fungal flora. Cladosporium, Curvularia and Stemphylium displayed a clear seasonal trend, while there were no clear seasonal trends for other fungal spore types. Diurnal variations were observed to be mainly having daytime maxima. Spearman Rank Correlation Coefficient analysis was conducted using various weather parameters. The various fungal types showed a negative correlation with heat index, dew point, wind velocity and wind chill. However, a positive correlation was found with humidity, rain and barometric pressure. In fact, Alternaria, Bipolaris and Periconia showed a negative correlation with temperature, while Cladosporium and Periconia showed a negative correlation with heat index, dew point, wind velocity and wind chill. The barometric pressure was positively correlated with Cladosporium. On the basis of these findings, it can be concluded that a number of fungal spores are present in the atmosphere of Karachi throughout the year, with certain atmospheric conditions influencing the release, dispersion, and sedimentation processes of some genera. It is expected that clinicians will use the identified fungal flora for diagnosis and treatment and/or adopt preventative measures for allergic individuals.     

Intervention study of airborne fungal spora in homes with portable HEPA filtration units

The concentrations and composition of airborne fungal spores in homes fitted with portable HEPA filtration units were examined to provide information to evaluate the importance of varying levels of fungal spores in residential environments in Perth, Australia. A novel method for simulating activity/impaction on carpeted environments was also investigated. Reductions in fungal (35%) and particulate (38%) levels were achieved in the air filter homes. Penicillium, Cladosporium and yeasts were the most common and widespread fungi recovered indoors and outdoors. Fungal range decreased over the study period but this could be due to an overall reduced dissemination of spores (less spores in the air).     

Application of flow cytometry and cell sorting to the bacterial analysis of environmental aerosol samples

Flow cytometry (FCM) combined with viability staining is a useful tool in discerning viable bacteria in environmental samples where traditional culture methods may fail. Contamination of aerosol samples with dust and other non-biological particles can interfere with accurate sample analysis and therefore there is a desire to exclude those particles from analysis. Particles were sorted according to their light scattering properties, cultured and isolates obtained. Isolates were cultured in suspension and reanalyzed by flow cytometry. The isolates were also analyzed and identified by DNA sequence analysis. Isolates with statistically similar light scattering properties shared common sequence identification. Isolates exhibited distinct light scattering profiles that roughly correlated with their originating gate, but often the peak of the profile was outside that gate.     

Study of heavy metals in some environmental samples

Fuels like coal and rubber are frequently used for brick burning. However, both coal and rubber contain heavy metals. These heavy metals may elutriate in the wake of fly ash or may adsorb or absorb in the product. The present work deals with the analysis of heavy metals in some samples collected from brick burning industries located in the vicinity of a metropolitan city, Peshawar, Pakistan. Samples from raw clay, product, chimney scale and fossil fuel & rubber were collected and leached with acid mixture. The leachates were concentrated and analyzed by atomic absorption spectrophotometer for the determination of chromium (Cr), lead (Pb), cadmium (Cd) and antimony (Sb). It was observed that heavy metals are present in clay, brick and chimney scale. However, significant amount of these metals was observed in chimney scale. It is inferred that such emanations laden with heavy metals are accompanying the stack gases which are being dumped in to the environment. In order to avoid environmental problems, strict environmental regulations shall be enforced and a constant check on these emanations to the environment must be made to ensure clean air act.     

Stability and storage problems in organotin speciation in environmental samples

The stability of both tributyltin (TBT) and triphenyltin (TPT) in water, sediment, oysters and cockles was studied over a period of 18 months using several storage conditions. Butyltins were stable in unacidified sea-water stored in polycarbonate bottles in the dark at 4 degrees C for 7 months, but half of the TBT concentration was lost after 540 d. A comparable preservation time was achieved for butyltins stored on C18 cartridges at room temperature. However, phenyltins extracted from sea-water were stable for only 60 d stored on cartridges and even more pronounced losses (about 90% after 540 d) occurred when they were stored in either polycarbonate or Pyrex glass bottles. Losses of organotins were observed in sediments after air drying and pasteurization treatments using a freeze-dried sediment as a comparator, whereas both butyltin and phenyltin species remained stable in sediments stored at -20 degrees C for the 18 months tested, irrespective of the treatment used for stabilization. Air drying followed by pasteurization was shown to be superior to other treatments for the stabilization of organotin compounds in sediments stored at higher temperatures, but 30% of TBT was lost after 540 d at 25 degrees C. Finally, butyltins were stable in both frozen cockles and oysters in the dark over a 7 month period and in freeze-dried samples stored at 4 degrees C for 5 months, but TBT losses of about 70% were observed after 540 d.     

Air sampling of fungal spores on filters. An investigation on passive sampling and viability

In this study, glycerol was tested as a collection substrate for passive bioaerosol sampling. Filters (mixed cellulose acetate and nitrate) were soaked in glycerol and exposed for an aerosol from three different fungal species: Penicillum commune, Aspergillus versicolor and Paecilomyces variotii. The passive sampling method was compared with a closed-face polycarbonate filter sampling method. Exposure was performed in an exposure chamber. The total number of spores was determined by microscopic techniques, and the cultivable number was determined by cultivation on Malt Extract Agar dishes. The glycerol soaked filter demonstrated a good correlation with the closed-face sampler with regard to the total count. Spores stored in a pumped filter cassette were not affected by storage for up to 7 days. On the other hand, the culturability of the spores was markedly decreased after 1 day when stored on glycerol soaked filters.     

Methodologies for determination of antimony in terrestrial environmental samples

Methodologies for the environmental analysis of total antimony and aqueous chemical speciation are critically reviewed, including preparation techniques for aqueous and solid matrices and the determination of solid state partitioning and recommendations are given for future research directions. Concentrations of total antimony commonly present in aqueous and solid environmental samples are readily determined using present day analytical techniques. This has resulted primarily from technological advances in microwave digestion for solid matrices and the development of plasma based analyte detection systems. ICP-AES and ICP-MS techniques are both utilised for the environmental analysis of total antimony concentrations. However, ICP-MS is increasingly favoured as a result of reduced spectral interferences and the potential for analyte detection in the pg mL(-1) range. Determination of aqueous antimony speciation presents a number of complex analytical challenges and highly selective separation and identification techniques are required prior to detection. The majority of published techniques including common applications of hydride generation are insufficiently selective for the determination of intrinsic chemical speciation and often only oxidation state data are obtained. The recent in-line applications of HPLC-ICP-MS offer the potential for highly selective separations of aqueous antimony species and determination of detailed chemical speciation data. However, considerable development work is required to optimise chromatographic separations and identify uncharacterised species resident in environmental systems. Analytical techniques to aid the determination of antimony's associations with solid environmental matrices include the application of chemical extraction procedures and leaching experiments. To date, this area of analytical research has received little attention and further studies are required to elucidate this aspect of antimony's environmental chemistry.     

Detection of airborne Legionella while showering using liquid impingement and fluorescent in situ hybridization (FISH)

Aerosols of water contaminated with Legionella bacteria constitute the only mode of exposure for humans. However, the prevention strategy against this pathogenic bacteria risk is managed through the survey of water contamination. No relationship linked the Legionella bacteria water concentration and their airborne abundance. Therefore, new approaches in the field of the metrological aspects of Legionella bioaerosols are required. This study was aimed at testing the main principles for bioaerosol collection (solid impaction, liquid impingement and filtration) and the in situ hybridization (FISH) method, both in laboratory and field assays, with the intention of applying such methodologies for airborne Legionella bacteria detection while showering. An aerosolization chamber was developed to generate controlled and reproducible L. pneumophila aerosols. This tool allowed the identification of the liquid impingement method as the most appropriate one for collecting airborne Legionella bacteria. The culturable fraction of airborne L. pneumophila recovered with the liquid impingement principle was 4 and 700 times higher compared to the impaction and filtration techniques, respectively. Moreover, the concentrations of airborne L. pneumophila in the impinger fluid were on average 7.0 x 10(5) FISH-cells m(-3) air with the fluorescent in situ hybridization (FISH) method versus 9.0 x 10(4) CFU m(-3) air with the culture method. These results, recorded under well-controlled conditions, were confirmed during the field experiments performed on aerosols generated by hot water showers in health institutions. This new approach may provide a more accurate characterization of aerobiocontamination by Legionella bacteria.     

Application of cryofocusing hydride generation and atomic fluorescence detection for dissolved mercury species determination in natural water samples

The concentration levels of mercury (Hg) species in natural water samples are usually low. Consequently, accurate analysis with low detection limits is still a major problem. In this work, a method was applied for the simultaneous direct determination of dissolved mercury species in water samples by on-line hydride generation (HG), cryogenic trapping (CT), gas chromatography (GC) and detection by atomic fluorescence spectrometry (AFS). The suitability of the method for real samples with different organic matter and chloride contents was evaluated by recovery experiments in synthetic and natural spiked water samples. The HG method was compared with other current available methods for mercury analysis with respect to the different fraction of mercury analysed, i.e. 'reactive', 'reducible' or total. HG derivatization and SnCl2 reduction (with and without previous oxidation with BrCl) were applied to synthetic and natural (spiked and non-spiked) water samples. The influence of chloride and dissolved organic matter concentrations was studied. The results suggest that the HG procedure is suitable for the simultaneous determination of Hg2+ and MeHg+ in surface water samples. Inorganic mercury analysed by HG (i.e. reducible) is close to the total inorganic mercury.     

Study of chemical composition and morphology of airborne particles in Chandigarh, India using EDXRF and SEM techniques

The elemental composition and morphology of aerosols, collected from March 95 to February 96 and March 96 to August 96 respectively in the city of Chandigarh, India is determined using Energy Dispersive X-ray fluorescence and scanning electron microscopic techniques. The elemental concentration levels are found to be higher by a factor of 2-7 in the spring season as compared to the rainy season. The concentration of spherical and non-spherical (i.e. elongated) aerosols is more in the spring season and is reduced drastically in the rainy season due to the prominent wash out effect of rains. More accurate particle classification and source identification is obtained when based on combination of chemical composition and particle morphology. Possible sources identified from this analysis are soil dust, Industrial activity, Agricultural and Garbage burning, Maritime aerosols and Automobile exhaust.