A simple polymerase chain reaction/restriction fragment length polymorphism assay capable of identifying medically relevant filamentous fungi

Investigation of adhesion status of Candida species to the surface of resin materials produced at different angles with additive manufacturing

BACKGROUND

The aim of this study was to evaluate the adhesion of Candida glabrata, Candida albicans, Candida krusei, Candida parapsilosis and Candida tropicalis yeasts to disk-shaped resin materials produced from resin which used in the production of surgical guide with 0, 45 and 90-degrees printing orientations by Liquid Crystal Display additive manufacturing technology.

METHODS

Disk-shaped specimens were printed with surgical guide resin using the Liquid Crystal Display production technique in 3 printing orientations (0, 45 and 90-degrees). Surface roughness and contact angle values were evaluated. Real-Time PCR analysis was performed to evaluate Candida adhesion (C. glabrata, C. albicans, C. krusei, C. parapsilosis and C. tropicalis) Field emission scanning electron microscope (FESEM) images of the materials were obtained.

RESULTS

Specimens oriented at 45-degrees demonstrated higher surface roughness (P < .05) and lower contact angle values than other groups. No significant difference was found in the adhesion of C. glabrata, C. albicans, and C. parapsilosis among specimens printed at 0, 45, and 90-degrees orientations (P > .05). A higher proportion of C. krusei and C. tropicalis was found in the specimens printed at orientation degrees of 45 = 90 < 0 with statistical significance. Analyzing the adhesion of all Candida species reveals no statistical disparity among the printing orientations.

CONCLUSIONS

The surface roughness, contact angle, and adhesion of certain Candida species are affected by printing orientations. Hence, careful consideration of the printing orientation is crucial for fabricating products with desirable properties. In 45-degree production, roughness increases due to the layered production forming steps, whereas in 0-degree production, certain Candida species exhibit high adhesion due to the formation of porous structures. Consequently, considering these factors, it is advisable to opt for production at 90-degrees, while also considering other anticipated characteristics.

Speciation of fungi using real time PCR with molecular beacons: Can we solve the enigma of diagnosis of invasive fungal disease?

BACKGROUND

Invasive fungal diseases (IFDs) are difficult to diagnose and associated with high mortality rates, especially in the immunosuppressed. Species of Aspergillus and Candida are the cause of majority of invasive fungal disease however IFDs are also caused by Fusarium, Zygomycetes, Trichosporon, etc. Early detection is crucial for appropriate antifungal therapy. Blood cultures usually fail to isolate filamentous fungi, while detection of circulating beta-d-glucan or galactomannan antigens show variable sensitivity and specificity. There is a need of reliable, sensitive and specific diagnostic tests for IFDs.

METHODS

A real-time Polymerase Chain Reaction (PCR) assay with a universal primer/molecular beacon system was developed for detecting and speciating most of the pathogenic fungi implicated in IFD. A single-reaction assay was designed targeting a carefully selected region of the ITS2 and ITS5 subunits of the fungal rDNA gene along with four molecular beacons capable of differential hybridization to the amplicons of different species. This generated a signature set of melting temperatures using the standard strains. The assay was tested on clinical specimens from patients with suspected invasive fungal disease.

RESULTS

The assay was tested on 72 clinical samples and 72 healthy controls. Of these, 22 clinical samples (6/8 proven; 13/29 probable; 3/35 possible IFD, classified by the EORTC/MSG criteria) were positive by PCR and generated a set of melting temperatures enabling identification of the causative fungus. The assay was negative in all healthy controls.

CONCLUSION

The molecular beacon assay is a promising tool providing a rapid method for detection and monitoring of invasive fungal disease in immunosuppressed patients.

PCR ITS-RFLP for Penicillium Species and Other Genera

Among numerous molecular methodologies developed for highly specific identification of filamentous fungi isolates, here we describe restriction digestion analysis of the ITS products as an easy method to identify isolates of filamentous fungi. This technique is a rapid and reliable method appropriate for routine identification of filamentous fungi. This can be used to screen large numbers of isolates from various environments in a short time. The use of different endonucleases allowed generating individual restriction profiles. The individual profiles obtained were combined into composite restriction patterns characteristic of a species. Eleven different genera can be differentiated and among them 41 different species.

Non-Botrytis grape-rotting fungi responsible for earthy and moldy off-flavors and mycotoxins

The grape microflora is complex and includes filamentous fungi, yeasts and bacteria with different physiological characteristics and effects on wine production. Most studies have focused on the wine microbiota, but a few studies have reported the ecology of grape microorganisms. Some of these organisms - such as non-Botrytis bunch rotting fungi, which greatly influence the safety or sensory quality of wine, due to the production of mycotoxins and off-flavors, respectively - are considered to be spoilage agents. We review here the diversity of filamentous fungi on grapes and the factors influencing their development, such as grape ripening stage, environmental factors (climate, rain and cultivation practices), grape variety and grape health status. We also discuss the pathways by which mycotoxins and off-flavors are produced, the control of the population, the metabolites responsible for wine spoilage and the methods for detecting and characterizing the microorganisms involved.

PCR ITS-RFLP: A useful method for identifying filamentous fungi isolates on grapes

Restriction digestion analysis of the ITS products was tested as an easy method to identify isolates of filamentous fungi on grapes. Endonucleases SduI, HinfI, MseI, HaeIII were used. Endonucleases BfmI, Cfr9I, Hpy188I, MaeII or PspGI were used as necessary to complete discrimination. The 43 species studied generated 42 different composite profiles. Only the species P. thomii and P. glabrum gave the same composite profile. 96.3% strains tested could be differentiated to the species level with only four enzymes. Hundred ninety nine strains of filamentous fungi were isolated from various vineyards in Burgundy and identified by this method. Penicillium (58.5%) was the genus the most frequently isolated and no strains of the genus Aspergillus was isolated. P. spinolusum was the most isolated species of Penicillium (22.70%). The species C. cladiosporioides, B. cinerea, E. nigrum, A. alternata, T. koningiopsis, P. diplodiella, C. herbarum, A. alternatum, T. cucumeris and F. oxysporum were also isolated. This technique is a rapid and reliable method appropriate for routine identification of filamentous fungi. This can be used to screen large numbers of isolates from various environments in a short time. This is the first exhaustive study of fungal diversity at species level in vineyard.

Quantitative PCR analysis of fungal DNA in Swedish day care centers and comparison with building characteristics and allergen levels

Abstract Sweden has had allergen-avoidance day care centers (AADCs) since 1979. The aim of this study was to measure fungal DNA by quantitative polymerase chain reaction (qPCR), a new method, in AADCs and ordinary day care centers (ODCs) and examine associations between allergen levels and building characteristics. Dust samples were collected by swabbing doorframes, vacuum-cleaning, and using Petri dishes. In total, 11 AADCs and 11 ODCs were studied (70 rooms). Total fungal DNA, measured by qPCR in the swab dust, was detected in 89%, Aspergillus or Penicillium (Asp/Pen) DNA in 34%, and Stachybotrys chartarum DNA in 6% of the rooms. Total fungal DNA was significantly higher in rooms with linoleum floor (P = 0.02), textile carpets (P = 0.03), reported dampness/molds (P = 0.02) and reported odor (P < 0.001) in the buildings, and significantly lower in wooden facade buildings (P = 0.003). Reported odor was related to the amount of sieved fine dust, reported dampness/molds and type of building construction. Total fungal DNA was related to cat, dog, horse and total allergen levels (P = 0.003) in the day care centers. In conclusion, total fungal DNA is related to reported dampness/molds, reported odor, and type of wall construction. The association between fungal and allergen contamination indicated a general 'hygiene factor' related to biological contaminants. Practical Implications The associations between fungal DNA, reported dampness/molds, and odor support the view that buildings with odor problems should be investigated for possible hidden fungal growth. There is a need to measure fungal biomass in different types of building constructions by monitoring fungal DNA. Analysis of fungal DNA with quantitative PCR can be a fast and practical way to study indoor fungal contamination. Swabbing dust from the doorframe of the main entrance to the room can be a convenient method of sampling dust for fungal DNA analysis. The high prevalence of reported dampness/molds and the common occurrence of fungal DNA indicate the need to improve the indoor environment of Swedish day care centers.

Analysis of fungal flora in indoor dust by ribosomal DNA sequence analysis, quantitative PCR, and culture

In recent years increasing attention has been given to the potential health effects of fungal exposure in indoor environments. We used large-scale sequencing of the fungal internal transcribed spacer region (ITS) of nuclear ribosomal DNA to describe the mycoflora of two office buildings over the four seasons. DNA sequencing was complemented by cultivation, ergosterol determination, and quantitative PCR analyses. Sequences of 1,339 clones were clustered into 394 nonredundant fungal operational taxonomical units containing sequences from 18 fungal subclasses. The observed flora differed markedly from that recovered by cultivation, the major differences being the near absence of several typical indoor mold genera such as Penicillium and Aspergillus spp. and a high prevalence of basidiomycetes in clone libraries. A total of 55% of the total diversity constituted of unidentifiable ITS sequences, some of which may represent novel fungal species. Dominant species were Cladosporium cladosporioides and C. herbarum, Cryptococcus victoriae, Leptosphaerulina americana and L. chartarum, Aureobasidium pullulans, Thekopsora areolata, Phaeococcomyces nigricans, Macrophoma sp., and several Malassezia species. Seasonal differences were observed for community composition, with ascomycetous molds and basidiomycetous yeasts predominating in the winter and spring and Agaricomycetidae basidiomycetes predominating in the fall. The comparison of methods suggested that the cloning, cultivation, and quantitative PCR methods complemented each other, generating a more comprehensive picture of fungal flora than any of the methods would give alone. The current restrictions of the methods are discussed.

MdACO expression during abscission: the use of 33P labeled primers in transcript quantitation

The last step of ethylene biosynthesis in apple is catalyzed by ACO (1-aminocyclopropane 1-carboxylic acid oxidase) encoded by MdACO1 and MdACO2. Both genes were expressed during early fruit development although at different level. Later on, the ACO transcript accumulation in persisting fruitlets decreased whereas in fruitlets undergoing abscission MdACO2 transcripts remained constant and those of MdACO1dramatically increased. The expression of MdACO was assessed by a particular type of semi-quantitative PCR involving 33P labeled primers and the following electrophoresis in polyacrylamide gel. The use of either the reverse primer or the anchored oligo dT13 produced clear and elegant results. Nevertheless, the initial quantity of labeled primer appeared to be a crucial factor for obtaining a wide range titration curve.

DNA and the classical way: Identification of medically important molds in the 21st century

The advent of the 21st century has seen significant advances in the methods and practices used for identification of medically important molds in the clinical microbiology laboratory. Historically, molds have been identified by using observations of colonial and microscopic morphology, along with tables, keys and textbook descriptions. This approach still has value for the identification of many fungal organisms, but requires expertise and can be problematic in determining a species identification that is timely and useful in the management of high-risk patients. For the increasing number of isolates that are uncommon, atypical, or unusual, DNA-based identification methods are being increasingly employed in many clinical laboratories. These methods include the commercially available GenProbe assay, methods based on the polymerase chain reaction such as single-step PCR, RAPD-PCR, rep-PCR, nested PCR, PCR-RFLP, PCR-EIA, and more recent microarray-based, Luminex technology-based, and real-time PCR-based methods. Great variation in assay complexity, targets, and detection methods can be found, and many of these methods have not been widely used or rigorously validated. The increasing availability of DNA sequencing chemistry has made comparative DNA sequence analysis an attractive alternative tool for fungal identification. DNA sequencing methodology can be purchased commercially or developed in-house; such methods display varying degrees of usefulness depending on the breadth and reliability of the databases used for comparison. The future success of sequencing-based approaches will depend on the choice of DNA target, the reliability of the result, and the availability of a validated sequence database for query and comparison. Future studies will be required to determine sequence homology breakpoints and to assess the accuracy of molecular-based species identification in various groups of medically important filamentous fungi. At this time, a polyphasic approach to identification that combines morphologic and molecular methods will ensure the greatest success in the management of patients with fungal infections.

A simple polymerase chain reaction-sequencing analysis capable of identifying multiple medically relevant filamentous fungal species

Due to the accumulating evidence that suggests that numerous unhealthy conditions in the indoor environment are the result of abnormal growth of the filamentous fungi (mold) in and on building surfaces it is necessary to accurately determine the organisms responsible for these maladies and to identify them in an accurate and timely manner. Historically, identification of filamentous fungal (mold) species has been based on morphological characteristics, both macroscopic and microscopic. These methods may often be time consuming and inaccurate, necessitating the development of identification protocols that are rapid, sensitive, and precise. To this end, we have devised a simple PAN-PCR approach which when coupled to cloning and sequencing of the clones allows for the unambiguous identification of multiple fungal organisms. Universal primers are used to amplify ribosomal DNA sequences which are then cloned and transformed into Escherichia coli. Individual clones are then sequenced and individual sequences analyzed and organisms identified. Using this method we were capable of identifying Stachybotrys chartarum, Penicillium purpurogenum, Aspergillus sydowii, and Cladosporium cladosporioides from a mixed culture. This method was found to be rapid, highly specific, easy to perform, and cost effective.