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Results for “Mycological Typing Techniques”

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At least 19 recordsLinked to original sources
PubMed2006

Comparative study of the new colorimetric VITEK 2 yeast identification card versus the older fluorometric card and of CHROMagar Candida as a source medium with the new card.

The new VITEK 2 colorimetric card was compared to the previous fluorometric card for identification of yeast. API 20C was considered the "gold standard." The new card consistently performed better than the older card. Isolates from CHROMagar Candida plates were identified equally as well as those from Sabouraud dextrose agar.

Candida↗
PubMed2004

Identification of pathogenic dematiaceous fungi and related taxa based on large subunit ribosomal DNA D1/D2 domain sequence analysis.

The nucleotide sequences of the D1/D2 domains of large subunit (26S) ribosomal DNA for 76 strains of 46 species of pathogenic dematiaceous fungi and related taxa were determined. Intra-species sequence diversity of medically important dematiaceous fungi including Phialophora verrucosa, Fonsecaea pedrosoi, Fonsecaea compacta, Cladophialophora carrionii, Cladophialophora bantiana, Exophiala dermatitidis, Exophiala jeanselmei, Exophiala spinifera, Exophiala moniliae, and Hortaea werneckii were extremely small; as few as 0 changes were detected in C. bantiana, Fonsecaea and Exophiala species, 1 bp in C. carrionii and H. werneckii, and 2 bp in P. verrucosa. Inter-species nucleotide diversity between most species was higher. These data suggested that the D1/D2 domain is sufficiently variable for identification of pathogenic dematiaceous fungi and relevant species. The phylogenetic trees constructed from the sequence data revealed that most human pathogenic species formed a single cluster and that Cladosporium and Phialophora species were distributed polyphyletically into several clusters.

Ascomycota↗
PubMed1999

Application of molecular typing methods to dermatophyte species that cause skin and nail infections.

Typing methods utilising DNA technology were applied to a collection of Trichophyton mentagrophytes and T. rubrum isolates from skin and nail infections. The methods included restriction enzyme analysis (REA), hybridisation with the DNA probe poly (dG-dT), randomly amplified polymorphic DNA (RAPD) by PCR and restriction analysis of a segment of PCR-amplified rDNA. All these tests successfully differentiated the species, but few intra-species differences were detected. REA demonstrated some isolate variation, but this was limited and difficult to interpret, making it unsuitable as a typing tool. RAPD demonstrated few variations amongst T. mentagrophytes and none in T. rubrum.

DNA Probes↗
PubMed2003

Reflections on the classification of yeasts for different end-users in biotechnology, ecology, and medicine.

The approach to yeast identification has significantly changed in just a few decades due to the rapid increase in basic biological knowledge, increased interest in the practical applications and biodiversity of this important microbial group, and enormous technological advances. While some conventional methods can still be validly applied, many molecular techniques have been developed that allow for strain classification on all taxonomic levels. A critical evaluation of the actual scope of each identification procedure will in the end determine the most appropriate use of the many protocols now available. Nonetheless, the oldest tool of microbiology, the microscope, is still a fundamental accessory for studies involving yeast biology, biodiversity and taxonomy.

Biotechnology↗
PubMed1997

Controversies in medical mycology.

Questions and controversies involving many aspects of medical mycology have increased in recent years. Case histories are described in which fungal infection causes unexpected and atypical problems. Molecular techniques of diagnosis need to be used alongside traditional culture methods. Increased drug use has led to genuine concerns and differing views regarding the definition and development of resistance by fungi. The use and value of combinational antifungal therapy and the employment of immunomodulatory agents concomitant with antimycotics have been debated. Nonetheless, good standards have been developed in the testing of antifungal agents. These, together with the commercial viability of antifungal drugs and hence increased interest in their development, mean that although we have entered the golden age of mycology we have also entered the golden age of antifungal therapy.

Adolescent↗
PubMed2002

Office practice-based confirmation of onychomycosis: a US nationwide prospective survey.

BACKGROUND: Onychomycosis is sufficiently prevalent to be seen and treated by primary care physicians. The diagnosis of onychomycosis is most often confirmed from nail specimens by microscopy and fungal culture done at a central laboratory; these are relatively expensive tests with a turnaround time of a month or more. This study was conducted (1) to evaluate the use of in-office dermatophyte test medium (DTM) culture, and (2) to determine the epidemiology of onychomycosis in a large, nationwide sample of patients who were not participants in a clinical trial. METHODS: A nationwide sample of primary care physicians and podiatrists enrolled 670 patients with clinical signs of toenail onychomycosis. Dermatophyte test medium cultures were performed in the office and the results were compared with fungal cultures performed by a central laboratory. RESULTS: Central laboratory fungal cultures were positive in 44% (n = 297) of patients and DTM cultures in 51% (n = 345). Dermatophytes accounted for 93% of the confirmed infections and nondermatophyte molds the rest. In the 617 patients with paired dermatophyte test medium and laboratory fungal culture results, the 2 tests were in agreement (both positive or both negative) in 68% of cases (kappa, 0.37; asymptotic SE, 0.04; 95% confidence interval, 0.299-0.441). CONCLUSIONS: A DTM culture is a relatively rapid, easy, and inexpensive method to confirm dermatophyte infections in patients with signs of onychomycosis in the primary care setting. Because the available drugs for treating onychomycosis are effective against all dermatophyte species, the confirmation of dermatophyte infection, without further identification of genus and species, is sufficient evidence to begin treatment.

Adolescent↗
PubMed2004

Occurrence of Candida strains in cases of paronychia.

A total of 43 patients, 11 males and 32 females, with paronychia of the fingernails were examined for the presence of Candida spp. The yeast species isolated were identified using standard laboratory methods, including germ-tube production, morphology on rice agar with Tween 80, and mainly fermentation and assimilation of saccharides. In the male group, two Candida species were detected: C. albicans as the dominant species in 9 patients and C. parapsilosis in 2 cases. Similarly, C. albicans was the prevalent species also in females (n = 17); other Candida species detected were C. parapsilosis (n = 7), C. tropicalis (5) and C. krusei (3). In addition to the genus Candida, the following anaerobic and aerobic microorganisms were isolated from patients of both groups: Fusobacterium spp., Bacteroides spp., Staphylococcus aureus, alpha-hemolytic streptococci, group A beta-hemolytic streptococci, Klebsiella pneumoniae, Neisseria spp. and Pseudomonas aeruginosa.

Adult↗
PubMed2006

FTIR spectroscopy in medical mycology: applications to the differentiation and typing of Candida.

The incidence of fungal infections, in particular candidiasis and aspergillosis, has considerably increased during the last three decades. This is mainly due to advances in medical treatments and technologies. In high risk patients (e.g. in haematology or intensive care), the prognosis of invasive candidiasis is relatively poor. Therefore, a rapid and correct identification of the infectious agent is important for an efficient and prompt therapy. Most clinical laboratories rely on conventional identification methods that are based on morphological, physiological and nutritional characteristics. However, these have their limitations because they are time-consuming and not always very accurate. Moreover, molecular methods may be required to determine the genetic relationship between the infectious strains, for instance in Candida outbreaks. In addition, the latter methods require time, expensive consumables and highly trained staff to be performed adequately. In this study, we have applied the FTIR spectroscopic approach to different situations encountered in routine mycological diagnosis. We show the potentials of this phenotypic approach, used in parallel with routine identification methods, for the differentiation of 3 frequently encountered Candida species (C. albicans, C. glabrata and C. krusei) by using both suspensions and microcolonies. This approach, developed for an early discrimination, may help in the initial choice of antifungal treatment. Furthermore, we demonstrate the feasibility of the method for intraspecies comparison (typing) of 3 Candida species (C. albicans, C. glabrata and C. parapsilosis), particularly when an outbreak is suspected.

Candida↗
PubMed2004

Polyphasic identification of yeasts isolated from bark of cork oak during the manufacturing process of cork stoppers.

A two-step protocol was used for the identification of 52 yeasts isolated from bark of cork oak at initial stages of the manufacturing process of cork stoppers. The first step in the identification was the separation of the isolates into groups by their physiological properties and RFLPs of the ITS-5.8S rRNA gene. The second step was the sequencing of the D1/D2 domains of the 26S rRNA gene of selected isolates representing the different groups. The results revealed a predominance of basidiomycetous yeasts (11 species), while only two species represented the ascomycetous yeasts. Among the basidiomycetous yeasts, members representing the species Rhodosporidium kratochvilovae and Rhodotorula nothofagi, that have been previously isolated from plant material, were the most abundant. Yeasts pertaining to the species Debaryomyces hansenii var. fabryii, Rhodotorula mucilaginosa and Trichosporon mucoides were isolated in small numbers.

Base Sequence↗
PubMed1999

Novel microtiter plate format for testing germ tube formation and proposal of a cost-effective scheme for yeast identification in a clinical laboratory.

The germ tube test is most widely used for presumptive identification of Candida albicans. Conventional testing is relatively time-consuming due to the hands-on time involved in preparing and viewing each isolate. In order to reduce work-load and costs we have developed a novel microtiter plate test format that offers several advantages: (i) use of removable strips of microtiter wells placed in lockwell frames, (ii) only one pipetting step for each isolate, (iii) direct micromorphological evaluation using an inverse microscope, (iv) use of a novel synthetic germ tube test medium, (v) reduction of the inoculum, permitting testing of minute colonies, (vi) thus, testing of different colonies in potentially mixed primary cultures of clinical specimens is encouraged and facilitated. Implementing this microtiter based germ tube test with simultaneous trehalase test for presumptive identification of Torulopsis (Candida) glabrata, we propose an identification scheme including this test format. This has been implemented in our routine laboratory permitting cost-effective presumptive identification of almost all clinically relevant yeast species.

Candida↗
PubMed2005

Molecular methods for the identification of Aspergillus species.

Invasive aspergillosis (IA) is a leading cause of morbidity and mortality in immunocompromised hosts. In some institutions, species of Aspergillus less susceptible to amphotericin B than Aspergillus fumigatus are becoming more common, making an accurate identification of species important. However, species identification has traditionally relied on macroscopic colony characteristics and microscopic morphology, which may require several days of culture. Additional sub-culturing on specialized media may be required to induce conidia formation; in some cases conidia may never form, confounding identification. Therefore, rapid, nucleic acid-based methods that identify species of Aspergillus independent of morphology are now being developed to augment or replace phenotypic identification methods. The most successful methods to date have employed polymerase chain reaction (PCR) amplification of target sequences within the ribosomal RNA gene complex, including the 28S ribosomal subunit (D1-D2 region) and the internal transcribed spacers 1 and 2 (ITS1 and ITS2 regions). We therefore developed a PCR-based assay to differentiate medically important species of Aspergillus from one another, and from other opportunistic moulds and yeasts, by employing universal, pan-fungal primers directed to conserved ribosomal genes and species-specific DNA probes directed to the highly variable ITS2 region. Amplicons were then detected in a simple, colorimetric enzyme immunoassay format (PCR-EIA). DNA sequencing of the ITS1 and ITS2 regions and of the D1-D2 region was also conducted for the differentiation of species by comparative GenBank sequence analysis. The PCR-EIA method was found to be rapid, sensitive, and specific for the identification and differentiation of the most medically important species of Aspergillus. In addition, methods to identify species of Aspergillus by comparative GenBank sequence analysis were found to be more reliable using the ITS1 and ITS2 regions than the D1-D2 region.

Aspergillosis↗
PubMed1992

The molecular analysis of synonymy among medically important yeasts within the genus Candida.

Three sets of medically important yeasts, Candida albicans, C. tropicalis, and C. krusei, were compared with their putative synonyms (C. langeronii and C. claussenii, C. paratropicalis, and Itssatchenkia orientalis, respectively) to determine if these synonyms are genetically distinguishable from each other. Pulsed-field electrophoresis and hybridization to species-specific probes were used to accomplish this goal. The species-specific probes for C. albicans and C. tropicalis have been previously described (27A and CT13.8, respectively) whereas the probe for C. krusei (CK3) was cloned in this study. No distinguishing characteristics between synonyms were identified, thus supporting the current taxonomic treatment of these organisms.

Candida↗
PubMed2006

Broad-spectrum respiratory tract pathogen identification using resequencing DNA microarrays.

The exponential growth of pathogen nucleic acid sequences available in public domain databases has invited their direct use in pathogen detection, identification, and surveillance strategies. DNA microarray technology has offered the potential for the direct DNA sequence analysis of a broad spectrum of pathogens of interest. However, to achieve the practical attainment of this potential, numerous technical issues, especially nucleic acid amplification, probe specificity, and interpretation strategies of sequence detection, need to be addressed. In this report, we demonstrate an approach that combines the use of a custom-designed Affymetrix resequencing Respiratory Pathogen Microarray (RPM v.1) with methods for microbial nucleic acid enrichment, random nucleic acid amplification, and automated sequence similarity searching for broad-spectrum respiratory pathogen surveillance. Successful proof-of-concept experiments, utilizing clinical samples obtained from patients presenting adenovirus or influenza virus-induced febrile respiratory illness (FRI), demonstrate the ability of this approach for correct species- and strain-level identification with unambiguous statistical interpretation at clinically relevant sensitivity levels. Our results underscore the feasibility of using this approach to expedite the early surveillance of diseases, and provide new information on the incidence of multiple pathogens.

Bacterial Typing Techniques↗
PubMed2006

Mycelium cultivation, chemical composition and antitumour activity of a Tolypocladium sp. fungus isolated from wild Cordyceps sinensis.

AIMS: To examine and illustrate the morphological characteristics and growth kinetics of Cs-HK1, a Tolypocladium fungus, isolated from wild Cordyceps sinensis in solid and liquid cultures, and the major chemical constituents and antitumour effects of Cs-HK1 mycelium. METHODS AND RESULTS: The Cs-HK1 fungus was isolated from the fruiting body of a wild C. sinensis and identified as a Tolypocladium sp. fungus. It grew rapidly at 22-25 degrees C on a liquid medium containing glucose, yeast extract, peptone and major inorganic salts, with a specific growth rate of 1.1 day(-1), reaching a cell density of 23.0 g dw l(-1) in 7-9 days. Exopolysaccharides accumulated in the liquid culture to about 0.3 g l(-1) glucose equivalent. In comparison with natural C. sinensis, the fungal mycelium had similar contents of protein (11.7-microg) and carbohydrate (654.6-microg) but much higher contents of polysaccharide (244.2 mg vs 129.5 mg), adenosine (1116.8-microg vs 264.6 microg) and cordycepin (65.7 microg vs 20.8 microg) (per gram dry weight). Cyclosporin A, an antibiotic commonly produced by Tolypocladium sp., was also detected from the mycelium extract. The hot water extract of mycelium showed low cytotoxic effect on B16 melanoma cells in culture (about 25% inhibition) but significant antitumour effect in animal tests, causing 50% inhibition of B16 cell-induced tumour growth in mice. CONCLUSIONS: The Tolypocladium sp. fungus, Cs-HK1, can be easily cultivated by liquid fermentation. The mycelium biomass contained the major bioactive compounds of C. sinensis, and the mycelium extract had significant antitumour activity. SIGNIFICANCE AND IMPACT OF THE STUDY: The Cs-HK1 fungus may be a new and promising medicinal fungus and an effective and economical substitute of the wild C. sinensis for health care.

Animals↗
PubMed2004

Changes in population structure of the soilborne fungus Gaeumannomyces graminis var. tritici during continuous wheat cropping.

A method was developed to assess the genetic structure of Gaeumannomyces graminis var. tritici (Ggt) populations and test the hypothesis of an association between disease level in the field with changes in pathogen populations. A long-term wheat monoculture experiment, established since 1994, generated different take-all epidemics with varying the number of wheat crop successions in the 1999-2000 cropping season. Genetic polymorphism in Ggt populations was investigated over natural, local epidemics. Four populations of 30 isolates were isolated from necrotic wheat roots in a first, third, fourth, and sixth wheat crop in the same year. Each Ggt isolate was characterized with RAPD (Random Amplification Polymorphism DNA) markers and AFLP (Amplified Fragment Length Polymorphism) fingerprinting. Seventeen multilocus genotypes based on the combination of RAPD and AFLP markers were identified among all these populations. The 120 isolates were divided into two main groups, G1 and G2, according to bootstrap values higher than 86%, except for an unique isolate from the third wheat crop. Within each group, populations ranged between 93 and 100% similarity. Both groups included isolates collected from the first, third, fourth or sixth wheat crop. However, G1 group profiles dominated amongst isolates sampled in the first and the sixth wheat crops, whereas G2 group profiles largely dominated amongst isolates collected from the third and fourth wheat crops. Aggressiveness of group G2 (38%) was significantly greater than that of G1 (29.5%). These results suggest that changes in Ggt population structure occur during continuous wheat cropping. The distinction of two Ggt groups provides a simple basis for further spatio-temporal analysis of Ggt population during polyetic take-all decline.

Ascomycota↗