Nucleotide sequence analysis of beta tubulin gene in a wide range of dermatophytes

Epidemiologic features and therapeutic strategies of kerion: A nationwide multicentre study

BACKGROUND

Kerion is a severe type of tinea capitis that is difficult to treat and remains a public health problem.

OBJECTIVES

To evaluate the epidemiologic features and efficacy of different treatment schemes from real-world experience.

METHODS

From 2019 to 2021, 316 patients diagnosed with kerion at 32 tertiary Chinese hospitals were enrolled. We analysed the data of each patient, including clinical characteristics, causative pathogens, treatments and outcomes.

RESULTS

Preschool children were predominantly affected and were more likely to have zoophilic infection. The most common pathogen in China was Microsporum canis. Atopic dermatitis (AD), animal contact, endothrix infection and geophilic pathogens were linked with kerion occurrence. In terms of treatment, itraconazole was the most applied antifungal agent and reduced the time to mycological cure. A total of 22.5% of patients received systemic glucocorticoids simultaneously, which reduced the time to complete symptom relief. Furthermore, glucocorticoids combined with itraconazole had better treatment efficacy, with a higher rate and shorter time to achieving mycological cure.

CONCLUSIONS

Kerion often affects preschoolers and leads to serious sequelae, with AD, animal contact, and endothrix infection as potential risk factors. Glucocorticoids, especially those combined with itraconazole, had better treatment efficacy.

Tinea corporis intrafamilial infection in pets due to Microsporum canis

Microsporum canis, one of the most widespread dermatophytes worldwide, is a zoonotic microorganism that transmits infection from reservoirs such as cats and dogs to humans. This microorganism is associated with Tinea corporis and other clinical manifestations; however, few studies have used genetic surveillance to determine and characterize the process of zoonotic transmission. In this study, we show a clear example of zoonotic transmission from a cat to an intrafamilial environment, where it caused Tinea corporis by infection with M. canis. Molecular characterization using the b-tubulin gene and Random Amplified Polymorphic DNA analysis made it possible to determine that the six isolates of M. canis obtained in this study belonged to the same genetic variant or clone responsible for reservoir-reservoir or reservoir-human transmission.

Molecular identification of keratinophilic fungi associated with hair scalp and antifungal activity of green-synthesis zinc oxide nanoparticles

A diverse population of fungi colonizes human hair and skin due to millions of years of functional integration and mutual adaptation. The human body, with its fungal communities, forms a complex entity. Microbial imbalance is promoted by instabilities in the host-mycobiota interaction system, which can be related to the development of various diseases. By morphological and molecular identification, 15 genera comprising 24 species were isolated from 18 scalp samples collected from girls. Yeast-like structures were the most common species in this study; they were recovered from six samples (33.3%). They were represented by five species: Arachniotus ruber; Cosmospora aurantiicola; Cutaneotrichosporon oleaginosum; Geotrichum candidum and Suhomyces tanzawaensis. For the synthesis of zinc oxide nanoparticles (ZnO NPs), an aqueous extract of Zingiber officinale was utilized as a reducing and capping agent. The prepared NPs tested by X-ray diffraction, they had a hexagonal wurtzite structure. Most of the ZnO NPs were spherical, and their diameter was about 38.9 nm using a transmission electron microscope. ZnO NPs of the Fourier-transform infrared spectroscopy spectra were recorded in the range of 400-4000 cm-1. UV-visible diffuse reflectance spectroscopy showed the 200-800 nm wavelength range. ZnO NPs showed the highest activity against Ambrosiella hartigii Ambh2; Cladosporium cladosporioides Cladcl12; C. cf. cucumerinum Cladcu13; S. tanzawaensis Suht34, with minimal inhibitory concentrations 1.25 × 103 µg/mL on the four isolates.

A Comparative Description of Dermatophyte Genomes: A State-of-the-Art Review

The nomenclature and phylogeny of dermatophytes is currently based on the nucleotide sequence polymorphisms of a few genomic regions. However, the limitations of this multilocus sequence-based approach makes dermatophyte species identification difficult. Variation and adaptation are key to the persistence of species. Nevertheless, this heterogeneity poses a genuine problem for the classification and nomenclature of dermatophytes. The relatively high intra-species and low inter-species polymorphisms of this keratinophilic group of fungi hampers both species delineation and identification. Establishing the taxonomic boundaries of dermatophyte species complexes remains controversial. Furthermore, until recently, knowledge of molecular biology, genetics and genomics remained limited. This systematic review highlights the added value of whole genome sequencing and analysis data in dermatophyte classification that might enhance identification and, consequently, the diagnosis and management of dermatophytoses. Our approach consisted in describing and comparing the dermatophyte mitochondrial genomes, secretomes (Adhesins, LysM domains, proteases) and metabolic pathways, with the aim to provide new insights and a better understanding of the phylogeny and evolution of dermatophytes.

Case report: A case of ocular infection caused by Corynespora cassiicola

Objective

The aim of this study is to identify the pathogen causing ocular infection in a Chinese patient and to describe its morphological characteristics.

Methods

Samples from the patient's intraoperative pus were collected for microscopic examination and culture. Morphology and drug sensitivities of the isolated fungus were analyzed. Ribosomal DNA (rDNA) sequencing was performed and blasted in GenBank.

Results

A strain of fungi was repeatedly isolated from pus samples in different types of medium. No conidia were shown when the isolate cultured on normal PDA medium, whereas pseudoseptate thick-walled conidia were shown when cultured on medium containing leaf leachate. The results of BLAST and phylogenetic trees based on internal transcribed spacer, beta-tubulin, translation elongation factor 1-alpha, and RNA polymerase II gene demonstrated that the isolated fungus was Corynespora cassiicola. Minimum inhibitory concentration results of this organism were as follows: anidulafungin, 0.06 μg/ml; amphotericin B, 0.12 μg/ml; micafungin, 0.06 μg/ml; caspofungin, 0.5 μg/ml; 5-fluorocytosine, >64 μg/ml; posaconazole, 2 μg/ml; voriconazole, 0.25 μg/ml; itraconazole, 0.5 μg/ml; fluconazole, 64 μg/ml.

Conclusion

The case was infected with Corynespora cassiicola and led to eye suppurative endophthalmitis and blindness. Combined applications of morphological and molecular biology techniques facilitate accurate diagnosis of fungal infections.

Phenotypic and Genotypic Identification of Dermatophytes from Mexico and Central American Countries

Dermatophytes are fungi included in the genera Trichophyton, Microsporum, Epidermophyton, Nannizzia, Paraphyton, Lophophyton, and Arthroderma. Molecular techniques have contributed to faster and more precise identification, allowing significant advances in phylogenetic studies. This work aimed to identify clinical isolates of dermatophytes through phenotypic (macro- and micromorphology and conidia size) and genotypic methods (sequences of ITS regions, genes of β tubulin (BT2), and elongation factor α (Tef-1α)) and determine the phylogenetic relationships between isolates. Ninety-four dermatophyte isolates from Costa Rica, Guatemala, Honduras, Mexico, and the Dominican Republic were studied. The isolates presented macro- and micromorphology and conidia size described for the genera Trichophyton, Microsporum, and Epidermophyton. Genotypic analysis classified the isolates into the genera Trichophyton (63.8%), Nannizzia (25.5%), Arthroderma (9.6%), and Epidermophyton (1.1%). The most frequent species were T. rubrum (26 isolates, 27.6%), T. interdigitale (26 isolates, 27.6%), and N. incurvata (11 isolates, 11.7%), N. gypsea and A. otae (nine isolates, 9.6%), among others. The genotypic methods clarified the taxonomic status of closely related species. For instance, the ITS and BT2 markers of T. rubrum/T. violaceum did not differ but the Tef-1α gene did. On the other hand, the three markers differed in T. equinum/T. tonsurans. Therefore, the ITS, BT2, and Tef-1α genes are useful for typing in phylogenetic analyses of dermatophytes, with Tef-1α being the most informative locus. It should be noted that isolate MM-474 was identified as T. tonsurans when using ITS and Tef-1α, but when using BT2, it was identified as T. rubrum. On the other hand, no significant difference was found when comparing the methods for constructing phylogenies, as the topologies were similar.

Dermatophytosis caused by Nannizzia nana (Microsporum nanum): a comprehensive review on a novel pathogen

Keratinophilic fungi are mostly soil-inhabiting organisms with occasional infections in humans and animals. Even though most dermatophytes are host-adapted, cross-species infections are common by zoophilic and geophilic dermatophytes. N. nana is considered an etiological agent of ringworm in pigs but has also been isolated from other animals, including humans. However, it also possesses many characteristics of geophilic dermatophytes including the ability to grow in soil. N. nana produces characteristic pear-shaped macroconidia and usually exhibits an ectothrix pattern of hair infection. It has been isolated from dermatitis lesions as well as from soil. N. nana infections in pigs are not of much concern as far as economy or health is concerned. But it has been associated with onychomycosis and gonathritis in humans, which are significant in human medicine. The shift in the predominance of dermatophytes in humans and the ability to evolve into a potential tinea pathogen necessitates more understanding of the physiology and genetics of N. nana. In this review, we have attempted a detailed analysis of the studies about N. nana, emphasizing growth and cultural characters, physiology, isolation, infection in humans and animals, molecular characterization and antifungal susceptibility.

Molecular epidemiology of Trichophyton infections among canines from Northern India

Dermatophytes are keratinophilic fungi that cause skin infections in both humans and animals. Recently, the incidence rates of fungal infections associated with Trichophyton spp. have been considered endemic in many locations. The aim of this study was to isolate and characterize Trichophyton spp. from canines and felines. In the present study, screened 442 canine (n = 386) and feline (n = 56) samples for dermatophytes. Among all the samples, ten isolates were identified as Trichophyton spp. based on micro-morphological features. For comparative analysis, we included three human strains of Trichophyton mentagrophytes complex. In vitro susceptibility of antifungal drugs indicated the highest sensitivity except for fluconazole. The canine and human strains were genetically characterized by sequencing three genes: the internal transcribed spacer region of rDNA, translation elongation factor 1- gene, and beta-tubulin. Based on sequence homology and phylogenetic analysis, the ten canine strains belonged to four different species/ genotypes such as T. mentagrophytes genotype VIII (T. indotineae) (n = 5), T. interdigitale (n = 2), T. simii (n = 2) and T. quinckeanum (n = 1). The three human strains used for comparative analysis were identified as T. mentagrophytes genotype VIII (n = 2) and T. benhamiae (n = 1). The study hence indicates that the T. mentagrophytes genotype VIII, considered as an endemic and emerging human pathogenic clone in India, is also the prevalent in animals.

Molecular epidemiology, virulence factors, and antifungal susceptibility of Candida inconspicua strains isolated from clinical samples in Turkey

In this study, it was aimed to evaluate the molecular epidemiology, virulence factors, and antifungal susceptibility of clinical Candida inconspicua isolates. All isolates were identified by phenotypic methods and sequence analysis of ITS 1-2, D1/D2, EF-1 alpha. Proteinase, phospholipase, and esterase activities, biofilm formation, and antifungal susceptibilities were determined. All thirty isolates identified as Candida norvegensis by phenotypic methods were reidentified as C. inconspicua by sequence analysis, demonstrating the inadequacy of phenotypic methods to differentiate these 2 species. The gene regions examined in terms of determining evolutionary relatedness did not show intraspecies nucleotide variations. Therefore, different molecular approaches are needed to evaluate molecular epidemiology. Esterase, phospholipase, and biofilm formation were found to be positive in 100%, 100%, and 36.6% of the strains, respectively. The MIC₅₀/MIC₉₀ values for fluconazole and flucytosine were found to be higher than the other tested antifungals, which should be taken into account in the treatment.

A simple multiplex polymerase chain reaction assay for rapid identification of the common pathogenic dermatophytes: Trichophyton interdigitale, Trichophyton rubrum, and Epidermophyton floccosum

Background and Purpose:

The most common etiological agents of human dermatophytosis in various parts of the world are Trichophyton rubrum, Trichophyton interdigitale, and Epidermophyton floccosum. The main aim of this study was to design and evaluate a simple and straightforward multiplex polymerase chain reaction (PCR) assay for reliable identification/differentiation of these species in clinical isolates.

Materials and Methods:

The reliable sequences of several molecular targets of dermatophytes species were used to design a multiplex PCR for the identification of common pathogenic dermatophytes. The isolates and clinical specimens examined in this study included seven standard strains of dermatophytes, 101 isolates of dermatophytes and non-dermatophyte molds/yeasts which had already been identified by sequencing or PCR-restriction fragment length polymorphism (RFLP), and 155 clinical samples from patients suspected of cutaneous mycoses.

Results:

Species-specific primer pairs for T. rubrum and T. interdigitale/T. mentagrophytes were designed based on the sequence data of the translation elongation factor 1-alpha gene, and the primers for E. floccosum targeted the specific sequence of the internal transcribed spacer region (ITS). The multiplex PCR successfully detected T. rubrum, T. interdigitale/T. mentagrophytes, and E. floccosum strains that were identified by sequencing or PCR-RFLP. However, the primer pairs selected for T. interdigitale/T. mentagrophytes cross-reacted with Trichophyton tonsurans. In testing the PCR system directly for clinical samples, the proportion of positive multiplex PCR was higher than positive culture (68.1% vs. 55.4%, respectively).

Conclusion:

The multiplex assay could detect three common agents out of several causal agents of dermatophytosis, namely T. rubrum, T. interdigitale, and E. floccosum. Therefore, by adding pan-dermatophyte primers it can be used as a comprehensive detection/identification test.

Generalized dermatophytosis caused by Trichophyton equinum in 8 juvenile black bears in California

From 2014-2019, 8 juvenile black bears (Ursus americanus) from different geographic regions were presented to the California Department of Fish and Wildlife because of emaciation, alopecia, and exfoliative dermatitis that resulted in death or euthanasia. Autopsy and histopathology revealed that all 8 bears had generalized hyperkeratotic dermatitis, folliculitis, and furunculosis. Skin structures were heavily colonized by fungal hyphae and arthrospores; fungal cultures of skin from 7 bears yielded Trichophyton equinum, a zoophilic dermatophyte reported only rarely in non-equid species. Additional skin conditions included mites (5), ticks (2), and coagulase-negative Staphylococcus sp. infections (2). No other causes of morbidity or mortality were identified. Molecular comparisons performed at the University of Texas Fungal Reference Laboratory determined that all isolates produced identical banding patterns, potentially representing a clonal population. Dermatophytosis is commonly localized and limited to the stratum corneum of the epidermis and hair follicles. Generalized disease with dermal involvement is rare in immunocompetent individuals; illness, malnutrition, age, or immunosuppression may increase susceptibility. Underlying causes for the severe disease impact in these bears were not evident after physical or postmortem examination. The mechanism by which bears from different geographic locations had severe, T. equinum-associated dermatophytosis from a potentially clonal dermatophyte could not be explained and warrants further investigation.

Aetiology of tinea capitis in China: A multicentre prospective study

BACKGROUND

Tinea capitis is still common in developing countries, such as China. Its pathogen spectrum varies across regions and changes over time.

OBJECTIVES

This study aimed to clarify the current epidemiological characteristics and pathogen spectrum of tinea capitis in China.

METHODS

A multicentre, prospective descriptive study involving 29 tertiary hospitals in China was conducted. From August 2019 to July 2020, 611 patients with tinea capitis were enrolled. Data concerning demography, risk factors and fungal tests were collected. The pathogens were further identified by morphology or molecular sequencing when necessary in the central laboratory.

RESULTS

Among all enrolled patients, 74.1% of the cases were 2- to 8-year-olds. The children with tinea capitis were mainly boys (56.2%) and more likely to have an animal contact history (57.4% vs. 35.3%, P = 0.012) and zoophilic dermatophyte infection (73.5%). The adults were mainly females (83.3%) and more likely to have anthropophilic agent infection (53.5%). The most common pathogen was zoophilic Microsporum canis (354, 65.2%), followed by anthropophilic Trichophyton violaceum (74, 13.6%). In contrast to the eastern, western and northeastern regions where zoophilic M. canis predominated, anthropophilic T. violaceum predominated in central China (69.2%, P < 0.0001), where the patients had the most tinea at other sites (20.3%) and dermatophytosis contact (25.9%) with the least animal contact (38.8%). Microsporum ferrugineum was the most common anthropophilic agent in the western area, especially in Xinjiang Province.

CONCLUSIONS

Boys aged approximately 5 years were mainly affected. Dermatologists are advised to pay more attention to the different transmission routes and pathogen spectra in different age groups from different regions.

A Polyphasic Approach to Classification and Identification of Species within the Trichophyton benhamiae Complex

In recent years, considerable advances have been made in clearing up the phylogenetic relationships within the Arthrodermataceae family. However, certain closely related taxa still contain poorly resolved species boundaries. Here, we tried to elucidate the species composition of the Trichophyton benhamiae species complex using a combined approach consisting of multi-gene phylogenetic analysis based on internal transcribed spacer (ITS) and beta-tubulin (BT) gene regions, morphological analysis, and spectral comparison using MALDI-ToF. We confirmed the existence of 11 different monophyletic clades within the complex representing either species or genetically distinct groups within species. MALDI-ToF spectrometry analysis revealed that most of these clades were readily distinguishable from one another; however, some closely related sister clades, such as T. europaeum and T. japonicum, were often misidentified as their counterpart. The distinct “yellow” and “white” phenotypes of T. benhamiae do not have a clear genetic basis and should thus be considered as different morphotypes of the same species. Strains traditionally considered T. benhamiae can be divided into three main clades: (i) T. benhamiae, (ii) T. europaeum/T. japonicum, and (iii) the phylogenetically distant T. africanum. While T. europaeum and T. japonicum are distinguishable based on their genotype, spectral and morphological analysis did not provide clear delimiting characteristics.

Molecular Epidemiology, Genetic Diversity, and Antifungal Susceptibility of Major Pathogenic Dermatophytes Isolated From Human Dermatophytosis

Background

Dermatophytes are a homogeneous group of species with low genetic diversity, and there are still many uncertainties about the boundaries among species.

Objectives

Aiming at clarifying the relationships among species in the genus and introducing suitable genes for multilocus sequence typing (MLST), a new MLST scheme approach was developed to characterize the major pathogenic dermatophytes.

Methods

We performed maximum parsimony (MP), MrBayes, RAxML, and eBURST analyses, based on the MLST scheme to scrutinize the evolution within 95 clinical isolates and four reference strains belonging to the four major dermatophytes species. Then, the discriminatory power, pairwise genetic distances, ratio dN/dS, and sequence types (STs) of these isolates were determined. Also, to study taxonomy, sequences of the internal transcribed spacer (ITS), Beta-tubulin (BT2), and translation elongation factor 1-α (TEF-1α) genes of other dermatophytes species available in the GenBank were analyzed.

Results

Findings of the present study indicated that three genes: BT2, ITS, and TEF−1α, which showed the greatest diversity among dermatophyte species, were suitable for MLST. The most prevalent STs were seen among the species of Trichophyton interdigitale. Also, two new genotypes, i.e., XXVII and XXVIII, were introduced for T. interdigitale and Trichophyton mentagrophytes. The least informative sites were found in Epidermophyton floccosum, Trichophyton rubrum, and T. mentagrophytes, while the most informative sites were observed in T. interdigitale. Furthermore, the most informative locus was TEF-1α. The phylogenetic tree, constructed by the combination of the three genes, shows a new topological pattern that confirms the derivation of the anthropophilic and zoophilic genera from the geophilic genus. Also, the phylogenetic analyses and pairwise distances of the combination of the three loci showed that Trichophyton tonsurans and Trichophyton equinum were a species complex, where T. equinum is derived from T. tonsurans.

Conclusions

Results of this study showed that MLST is very effective in determining the boundaries between species and taxonomy. Considering that there is no database for MLST dermatophytes, further studies are needed to determine the suitable genes for MLST. Also, the determination of STs in epidemiological studies and raising epidemiological information are helpful. This study was a new starting point to determine the ST and a foundation for a dermatophyte MLST database.

Taxonomy of the Trichophyton mentagrophytes/T. interdigitale Species Complex Harboring the Highly Virulent, Multiresistant Genotype T. indotineae

A severe outbreak of highly virulent and multi-resistant dermatophytosis by species in the Trichophyton mentagrophytes/T. interdigitale complex is ongoing in India. The correct identity of the etiologic agent is a much-debated issue. In order to define species limits, a taxonomic study was undertaken combining molecular, morphological, and physiological characteristics as evidence of classification. Molecular characteristics show that T. mentagrophytes s. str. and T. interdigitale s. str. can be distinguished with difficulty from each other, but are unambiguously different from the Indian genotype, T. indotineae by sequences of the HMG gene. The entities were confirmed by multilocus analysis using tanglegrams. Phenotypic characters of morphology and physiology are not diagnostic, but statistically significant differences are observed between the molecular siblings. These properties may be drivers of separate evolutionary trends. Trichophyton mentagrophytes represents the ancestral, homothallic cloud of genotypes with a probable geophilic lifestyle, while T. indotineae and T. interdigitale behave as anthropophilic, clonal offshoots. The origin of T. indotineae, which currently causes a significant public health problem, is zoonotic, and its emergence is likely due to widespread misuse of antifungals.

Investigation of in vitro antifungal susceptibility testing and genetic diversity of clinical isolates of Trichophyton benhamiae and Trichophyton eriotrephon in Iran

BACKGROUND

Trichophyton benhamiae is a zoophilic dermatophyte, known as one of the causative agents of dermatophytosis.

OBJECTIVES

The purpose of this study was to explore the genotypes of T. benhamiae strains isolated from geographically different areas of Iran and also to evaluate in vitro antifungal susceptibility profile of these strains against seven antifungal drugs.

METHODS

Twenty-two strains of T. benhamiae and two strains of T. eriotrephon were isolated from patients with distinct types of dermatophytosis. DNA extraction and amplification of rDNA regions using ITS1 and ITS4 primers were conducted on the isolates. The in vitro antifungal susceptibility of posaconazole (PSC), voriconazole (VRC), itraconazole (ITC), ketoconazole (KET), caspofungin (CAS), terbinafine (TRB) and griseofulvin (GRZ) was evaluated according to CLSI M38-A2 protocol.

RESULTS

The multiple alignment of the ITS-rDNA sequences of T. benhamiae indicated a mean similarity of 99.5%, with 0-3 interspecies nucleotide difference. The geometric mean (GM) values of minimum inhibitory concentrations (MICs) and minimum effective concentrations (MECs) across the all isolates were respectively: TRB: 0.025 mg/L, PSC: 0.032 mg/L, ITC: 0.050 mg/L and VRC: 0.059 mg/L with lower values and CAS: 0.31 mg/L, KTZ: 0.56 mg/L and GRZ: 0.76 mg/L with higher values.

CONCLUSION

Diverse ITS sequence types of T. benhamiae were shown in different geographical regions of Iran. The TRB, PSC and ITC were the most effective drugs against T. benhamiae strains, respectively. Furthermore, in our study, two strains of T. eriotrephon as a scarce dermatophyte species were described.

New molecular marker for phylogenetic reconstruction of black yeast-like fungi (Chaetothyriales) with hypothetical EIF2AK2 kinase gene

In eukaryotes, phosphorylation of the α-subunit of eIF2 is a mechanism to adjust cellular gene expression profiles in response to specific signals. The eIF2α kinases are a group of serine-threonine kinases that perform important functions in response to infection, proteotoxicity, and nutrient scavenging. The conserved nature of eIF2α kinases among fungi makes them potential evolutionary markers, which may contribute to deeper understanding of taxonomy and evolution. To date, only few studies are available of eIF2α kinases in black yeasts, which are members of Chaetothyriales containing potential agents of a gamut of major human diseases, such as chromoblastomycosis, phaeohyphomycosis and mycetoma. To establish the phylogenetic validity of sequences of eIF2α kinases hypothetical genes, we compared these genes between members of different classes of fungi, including black yeasts and allies, aiming at evaluation of the phylogeny of this group using an alternative molecular marker, compared to standard ribosomal genes. Trees generated with eIF2α kinase sequences of fungi were compared with those generated by ribosomal internal transcribed spacers (ITS rDNA) sequences from the same species. Sequences used were obtained from the protein Non-redundant database of NCBI, were aligned using CLUSTALX v1.8 and alignments were analyzed with RAxML v8.2.9 on the CIPRES Science Gateway portal. The trees generated had similar topologies, demonstrating that eIF2α kinases hypothetical gene sequences present a coherent reflection of evolution among fungi, compared to trees reconstructed by the use of ribosomal sequences. Our preliminary findings with a limited dataset strongly suggest that the evolution of kinases among black yeasts follows a similar path as revealed by ribosomal data, which underlines the validity of current taxonomy of black yeasts and relatives.

DNA topoisomerase 2 gene polymorphism in dermatophytes

BACKGROUND

Dermatophytes are a group of keratinophilic fungi of medical importance. Despite a relatively long history of molecular taxonomic studies, there is still a need for information on genetic polymorphism in wider variety of genomic loci.

OBJECTIVES

Our goal was to study partial DNA topoisomerase 2 gene (TOP2) polymorphism in dermatophytes.

METHODS

We performed DNA sequencing of TOP2 in 26 dermatophyte species along with ribosomal internal transcribed spacer (ITS) sequencing.

RESULTS

The number of polymorphic sites in TOP2 data set was similar to that one in ITS data set. Nannizzia species formed paraphyletic group in TOP2 tree. Trichophyton simii was paraphyletic in concatenated TOP2-ITS tree, one of its two clades contained solely Iranian isolates.

CONCLUSIONS

Our results revealed several unresolved problems in the taxonomy of dermatophytes, including probable polyphyly of the genus Nannizzia and the species T simii.

Epidermophyton floccosum: nucleotide sequence analysis and antifungal susceptibility testing of 40 clinical isolates

Purpose. Epidermophyton floccosum is an anthropophilic dermatophyte species, which is one of the common causative agents of dermatophytosis in different parts of the world. The aim of the present investigation was to evaluate the genetic diversity of E. floccosum strains isolated from different parts of Iran and to define the in vitro susceptibility profiles of seven antifungal drugs against these clinical isolates.Methodology. Forty clinical strains of E. floccosum isolated from 40 patients with dermatophytosis were subjected to DNA extraction and PCR amplification of the ITS rDNA region using universal primers ITS1 and ITS4. The in vitro activities of griseofulvin, itraconazole, voriconazole, posaconazole, caspofungin, ketoconazole and terbinafine were determined using a broth microdilution method according to the CLSI-M-38A2 protocol.Results. A mean genetic similarity of 99.5 % was found between E. floccosum strains, with intraspecies differences ranging from 0 to 3 nt. The geometric mean (GM) MICs and minimum effective concentrations (MECs) across all isolates were, in increasing order, as follows: terbinafine (GM=0.018 mg l^-1), posaconazole (GM=0.022 mg l^-1), itraconazole (GM=0.034 mg l^-1) and voriconazole (GM=0.045 mg l^-1), which had low MICs against all tested strains, whereas caspofungin (GM=0.22 mg l^-1), ketoconazole (GM=0.41 mg l^-1) and griseofulvin (GM=0.62 mg l^-1) demonstrated higher MICs.Conclusion. Our study showed low intraspecies variation within strains of E. floccosum. Furthermore, terbinafine, posaconazole, itraconazole and voriconazole were shown to be the most potent antifungal drugs against E. floccosum strains.

Species boundaries in the Trichophyton mentagrophytes / T. interdigitale species complex

The fungi Trichophyton mentagrophytes and T. interdigitale are closely related species, causing superficial infections in humans and other mammals. The status of these taxa is a field of long-lasting debates. To clarify their phylogenetic relationships within the genus Trichophyton and sharpen the species boundaries, we performed sequencing of four T. mentagrophytes genomes and also evaluated three previously published multilocus data sets. We performed computational species delimitation analysis on all available in GenBank internal transcribed spacer region (ITS) sequences of Trichophyton spp. Phylogenomic data, phylogenetic network, and species delimitation analyses implied that T. mentagrophytes and T. interdigitale belong to the same phylogenetic species. However, we argue that taxonomic status quo should be retained, from the perspective of epidemiological data and the principle of taxonomic stability. Since there is a correlation between ITS genotype and epidemiological source of an isolate, restriction of T. interdigitale to purely anthropophilic ITS genotypes seems to be reasonable.

Perspectives on misidentification of Trichophyton interdigitale/Trichophyton mentagrophytes using internal transcribed spacer region sequencing: Urgent need to update the sequence database

The taxonomy of the dermatophytes has been revisited using a novel multilocus phylogenetic approach, and several neotypes and reference strains have been assigned for Trichophyton species. Single gene sequencing, that is the ITS region, for identification of highly related species T. mentagrophytes/T. interdigitale, warrant reassessment. The sequence database (Westerdijk and NCBI) needs to be updated as several incorrect/obsolete entries of reference and neotype strains of T. interdigitale/T. mentagrophytes hampers correct identification of this complex.

Emerging Insights into the Occupational Mycobiome

PURPOSE OF REVIEW

The evolution of molecular-based methods over the last two decades has provided new approaches to identify and characterize fungal communities or "mycobiomes" at resolutions previously not possible using traditional hazard identification methods. The recent focus on fungal community assemblages within indoor environments has provided renewed insight into overlooked sources of fungal exposure. In occupational studies, internal transcribed spacer (ITS) region sequencing has recently been utilized in a variety of environments ranging from indoor office buildings to agricultural commodity and harvesting operations.

RECENT FINDINGS

Fungal communities identified in occupational environments have been primarily placed in the phylum Ascomycota and included classes typically identified using traditional fungal exposure methods such as the Eurotiomycetes, Dothideomycetes, Sordariomycetes, and Saccharomycetes. The phylum Basidiomycota has also been reported to be more prevalent than previously estimated and ITS region sequences have been primarily derived from the classes Agaricomycetes and Ustilaginomycetes. These studies have also resolved sequences placed in the Basidiomycota classes Tremellomycetes and Exobasidiomycetes that include environmental and endogenous yeast species. These collective datasets have shown that occupational fungal exposures include a much broader diversity of fungi than once thought. Although the clinical implications for occupational allergy are an emerging field of research, establishing the mycobiome in occupational environments will be critical for future studies to determine the complete spectrum of worker exposures to fungal bioaerosols and their impact on worker health.

Characterization of beta-tubulin DNA sequences within Candida parapsilosis complex

Background and Purpose:

Candida parapsilosis is a common cause of candidemia in children and patients with onco-hematological diseases, septic arthritis, peritonitis, vaginitis, and nail and skin infections. Regarding this, the present study was condcuted to evaluate intra- and inter-species variation within beta-tubulin DNA sequence of C. parapsilosis complex in order to establish the utilization of this gene in the identification and phylogenetic analysis of the species.

Materials and Methods:

A total of 23 isolates representing three different species of C. parapsilosis complex were used in this study, all of which were identifed by ITS-sequencing. For the successful amplification of beta-tubulin gene, a newly designed set of pan-Candida primers was used, followed by bilaterally sequence analysis for pairwise comparisons, determination of multiple alignments, evaluation of sequence identity levels, counting sequence difference, and construction of phylogenetic tree.

Results:

The multiple alignment of 623-629 bp-long nucleotide (nt) sequences reflecting the beta-tubulin gene indicated an inter-species divergence ranging within 0-68 nt in C. parapsilosis, C. orthopsilosis, and C. metapsilosis with a mean similarity of 84.7% among the species. Meanwhile, the intra-species differences of 0-20 and 0-6 nt were found between the strains of C. parapsilosis and C. orthopsilosis, respectively. The phylogenetic tree topology was characterized by a clade made up by C. parapsilosis and C. orthopsilosis, while C. metapsilosis formed a related but separate lineage.

Conclusion:

Our data provided the basis for further discoveries of the relationship between the species belonging to C. parapsilosis complex. Furthermore, the findigns of the prsent study revealed the efficiency of beta-tubulin DNA sequence data in the identification and taxonomy of C. parapsilosis and other pathogenic yeasts.

Majocchi's granuloma: current perspectives

Majocchi’s granuloma (MG) is a rare fungal infection of the dermis that is mainly caused by dermatophytes (in ≥95% of cases); the most frequently identified cause is anthropophilic Trichophyton rubrum. In the rest of the cases, the causes are non-dermatophytic fungi such as Aspergillus species. This review aimed to provide information about the current perspectives on MG regarding its clinical characteristics, predisposing factors, laboratory diagnosis, and treatment strategies. Although the lower extremities were reported to be the most common site of infection, facial involvement has been predominant in the past 5 years. Our literature research showed that the most common predisposing factor (55%) is the use of topical steroid creams without potassium hydroxide examination during treatment of erythematous squamous dermatoses. A reliable diagnosis of MG is based on histopathological examination, including fungal culture and molecular analyses. MG should be treated not only with topical agents but also with systemic antifungal agents that are continued until the lesions are completely resolved. In systemic treatment, the most preferred drug is terbinafine, because of its efficacy, side effects, and safety.

Skin Fungi from Colonization to Infection

Humans are exceptional among vertebrates in that their living tissue is directly exposed to the outside world. In the absence of protective scales, feathers, or fur, the skin has to be highly effective in defending the organism against the gamut of opportunistic fungi surrounding us. Most (sub)cutaneous infections enter the body by implantation through the skin barrier. On intact skin, two types of fungal expansion are noted: (A) colonization by commensals, i.e., growth enabled by conditions prevailing on the skin surface without degradation of tissue, and (B) infection by superficial pathogens that assimilate epidermal keratin and interact with the cellular immune system. In a response-damage framework, all fungi are potentially able to cause disease, as a balance between their natural predilection and the immune status of the host. For this reason, we will not attribute a fixed ecological term to each species, but rather describe them as growing in a commensal state (A) or in a pathogenic state (B).

Phylogeny of dermatophytes with genomic character evaluation of clinically distinct Trichophyton rubrum and T. violaceum

Trichophyton rubrum and T. violaceum are prevalent agents of human dermatophyte infections, the former being found on glabrous skin and nail, while the latter is confined to the scalp. The two species are phenotypically different but are highly similar phylogenetically. The taxonomy of dermatophytes is currently being reconsidered on the basis of molecular phylogeny. Molecular species definitions do not always coincide with existing concepts which are guided by ecological and clinical principles. In this article, we aim to bring phylogenetic and ecological data together in an attempt to develop new species concepts for anthropophilic dermatophytes. Focus is on the T. rubrum complex with analysis of rDNA ITS supplemented with LSU, TUB2, TEF3 and ribosomal protein L10 gene sequences. In order to explore genomic differences between T. rubrum and T. violaceum, one representative for both species was whole genome sequenced. Draft sequences were compared with currently available dermatophyte genomes. Potential virulence factors of adhesins and secreted proteases were predicted and compared phylogenetically. General phylogeny showed clear gaps between geophilic species of Arthroderma, but multilocus distances between species were often very small in the derived anthropophilic and zoophilic genus Trichophyton. Significant genome conservation between T. rubrum and T. violaceum was observed, with a high similarity at the nucleic acid level of 99.38 % identity. Trichophyton violaceum contains more paralogs than T. rubrum. About 30 adhesion genes were predicted among dermatophytes. Seventeen adhesins were common between T. rubrum and T. violaceum, while four were specific for the former and eight for the latter. Phylogenetic analysis of secreted proteases reveals considerable expansion and conservation among the analyzed species. Multilocus phylogeny and genome comparison of T. rubrum and T. violaceum underlined their close affinity. The possibility that they represent a single species exhibiting different phenotypes due to different localizations on the human body is discussed.

How to boost marine fungal research: A first step towards a multidisciplinary approach by combining molecular fungal ecology and natural products chemistry

Marine fungi have attracted attention in recent years due to increased appreciation of their functional role in ecosystems and as important sources of new natural products. The concomitant development of various "omic" technologies has boosted fungal research in the fields of biodiversity, physiological ecology and natural product biosynthesis. Each of these research areas has its own research agenda, scientific language and quality standards, which have so far hindered an interdisciplinary exchange. Inter- and transdisciplinary interactions are, however, vital for: (i) a detailed understanding of the ecological role of marine fungi, (ii) unlocking their hidden potential for natural product discovery, and (iii) designing access routes for biotechnological production. In this review and opinion paper, we describe the two different "worlds" of marine fungal natural product chemists and marine fungal molecular ecologists. The individual scientific approaches and tools employed are summarised and explained, and enriched with a first common glossary. We propose a strategy to find a multidisciplinary approach towards a comprehensive view on marine fungi and their chemical potential.

Characterization of the translation elongation factor 1-α gene in a wide range of pathogenic Aspergillus species

PURPOSE

We aimed to evaluate the resolving power of the translation elongation factor (TEF)-1α gene for phylogenetic analysis of Aspergillus species.

METHODOLOGY

Sequences of 526 bp representing the coding region of the TEF-1α gene were used for the assessment of levels of intra- and inter-specific nucleotide polymorphism in 33 species of Aspergillus, including 57 reference, clinical and environmental strains.

RESULTS

Analysis of TEF-1α sequences indicated a mean similarity of 92.6 % between the species, with inter-species diversity ranging from 0 to 70 nucleotides. The species with the closest resemblance were A. candidus/A. carneus, and A. flavus/A. oryzae/A. ochraceus, with 100 and 99.8 % identification, respectively. These species are phylogenetically very close and the TEF-1α gene appears not to have sufficient discriminatory power to differentiate them. Meanwhile, intra-species differences were found within strains of A. clavatus, A. clavatonanicus, A. candidus, A. fumigatus, A. terreus, A. alliaceus, A. flavus, Eurotium amstelodami and E. chevalieri. The tree topology with strongly supported clades (≥70 % bootstrap values) was almost compatible with the phylogeny inferred from analysis of the DNA sequences of the beta tubulin gene (BT2). However, the backbone of the tree exhibited low bootstrap values, and inter-species correlations were not obvious in some clades; for example, tree topologies based on BT2 and TEF-1α genes were incompatible for some species, such as A. deflectus, A. janus and A. penicillioides.

CONCLUSION

The gene was not phylogenetically more informative than other known molecular markers. It will be necessary to test other genes or larger genomic regions to better understand the taxonomy of this important group of fungi.

Epidemiological status of dermatophytosis in Guilan, north of Iran

Background and Purpose:

The epidemiological features of dermatophytoses have been characterized in many geographical locations of Iran, but not in Guilan, North of Iran. This study was carried out to determine the distribution pattern of dermatophytoses and their relevant agents in Guilan, North of Iran, over a period of one year, from April 2010 to April 2011.

Materials and Methods:

The clinical samples of skin, hair, and nail from 889 outpatients (317 men vs. 572 women) were used for direct microscopy and culture. All the culture-positive samples were then subjected to amplification of the internal transcribed spacer (ITS) of the nuclear rDNA followed by a restriction fragment length polymorphism (RFLP) assay to verify the causative agents.

Results:

The infection was confirmed in 90 (44.3%) males and 113 (55.7%) females. The most common type of dermatophytoses was tinea cruris (42.9%), followed by tinea pedis (20.2%), tinea corporis (11.3%), tinea unguium (7.4%), tinea faciei (6.9%), tinea manuum (6.4%), and tinea capitis (4.9%). ITS-RFLP based of the identification of isolates, showed that the infections were significantly associated with anthropophilic species, of Trichophyton rubrum (41.9%), Epidermophyton floccosum (19.7%), T. tonsurans (5.4%), and T.violaceum (2%). Other causative agents were T. interdigitale (22.6%), Microsporum canis (4.9%), T. verrucosum (2.5%), and M. gypseum (1%).

Conclusion:

The higher prevalence of T. rubrum, as the agent of dermatophytoses, than other species has never been reported from Iran and is of public health concern because of the chronic nature of infections with anthropophilic species. To thoroughly investigate the epidemiological trend of dermatophytoses in Iran, further periodical and molecular-based studies are necessary.

Toward a Novel Multilocus Phylogenetic Taxonomy for the Dermatophytes

Type and reference strains of members of the onygenalean family Arthrodermataceae have been sequenced for rDNA ITS and partial LSU, the ribosomal 60S protein, and fragments of β-tubulin and translation elongation factor 3. The resulting phylogenetic trees showed a large degree of correspondence, and topologies matched those of earlier published phylogenies demonstrating that the phylogenetic representation of dermatophytes and dermatophyte-like fungi has reached an acceptable level of stability. All trees showed Trichophyton to be polyphyletic. In the present paper, Trichophyton is restricted to mainly the derived clade, resulting in classification of nearly all anthropophilic dermatophytes in Trichophyton and Epidermophyton, along with some zoophilic species that regularly infect humans. Microsporum is restricted to some species around M. canis, while the geophilic species and zoophilic species that are more remote from the human sphere are divided over Arthroderma, Lophophyton and Nannizzia. A new genus Guarromyces is proposed for Keratinomyces ceretanicus. Thirteen new combinations are proposed; in an overview of all described species it is noted that the largest number of novelties was introduced during the decades 1920–1940, when morphological characters were used in addition to clinical features. Species are neo- or epi-typified where necessary, which was the case in Arthroderma curreyi, Epidermophyton floccosum, Lophophyton gallinae, Trichophyton equinum, T. mentagrophytes, T. quinckeanum, T. schoenleinii, T. soudanense, and T. verrucosum. In the newly proposed taxonomy, Trichophyton contains 16 species, Epidermophyton one species, Nannizzia 9 species, Microsporum 3 species, Lophophyton 1 species, Arthroderma 21 species and Ctenomyces 1 species, but more detailed studies remain needed to establish species borderlines. Each species now has a single valid name. Two new genera are introduced: Guarromyces and Paraphyton. The number of genera has increased, but species that are relevant to routine diagnostics now belong to smaller groups, which enhances their identification.

Trichophyton erinacei in pet hedgehogs in Spain: Occurrence and revision of its taxonomic status

Hedgehogs have increased in popularity as pets in Spain but there are no data of infection rates of this exotic animal with dermatophytes in our country. During the period of 2008-2011 a total of 20 pet hedgehogs (19 African pygmy hedgehogs and 1 Egyptian long-eared hedgehog) suspected of having dermatophytoses were studied. This is the first survey of the occurrence of T. erinacei in household hedgehogs in Spain. The T. erinacei infection rate was 50% (9 out of 19 African pygmy hedgehogs, and the one Egyptian long-eared hedgehog surveyed). Morphological identification of the isolates was confirmed by molecular analysis. All the strains had the same ITS sequence and showed 100% sequence similarity to T. erinacei type strain CBS 511.73 (AB 105793). The Spanish isolates were confirmed as T. erinacei urease positive. On the basis of ITS sequences, T. erinacei is a species close to but separate from the taxa included in the A. benhamiae complex. Review of the current literature on DNA-based methods for identification of species included in this complex has highlighted the urgent need to reach a consensus in species circumscription and classification system accepted by all mycologists.

Molecular Markers Useful for Intraspecies Subtyping and Strain Differentiation of Dermatophytes

Dermatophytosis is a very common skin disorder and the most frequent infection encountered by practicing dermatologists. The identification, pathogenicity, biology, and epidemiology of dermatophytes, the causative agents of dermatophytosis, are of interest for both dermatologists and medical mycologists. Recent advances in molecular methods have provided new techniques for identifying dermatophytes, including intraspecies variations. Intraspecies subtyping and strain differentiation have made possible the tracking of infections, the identification of common sources of infections, recurrence or reinfection after treatment, and analysis of strain virulence and drug resistance. This review describes molecular methods of intraspecies subtyping and strain differentiation, including analyses of mitochondrial DNA and non-transcribed spacer regions of ribosomal RNA genes, random amplification of polymorphic DNA, and microsatellite markers, along with their advantages and limitations.

Kerion and Tinea Corporis Caused by Rabbit-Derived Trichophyton interdigitale in Three Siblings and One Consulting Doctor Using β-Tubulin Gene to Identify the Pathogen

Trichophyton interdigitale is generally deemed as an anamorph of Arthroderma vanbreuseghemii based on internal transcribed spacer (ITS) sequencing, but recently their anamorph/teleomorph connection should be cautioned based on β-tubulin phylogeny. We report three siblings and one consulting doctor who developed kerion and tinea corporis after contact with domestic rabbits. Seven same strains were isolated from four patients and three regions of a sick rabbit. The ITS and D1/D2 sequences of our isolate were 99 % homologous to A. Vanbreuseghemii, while β-tubulin sequence was 100 % identical to T. interdigitale. Our isolate was identified as T. interdigitale based on maximum likelihood analysis of β-tubulin. Random amplified polymorphic DNA revealed that the band patterns of five isolated strains and another rabbit-derived strain WCH023 were identical for OPF-03 and OPF-12. Skin lesions of all patients resolved completely for 2- to 6-week therapy of oral terbinafine and topical 1 % bifonazole or 1 % terbinafine cream. This study demonstrates that T. interdigitale of rabbit origin can cause various types of human dermatophytosis by mild scratch. Terbinafine may be the first choice for dermatophytosis caused by T. interdigitale.

Development a diagnostic pan-dermatophyte TaqMan probe real-time PCR assay based on beta tubulin gene

Early differentiation of dermatophytosis from other cutaneous mycoses is essential to avoid inaccurate therapy. DNA-based techniques including real-time PCR have increasingly been considered for detection of fungal elements in clinical specimens. In this study, after partial sequence analysis of beta tubulin (BT2) gene in 13 common and rare pathogenic dermatophyte species, a pan-dermatophyte primer and probe set was designed in a TaqMan probe-based PCR format. The sensitivity and specificity of the system was tested with 22 reference strains of dermatophytes, 234 positive clinical specimens, 32 DNA samples extracted from normal nails, several fungi other than dermatophytes and human DNAs. Analytical detection limit of the designed PCR on serially diluted DNAs of prepared recombinant plasmid indicated that only five molecules per sample are the minimum number for reliable detection by the assay. A total of 226 out of 234 (96.5%) DNAs extracted from clinical samples, but none of the 32 nail samples, from healthy volunteers were positive in PCR. The real-time PCR targeted beta tubulin gene established in this study could be a sensitive diagnostic tool which is significantly faster than the conventional culture method and should be useful in the clinical settings, in large-scale epidemiological studies and in clinical trials of antifungal therapy.

Reconstruction of phylogenetic relationships in dermatomycete genus Trichophyton Malmsten 1848 based on ribosomal internal transcribed spacer region, partial 28S rRNA and beta-tubulin genes sequences

Trichophyton spp. are important causative agents of superficial mycoses. The phylogeny of the genus and accurate strain identification, based on the ribosomal ITS region sequencing, are still under development. The present work is aimed at (i) inferring the genus phylogeny from partial ITS, LSU and BT2 sequences (ii) description of ribosomal ITS region polymorphism in 15 strains of Trichophyton interdigitale. We performed DNA sequence-based species identification and phylogenetic analysis on 48 strains belonging to the genus Trichophyton. Phylogenetic relationships were inferred by maximum likelihood and Bayesian methods on concatenated ITS, LSU and BT2 sequences. Ribosomal ITS region polymorphisms were assessed directly on the alignment. By phylogenetic reconstruction, we reveal major anthropophilic and zoophilic species clusters in the genus Trichophyton. We describe several sequences of the ITS region of T. interdigitale, which do not fit in the traditional polymorphism scheme and propose emendations in this scheme for discrimination between ITS sequence types in T. interdigitale. The new polymorphism scheme will allow inclusion of a wider spectrum of isolates while retaining its explanatory power. This scheme was also found to be partially congruent with NTS typing technique.

Detection and identification of Trichophyton tonsurans from clinical isolates and hairbrush samples by loop-mediated isothermal amplification system

Since the 1990s, there have been reports of the spread of dermatophytosis caused by Trichophyton tonsurans among contact sports athletes in several countries, including Japan. This study was performed to develop a loop-mediated isothermal amplification (LAMP) system for rapid and accurate detection and identification of T. tonsurans from clinical isolates or hairbrush samples for diagnosis and to prevent the spread of infection. A specific primer set was prepared by comparing the whole genome sequence of T. tonsurans with those of six other closely related dermatophytes. After confirming the sensitivity and specificity of this system, LAMP assay was performed using 37 clinical samples obtained from three healthy volunteers and 24 judo athletes. A total of 155 fungal isolates (56 strains of various standard fungi, 96 identified T. tonsurans isolates, three hairbrush-cultured isolates from judo athletes) and 37 hairbrush samples (34 samples from 24 judo athletes, and three samples from three healthy volunteers) were used for culture and LAMP assay, respectively. The assay showed no cross-reactivity to standard strains other than T. tonsurans. The detection limit was 100 copies of DNA template per tube. All of the 96 T. tonsurans isolates were amplified, and all samples from healthy volunteers showed negative results. Four of the 34 hairbrush samples obtained from judo athletes showed positive results in LAMP assay, and two of the four were positive in both culture and LAMP assay. We developed a rapid LAMP system with high specificity and sensitivity for diagnosis of T. tonsurans infection.

Phylogenetic analysis of dermatophyte species using DNA sequence polymorphism in calmodulin gene

Use of phylogenetic species concepts based on rDNA internal transcribe spacer (ITS) regions have improved the taxonomy of dermatophyte species; however, confirmation and refinement using other genes are needed. Since the calmodulin gene has not been systematically used in dermatophyte taxonomy, we evaluated its intra- and interspecies sequence variation as well as its application in identification, phylogenetic analysis, and taxonomy of 202 strains of 29 dermatophyte species. A set of primers was designed and optimized to amplify the target followed by bilateral sequencing. Using pairwise nucleotide comparisons, a mean similarity of 81% was observed among 29 dermatophyte species, with inter-species diversity ranging from 0 to 200 nucleotides (nt). Intraspecies nt differences were found within strains of Trichophyton interdigitale, Arthroderma simii, T. rubrum and A. vanbreuseghemii, while T. tonsurans, T. violaceum, Epidermophyton floccosum, Microsporum canis, M. audouinii, M. cookei, M. racemosum, M. gypseum, T. mentagrophytes, T schoenleinii, and A. benhamiae were conserved. Strains of E. floccosum/M. racemosum/M. cookei, A. obtosum/A. gertleri, T. tonsurans/T. equinum and a genotype of T. interdigitale had identical calmodulin sequences. For the majority of the species, tree topology obtained for calmodulin gene showed a congruence with coding and non-coding regions including ITS, BT2, and Tef-1α. Compared with the phylogenetic tree derived from ITS, BT2, and Tef-1α genes, some species such as E. floccosum and A. gertleri took relatively remote positions. Here, characterization and obtained dendrogram of calmodulin gene on a broad range of dermatophyte species provide a basis for further discovery of relationships between species. Studies of other loci are necessary to confirm the results.

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.

Dermatophytosis due to Microsporum incurvatum: Notification and Identification of a Neglected Pathogenic Species

A 4-year-old Iranian boy developed erythematous, itchy and annular lesion on his face. Microscopic examination of the scraped samples with 10 % potassium hydroxide (KOH) revealed fungal septate hyphae and arthroconidia. The etiological agent was found to be Microsporum gypseum in mycological examinations. Amplification and restriction digestion of the internal transcribed spacers (ITS) of rDNA was not helpful for identification, but in ITS sequencing the isolate showed 98 % homology to Microsporum incurvatum strain CBS 172.64. Empirical treatment of the patient with griseofulvin for 4 weeks was successful. Other than our isolate, the ITS1 sequences of 38 strains from related species were retrieved from GenBank and phylogenetic tree using maximum likelihood method was constructed. The case isolate clustered apart from other strains of M. incurvatum. Pairwise comparison of ITS1 showed intraspecies variations of 0-13 nucleotides among M. incurvatum strains and an extensive interspecies variation of 33-80 bp and remarkable interspecies size polymorphism between the three sister species in the M. gypseum complex. The high level of ITS1 intraspecific variation is suitable for species identification rather than phylogeographic analysis of M. gypseum complex.

Translation elongation factor 1-α gene as a potential taxonomic and identification marker in dermatophytes

Intra- and interspecies variations of the translation elongation factor 1-α (Tef-1α) gene were evaluated as a new identification marker in a wide range of dermatophytes, which included 167 strains of 30 species. An optimized pan-dermatophyte primer pair was designed, and the target was sequenced. Consensus sequences were used for multiple alignment and phylogenetic tree analysis and the levels of intra- and interspecific nucleotide polymorphism were assessed. Between species, the analyzed part of the Tef-1α gene varied in length from 709 to 769 nucleotides. Significant numbers of species including Trichophyton rubrum, T. tonsurans, T. schoenleinii, T. concentricum, T. violaceum, Epidermophyton floccosum, Microsporum ferrugineum, M. canis, M. audouinii, T. equinum, T. eriotrephon, and T. erinacei were invariant in Tef-1α and had sufficient barcoding distance with neighboring species. Although overall consistency was found between ITS phylogeny as the current molecular marker of dermatophytes and Tef-1α, a higher discriminatory power of Tef-1α appeared particularly useful in some clades of closely related species such as the A. vanbreuseghemii, T. rubrum, A. benhamiae, and A. otae complexes. Nevertheless, we stress that a single gene can not specify species borderlines among dermatophytes and multiple lines of evidence based on a multilocus inquiry may ascertain an incontrovertible evaluation of kinship.