Identification of moulds in the diagnostic laboratory—an algorithm implementing molecular and phenotypic methods

Cutaneous Invasive Fungal Infections with Saksenaea Species in Immunocompetent Patients in Europe: A Systematic Review and Case Report

Invasive fungal infections from Saksenaea, a fungus belonging to the Mucorales, have been rarely reported in central European climate zones. This study aims to raise awareness of invasive cutaneous infections with Saksenaea species. The first case of a cutaneous infection was diagnosed in Switzerland in an immunocompetent 79-year-old patient. A minor skin trauma of her left lower leg led to a fulminant infection causing necrosis and extensive loss of tissue. The combination of surgical debridement and administration of antifungal agents averted a prolonged course with a possible worse outcome. A pedicled hemisoleus muscle flap was used to reconstruct the defect and treatment was continued for 63 days.

Identification of filamentous fungi including dermatophytes using MALDI-TOF mass spectrometry

Identification of filamentous fungi based on morphological features is the most available approach used in clinical mycology laboratories. However, MALDI-TOF mass spectrometry is currently invaluable for identification of microorganisms because of its rapidity, simplicity, and accuracy. This study aimed to find the optimal way of identifying filamentous fungi using MALDI-TOF MS.The sample comprised 193 isolates of filamentous fungi. The identification started with morphological assessment. Then isolates were identified using MALDI-TOF MS, both directly from culture and following culture in liquid media with extraction. Subsequently, identification of 20 selected isolates was compared by sequencing of the benA gene, ITS1-5,8-ITS2, and D1-D2 LSU regions.Based on morphological criteria, 17 genera of fungi were identified. With MALDI-TOF MS performed directly from culture, nine isolates were identified to the genus level and 184 to the species level, with a total of 75 species being noted. With the MALDI-TOF MS extraction method, 190 isolates were identified to the species level, with 43 species being noted. The rates of agreement between identification using morphology and the MALDI-TOF MS direct method were 58.55% at the genus level and 22.24% at the species level. The rates of agreement between identification using morphology and the MALDI-TOF MS extraction method were 84.97% at the genus level and 46.11% at the species level. Using sequencing, 87.5% agreement was found for identification with the MALDI-TOF MS extraction method, as compared with only 43.75% for the direct method.The results suggest that the optimal approach to identification of filamentous fungi is a combination of morphological features and MALDI-TOF MS using the extraction method.

Biological Activity of Extracts from Aromatic Plants as Control Agents against Spoilage Molds Isolated from Sheep Cheese

The aim of this work was to assess the antifungal and antioxidant activity of essential oils and ethanolic extracts from distilled solid by-products from aromatic plants (Artemisia dracunculus, Hyssopus officinalis, Lavandula stoechas, Origanum vulgare and Satureja montana) against 14 fungi strains isolated from sheep cheese and identified at species level using DNA barcoding based on β-tubulin sequence analysis. In addition, capacity of fungi to produce ochratoxin A, patulin, cyclopiazonic acid and sterigmatocystin was analyzed. Of the isolates, 85.7% belonged to Penicillium (P. commune/biforme, P. crustosum) and 14.3% to Aspergillus (A. puulaauensis and A. jensenii), the first time that these Aspergillus species have been found in sheep's cheese. All P. commune isolates were producers of cyclopiazonic acid, and the two Aspergillus strains produced sterigmatocystin, but the others did not produce any tested mycotoxin. Among the essential oils tested, oregano, savory and tarragon had a significant antifungal activity against all the isolated strains, but no ethanolic extract showed antifungal activity. By contrast, ethanolic extracts showed great potential as antioxidants. The identification of new molds in cheese will help the dairy industry to know more about those molds affecting the sector, and the use of aromatic plants in the control of fungal spoilage could be a suitable alternative to chemical preservatives used in the agri-food industry.

Floral Colonization Dynamics and Specificity of Aureobasidium pullulans Strains Used to Suppress Fire Blight of Pome Fruit

Aureobasidium pullulans is used as a biocontrol agent for fire blight protection in organic apple and pear production. We assessed colonization of pome flowers by A. pullulans in orchards located near Corvallis, OR and Wenatchee, WA. Blossom Protect, a mix of A. pullulans strains CF10 and CF40, and its citrate-based companion, Buffer Protect, were sprayed at 70% bloom. Later in bloom, the population size of putative A. pullulans on flowers was estimated by dilution plating; plate scrapings of putative A. pullulans were then sampled and subjected to a PCR analysis. Sequenced PCR amplicons of the internal transcribed spacer region and the elongase gene confirmed the presence of A. pullulans, whereas a multiplex PCR with primers specific to CF10 and CF40 was used to determine the presence of the introduced strains. At Corvallis, a wet spring environment, A. pullulans, was recovered from most (>90%) Bartlett pear and Golden Delicious apple flowers sampled from experimental trees, regardless of whether the trees were treated with Blossom Protect. Nevertheless, population size estimates of A. pullulans on the flowers were correlated with the number of times Blossom Protect was sprayed on the trees. At Wenatchee, an arid spring environment, A. pullulans was detected on most flowers from trees treated with Blossom Protect, but only on a minority of flowers from nontreated controls. In both locations, the combined incidence of strains CF10 and CF40 on flowers averaged 89% on Blossom Protect-treated trees, but only 27% on adjacent, nontreated trees. During subsequent trials, the efficacy of Blossom Protect for fire blight control was compared with alternative yeast isolates, with each applied with Buffer Protect; local isolates of A. pullulans and Cryptococcus neoformans and a postharvest biocontrol strain of Cystofilobasidium infirmominiatum were used All yeast strains suppressed fire blight to a degree; however, in each of four trials, the level of suppression was highest with Blossom Protect, and it was significantly superior (P ≤ 0.05) to other yeast isolates in two of the trials. Because A. pullulans strains CF10 and CF40 were detected primarily on flowers on trees treated with Blossom Protect, and because they were detected much less frequently on nearby nontreated tress, we recommend treating every tree row with Blossom Protect at least once for organic fire blight suppression.

Polyphasic identification of Penicillium spp. isolated from Spanish semi-hard ripened cheeses

Fifteen samples of semi-hard ripened cheeses, both spoiled (10) and unspoiled (5), and obtained from cheese factories located in Northwest of Spain, were analysed by a dilution plating technique and direct sampling. A total of 32 isolates were identified at species level by a polyphasic approach (phenotypic characterization, partial extrolite analysis and molecular identification). Most isolates (65.6%) belonged to the species P. commune; other species found were P. solitum, P. chrysogenum, P. nordicum, P. expansum and P. cvjetkovicii. All of the P. commune isolates were able to produce cyclopiazonic acid, while the P. nordicum and the P. expansum isolates were producers of ochratoxin A and patulin respectively. Despite this, the role of P. commune as beneficial fungi in cheese ripening should be investigated. Molecular identification based on BenA sequence analysis was able to identify the majority of isolates. The three mycotoxins investigated can be considered key for identification. The polyphasic approach seems to be a very valuable tool for identification of isolates of this complex genus.

Contribution of the internal transcribed spacer regions to the detection and identification of human fungal pathogens

Fungi are morphologically and phylogenetically diverse. There identification is largely based on phenotypic methods. Thus, related species, phenotypic variants and rare species may be unidentified. So, molecular methods have been introduced for identification of pathogenic molds to overcome these problems. In this study, we report the contribution of molecular tools (PCR sequencing) to identify fungal pathogens in both clinical and environmental samples. A total of 82 mold isolates were used (50 clinical samples and 32 environmental samples). PCR and direct sequencing, targeting the internal transcribed spacer (ITS) regions, were performed. We employed comparative sequence analysis to identify molds by using the GenBank database. 89% of isolates were identified by phenotypic methods. PCR- sequencing allowed the fungal identification in all cases. The concordance between molecular and morphological identification was obtained for 33 cases (40.2%). In 36 cases (43.9%), the molecular study gave the exact species identification. PCR sequencing allowed as revising mycological identification for 13 fungi strains (15.9%). The concordance of identification at species level by phenotypic method and by sequence analysis was obtained for 28% of clinical samples and for 59% of environmental samples. The phylogenetic tree for the ITS sequences showed six different clusters that are composed of isolates belonging to the same genus or species. PCR sequencing has been shown to be useful for the detection of the presence of fungal DNA in both environmental and clinical samples. It is rapid and more sensitive for the identification of medically important fungi.

Development and optimization of a group-specific loop-mediated isothermal amplification (LAMP) assay for the detection of patulin-producing Penicillium species

The mycotoxin patulin is a toxic fungal secondary metabolite occurring in food worldwide. Methods for rapid, simple and specific detection of patulin-producing fungi in food and feed are therefore urgently needed. In the current study, a loop-mediated isothermal amplification (LAMP) assay based on the isoepoxydon dehydrogenase (idh) gene of the patulin biosynthetic pathway was developed and optimized for the group-specific detection of patulin-producing Penicillium species. By testing purified DNA of 174 fungal strains representing 31 genera, the assay was demonstrated to be highly specific for the detection of patulin-producing species in Penicillium, Byssochlamys and Paecilomyces. The assay had a detection limit of 2.5 pg of purified genomic DNA of P. expansum per reaction. Moreover, the assay was demonstrated to detect patulin-producers when conidia were directly added to the master mix as template without any sample preparation. The applicability of the assay in food analyses was successfully tested on artificially contaminated grapes and apples requiring minimal sample preparation. A screening of grapes from the 2018 harvest from different locations in Germany revealed no presence of patulin-producers. The developed LAMP assay is a promising tool for rapid diagnosis in quality control applications in the food and beverage industry.

Evaluation of the Bruker Biotyper Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry System for Identification of Aspergillus Species Directly from Growth on Solid Agar Media

We evaluated the accuracy of the Bruker Biotyper matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) system at identifying clinical isolates of Aspergillus species that were grown on agar media. A total of 381 non-duplicate Aspergillus isolates representing 21 different Aspergillus species identified by molecular analysis were included in this study. The Bruker Biotyper MALDI-TOF MS system was able to identify 30.2% (115/381) of the isolates to the species level (score values of ≥2.000) and 49.3% to the genus level (score values of 1.700–1.999). When the identification cutoff value was lowered from ≥2.000 to ≥1.700, the species-level identification rate increased to 79.5% with a slight rise of false identification from 2.6 to 5.0%. From another aspect, a correct species-level identification rate of 89% could be reached by the Bruker Biotyper MALDI-TOF MS system regardless of the score values obtained. The Bruker Biotyper MALDI-TOF MS system had a moderate performance in identification of Aspergillus directly inoculated on solid agar media. Continued expansion of the Bruker Biotyper MALDI-TOF MS database and adoption of alternative cutoff values for interpretation are required to improve the performance of the system for identifying highly diverse species of clinically encountered Aspergillus isolates.

Similar efficacy of broad-range ITS PCR and conventional fungal culture for diagnosing fungal infections in non-immunocompromised patients

Background

Broad-range fungal inter spacer region (ITS) polymerase chain reaction (PCR) has been evaluated for the detection and identification of fungi in clinical specimens from severely immunocompromised patients, but not in non-selected patients. Thus, the aim of this study was to compare the diagnostic performance of ITS PCR with that of fungal culture and to investigate its clinical impact on the diagnosis of fungal infections in non-immunocompromised patients. The corresponding patients’ data were retrieved by detailed medical chart reviews.

Results

Results from 251 specimens showed a high concordance of 89.6 % for ITS PCR and fungal culture. The analytical sensitivity and specificity of ITS PCR considering culture as gold standard were 87.7 and 90.3 %, respectively, the positive and negative predictive value (PPV and NPV) were 76 and 95.5 %, respectively. Assessing the clinical probability of a fungal infection based on detailed chart reviews, PCR had a clinical sensitivity of 88.9 %, a specificity of 86.3 %, a PPV of 64.0 % and a NPV of 96.6 %. The overall performance of fungal broad-range PCR was similar to that of culture.

Conclusions

Our data show that, in non-selected and non-immunocompromised patients, the performance of ITS PCR is similar to that of culture for detecting fungal infections, not the least because sensitivity of culture in patients under antifungal treatment is surprisingly high. Compared to culture, PCR has the advantage of a rapid time-to-result (approximately two working days), proper identification of rare pathogens, prompt initiation of a species-targeted antifungal treatment, and prospects for automation.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-016-0752-1) contains supplementary material, which is available to authorized users.

Molecular diagnostic methods for invasive fungal disease: the horizon draws nearer?

Rapid, accurate diagnostic laboratory tests are needed to improve clinical outcomes of invasive fungal disease (IFD). Traditional direct microscopy, culture and histological techniques constitute the 'gold standard' against which newer tests are judged. Molecular diagnostic methods, whether broad-range or fungal-specific, have great potential to enhance sensitivity and speed of IFD diagnosis, but have varying specificities. The use of PCR-based assays, DNA sequencing, and other molecular methods including those incorporating proteomic approaches such as matrix-assisted laser desorption ionisation-time of flight mass spectroscopy (MALDI-TOF MS) have shown promising results. These are used mainly to complement conventional methods since they require standardisation before widespread implementation can be recommended. None are incorporated into diagnostic criteria for defining IFD. Commercial assays may assist standardisation. This review provides an update of molecular-based diagnostic approaches applicable to biological specimens and fungal cultures in microbiology laboratories. We focus on the most common pathogens, Candida and Aspergillus, and the mucormycetes. The position of molecular-based approaches in the detection of azole and echinocandin antifungal resistance is also discussed.

Abiotic determinants of the historical buildings biodeterioration in the former Auschwitz II-Birkenau concentration and extermination camp

The paper presents the results of a study conducted at the Auschwitz-Birkenau State Museum in Oświęcim on the occurrence of biodeterioration. Visual assessment of the buildings revealed signs of deterioration of the buildings in the form of dampness, bulging and crumbling plaster, and wood fiber splitting. The external surfaces, and especially the concrete strips and ground immediately adjoining the buildings, were colonized by bryophytes, lichens, and algae. These organisms developed most intensively close to the ground on the northern sides of the buildings. Inside the buildings, molds and bacteria were not found to develop actively, while algae and wood-decaying fungi occurred locally. The factors conducive to biological corrosion in the studied buildings were excessive dampness of structural partitions close to the ground and a relative air humidity of above 70%, which was connected to ineffective moisture insulation. The influence of temperature was smaller, as it mostly affected the quantitative composition of the microorganisms and the qualitative composition of the algae. Also the impact of light was not very strong, but it was conducive to algae growth.

Use of the Bruker MALDI Biotyper for identification of molds in the clinical mycology laboratory

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is increasingly used for the identification of bacteria and fungi in the diagnostic laboratory. We evaluated the mold database of Bruker Daltonik (Bremen, Germany), the Filamentous Fungi Library 1.0. First, we studied 83 phenotypically and molecularly well-characterized, nondermatophyte, nondematiaceous molds from a clinical strain collection. Using the manufacturer-recommended interpretation criteria, genus and species identification rates were 78.3% and 54.2%, respectively. Reducing the species cutoff from 2.0 to 1.7 significantly increased species identification to 71.1% without increasing misidentifications. In a subsequent prospective study, 200 consecutive clinical mold isolates were identified by the MALDI Biotyper and our conventional identification algorithm. Discrepancies were resolved by ribosomal DNA (rDNA) internal transcribed spacer region sequence analysis. For the MALDI Biotyper, genus and species identification rates were 83.5% and 79.0%, respectively, when using a species cutoff of 1.7. Not identified were 16.5% of the isolates. Concordant genus and species assignments of MALDI-TOF MS and the conventional identification algorithm were observed for 98.2% and 64.2% of the isolates, respectively. Four erroneous species assignments were observed using the MALDI Biotyper. The MALDI Biotyper seems highly reliable for the identification of molds when using the Filamentous Fungi Library 1.0 and a species cutoff of 1.7. However, expansion of the database is required to reduce the number of nonidentified isolates.

Identification of clinically relevant fungi and prototheca species by rRNA gene sequencing and multilocus PCR coupled with electrospray ionization mass spectrometry

BACKGROUND

Multilocus PCR coupled with electrospray ionization mass spectrometry (PCR/ESI-MS) is a new strategy for pathogen identification, but information about its application in fungal identification remains sparse.

METHODS

One-hundred and twelve strains and isolates of clinically important fungi and Prototheca species were subjected to both rRNA gene sequencing and PCR/ESI-MS. Three regions of the rRNA gene were used as targets for sequencing: the 5' end of the large subunit rRNA gene (D1/D2 region), and the internal transcribed spacers 1 and 2 (ITS1 and ITS2 regions). Microbial identification (Micro ID), acquired by combining results of phenotypic methods and rRNA gene sequencing, was used to evaluate the results of PCR/ESI-MS.

RESULTS

For identification of yeasts and filamentous fungi, combined sequencing of the three regions had the best performance (species-level identification rate of 93.8% and 81.8% respectively). The highest species-level identification rate was achieved by sequencing of D1/D2 for yeasts (92.2%) and ITS2 for filamentous fungi (75.8%). The two Prototheca species could be identified to species level by D1/D2 sequencing but not by ITS1 or ITS2. For the 102 strains and isolates within the coverage of PCR/ESI-MS identification, 87.3% (89/102) achieved species-level identification, 100% (89/89) of which were concordant to Micro ID on species/complex level. The species-level identification rates for yeasts and filamentous fungi were 93.9% (62/66) and 75% (27/36) respectively.

CONCLUSIONS

rRNA gene sequencing provides accurate identification information, with the best results obtained by a combination of ITS1, ITS2 and D1/D2 sequencing. Our preliminary data indicated that PCR/ESI-MS method also provides a rapid and accurate identification for many clinical relevant fungi.

Optimization of water curing for the preservation of chestnuts (Castanea sativa Mill.) and evaluation of microbial dynamics during process

Chestnuts are very perishable fruits, whose quality may be compromised during postharvest handling. Damage can be caused both by insects and fungi. Water curing, a commonly used postharvest method, is based on soaking fruits in water typically for about one week. Factors that affect effectiveness of water curing have only been explained partially. A decrease in pH, likely imputable to a light fermentation caused by lactic acid bacteria, may inhibit the growth of moulds. In this study a Lactobacillus pentosus strain was selected for its ability to inhibit fungi, and used as a starter culture during water curing. As second goal, a reduction of the environmental impact of the process was evaluated by using water that had been re-cycled from a previous curing treatment. Experiments were performed on pilot as well as on farm scale. In all trials, microbial dynamics were evaluated by means of a polyphasic approach including conventional and molecular-based analyses. According to results, the employment of an adjunct culture appears as a very promising opportunity. Even if no reduction in the duration of the process was achieved, waters exhibited a minor microbial complexity and fruits did not lose the natural lustre after the process.

Identification of dermatophytes by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

In this study we evaluated the suitability of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for the identification of dermatophytes in diagnostic laboratories. First, a spectral database was built with 108 reference strains belonging to 18 species of the anamorphic genera Epidermophyton, Microsporum and Trichophyton. All strains were well characterized by morphological criteria and ITS sequencing (gold standard). The dendrogram resulting from MALDI-TOF mass spectra was almost identical with the phylogenetic tree based on ITS sequencing. Subsequently, MALDI-TOF MS SuperSpectra were created for the identification of Epidermophyton floccosum, Microsporium audouinii, M. canis, M. gypseum (teleomorph: Arthroderma gypseum), M. gypseum (teleomorph: A. incurvatum), M. persicolor, A. benhamiae (Tax. Entity 3 and Am-Eur. race), T. erinacei, T. interdigitale (anthropophilic and zoophilic populations), T. rubrum/T. violaceum, T. tonsurans and T. terrestre. Because T. rubrum and T. violaceum did not present enough mismatches, a SuperSpectrum covering both species was created, and differentiation between them was done by comparison of eight specific peptide masses. In the second part of this study, MALDI-TOF MS with the newly created SuperSpectra was tested using 141 clinical isolates representing nine species. Analyses were done with 3-day-old cultures. Results were compared to morphological identification and ITS sequencing; 135/141 (95.8%) strains were correctly identified by MALDI-TOF MS compared to 128/141 (90.8%) by morphology. Therefore, MALDI-TOF MS has proven to be a useful and rapid identification method for dermatophytes.

Identification of clinical mold isolates by sequence analysis of the internal transcribed spacer region, ribosomal large-subunit D1/D2, and β-tubulin

Background

The identification of molds in clinical laboratories is largely on the basis of phenotypic criteria, the classification of which can be subjective. Recently, molecular methods have been introduced for identification of pathogenic molds in clinical settings. Here, we employed comparative sequence analysis to identify molds.

Methods

A total of 47 clinical mold isolates were used in this study, including Aspergillus and Trichophyton. All isolates were identified by phenotypic properties, such as growth rate, colony morphology, and reproductive structures. PCR and direct sequencing, targeting the internal transcribed spacer (ITS) region, the D1/D2 region of the 28S subunit, and the β-tubulin gene, were performed using primers described previously. Comparative sequence analysis by using the GenBank database was performed with the basic local alignment search tool (BLAST) algorithm.

Results

For Aspergillus, 56% and 67% of the isolates were identified to the species level by using ITS and β-tubulin analysis, respectively. Only D1/D2 analysis was useful for Trichophyton identification, with 100% of isolates being identified to the species level. Performances of ITS and D1/D2 analyses were comparable for species-level identification of molds other than Aspergillus and Trichophyton. In contrast, the efficacy of β-tubulin analysis was limited to genus identification because of the paucity of database information for this gene.

Conclusions

The molecular methods employed in this study were valuable for mold identification, although the different loci used had variable usefulness, according to mold genus. Thus, a tailored approach is recommended when selecting amplification targets for molecular identification of molds.

Molecular methods for pathogen and microbial community detection and characterization: current and potential application in diagnostic microbiology

Clinical microbiology laboratories worldwide have historically relied on phenotypic methods (i.e., culture and biochemical tests) for detection, identification and characterization of virulence traits (e.g., antibiotic resistance genes, toxins) of human pathogens. However, limitations to implementation of molecular methods for human infectious diseases testing are being rapidly overcome allowing for the clinical evaluation and implementation of diverse technologies with expanding diagnostic capabilities. The advantages and limitation of molecular techniques including real-time polymerase chain reaction, partial or whole genome sequencing, molecular typing, microarrays, broad-range PCR and multiplexing will be discussed. Finally, terminal restriction fragment length polymorphism (T-RFLP) and deep sequencing are introduced as technologies at the clinical interface with the potential to dramatically enhance our ability to diagnose infectious diseases and better define the epidemiology and microbial ecology of a wide range of complex infections.

Molecular profiling of fungal communities in moisture damaged buildings before and after remediation--a comparison of culture-dependent and culture-independent methods

Background

Indoor microbial contamination due to excess moisture is an important contributor to human illness in both residential and occupational settings. However, the census of microorganisms in the indoor environment is limited by the use of selective, culture-based detection techniques. By using clone library sequencing of full-length internal transcribed spacer region combined with quantitative polymerase chain reaction (qPCR) for 69 fungal species or assay groups and cultivation, we have been able to generate a more comprehensive description of the total indoor mycoflora. Using this suite of methods, we assessed the impact of moisture damage on the fungal community composition of settled dust and building material samples (n = 8 and 16, correspondingly). Water-damaged buildings (n = 2) were examined pre- and post- remediation, and compared with undamaged reference buildings (n = 2).

Results

Culture-dependent and independent methods were consistent in the dominant fungal taxa in dust, but sequencing revealed a five to ten times higher diversity at the genus level than culture or qPCR. Previously unknown, verified fungal phylotypes were detected in dust, accounting for 12% of all diversity. Fungal diversity, especially within classes Dothideomycetes and Agaricomycetes tended to be higher in the water damaged buildings. Fungal phylotypes detected in building materials were present in dust samples, but their proportion of total fungi was similar for damaged and reference buildings. The quantitative correlation between clone library phylotype frequencies and qPCR counts was moderate (r = 0.59, p < 0.01).

Conclusions

We examined a small number of target buildings and found indications of elevated fungal diversity associated with water damage. Some of the fungi in dust were attributable to building growth, but more information on the material-associated communities is needed in order to understand the dynamics of microbial communities between building structures and dust. The sequencing-based method proved indispensable for describing the true fungal diversity in indoor environments. However, making conclusions concerning the effect of building conditions on building mycobiota using this methodology was complicated by the wide natural diversity in the dust samples, the incomplete knowledge of material-associated fungi fungi and the semiquantitative nature of sequencing based methods.

Molecular identification of Pilobolus species from Yellowstone National Park

Pilobolus, a widely distributed coprophilous fungus, grows on herbivore dung. Species of Pilobolus traditionally are described with imprecise morphological characteristics potentially leading to misidentification. In this study we used PCR analysis of taxonomically informative sequences to provide more consistent species identification from isolates obtained in Yellowstone National Park. We collected Pilobolus park-wide from six taxa of herbivores over 9 y. Multiple transfers of single sporangium isolates provided pure cultures from which DNA was extracted. Sequence analysis of internal transcribed spacer (ITS) regions of DNA that code for rRNA genes were used to distinguish among similar species. We describe several species of Pilobolus associated with herbivores in various habitats, including two species not previously reported, P. heterosporus and P. sphaerosporus. Our results show that phylogenetic species identification of Pilobolus based on sequence analysis of pure culture isolates provides a more reliable means of identifying species than traditional methods.

Systematic internal transcribed spacer sequence analysis for identification of clinical mold isolates in diagnostic mycology: a 5-year study

The implementation of internal transcribed spacer (ITS) sequencing for routine identification of molds in the diagnostic mycology laboratory was analyzed in a 5-year study. All mold isolates (n = 6,900) recovered in our laboratory from 2005 to 2009 were included in this study. According to a defined work flow, which in addition to troublesome phenotypic identification takes clinical relevance into account, 233 isolates were subjected to ITS sequence analysis. Sequencing resulted in successful identification for 78.6% of the analyzed isolates (57.1% at species level, 21.5% at genus level). In comparison, extended in-depth phenotypic characterization of the isolates subjected to sequencing achieved taxonomic assignment for 47.6% of these, with a mere 13.3% at species level. Optimization of DNA extraction further improved the efficacy of molecular identification. This study is the first of its kind to testify to the systematic implementation of sequence-based identification procedures in the routine workup of mold isolates in the diagnostic mycology laboratory.

Sequence-based identification of filamentous basidiomycetous fungi from clinical specimens: a cautionary note

The species-level identification of sterile and/or arthroconidium-forming filamentous fungi presumed to be basidiomycetes based upon morphological or physiological features alone is usually not possible due to the limited amount of hyphal differentiation. Therefore, a reliable molecular approach capable of the unambiguous identification of clinical isolates is needed. One hundred sixty-eight presumptive basidiomycetes were screened by sequence analysis of the internal transcribed spacer (ITS) and D1/D2 ribosomal DNA regions in an effort to obtain a species identification. Through the use of this approach, identification of a basidiomycetous fungus to the species level was obtained for 167/168 of the isolates. However, comparison of the BLAST results for each isolate for both regions revealed that only 28.6% (48/168) of the isolates had the same species identification by use of both the ITS and the D1/D2 regions, regardless of the percent identity. At the less stringent genus-only level, the identities for only 48.8% (82/168) of the isolates agreed for both regions. Investigation of the causes for this low level of agreement revealed that 14% of the species lacked an ITS region deposit and 16% lacked a D1/D2 region deposit. Few GenBank deposits were found to be complete for either region, with only 8% of the isolates having a complete ITS region and 10% having a complete D1/D2 region. This study demonstrates that while sequence-based identification is a powerful tool for many fungi, sequence data derived from filamentous basidiomycetes should be interpreted carefully, particularly in the context of missing or incomplete GenBank data, and, whenever possible, should be evaluated in light of compatible morphological features.