Evaluation of interference to conventional and real-time PCR for detection and quantification of fungi in dust

Advances in polymerase chain reaction (PCR) have permitted accurate, rapid and quantitative identification of microorganisms in pure cultures regardless of viability or culturability. In this study, a simple sample processing method was investigated for rapid identification and quantification of fungal spores from dust samples using both conventional and real-time PCR. The proposed method was evaluated for susceptibility to interference from environmental dust samples. Stachybotrys chartarum and Aspergillus fumigatus were used as test organisms. The sensitivity of detection in pure culture was 0.1 spore DNA equivalents per PCR reaction corresponding to 20 spores ml(-1) in the sample. However, 1 spore DNA equivalent per PCR reaction corresponding to 200 spores ml(-1) in the sample was the lowest amount of spores tested without interference in dust samples spiked with spores of either fungal species. The extent of inhibition was calculated using conventional and real-time PCR reactions containing fungal spores, specific primers, specific probes (for real-time PCR) and various amounts of dust. The results indicate that the extent of inhibition by dust on PCR varies with the type and amount of dust, and number of spores. No interference in the analysis of spiked samples was detected from 0.2 mg ml(-1) of four real-life dust samples at p-value >0.05 using 2 x 10(4) spores for conventional PCR and 2 x 10(5) spores for real-time PCR. However, samples containing >0.2 mg ml(-1) real-life dust compromised the PCR assay. These results suggest the potential usefulness of a simple sample processing method in conjunction with PCR for monitoring the fungal content of aerosols collected from indoor environments.     

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.     

实时荧光定量PCR法快速测定水中微囊藻

以铜绿微囊藻（Microcystis aeruginosa）16S rRNA基因片段为靶序列设计一对特异性引物,采用Real-time PCR法,对铜绿微囊藻进行定性、定量检测。试验表明,仅含铜绿微囊藻DNA模板的样品有特异性扩增,扩增产物熔解曲线平稳,峰尖且窄,熔解温度为（87±1）℃。以重组质粒pMD-18T-16S为标准品,检测区间为1．1×102 copies/mL～1．1×108 copies/mL,所得标准曲线符合制备实时定量PCR标准曲线的要求,对标准品进行测定,方法检出限为11 copies/mL。用该标准曲线对实验室培养获得的铜绿微囊藻DNA样品进行定量检测,与显微镜计数结果基本一致。     

Molecular detection of three gastroenteritis viruses in urban surface waters in Beijing and correlation with levels of fecal indicator bacteria

To assess the presence of three gastroenteritis viruses responsible for human acute gastroenteritis in surface water, a 1-year study was carried out in the city of Beijing, China. A total of 108 urban surface water samples were collected from nine collection sites which were defined with a global positioning system in rivers or lakes from September 2006 to August 2007. The water samples were subjected to virus concentration using an HA electronegative filter, followed by polymerase chain reaction (PCR) for rotavirus (RV) astrovirus (AV), and norovirus (NV). It showed that the number of viruses detected in water samples from different sites was variable, totaling 63 virus strains, with rotavirus (48.1%) verified as the most prevalent detected, followed by astrovirus (AV, 5.6%), and norovirus (NV, 4.6%). RV was also quantified by real-time PCR and the concentration of RV ranged from 0 to 18.27 genome copies·L(-1). And the distributions of RV in surface water were abundant in cold weather (from September to February) while less prevailing in warm weather (from March to August). The high detection rate of RV we encountered in this study provided convincing evidence that RV circulated at a certain frequency in the Beijing population. There was no statistically significant correlation between RV levels and both fecal coliform (R (2)?=?0.02) and Enterococcus faecalis (R (2)?=?0.02) densities. Our study suggests prolonged virus persistence in aquatic environments and emphasizes the enteric virus group as the most reliable for environmental monitoring.     

Multiplex-PCR and PCR-RFLP assays to monitor water quality against pathogenic bacteria

In this work we developed and optimized two molecular-based approaches to monitor rapidly, sensitively and specifically bacterial pathogens from three different genera, Escherichia coli, Pseudomonas aeruginosa, and Salmonella spp., directly in waters. To achieve this aim, firstly a multiplex-PCR assay (M-PCR) was optimized using a primer pair specific for each pathogen. Secondly, as a molecular confirmatory test after isolation of the pathogens by classical microbiological methods, PCR-RFLP of their amplified 16S rDNA genes was performed. It was observed from the results that the developed M-PCR assay has significant impact on the ability to detect sensitively, rapidly and specifically the three pathogens directly in water within a short time (5 h from sampling to obtain final results), therefore it represents a considerable advancement over other known more time-consuming and less-sensitive methods for identification and characterization of these kinds of pathogens.     

Real-time PCR for detection of the Aspergillus genus

Aspergillus is a genus of mold that has strong indoor sources, including several species capable of acting as opportunistic pathogens. Previous studies suggest that Aspergillus could serve as an indicator for abnormal mold growth or moisture, making it an important genus for environmental monitoring. Here, a quantitative polymerase chain reaction (qPCR, or real-time PCR) assay is presented for Aspergillus. The assay shows good specificity for the genus, detecting all Aspergillus species tested, although a few non-Aspergillus species are also amplified. Sensitivity testing demonstrates that DNA representing one conidium can be detected. A validation study compared qPCR results against direct microscopy counts using A. fumigatus conidia aerosolized into a laboratory chamber. The assay was then used to quantify Aspergillus in indoor air samples, demonstrating its utility for environmental monitoring. Analysis of a small number of clinical sputum samples showed complete agreement with culturing results.     

Simultaneous determination of malachite green, enrofloxacin and ciprofloxacin in fish farming water and fish feed by liquid chromatography with solid-phase extraction

An effective and sensitive method for simultaneous analysis of malachite green (MG), enrofloxacin (ENFLX) and ciprofloxacin (CPFLX) by liquid chromatography-diode array detection with solid-phase extraction (SPE) is developed. The conditions of SPE and LC were investigated and optimised. The effective separation of these compounds was achieved using a ZY1104 C18 column (250 × 4.6 mm, 5 μm) with 20 mM tetrabutyl ammonium bromide (pH 3.0)-acetonitrile as mobile phase and gradient elution. The diode array detection was used at 278 nm for ENFLX and CPFLX and at 613 nm for MG. Under the optimal conditions, the method LOD values of MG, ENFLX and CPFLX were 0.01, 0.07 and 0.10 μg L(?-1) for fish farming water samples and 1.5, 10.5 and 15 μg kg(?-1) for fish feed samples, respectively. The relative recoveries of the three analytes were achieved to be 76.7-82.3% with the RSDs (n = 5) of 3.2-4.6% for spiked fish farming water samples and 78.8-93.7% with the RSDs (n = 5) of 3.1-4.8% for spiked fish feed samples.     

Microbial contamination of dental unit waterlines in Istanbul, Turkey

The water used in dental unit waterlines (DUWLs) acts as a coolant for the high-speed equipment and as an irrigant during dental treatments. There are kind of water tanks. DUWLs provide a favorable environment for microbial biofilm and multiplation primarily due to the high surface in the tubing and the character of fluid dynamics in narrow, smooth-walled waterlines. Biofilms can harbour opportunist pathogens such as Legionella sp., Pseudomonas sp. Several studies have shown that DUWLs have high levels of microbial contamination. Presence of high level of microbial contamination is an important problem for dentists and dental patients who are immunocompromised. We collected water samples from DUWLs of 20 private dental offices. We have determined that only 2 (3.4%) out of 59 dental unit water samples were found to meet the standard (<200 CFU.ml(-1)) for DUWLs water quality by American Dental Association (ADA). Of the 59 water samples examined, 14 (24%) were positive for Pseudomonas sp. and 18 (30.5%) were positive for fungi. The most common 14 bacterial strains and seven fungi were isolated. Of bacterial strains, 57.1% were identified: Majority of the bacterial species isolated from our samples was identified as Pseudomonas fluorescens, Pasteurella haemolytica, Photobacterium damsela, Ochrobacter anthropi, Moraxella sp., Aspergillus flavus, Penicillium expansum. Legionella sp. were not detected in all water samples.     

Detection and quantification of Cladosporium in aerosols by real-time PCR

Cladosporium is one of the most common airborne molds found in indoor and outdoor environments. Cladosporium spores are important aeroallergens, and prolonged exposure to elevated spore concentrations can provoke chronic allergy and asthma. To accurately quantify the levels of Cladosporium in indoor and outdoor environments, two real-time PCR systems were developed in this study. The two real-time PCR systems are highly specific and sensitive for Cladosporium detection even in a high background of other fungal DNAs. These methods were employed to quantify Cladosporium in aerosols of five different indoor environments. The investigation revealed a high spore concentration of Cladosporium (10(7) m(-3)) in a cow barn that accounted for 28-44% of the airborne fungal propagules. In a countryside house that uses firewood for heating and in a paper and pulp factory, Cladosporium was detected at 10(4) spores m(-3), which accounted for 2-6% of the fungal propagules in the aerosols. The concentrations of Cladosporium in these three indoor environments far exceeded the medical borderline level (3000 spores m(-3)). In a power station and a fruit and vegetable storage, Cladosporium was found to be a minor component in the aerosols, accounted for 0.01-0.1% of the total fungal propagules. These results showed that monitoring Cladosporium in indoor environments is more important than in outdoor environments from the public health point of view. Cladosporium may not be the dominant fungi in some indoor environments, but its concentration could still be exceeding the threshold value for clinical significance. The methods developed in this study could facilitate accurate detection and quantification of Cladosporium for public health related risk assessment.     

Mercury concentration in fish from Piracicaba River (Minas Gerais, Brazil)

Mercury emissions from some upstream gold mining areas and recent findings of high natural Hg levels in sediments motivated studies on the Hg cycle in the Minas Gerais state. The study presents the total mercury amount found in Geophagus brasiliensis' muscular tissue (wet weight) and sediments from Piracicaba River. Mercury was analyzed using acid digestion followed by determination of total mercury by cold vapour atomic absorption spectrophotometry. This study was also complemented with the analysis of the limnological parameters (water temperature, conductivity, total dissolved solids, suspended particles, pH, dissolved oxygen, maximum depth, photic index and total carbon). The mercury concentration in sediments samples was higher than the mercury concentration in muscular tissue of fish. The lowest Hg level measured in fish was 0.0147 microg g( - 1), while the highest was 0.101 microg g( - 1). In the sediment samples, the lowest and highest levels were 0.02 microg g( - 1) and 0.16 microg g( - 1), respectively. The Hg concentrations in fish and sediment were both under the maximum limit permitted by the World Health Organization.     

Total mercury levels in nine species of freshwater fish from two hydroelectric reservoirs and a crater lake in Ghana

Total mercury (Hg) concentrations were determined in the muscle tissue of fish from three reservoirs in Ghana, namely, Lake Bosomtwi, Kpong and Akosombo Hydroelectric Reservoirs. A total of 165 fish samples covering nine species were collected and analysed for total mercury. A mixture of HNO3, H2SO4 and HClO4 were used for complete oxidation of organic tissues. Hg was detected by the Cold Vapour Atomic Absorption Spectrometry technique using an automatic mercury analyzer. Total mercury concentrations in microg g(-1) (wet weight) ranged from below 0.001 to 0.070 for fish from Lake Bosomtwi, 0.010 to 0.275 for fish from Kpong Reservoir and from below 0.001 to 0.042 for fish from Akosombo Reservoir. All the results obtained are below the World Health Organization limit of 0.5 microg g(-1). The low levels of total mercury obtained in this study suggest that the three aquatic environments have not been significantly impacted by mercury contamination.     

Removal and recovery of metals from a coal pile runoff

The removal and recovery of heavy metals from a coal pilerunoff water using a mixture of multiple metal-tolerantbacterial strains of ATCC 55673, and ATCC 55674 and a Pseudomonas sp. was investigated. The analysis of elementalcomposition of metal precipitates recovered from the bacterialbiomass by transmission electron microscopy and energy dispersiveX-ray analysis revealed the presence of metals originally presentin the wastewater. In addition, analysis of metals in culturesupernatant and bacterial biomass by inductively coupled plasmaemission spectroscopy (ICP-ES) indicated a removal range of 82-100% and a recovery of 15-58% of metals from the wastewater and bacterial biomass, respectively.     

Development of an enzyme-linked immunosorbent assay for screening contamination by chlorophenols in environmental waters

The development of an immunoassay for screening contamination by chlorophenols is presented. Two haptens were synthesized and conjugated to immunizing proteins to raise rabbit polyclonal antibodies. The antibody-coated format (direct) gave better sensitivity than the conjugate-coated format (indirect) if 2,4,6-trichlorophenol is used as target analyte. The measurement range was 86.4 microg l(-1) to 0.7 microg l(-1), with an average I50 of 7.8 microg l(-1) and a detection limit of 0.2 microg l(-1). The assay detects the presence of trichloropyridinol and other chlorophenols such as di-, tetra- and pentachlorophenols constituting thus a suitable tool for the early warning of the presence of such family contaminants. The optimized method permits the detection of the most important chlorophenols in a fast and reproducible way using no more than one antibody and a single assay. The results achieved with water samples spiked with different chlorophenols fit with a multiple linear regression model when expressing the total concentration of chlorophenols as equivalent of 2,4,6-trichlorophenol (P < 0.01), demonstrating the usefulness of the assay as a screening tool to detect contamination by chlorophenols.     

Biomonitoring of polychlorinated biphenyls (PCBs) in heavily polluted aquatic environment in different fish species

The distribution and concentrations of polychlorinated biphenyls (PCBs) were determined in fish species (European perch Perca fluviatilis, northern pike Esox lucius, pike perch Sander lucioperca, wels catfish Silirus glanus, common carp Cyprinus carpio, European eel Anguilla anguilla, freshwater bream Abramis brama, goldfish Carassius auratus, and roach Rutilus rutilus) in a heavily polluted water reservoir Zemplínska ?írava (Slovakia). The study performed at two different time points 5?years apart (2004 and 2009) revealed serious PCB contamination of fish muscle tissue and significant interspecies as well as tissue-specific differences in PCB uptake by fish. Total PCBs broadly correlated with the trophic position of individual fish species within a food chain (P??0.05). The study has shown that the kind of fish, its feeding habit, and specific conditions of the habitat are mutually interrelated factors that are responsible for significant variations in fish body burdens. A tendency to PCB biomagnification was also proved in some fish species of this water reservoir.     

Genetic damage induced by lead chloride in different tissues of fresh water climbing perch Anabas testudineus (Bloch)

The present investigation was undertaken to study the induction of DNA damage by lead chloride (PbCl(2)) in freshwater climbing perch Anabas testudineus using alkaline single cell gel electrophoresis (comet assay). Based on the LC(50) values of lead chloride of A. testudineus three different concentrations viz., 0.1, 1.0 and 2.0 mg/L were selected to expose fish. The DNA damage was observed in the gill, kidney and liver tissue as the percentage of DNA in comet tails and comet heads in the tissue of the exposed fish. DNA damage at different concentrations showed sensitivity to particular tissue. The liver tissue exhibited significantly (p < 0.01) higher DNA damage, followed by kidney and gill. However, the DNA damage was found to be dose dependent; at 2 mg/L of PbCl(2) the tail and head DNA of liver tissue were 57.84% and 39.49%, in kidney tissue the values were 52.36% and 44.97% whereas in gill tissue the values were 48.86% and 48.96% respectively. The current study explored the utility of the comet assay for in vivo laboratory studies using A. testudineus species for screening the genotoxic potential of lead chloride.     

长江上游合江江段鱼类早期资源与向家坝水库生态调度效果初步研究

合江江段是长江上游干流保持河流生境、适宜喜流水性鱼类栖息的重要江段.为了掌握合江江段鱼类早期资源动态,分析向家坝水库生态调度的效果,于2020年向家坝水库生态调度前后,开展了鱼类早期资源逐日监测.研究期间,共采集到鱼类早期资源5目10科38种(属),其中仔鱼29种(属)、鱼卵19种(属),包括特有鱼类6种.广适应性和喜...     

Molecular quantification of virulence gene-containing Aeromonas in water samples collected from different drinking water treatment processes

Pathogenic species of Aeromonas produce a range of virulence factors, including aerolysin, cytotonic enterotoxins, and serine protease, to cause acute gastroenteritis and wound infections in humans and animals. Recognizing that not all Aeromonas strains are pathogenic, in this study, we proposed to evaluate Aeromonas removal effectiveness based on the presence of virulence gene-containing Aeromonas as a proper means to assess microbial risk of Aeromonas. We developed and applied real-time PCR assays to quantify serine protease (ser) gene- and heat-labile cytotonic enterotoxin (alt) gene-containing Aeromonas in water samples. Among 18 Aeromonas isolates from the source water, only three isolates possessed all three genes (aer, ser, and alt). A higher percent of isolates has either ser gene (89%) or alt gene (72%) compared to the percent of isolates containing aer gene (44%). Results of this study suggested that several different conventional and unconventional drinking water treatment processes could effectively remove Aeromonas from source water. As the comprehensive knowledge of the distribution of virulence factors in different Aeromonas species is currently not available, using real-time PCR to quantify various virulence factor genes in water samples and/or isolates can be a practical means for better assessment of microbial risks in water.     

Assessment of pathogenic bacteria in water and sediment from a water reservoir under tropical conditions (Lake Ma Vallée), Kinshasa Democratic Republic of Congo

This study was conducted to assess potential human health risks presented by pathogenic bacteria in a protected multi-use lake-reservoir (Lake Ma Vallée) located in west of Kinshasa, Democratic Republic of Congo (DRC). Water and surface sediments from several points of the Lake were collected during summer. Microbial analysis was performed for Escherichia coli, Enterococcus (ENT), Pseudomonas species and heterotrophic plate counts. PCR amplification was performed for the confirmation of E. coli, ENT, Pseudomonas spp. and Pseudomonas aeruginosa isolated from samples. The results reveal low concentration of bacteria in water column of the lake, the bacterial quantification results observed in this study for the water column were below the recommended limits, according to WHO and the European Directive 2006/7/CE, for bathing water. However, high concentration of bacteria was observed in the sediment samples; the values of 2.65?×?10³, 6.35?×?10³, 3.27?×?10³ and 3.60?×?10⁸ CFU g^?1 of dry sediment for E. coli, ENT, Pseudomonas spp. and heterotrophic plate counts, respectively. The results of this study indicate that sediments of the Lake Ma Vallée can constitute a reservoir of pathogenic microorganisms which can persist in the lake. Possible resuspension of faecal indicator bacteria and pathogens would affect water quality and may increase health risks to the population during recreational activities. Our results indicate that the microbial sediment analysis provides complementary and important information for assessing sanitary quality of surface water under tropical conditions.