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Diguta CF, Rousseaux S, Weidmann S, Bretin N, Vincent B, Guilloux-Benatier M, Alexandre H. Development of a qPCR assay for specific quantification of Botrytis cinerea on grapes. FEMS Microbiol Lett 2010; 313:81-7. [DOI: 10.1111/j.1574-6968.2010.02127.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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52
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Watanabe M, Lee K, Goto K, Kumagai S, Sugita-Konishi Y, Hara-Kudo Y. Rapid and effective DNA extraction method with bead grinding for a large amount of fungal DNA. J Food Prot 2010; 73:1077-84. [PMID: 20537263 DOI: 10.4315/0362-028x-73.6.1077] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
To identify a rapid method for extracting a large amount of DNA from fungi associated with food hygiene, extraction methods were compared using fungal pellets formed rapidly in liquid media. Combinations of physical and chemical methods or commercial kits were evaluated with 3 species of yeast, 10 species of ascomycetous molds, and 4 species of zygomycetous molds. Bead grinding was the physical method, followed by chemical methods involving sodium dodecyl sulfate (SDS), cetyl trimethyl ammonium bromide (CTAB), and benzyl chloride and two commercial kits. Quantity was calculated by UV absorbance at 260 nm, quality was determined by the ratio of UV absorbance at 260 and 280 nm, and gene amplifications and electrophoresis profiles of whole genomes were analyzed. Bead grinding with the SDS method was the most effective for DNA extraction for yeasts and ascomycetous molds, and bead grinding with the CTAB method was most effective with zygomycetous molds. For both groups of molds, bead grinding with the CTAB method was the best approach for DNA extraction. Because this combination also is relatively effective for yeasts, it can be used to extract a large amount of DNA from a wide range of fungi. The DNA extraction methods are useful for developing gene indexes to identify fungi with molecular techniques, such as DNA fingerprinting.
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Affiliation(s)
- M Watanabe
- Division of Microbiology, National Institute of Health Sciences, Kamiyoga 1-18-1, Setagaya-ku, Tokyo 158-8501, Japan.
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el Khoury A, Atoui A. Ochratoxin a: general overview and actual molecular status. Toxins (Basel) 2010; 2:461-93. [PMID: 22069596 PMCID: PMC3153212 DOI: 10.3390/toxins2040461] [Citation(s) in RCA: 267] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2010] [Revised: 03/05/2010] [Accepted: 03/08/2010] [Indexed: 11/16/2022] Open
Abstract
Ochratoxin A (OTA) is a mycotoxin produced by several species of Aspergillus and Penicillium fungi that structurally consists of a para-chlorophenolic group containing a dihydroisocoumarin moiety that is amide-linked to L-phenylalanine. OTA is detected worldwide in various food and feed sources. Studies show that this molecule can have several toxicological effects such as nephrotoxic, hepatotoxic, neurotoxic, teratogenic and immunotoxic. A role in the etiology of Balkan endemic nephropathy and its association to urinary tract tumors has been also proved. In this review, we will explore the general aspect of OTA: physico-chemical properties, toxicological profile, OTA producing fungi, contaminated food, regulation, legislation and analytical methods. Due to lack of sufficient information related to the molecular background, this paper will discuss in detail the recent advances in molecular biology of OTA biosynthesis, based on information and on new data about identification and characterization of ochratoxin biosynthetic genes in both Penicillium and Aspergillus species. This review will also cover the development of the molecular methods for the detection and quantification of OTA producing fungi in various foodstuffs.
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Affiliation(s)
- André el Khoury
- Centre d’analyses et de recherches, Faculté des Sciences, Université Saint-Joseph, Beyrouth, Lebanon
| | - Ali Atoui
- Lebanese Atomic Energy Commission-CNRS, P.O. Box 11-8281, Riad El Solh, 1107 2260 Beirut, Lebanon
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55
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Advances in molecular detection of Aspergillus: an update. Arch Microbiol 2010; 192:409-25. [DOI: 10.1007/s00203-010-0563-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2009] [Revised: 11/01/2009] [Accepted: 03/10/2010] [Indexed: 10/19/2022]
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Oliveira M, Amorim MI, Ferreira E, Delgado L, Abreu I. Main airborne Ascomycota spores: characterization by culture, spore morphology, ribosomal DNA sequences and enzymatic analysis. Appl Microbiol Biotechnol 2010; 86:1171-81. [PMID: 20143229 DOI: 10.1007/s00253-010-2448-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2009] [Revised: 01/04/2010] [Accepted: 01/10/2010] [Indexed: 10/19/2022]
Abstract
The aim of this work was to identify the main allergy-related Ascomycetes fungal spores present in the atmosphere of Porto, using different and complementary techniques. The atmospheric sampling, performed in the atmosphere of Porto (Portugal) from August 2006 to July 2008, indicated Cladosporium, Penicillium, Aspergillus and Alternaria as the main fungal spore taxa. Alternaria and Cladosporium peaks were registered during summer. Aspergillus and Penicillium highest values were registered from late winter to early spring. Additionally, the Andersen sampler allowed the culture and isolation of the collected viable spores subsequently used for different identification approaches. The internal-transcribed spacer region of the nuclear ribosomal repeat unit sequences of airborne Ascomycetes fungi isolates revealed 11 taxonomically related fungal species. Among the identified taxa, Penicillum and Aspergillus presented the highest diversity, while only one species of Cladosporium and Alternaria, respectively, were identified. All selected fungal spore taxa possessed phosphatase, esterase, leucine arylamidase and beta-glucosidase enzymatic activity, while none had lipase, cystine arylamidase, trypsin or beta-glucuronidase activity. The association between the spore cell wall morphology, DNA-based techniques and enzymatic activity approaches allowed a more reliable identification procedure of the airborne Ascomycota fungal spores.
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Affiliation(s)
- Manuela Oliveira
- Biology Department, Faculty of Sciences, University of Porto, Porto, Portugal
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Yamamoto N, Kimura M, Matsuki H, Yanagisawa Y. Optimization of a real-time PCR assay to quantitate airborne fungi collected on a gelatin filter. J Biosci Bioeng 2010; 109:83-8. [DOI: 10.1016/j.jbiosc.2009.06.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2009] [Revised: 05/26/2009] [Accepted: 06/15/2009] [Indexed: 11/30/2022]
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Buchheidt D, Hummel M, Schleiermacher D, Spiess B, Hehlmann R. Current Molecular Diagnostic Approaches to Systemic Infections withAspergillusSpecies in Patients with Hematological Malignancies. Leuk Lymphoma 2009; 45:463-8. [PMID: 15160907 DOI: 10.1080/10428190310001593210] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Within the recent years, novel molecular methods, especially PCR assays, have been developed to improve the diagnosis of invasive aspergillosis in patients with malignant hematological diseases being at high risk for this life-threatening infection. Early diagnosis and treatment are essential for adequate therapeutical management, which however, often remains difficult since most of the diagnostic tools used clinically at present either lack specificity or acceptable sensitivity. The clinical value, advantages and remaining problems of recently developed molecular approaches to detect the emerging fungal pathogen are reviewed.
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Affiliation(s)
- Dieter Buchheidt
- 3.Medizinische Klinik, Universitätsklinikum Mannheim, Ruprecht-Karls- Universität Heidelberg, Germany.
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Yamamoto N, Matsuzaka Y, Kimura M, Matsuki H, Yanagisawa Y. Comparison of dry- and wet-based fine bead homogenizations to extract DNA from fungal spores. J Biosci Bioeng 2009; 107:464-70. [PMID: 19332310 DOI: 10.1016/j.jbiosc.2008.12.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2008] [Revised: 11/05/2008] [Accepted: 12/06/2008] [Indexed: 11/19/2022]
Abstract
The present study explored DNA extraction kinetics from fungal spores, i.e., Aspergillus niger, Penicillium chrysogenum and Cladosporium sphaerospermum, by fine bead mill homogenization. In particular, the study aimed to investigate basic differences between the dry- and wet-based methods. The results showed higher initial rates of the DNA extractions by the dry-based method than by the wet-based method, due to higher collision efficiency among fine beads and fungal spores. Based on the experimental results, we constructed kinetic models. While the results by the wet-based method were fitted well with an existing first-order release-degradation model, the results by the dry-based method were not fitted well. Meanwhile, a newly constructed first-order release-degradation model, assuming a proportion of the DNA remained inside the disrupted spore cells and protected from further sheer stress, showed good correlations. The real-time PCR assays showed the PCR efficiencies of the DNA obtained by the dry-based method were higher than those by the wet-based method likely due to increased moderate fragmentation of the DNA by the dry-based method. Thus, although wet-based methods have been commonly used, dry-based methods might also be applicable to achieve efficient extraction and PCR amplification of fungal DNA.
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Affiliation(s)
- Naomichi Yamamoto
- Department of Nursing, School of Health Sciences, Tokai University, Bohseidai, Isehara-shi, Kanagawa, Japan.
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60
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Rabbani M, Sadeghi HM, Karjoo Z. Molecular detection of Streptomyces griseus isolated from Isfahan soil. Pak J Biol Sci 2009; 10:3374-9. [PMID: 19090153 DOI: 10.3923/pjbs.2007.3374.3379] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The aim of the present study was to detect Streptomyces griseus from Isfahan soil using biochemical, morphological and molecular techniques. Soil samples were collected from different regions (compost, 50 year old garden, river bed, clove, wheat farms and domestic yards) of Isfahan in two different seasons. One gram of each sample was serially diluted and cultivated in a primary isolation medium. Morphological shapes of colonies and vegetative hyphae were initially used to separate the grown bacteria of the samples. Various biochemical tests based on Bergey's manual of systemic bacteriology were performed to separate the Streptomyces from other related Genera. In order to further separate Streptomyces grisesus, Polymerase Chain Reaction (PCR) was used to detect the presence of aphE and strA genes in isolated colonies. Biochemical and morphological results, showed the presence of several species of Streptomyces in the collected samples. The expected band of 924 bp belonging to strA gene was observed in the positive control bacterial DNA (PTCC 1125). Several other bands were also observed in the positive control sample. From the total of 10 colonies that undergone molecular detection for the presents of strA gene, 6 colonies (W1, W3, W5, F4, F5, F26) showed only one band at 750 bp and four (W1, W3, F5, F26) showed an extra band of approximately 924 bp band as well. The expected band of 671 bp belonging to aphE gene was detected in positive control bacterial DNA (PTCC 1125). None of the soil samples, however, showed the presence of the aphE gene (data not shown).
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Affiliation(s)
- M Rabbani
- Department of Pharmaceutical Biotechnology, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
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Cruz P, Buttner MP. Development and evaluation of a real-time quantitative PCR assay for Aspergillus flavus. Mycologia 2008; 100:683-90. [PMID: 18959152 DOI: 10.3852/08-022] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Aspergillus flavus is a ubiquitous mold and the most common mold contaminating foodstuffs. Many strains of A. flavus produce aflatoxins. In addition it is an allergen and an opportunistic pathogen of animals and plants. A. flavus often is underestimated in traditional culture analyses due to the expertise required and the cost associated with speciating members of the genus Aspergillus. The goal of this study was to develop and validate a primer and probe set for the rapid detection and quantitation of A. flavus in pure culture using real-time quantitative polymerase chain reaction (QPCR) amplification. Unique DNA regions were located in the genome of the target organism by sequence comparison with the GenBank database, and several candidate oligonucleotides were identified from the scientific literature for potential use with the TaqMan QPCR technology. Three primer and probe sets were designed and validated for specificity and sensitivity in laboratory experiments. Initial screening to test for sensitivity was performed with seven A. flavus isolates and selected nontarget fungi. Specificity testing was conducted with the selected primer and probe set, which amplified all nine A. flavus isolates tested, including an aflatoxin producing strain. The primers did not amplify DNA extracted from 39 other fungal species (comprising 16 genera), including 18 other Aspergillus species and six Penicillium species. No amplification of human or bacterial DNA was observed; however cross-reactivity was observed with Aspergillus oryzae. PCR analysis of DNA dilutions and the use of an internal positive control demonstrated that 67% of the fungal DNA samples assayed contained PCR inhibitors. The assay validated for the target organism is capable of producing PCR results in less than 1 h after DNA extraction. The results of this research demonstrate the capabilities of QPCR for the enhanced detection and enumeration of fungi of significance to human health.
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Affiliation(s)
- Patricia Cruz
- Microbiology Division, Harry Reid Center for Environmental Studies, University of Nevada, Las Vegas, 4505 S. Maryland Parkway, Box 4009, Las Vegas, Nevada 89154-4009, USA.
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Macher J, Chen B, Rao C. Field evaluation of a personal, bioaerosol cyclone sampler. JOURNAL OF OCCUPATIONAL AND ENVIRONMENTAL HYGIENE 2008; 5:724-734. [PMID: 18780236 DOI: 10.1080/15459620802400159] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
A personal cyclone sampler (cyclone) was operated continuously alongside a 25-mm filter sampler (filter), a slit impactor (Burkard slide), and a high-volume cyclone sampler (Burkard cyclone) at an outdoor location with abundant naturally occurring fungi (N = 30; sampling time: 12.5 +/- 2.3 hr). Air concentrations (spore m(-3)) of 28 fungal groups were determined for all samplers by microscopy. Cyclone performance was judged using various indices to determine if it agreed with the other samplers in determination of the frequencies with which the fungal groups were observed, as well as their proportions of the total air concentration. Fungal diversity estimates were similar for all samplers and in the range of what has been reported nationally, i.e., observation of 9-11 equal groups per sample, but spore concentration dominated by 2-3 groups. Plots of paired cyclone:comparison sampler ratios against average concentrations identified biases. For example, ratios were correlated with concentration and there was greater uncertainty at lower concentrations. Mean ratios for cyclone:filter comparisons were not significantly different from one for ascospores, Aspergillus-Penicillium spp., basidiospores, Cladosporium spp., or total spore m(-3). However, agreement was less consistent with the Burkard slide (0.74, 1.12, 0.91, 1.09, and 0.92, respectively) and the Burkard cyclone (2.31, 1.62, 1.43, 1.91, and 1.33, respectively). Concentrations of cell equivalent m(-3) also were determined for the filter and two cyclone samples by polymerase chain reaction. Cell equivalents for Aspergillus fumigatus and Penicillium brevicompactum were compared with Aspergillus-Penicillium spp. spores, and Cladosporium cladosporioides and Cladosporium herbarum cell equivalents were compared with Cladosporium spp. spores. Cell equivalent:spore ratios below one for A. fumigatus and P. brevicompactum indicated that these species comprised smaller factions of total spores or were collected less efficiently than the larger C. cladosporioides and C. herbarum spores. The personal cyclone was shown to be suitable for collection of ambient airborne fungal spores and for analysis by microscopy and polymerase chain reaction.
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Affiliation(s)
- Janet Macher
- California Department of Public Health, Environmental Health Laboratory, Richmond, California 94804-6403, USA.
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Macher J, Chen B, Rao C. Chamber evaluation of a personal, bioaerosol cyclone sampler. JOURNAL OF OCCUPATIONAL AND ENVIRONMENTAL HYGIENE 2008; 5:702-712. [PMID: 18720289 DOI: 10.1080/15459620802380351] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
A personal cyclone sampler (cyclone) was operated in a 0.9-m3 chamber, side by side with a 25-mm filter sampler (filter) and either a slit impactor (Air-O-Cell) or a single-stage, multiple-hole, agar impactor (N6). Aerosols of two fungal spores were collected for 5 min to 5 hr-Aspergillus versicolor: 10, 20, 40, 80, 160, and 320 min; concentration: 10(2)-10(5) spore m(-3); Scopulariopsis brevicaulis: 5, 10, 15, 20, 25, and 30-min; concentration: 10(3)-10(5) spore m(-3) (six replicates for each sampling time). For each fungus, air concentrations were determined by a 15-channel optical particle counter (particle m(-3); N = 36), microscopy (spore m(-3); cyclone and filter, N = 36; Air-O-Cell, N = 18), culture (colony forming unit m(-3); cyclone and filter, N = 36; N6, N = 18), and polymerase chain reaction (cell equivalent m(-3); cyclone and filter, N = 36). Samplers were significantly correlated with each other as were the three analyses (correlation coefficients = 0.79-1.00 and 0.87-0.98, respectively). Ratios were calculated for simultaneous measurements with the cyclone and comparison samplers and for paired colony:spore, colony:cell equivalent, and cell equivalent:spore measurements for the cyclone and filter samples. The cyclone equaled or underestimated the other samplers for both fungi and all analyses (mean ratio: 0.75-1.04). A. versicolor colony and cell equivalent measurements exceeded spore measurements although microscopy should detect all spores not just culturable ones, perhaps due to difficulty observing the smaller spores or detection of DNA in cell fragments in addition to intact spores. Plots of the ratios of paired measurements against their averages identified biases between samplers and analyses. For example, ratios were correlated with spore concentration, and there was greater uncertainty at lower concentrations. These chamber tests have shown that the cyclone is suitable for collection of airborne fungal spores over a wide concentration range and time period and for analysis by microscopy, culture, and polymerase chain reaction.
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Affiliation(s)
- Janet Macher
- California Department of Public Health, Environmental Health Laboratory, Richmond, California, USA
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64
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First Isolation of the Anamorphic Basidiomycetous Yeast Trichosporon faecale in Germany, from the Skin of a Patient with Tinea pedis. Mycopathologia 2008; 165:149-53. [DOI: 10.1007/s11046-008-9092-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2007] [Accepted: 01/25/2008] [Indexed: 11/26/2022]
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65
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Detection of Stachybotrys chartarum using rRNA, tri5, and beta-tubulin primers and determining their relative copy number by real-time PCR. ACTA ACUST UNITED AC 2008; 112:845-51. [PMID: 18499423 DOI: 10.1016/j.mycres.2008.01.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2007] [Revised: 12/19/2007] [Accepted: 01/10/2008] [Indexed: 11/18/2022]
Abstract
Highly conserved regions are attractive targets for detection and quantitation by PCR, but designing species-specific primer sets can be difficult. Ultimately, almost all primer sets are designed based upon literature searches in public domain databases, such as the National Center for Biotechnology Information (NCBI). Prudence suggests that the researcher needs to evaluate as many sequences as available for designing species-specific PCR primers. In this report, we aligned 11, 9, and 16 DNA sequences entered for Stachybotrys spp. rRNA, tri5, and beta-tubulin regions, respectively. Although we were able to align and determine consensus primer sets for the 9 tri5 and the 16 beta-tubulin sequences, there was no consensus sequence that could be derived from alignment of the 11 rRNA sequences. However, by judicious clustering of the sequences that aligned well, we were able to design three sets of primers for the rRNA region of S. chartarum. The two primer sets for tri5 and beta-tubulin produced satisfactory PCR results for all four strains of S. chartarum used in this study whereas only one rRNA primer set of three produced similar satisfactory results. Ultimately, we were able to show that rRNA copy number is approximately 2-log greater than for tri5 and beta-tubulin in the four strains of S. chartarum tested.
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Characterization of fungi in chronic rhinosinusitis using polymerase chain reaction and sequencing. Eur Arch Otorhinolaryngol 2007; 265:651-5. [DOI: 10.1007/s00405-007-0529-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2007] [Accepted: 10/30/2007] [Indexed: 11/25/2022]
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Falacy JS, Grove GG, Mahaffee WF, Galloway H, Glawe DA, Larsen RC, Vandemark GJ. Detection of Erysiphe necator in Air Samples Using the Polymerase Chain Reaction and Species-Specific Primers. PHYTOPATHOLOGY 2007; 97:1290-1297. [PMID: 18943687 DOI: 10.1094/phyto-97-10-1290] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
ABSTRACT A polymerase chain reaction (PCR) assay employing species-specific primers was developed to differentiate Erysiphe necator from other powdery mildews common in the northwest United States. DNA was extracted from mycelia, conidia, and/or chasmothecia that were collected from grape leaves with a Burkard cyclonic surface sampler. To differentiate E. necator from other erysiphaeceous fungi, primer pairs Uncin144 and Uncin511 were developed to select unique sequences of the internal transcribed spacer regions of E. necator. Using these primers in PCR amplifications, a 367-bp amplicon specific to E. necator was generated, but no amplicons were generated from other erysiphaceous species collected from 48 disparate hosts representing 26 vascular plant families. The PCR limit of detection was one to five conidia of E. necator placed directly into reaction mixtures or 100 to 250 conidia placed on glass rods coated with silicon grease. During field studies, this PCR assay facilitated the detection of E. necator inoculum in air samples within hours of sample rod collection and prior to disease onset. Amplification of E. necator DNA did not occur when the PCR assay was conducted on vineyard air samples collected while grapes were dormant or during periods when vine growth occurred but E. necator remained dormant. The initial PCR detection of E. necator of the season occurred during seasonal ascospore releases caused by precipitation events between bud burst and the prebloom period during the 3 years of the study. Detection ceased for 7 to 11 days following ascospore release and then resumed several days prior to the observance of microscopic symptoms and signs of powdery mildew in the field. Results of this study represent the initial step toward the goal of incorporating an inoculum availability component into current and future grapevine powdery mildew risk assessment models.
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Paterson RRM. Internal amplification controls have not been employed in fungal PCR hence potential false negative results. J Appl Microbiol 2007; 102:1-10. [PMID: 17184314 DOI: 10.1111/j.1365-2672.2006.03220.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Polymerase chain reaction (PCR) is subject to false negative results. Samples of fungi with the genes of interest (e.g. a disease or mycotoxin) may be categorized as negative and safe as a consequence. Fungi are eukaryotic organisms that are involved in many fields of human activity such as antibiotic, toxin and food production. Certain taxa are implicated in human, animal and plant diseases. However, fungi are difficult to identify and PCR techniques have been proposed increasingly for this purpose. Internal amplification controls (IACs) will ameliorate the situation and need to become mandatory. These are nucleic acids that posses a sequence which will provide a PCR product (i) using the same primers employed for the target gene, and (ii) that will not coincide on the gel with the product of the target gene. Only one group of workers employed an IAC, to respond to potential inhibition, which was reported in 1995 from this present assessment of numerous reports. Inhibitors in cultures need to be minimized, and secondary metabolites are an obvious source. The fields reviewed herein include medical mycology, mycotoxicology, environmental mycology and plant mycology. The conclusion is that previous reports are compromised because IACs have not been employed in fungal PCR; future research must include this control at an early stage.
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Affiliation(s)
- R R M Paterson
- Centro de Engenharia Biológica, Micoteca da Universidade do Minho, Braga, Portugal.
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Nieguitsila A, Deville M, Jamal T, Halos L, Berthelemy M, Chermette R, Latouche S, Arné P, Guillot J. Evaluation of fungal aerosols using Temporal Temperature Gradient Electrophoresis (TTGE) and comparison with culture. J Microbiol Methods 2007; 70:86-95. [PMID: 17512067 DOI: 10.1016/j.mimet.2007.03.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2006] [Revised: 03/23/2007] [Accepted: 03/28/2007] [Indexed: 10/23/2022]
Abstract
Information obtained from fungal air samples can assist in the assessment of health hazards and can be useful in proactive indoor air quality monitoring. The objective of the present study was to evaluate the PCR-TTGE technique for the analysis of fungal diversity in the air. Eleven air samples were collected in five different sites using the bioimpactor CIP 10-M (Arelco). After a 2 hours sampling period, the collection liquid was recovered for subsequent cultivation and PCR-TTGE. A set of three fungi-specific primers (Fungcont 1, Fungcont 2+GC and Fungcont 3) was designed for the partial amplification of the 18S rRNA gene. The amplification was obtained in a single reaction tube by a semi-nested PCR. For identification, the TTGE bands were extracted and sequenced. PCR-TTGE allowed the clear separation of amplicons corresponding to distinct fungal species (both Ascomycota and Basidiomycota) that may be encountered in air. The number of fungal taxa detected after culture was systematically higher than the number of taxa found using PCR-TTGE. However, few fungal species were detected by PCR-TTGE and not by cultivation, suggesting that the combination of these approaches may provide a better analysis of fungal diversity in air samples than either method alone.
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Affiliation(s)
- Adélaïde Nieguitsila
- INRA, AFSSA, ENVA, UPVM, UMR 956, Ecole Nationale Vétérinaire d'Alfort, Maisons-Alfort, France
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70
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Brandi G, Sisti M, Paparini A, Gianfranceschi G, Schiavano GF, De Santi M, Santoni D, Magini V, Romano-Spica V. Swimming pools and fungi: an environmental epidemiology survey in Italian indoor swimming facilities. INTERNATIONAL JOURNAL OF ENVIRONMENTAL HEALTH RESEARCH 2007; 17:197-206. [PMID: 17479383 DOI: 10.1080/09603120701254862] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
A growing number of people attend swimming facilities for recreational activities, rehabilitative treatments, or sport. Filamentous fungi and yeast can be isolated from contaminated air, water and surfaces and may represent a biological risk for employees and users. Here we investigated the occurrence of mycotic species, in a sample of Italian swimming pools (n = 10). Detection and identification of isolated species were achieved by cultural and morphological methods. Results revealed moderate mycotic titres and a high biodiversity. Penicillium spp., Aspergillus spp., Cladosporium spp. and Alternaria sp., were constantly detected in air and surfaces sampled by the swimming area, while pathogenic yeast Candida albicans was never detected. Fusarium spp. was the most common taxon isolated from surfaces. For one facility, we typed the genotypic profiles and studied, by genetic typing, the spatial and temporal distribution of isolates. Phylogenetic relationships between species were analysed by alignment of small ribosomal subunit RNA sequences.
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Affiliation(s)
- Giorgio Brandi
- Institute of Toxicological Hygienic and Environmental Sciences, University of Urbino Carlo Bo, Urbino (PU), Italy
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71
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Wang Y, Chen W, Li X, Cheng B. Degenerated primer design to amplify the heavy chain variable region from immunoglobulin cDNA. BMC Bioinformatics 2006; 7 Suppl 4:S9. [PMID: 17217527 PMCID: PMC1780117 DOI: 10.1186/1471-2105-7-s4-s9] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The amplification of variable regions of immunoglobulins has become a major challenge in the cloning of antibody genes, whether from hybridoma cell lines or splenic B cells. Using conventional protocols, the heavy-chain variable region genes often are not amplified successfully from the hybridoma cell lines. RESULTS A novel method was developed to design the degenerated primer of immunoglobulin cDNA and to amplify cDNA ends rapidly. Polymerase chain reaction protocols were performed to recognize the VH gene from the hybridoma cell line. The most highly conserved region in the middle of the VH regions of the Ig cDNA was identified, and a degenerated 5'primer was designed, using our algorithms. The VH gene was amplified by both the 3'RACE and 5'RACE. The VH sequence of CSA cells was 399 bp. CONCLUSION The new protocol rescued the amplifications of the VH gene that had failed under conventional protocols. In addition, there was a notable increase in amplification specificity. Moreover, the algorithm improved the primer design efficiency and was shown to be useful both for building VH and VL gene libraries and for the cloning of unknown genes in gene families.
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Affiliation(s)
- Ying Wang
- Center for Laboratory Medicine, First Teaching Hospital of Medical School, Xi'an Jiaotong University, Xi'an 710061, China
| | - Wei Chen
- Center for Laboratory Medicine, First Teaching Hospital of Medical School, Xi'an Jiaotong University, Xi'an 710061, China
| | - Xu Li
- Center for Laboratory Medicine, First Teaching Hospital of Medical School, Xi'an Jiaotong University, Xi'an 710061, China
| | - Bing Cheng
- Department of Biomedical Engineering, Xi'an Jiaotong University, Xi'an 710049, China
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72
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Rao AK, Mathers PH, Ramadan HH. Detection of fungi in the sinus mucosa using polymerase chain reaction. Otolaryngol Head Neck Surg 2006; 134:581-5. [PMID: 16564376 DOI: 10.1016/j.otohns.2005.10.047] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2005] [Indexed: 11/24/2022]
Abstract
OBJECTIVE To compare the presence of fungi in the sinus mucosa of patients with and without chronic rhinosinusitis. STUDY DESIGN AND SETTING Prospective observational study using polymerase chain reaction and conventional culture to detect fungi in the sinus mucosa. Middle meatus mucosal samples were collected from 31 patients with chronic rhinosinusitis and 14 control subjects. RESULTS Fungi were detected in 6.5% of subjects with chronic rhinosinusitis and in none of the control subjects using polymerase chain reaction. Fungi were detected in 29% of subjects with the combination of inhalant allergies, nasal polyposis, and asthma. Fungi were detected in none of the subjects without the combination of these three comorbidities (P = 0.03). CONCLUSION Polymerase chain reaction assay appears to be able to detect fungi in chronic rhinosinusitis. SIGNIFICANCE Fungi may not be implicated in the pathogenesis of most chronic rhinosinusitis. EBM RATING B-3b.
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Affiliation(s)
- Arvin K Rao
- Department of Otolaryngology-Head and Neck Surgery, West Virginia University School of Medicine, Morgantown, West Virginia 26506-9200, USA
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73
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Niemeier RT, Sivasubramani SK, Reponen T, Grinshpun SA. Assessment of fungal contamination in moldy homes: comparison of different methods. JOURNAL OF OCCUPATIONAL AND ENVIRONMENTAL HYGIENE 2006; 3:262-73. [PMID: 16595378 PMCID: PMC2233946 DOI: 10.1080/15459620600637333] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
In an effort to better understand the relationship between different fungal sampling methods in the indoor environment, four methods were used to quantify mold contamination in 13 homes with visible mold. Swab, fungal spore source strength tester (FSSST), and air samples (total of 52 samples) were analyzed using both the microscopic (total spore count) and culture-based (CFU count) enumeration techniques. Settled dust samples were analyzed for culturable fungi only, as the microscopic enumeration was restricted by the masking effect. The relationships between the data obtained with the different sampling methods were examined using correlation analysis. Significant relationships were observed between the data obtained from swab and FSSST samples both by the total counting (r = 0.822, p < 0.05) and by the CFU counting (r = 0.935, p < 0.01). No relationships were observed between air and FSSST samples or air and settled dust samples. Percentage culturability of spores for each sampling method was also calculated and found to vary greatly for all three methods (swab: 0.03% to 63%, FSSST: 0.1% to > 100%, air: 0.7% to 79%). These findings confirm that reliance on one sampling or enumeration method for characterization of an indoor mold source might not provide an accurate estimate of fungal contamination of a microenvironment. Furthermore, FSSST sampling appears to be an effective measurement of a mold source in the field, providing an upper bound estimate of potential mold spore release into the indoor air. Because of the small sample size of this study, however, further research is needed to better understand the observed relationships in this study.
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Affiliation(s)
- R Todd Niemeier
- Department of Environmental Health, Center for Health-Related Aerosol Studies, University of Cincinnati, Cincinnati, Ohio 45267-0056, USA
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74
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Dao HP, Mathieu F, Lebrihi A. Two primer pairs to detect OTA producers by PCR method. Int J Food Microbiol 2005; 104:61-7. [PMID: 15975678 DOI: 10.1016/j.ijfoodmicro.2005.02.004] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2004] [Revised: 12/27/2004] [Accepted: 02/19/2005] [Indexed: 11/27/2022]
Abstract
Fungi contaminating foods and feeds may produce many mycotoxins including ochratoxin A (OTA). Early and rapid detection of potential OTA producing fungi is important to reduce the negative impacts of OTA. In this study, two PCR specific primer pairs, AoLC35-12L/AoLC35-12R and AoOTAL/AoOTAR, were designed from a DNA sequence of a polyketide synthase gene in Aspergillus ochraceus NRRL 3174. On 14 different fungi tested by PCR, AoLC35-12L/AoLC35-12R amplified a unique band from either OTA or citrinin producers while AoOTAL/AoOTAR amplified one PCR product only from A. ochraceus. So these primers could be used to detect both OTA and citrinin producing fungi (AoLC35-12L/AoLC35-12R) or only A. ochraceus (AoOTAL/AoOTAR) from foodstuffs using PCR method.
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Affiliation(s)
- Huy Phong Dao
- Equipe Génie des Systèmes Microbiens, Laboratoire de Génie Chimique UMR5503 (CNRS/INPT/UPS), Ecole Nationale Supérieure Agronomique de Toulouse, Institut National Polytechnique de Toulouse, 1, avenue de l'Agrobiopôle, BP107, 31326 Castanet Tolosan, France
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75
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Gadanho M, Sampaio JP. Application of temperature gradient gel electrophoresis to the study of yeast diversity in the estuary of the Tagus river, Portugal. FEMS Yeast Res 2005; 5:253-61. [PMID: 15556087 DOI: 10.1016/j.femsyr.2004.09.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2004] [Revised: 09/10/2004] [Accepted: 09/22/2004] [Indexed: 11/30/2022] Open
Abstract
Temperature gradient gel electrophoresis (TGGE) was employed for the assessment of yeast diversity in the estuary of the Tagus river (Portugal). The molecular detection of yeasts was carried out directly from water samples and, in parallel, a cultivation approach by means of an enrichment step was employed. A nested PCR was employed to obtain a fungal amplicon containing the D2 domain of the 26S rRNA gene. For identification the TGGE bands were extracted, re-amplified, and sequenced. Fourteen fungal taxa were detected and all except one were yeasts. Most yeast sequences corresponded to members of the Ascomycota and only three belonged to the Basidiomycota. Five yeasts (four ascomycetes and one basidiomycete) could not be identified to the species level due to the uniqueness of their sequences. The number of species detected after enrichment was higher than the number of taxa found using the direct detection method. This suggests that some yeast populations are present in densities that are below the detection threshold of the method. With respect to the analysis of the yeast community structure, our results indicate that the dominant populations belong to Debaryomyces hansenii, Rhodotorula mucilaginosa, Cryptococcus longus, and to an uncultured basidiomycetous yeast phylogenetically close to Cr. longus. The combined analysis of direct detection and cultivation approaches indicates a similar community structure at the two sampled sites since nine species were present at both localities.
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Affiliation(s)
- Mário Gadanho
- Centro de Recursos Microbiológicos, Secção Autónoma de Biotecnologia, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
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76
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Keswani J, Kashon ML, Chen BT. Evaluation of interference to conventional and real-time PCR for detection and quantification of fungi in dust. ACTA ACUST UNITED AC 2005; 7:311-8. [PMID: 15798797 DOI: 10.1039/b415498c] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
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.
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Affiliation(s)
- Jyoti Keswani
- Health Effects Laboratory Division, Exposure Assessment Branch, Centers for Disease Control and Prevention, National Institute for Occupational Safety and Health, 1095 Willowdale Road, M/S L-3030, Morgantown, WV 26505, USA.
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77
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Abstract
In recent years novel molecular methods, notably polymerase chain reaction (PCR) assays, have been developed to improve the diagnosis of life-threatening invasive aspergillosis in patients at high risk, especially patients with malignant hematological disease. Early diagnosis and treatment are essential for adequate therapeutic management. Management, however, often remains difficult since most of the diagnostic tools used clinically at present either lack specificity or acceptable sensitivity. The clinical value, advantages and remaining problems of PCR approaches to detect the emerging fungal pathogen are reviewed.
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Affiliation(s)
- D Buchheidt
- 3 Medizinische Klinik, Universitätsklinikum Mannheim, Ruprecht-Karls-Universität Heidelberg, Germany.
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78
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Abstract
Air sampling provides information about the bioaerosol composition of the atmosphere. Principal methods of volumetric sample collection include impaction, impingement, and filtration. Many instruments have been developed based on these collection methods. The most widely used devices are slit impactors, rotating arm impactors, and sieve impactors. Samples can be analyzed by various methods, with microscopy and culturing the most important approaches; however, immunoassays, molecular methods such as polymerase chain reaction, and other new techniques are becoming more widely used to analyze samples.
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Affiliation(s)
- Estelle Levetin
- Faculty of Biological Science, The University of Tulsa, 600 S. College, Tulsa, OK 74104, USA.
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79
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Niessen L, Schmidt H, Vogel RF. The use of tri5 gene sequences for PCR detection and taxonomy of trichothecene-producing species in the Fusarium section Sporotrichiella. Int J Food Microbiol 2004; 95:305-19. [PMID: 15337595 DOI: 10.1016/j.ijfoodmicro.2003.12.009] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Purified DNA from isolates of Fusarium poae, Fusarium sporotrichioides, Fusarium kyushuense and Fusarium langsethiae was used as a template to amplify a 658-bp fragment from the trichodiene synthase (tri5) gene of these fungi with the gene-specific PCR primer pair Tox5-1/Tox5-2. Fragments obtained were isolated and sequenced. DNA sequence alignments revealed high similarity between the sequences derived from F. sporotrichioides and F. langsethiae (98.7%) and less similarity between the latter species and F. poae (90.9%). Phylogenetic analysis of the aligned sequences using the tri5 sequence of Fusarium pseudograminearum as an outgroup revealed clear separation between one group consisting of F. poae and F. kyushuense and another consisting of F. sporotrichioides and F. langsethiae. The two latter species could not be distinguished phylogenetically on the basis of their tri5 sequences. Taxon-specific reverse primers were designed from the aligned sequences and combined with the tri5 gene-specific forward primer Tox5-1. The new reverse primers enabled specific amplification of a fragment of approximately 400 bp from DNA isolated from F. sporotrichioides, F. poae, F. langsethiae and F. kyushuense, respectively. All primers were tested for cross-reactivity with DNA from 26 fungal species potentially capable of producing trichothecenes. Only the primer designed for F. langsethiae cross-reacted with F. sporotrichioides. PCR assays were applied in analysis of artificially and naturally infected samples of barley and oats. On artificially infected barley, species were selectively detected by the corresponding primers. In naturally infected oats, F. langsethiae was identified by the combination of two PCR assays designed for detection of F. sporotrichioides and F. langsethiae, respectively.
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Affiliation(s)
- Ludwig Niessen
- Technische Universität München, Lehrstuhl für Technische Mikrobiologie, Weihenstephaner Steig 16, D-85350 Freising, Germany.
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80
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Rintala H, Hyvärinen A, Paulin L, Nevalainen A. Detection of streptomycetes in house dust--comparison of culture and PCR methods. INDOOR AIR 2004; 14:112-119. [PMID: 15009417 DOI: 10.1111/j.1600-0668.2003.00219.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Streptomycetes are gram-positive, spore producing, filamentous bacteria common in soil, but also present in indoor environments. They are potent producers of secondary metabolites and inducers of inflammatory responses in vitro. Polymerase chain reaction (PCR)- and culture-based detection methods for streptomycetes in house dust samples were compared. A total of 47 dust samples were investigated, and the presence of streptomycetes was determined by cultivation on tryptone-yeast-extract-glucose agar and PCR. The 16S rRNA gene of actinomycete isolates from house dust was partially sequenced to investigate if they belong to the genus Streptomyces. Both PCR and culture showed more frequent occurrence of streptomycetes in moisture-damaged homes, although the results did not correlate well. The occurrence of streptomycetes in house dust was associated with moisture damage of the home. The amount of Streptomyces-specific PCR amplification product was significantly higher in dust from moisture-damaged homes than in homes with no moisture damage (P < 0.05, Mann-Whitney U test). A correlation between streptomycetes and moisture damage, although not statistically significant, was also observed when using binary data, e.g. presence or absence of streptomycetes or moisture damage (P = 0.054 for PCR, and P = 0.127 for culture, Fisher's exact test). Altogether, the presence of streptomycetes in house dust seems to indicate the presence of moisture damage in the building.
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Affiliation(s)
- H Rintala
- Laboratory of Environmental Microbiology, National Public Health Institute (KTL), PO Box 95, FIN-70701 Kuopio, Finland.
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81
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Li DW, Yang CS. Fungal Contamination as a Major Contributor to Sick Building Syndrome. ADVANCES IN APPLIED MICROBIOLOGY 2004; 55:31-112. [PMID: 15350790 DOI: 10.1016/s0065-2164(04)55002-5] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- De-Wei Li
- P & K Microbiology Services, Inc., 1936 Olney Ave Cherry Hill, New Jersey 08003, USA
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82
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Wu Z, Tsumura Y, Blomquist G, Wang XR. 18S rRNA gene variation among common airborne fungi, and development of specific oligonucleotide probes for the detection of fungal isolates. Appl Environ Microbiol 2003; 69:5389-97. [PMID: 12957927 PMCID: PMC194989 DOI: 10.1128/aem.69.9.5389-5397.2003] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In this study, we sequenced 18S rRNA genes (rDNA) from 49 fungal strains representing 31 species from 15 genera. Most of these species are common airborne fungi and pathogens that may cause various public health concerns. Sequence analysis revealed distinct divergence between Zygomycota and Ascomycota. Within Ascomycota, several strongly supported clades were identified that facilitate the taxonomic placement of several little-studied fungi. Wallemia appeared as the group most diverged from all the other Ascomycota species. Based on the 18S rDNA sequence variation, 108 oligonucleotide probes were designed for each genus and species included in this study. After homology searches and DNA hybridization evaluations, 33 probes were verified as genus or species specific. The optimal hybridization temperatures to achieve the best specificity for these 33 probes were determined. These new probes can contribute to the molecular diagnostic research for environmental monitoring.
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Affiliation(s)
- Zhihong Wu
- National Institute for Working Life, SE-907 13 Umeå, Sweden
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83
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Sebastian A, Larsson L. Characterization of the microbial community in indoor environments: a chemical-analytical approach. Appl Environ Microbiol 2003; 69:3103-9. [PMID: 12788704 PMCID: PMC161488 DOI: 10.1128/aem.69.6.3103-3109.2003] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
An integrated procedure is presented whereby gas chromatography-ion trap mass spectrometry is used to determine chemical markers of gram-negative bacterial lipopolysaccharide (3-hydroxy fatty acids with 10 to 18 carbon atoms), gram-positive bacteria (branched-chain fatty acids with 15 and 17 carbon atoms), bacterial peptidoglycan (muramic acid), and fungal biomass (ergosterol) in samples of settled house dust. A hydrolysate of (13)C-labeled cyanobacterial cells is used as an internal standard for the first three markers. These analyses require two dust samples, one for 3-OH fatty acids, branched-chain fatty acids, and muramic acid and another for ergosterol. The method may be used to characterize microbial communities in environmental samples.
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Affiliation(s)
- Aleksandra Sebastian
- Department of Medical Microbiology, Dermatology and Infection, University of Lund, S-223 62 Lund, Sweden
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84
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Abstract
Stachybotrys is a toxin-producing fungus that grows indoors when both water and cellulose are available. Epidemiologic evidence has demonstrated an association between acute pulmonary hemorrhage in infants and exposure to Stachybotrys and other fungi in water-damaged home environments. In recent years, advances in understanding of this association have occurred in six major areas: animal models, biologic mechanism of lung injury, dose-response relationship, isolation from diseased patients, detection methods, and intervention. The association demonstrates strength, consistency, coherence, and specificity. While additional data are gathered, a preventive approach to reducing the exposure of infants with pulmonary hemorrhage is suggested.
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Affiliation(s)
- Ruth A Etzel
- Division of Occupational and Environmental Health, George Washington University School of Public Health and Health Services, Washington, DC USA.
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85
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Abstract
Changes in climate are altering pollen distribution. Predictive modeling can be used to forecast long- and short-term changes in pollen concentrations. Increasing evidence confirms the presence of pollen allergens on small, respirable particles in the air, explaining the occurrence of pollen-season increases in asthma. Like pollens, aboveground indoor fungal aerosols primarily reflect outdoor concentrations. Basement spore concentrations might be higher and reflective of local sources. Fungal presence in the indoor or outdoor air can be monitored on an area basis or with personal monitors. The samples can be analyzed by means of microscopy, culture, DNA probes, HPLC, or immunodetection. Total fungal biomass can be estimated on the basis of measurements of ergosterol or glucan in environmental samples. Unfortunately, there are no generally accepted standards for interpretation of fungal levels in indoor or outdoor air. At present, the best approach to indoor fungal control is moisture control in the indoor environment. This will essentially prevent fungal growth, except from extraordinary events.
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Affiliation(s)
- Harriet A Burge
- Harvard School of Public Health, Landmark Center, Room 404M, West, 401 Park Drive, PO Box 15677, Boston, MA 02215, USA
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86
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Wu Z, Blomquist G, Westermark SO, Wang XR. Application of PCR and probe hybridization techniques in detection of airborne fungal spores in environmental samples. JOURNAL OF ENVIRONMENTAL MONITORING : JEM 2002; 4:673-8. [PMID: 12400913 DOI: 10.1039/b203048a] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Specific PCR amplification and probe hybridization techniques were applied to examine the compositions of airborne fungi in samples from three different environments. The results from microscopic and CFU counting were compared to those of the molecular-based detections. The detection sensitivity for PCR amplifications was 9 to 73 spores and 1.3 to 19.3 CFUs per PCR reaction. The hybridization detection limit was 2 to 4 spores and 0.2 to 1.2 CFU. The hybridization method was more sensitive than PCR amplification and showed less variation among samples. Using specific PCR primers and probes we identified the presence of several fungal groups and species in the air samples. Specific detections through probe hybridization to PCR products amplified with universal or group-specific fungal primers have promising applications in the examination of air samples for environmental monitoring.
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Affiliation(s)
- Zhihong Wu
- Programme for Chemical Exposure Assessment, National Institute for Working Life, Umeå, Sweden
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87
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Möller EM, Peltola J. Isolation of high-molecular-weight DNA from mycelium and the recalcitrant and heavily pigmented spores of Stachybotrys chartarum. Anal Biochem 2001; 297:99-101. [PMID: 11567533 DOI: 10.1006/abio.2001.5320] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- E M Möller
- Institute of Plant Breeding, Seed Science, and Population Genetics, University of Hohenheim, D-70593 Stuttgart, Germany.
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