Application of PCR to distinguish common species of dermatophytes

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.

Multiplex real-time PCR for skin fungal infections: The diagnostic reliability in a one-year non-interventional study

The skin fungal infection diagnostic workflow currently includes microscopic and culture-based methods as the gold standard. Recent published data described the possible limitations of these conventional techniques documenting the possibility of reducing response time intervals. The present study reports an evaluation of the DermaGenius® (DG) multiplex kit (PathoNostics) for rapid C. albicans and dermatophytes identification directly from skin samples. The investigations involved 90 specimens that underwent DNA extraction and amplification simultaneously to microscopic and culture methods. According to current guidelines, we defined a dermatophytic skin infection as the simultaneous presence of clinical evidence of skin lesions and positive results for dermatophyte elements from microscopy and/or cultures. The collected data remarked on the advantages of the molecular assay, especially in terms of sensitivity and rapidity. A statistical evaluation analysed a comparison between conventional and innovative diagnostic methods. The sensitivity, specificity, positive predictive value, and negative predictive value of DG-PCR in the cutaneous dermatophytosis were, respectively, 94.7%, 78.8%, 88.5%, and 89.6%. Based on our experience, the molecular technique could represent a diagnostic confirmation in the case of previous antifungal treatment, little biological material available, or urgent clinical conditions.

Detection of LAP1 and LAP2 genes from Trichophyton rubrum

Samples of hair, nails and skin were collected, representing people of different ages and races. The number of isolated people gathered between October 2021 and February 2022 from Al-Hussein Teaching Hospital and a private clinic under the supervision of doctors(118) species was examined. Dermatophytes were found in 80 of them; among the 80 positive Trichophyton rubrum species, 30 were produced, which represents less than half of the dermatophytes for each of the 80 positive species (14 cutaneous, nine hair and seven nail isolates)the study's findings included hair hole testing, which came back negative, and urea degradation testing. The results were either negative or inconsistent across the isolates; the growth test in the PDA was positive, the virulence factors that enable the fungus to penetrate host tissues were studied during leucine aminopeptidase (LAP1) and (LAP2), it was observed that there were no significant differences in gene isolates of T. rubrum. Keywords: LAP1; LAP2; genus Trichophyton rubrum.

Detection of Microsporum canis and Trichophyton mentagrophytes by loop-mediated isothermal amplification (LAMP) and real-time quantitative PCR (qPCR) methods

BACKGROUND

Dermatophytes are infectious zoonotic fungal agents that are common in animals worldwide. A new loop-mediated isothermal amplification (LAMP) method and quantitative (q)PCR can be used for identifying these agents. Both methods have high specificity and sensitivity, and are simple and quick to use.

HYPOTHESIS/OBJECTIVES

To develop a LAMP and a rapid multiplex qPCR method for detecting Microsporum canis and Trichophyton mentagrophytes, which are the most common fungal species isolated from cats and dogs.

MATERIAL AND METHODS

Both methods targeted the CHS-1 gene. Their specificity and sensitivity were tested using 64 M. canis and 44 T. mentagrophytes field strains. The validation of the methods was performed using 250 clinical fungal-positive hair samples.

RESULTS

The specificity value was 100% for both methods. For LAMP, the sensitivity value was 96.9% for M. canis and 93.2% for T. mentagrophytes. For qPCR, the sensitivity values were 98.4% for M. canis and 97.7% for T. mentagrophytes. Similar specificity and sensitivity results were obtained from the validation study using 250 clinical hair samples. LAMP and multiplex qPCR took 30 and 45 min (respectively) for both targets. The limit of detection (LOD) assays for both targets were 10 and 1 spore/mL for LAMP and multiplex qPCR, respectively.

CONCLUSION

These findings demonstrate that the LAMP and multiplex qPCR methods targeting CHS-1 gene developed in this study can be used both for point-of-care testing and in the laboratory for detecting M. canis and T. mentagrophytes with high specificity and sensitivity with an internal control.

The taxonomy of the Trichophyton rubrum complex: a phylogenomic approach

The medically relevant Trichophyton rubrum species complex has a variety of phenotypic presentations but shows relatively little genetic differences. Conventional barcodes, such as the internal transcribed spacer (ITS) region or the beta-tubulin gene, are not able to completely resolve the relationships between these closely related taxa. T. rubrum, T. soudanense and T. violaceum are currently accepted as separate species. However, the status of certain variants, including the T. rubrum morphotypes megninii and kuryangei and the T. violaceum morphotype yaoundei, remains to be deciphered. We conducted the first phylogenomic analysis of the T. rubrum species complex by studying 3105 core genes of 18 new strains from the BCCM/IHEM culture collection and nine publicly available genomes. Our analyses revealed a highly resolved phylogenomic tree with six separate clades. Trichophyton rubrum, T. violaceum and T. soudanense were confirmed in their status of species. The morphotypes T. megninii, T. kuryangei and T. yaoundei all grouped in their own respective clade with high support, suggesting that these morphotypes should be reinstituted to the species-level. Robinson-Foulds distance analyses showed that a combination of two markers (a ubiquitin-protein transferase and a MYB DNA-binding domain-containing protein) can mirror the phylogeny obtained using genomic data, and thus represent potential new markers to accurately distinguish the species belonging to the T. rubrum complex.

A Household Microsporum canis Dermatophytosis Suggested by Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight Mass Spectrometry Analysis

Case series

Patients: Female, 4-year-old • her family (father, mother, sister)

Final Diagnosis: Microsporum canis dermatophytosis

Symptoms: Itiching

Medication: —

Clinical Procedure: Time-of-flight mass spectrometry (TOF-MS)

Specialty: Infectious Diseases

Comparison of subclinical dermatophyte infection in short- and long-haired cats

Background and Aim

Long-haired cats may have an increased risk of dermatophytosis due to insufficient grooming and their thick hair coat trapping fungal spores. The prevalence of subclinical dermatophytosis in long-haired cats was evaluated using fungal culture and Wood's lamp test. Hematology and blood chemistry results were compared between cats negative and positive for dermatophytosis.

Materials and Methods

A total of 127 cats (median age, 3 years [range, 10 months-10 years]) without feline leukemia virus or feline immunodeficiency virus infection were classified into short-haired (n=64) and long-haired (n=63) groups. Hair samples were cultured on a fungal culture medium (dermatophyte test medium, enhanced sporulation agar, and Sabouraud agar).

Results

The prevalence of dermatophytosis in short-haired and long-haired cats was 6.25% (95% confidence interval [CI], 2.15-12.28) and 34.92% (95% CI, 22.94-46.90), respectively. The odds of long-haired cats having dermatophytosis were 8.05 (95% CI, 2.44-33.97) times greater than that in short-haired cats. The number of positive dermatophytosis found in domestic short-haired cats (2/50, 4.0%) was significantly lower than that in Persian cats (17/47, 36.17%; p<0.001) and long-haired mixed breed cats (3/7, 42.86%; p=0.011). The overall sensitivity and specificity of the Wood's lamp test for diagnosing Microsporum canis infection were 37.5% (95% CI, 21.2-57.3%) and 96.1% (95% CI, 90.4-98.5%), respectively. Cats with dermatophytosis had significantly lower hematocrit and serum albumin levels than cats without dermatophytosis.

Conclusion

Subclinical dermatophytosis was more common in long-haired cats; therefore, dermatophyte examinations should be performed routinely.

Recent advances in the diagnosis of dermatophytosis

Dermatophytosis is a disease of global significance caused by pathogenic keratinolytic fungi called dermatophytes in both animals and humans. The recent taxonomy of dermatophytes classifies them into six pathogenic genera, namely Microsporum, Trichophyton, Epidermophyton, Nannizzia, Lophophyton and Arthroderma. It is because of the delayed diagnostic nature and low accuracy of dermatophyte detection by conventional methods that paved the path for the evolution of molecular diagnostic techniques, which provide the accurate and rapid diagnosis of dermatophytosis for an appropriate, timely antifungal therapy that prevents the nonspecific over-the-counter self-medication. This review focuses on the importance of rapid and accurate diagnosis of dermatophytosis, limitations of conventional methods, selection of targets in diagnosis, and factors affecting sensitivity and specificity of various molecular diagnostic technologies in the diagnosis of dermatophytosis. Generally, all the molecular techniques have a significant edge over the conventional methods of culture and microscopy in the dermatophytosis diagnosis. However, in mycology laboratory, the suitability of any molecular diagnostic technique in the diagnosis of dermatophytosis is driven by the requirement of time, economy, complexity, the range of species spectrum detected and the scale of diagnostic output required. Thus, various choices involved in the pursuit of a diagnosis of dermatophytosis are determined by the available conditions and the facilities in the laboratory.

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 Distinction in the Trichophyton rubrum Complex

The Trichophyton rubrum species complex comprises commonly encountered dermatophytic fungi with a worldwide distribution. The members of the complex usually have distinct phenotypes in culture and cause different clinical symptoms, despite high genome similarity. In order to better delimit the species within the complex, molecular, phenotypic, and physiological characteristics were combined to reestablish a natural species concept.

The Trichophyton rubrum species complex comprises commonly encountered dermatophytic fungi with a worldwide distribution. The members of the complex usually have distinct phenotypes in culture and cause different clinical symptoms, despite high genome similarity. In order to better delimit the species within the complex, molecular, phenotypic, and physiological characteristics were combined to reestablish a natural species concept. Three groups, T. rubrum, T. soudanense, and T. violaceum, could be distinguished based on the sequence of the internal transcribed spacer (ITS) ribosomal DNA barcode gene. On average, strains within each group were similar by colony appearance, microscopy, and physiology, but strains between groups showed significant differences. Trichophyton rubrum strains had higher keratinase activity, whereas T. violaceum strains tended to be more lipophilic; however, none of the phenotypic features were diagnostic. The results of matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) and amplified fragment length polymorphism (AFLP) were partially consistent with the ITS data but failed to distinguish the species unambiguously. Despite their close similarity, T. violaceum, T. soudanense, and T. rubrum can be regarded as independent species with distinct geographical distributions and clinical predilections. Trichophyton soudanense is pheno- and genotypically intermediate between T. rubrum and T. violaceum. For routine diagnostics, ITS sequencing is recommended.

Padronização de uma PCR para diagnóstico molecular de Microsporum canis em amostras de pelos e crostas de cães e gatos

RESUMO Objetivou-se neste estudo padronizar um protocolo de reação em cadeia da polimerase (PCR) para detecção de Microsporum canis em amostras de pelos e/ou crostas de cães e gatos. Foram selecionadas 48 amostras previamente identificadas por meio de cultura. Destas, 23 foram positivas para dermatófitos no cultivo. Padronizou-se a PCR a partir de primers desenhados para o alvo M. canis. Sessenta e um por cento (14/23) das amostras positivas para dermatófitos foram identificadas como M. canis em cultura. Desse total, 71,4% (10/14) apresentaram um fragmento de 218pb compatível com o esperado para a espécie fúngica alvo dessa reação. Observou-se uma sensibilidade de 71,4% e especificidade de 100% na PCR, além de uma boa concordância entre essas técnicas de diagnóstico (Kappa: 0,78; P<0,0001). O protocolo utilizado neste estudo apresentou alta especificidade na detecção de M. canis diretamente de amostras de pelos e/ou crostas de cães e gatos, viabilizando um diagnóstico mais rápido e específico, podendo esse protocolo ser empregado como um método confirmatório para agilizar a detecção de M. canis.

Diagnosis and treatment of dermatophytosis in dogs and cats.: Clinical Consensus Guidelines of the World Association for Veterinary Dermatology

BACKGROUND

Dermatophytosis is a superficial fungal skin disease of cats and dogs. The most common pathogens of small animals belong to the genera Microsporum and Trichophyton. It is an important skin disease because it is contagious, infectious and can be transmitted to people.

OBJECTIVES

The objective of this document is to review the existing literature and provide consensus recommendations for veterinary clinicians and lay people on the diagnosis and treatment of dermatophytosis in cats and dogs.

METHODS

The authors served as a Guideline Panel (GP) and reviewed the literature available prior to September 2016. The GP prepared a detailed literature review and made recommendations on selected topics. The World Association of Veterinary Dermatology (WAVD) provided guidance and oversight for this process. A draft of the document was presented at the 8th World Congress of Veterinary Dermatology (May 2016) and was then made available via the World Wide Web to the member organizations of the WAVD for a period of three months. Comments were solicited and posted to the GP electronically. Responses were incorporated by the GP into the final document.

CONCLUSIONS

No one diagnostic test was identified as the gold standard. Successful treatment requires concurrent use of systemic oral antifungals and topical disinfection of the hair coat. Wood's lamp and direct examinations have good positive and negative predictability, systemic antifungal drugs have a wide margin of safety and physical cleaning is most important for decontamination of the exposed environments. Finally, serious complications of animal-human transmission are exceedingly rare.

Development of a high-resolution melting analysis assay for rapid and high-throughput identification of clinically important dermatophyte species

Accurate identification of dermatophyte species is important both for epidemiological studies and for implementing antifungal treatment strategies. Although nucleic acid amplification-based assays have several advantages over conventional mycological methods, a major disadvantage is their high cost. The aim of this study was to develop a rapid and accurate real-time PCR-based high-resolution melting (HRM) assay for differentiation of the most common dermatophyte species. The oligonucleotide primers were designed to amplify highly conserved regions of the dermatophyte ribosomal DNA. Analysis of a panel containing potentially interfering fungi demonstrated no cross reactivity with the assay. To evaluate the performance characteristics of the method, a total of 250 clinical isolates were tested in comparison with the long-established PCR-RFLP method and the results were reassessed using DNA sequencing, as the reference standard method. The assay is able to type dermatophytes using normalised melting peak, difference plot analysis or electrophoresis on agarose gel methods. The results showed that, in comparison to PCR-RFLP, the developed HRM assay was able to differentiate at least 10 common dermatophytes species with a higher speed, throughput and accuracy. These results indicate that the HRM assay will be a useful sensitive, high throughput and cost-effective method for differentiating the most common dermatophyte species.

Dermatophyte surveillance in cats in three animal shelters in Ontario, Canada

Objectives The aim of the study was to determine the prevalence of dermatophyte shedding in cats admitted to three Ontario animal shelters from February to May 2013. Methods Four hundred cats were sampled within 48 h of admission, using a standard toothbrush sampling technique. Dermatophyte culture was performed. Results Dermatophytes were not identified in any of the 400 cats (0-0.9% one-sided exact 97.5% confidence interval). Conclusions and relevance These results imply that dermatophyte shedding is rare in cats admitted to Ontario animal shelters. Consequently, identification of infected animals, particularly multiple animals, represents an unusual occurrence that may justify prompt and intensive control measures.

Use of Restriction Fragment Length Polymorphism to Rapidly Identify Dermatophyte Species Related to Dermatophytosis

BACKGROUND

Dermatophytes are a group of keratinophilic fungi worldwide, which can infect the skin, hair and nails of humans and animals. This genus includes several species that present different features of dermatophytosis. Although, laboratory diagnosis of dermatophytes is based on direct microscopy, biochemical tests and culture, these manners are expensive, time consuming and need skilled staff. Therefore, molecular methods like PCR-RFLP are the beneficial tools for identification, which are rapid and sensitive. Thus, dermatophyte species are able to generate characteristic band patterns on agarose gel electrophoresis using PCR-RFLP technique, which leads to successful identification at the species level within a 5-hour period.

OBJECTIVES

The purpose of this study was to study inter- and intraspecific genomic variations for identification of clinically important dermatophyte species obtained from clinical specimens in Isfahan, Iran using PCR-RFLP.

MATERIALS AND METHODS

From March 2011 to August 2012, 135 clinical isolates were collected from infected patients at Isfahan, Iran. ITS1-5.8S-ITS2 region of rDNA was amplified using universal fungal primers. Subsequently, amplified products were digested by the MvaI restriction enzyme. Using discriminating band profiles on agarose gel, dermatophyte species were identified. However, DNA sequencing was used for unidentifiable strains.

RESULTS

The specimens were obtained from skin scrapings (70.3%), nail (24.4%) and hair (5.1%) clippings. Most patients were between 21 - 30 years and the ratio of male to female was 93/42. Trichophyton interdigitale was the commonest isolate (52.5%) in our findings, followed by Epidermophyton floccosum (24.4%), T. rubrum (16.2%), Microsporum canis (2.2%), T. erinacei (1.4%), T. violaceum (1.4%), T. tonsurans (0.7%) and M. gypseum (0.7%) based on PCR-RFLP.

CONCLUSIONS

Combination of traditional methods and molecular techniques considerably improves identification of dermatophytes in the species level in clinical laboratories, which can lead to properly antifungal therapy and successful management of infections. However, restriction and specificity and sensitivity should be lowered and increased, respectively, to be useful for a wide variety of clinical applications.

Application of PCR fingerprinting using (GACA)4 primer in the rapid discrimination of dermatophytes

BACKGROUND

Superficial fungal infections have a major impact on cosmetic health, affecting more than 20-25% of the global population, which is predominantly caused by dermatophytes. As per literature search, molecular strain typing of dermatophytes has not been investigated in India. Therefore, the present study was carried out to characterise the dermatophyte species and strains by molecular methods.

OBJECTIVE

To analyse the genotype variability by applying polymerase chain reaction (PCR) fingerprinting using a simple sequence repetitive oligonucleotide (GACA)4 primer to identify the species and strain variations among the dermatophytes isolated from a tertiary care centre in Chennai.

MATERIALS AND METHODS

From January 2010 to December 2010, 81 dermatophytes were isolated and included for the present study. A simple sequence repetitive oligonucleotide (GACA)4 was used as a single primer in the amplification process.

RESULTS

The (GACA)4-based PCR successfully amplified all the clinical isolates. Trichophyton rubrum and T. rubrum var. raubitschekii produced identical band profiles, where the latter could not be differentiated from the T. rubrum, which are being reported for the first time from south India. Epidermophyton floccosum produced species-specific band profiles. Intra-species variability was not observed among the T. rubrum and E. floccosum isolates. T. mentagrophytes produced three simple, distinct band patterns, which are surprisingly different from the earlier studies.

CONCLUSION

The PCR-based genotype using the short primer is rapid and precise in direct identification of dermatophyte isolates by one-step PCR to the species level and strain discrimination of the T. mentagrophytes variants.

Dermatophyte and non dermatophyte fungi in Riyadh City, Saudi Arabia

Background

Dermatophytes are a scientific label for a group of three genera (Microsporum, Epidermophyton and Trichophyton) of fungus that causes skin disease in animals and humans. Conventional methods for identification of these fungi are rapid and simple but are not accurate comparing to molecular methods.

Objective

This study aimed to isolate human pathogenic dermatophytes which cause dermatophytosis in Riyadh City, Saudi Arabia and to identify these fungi by using conventional and molecular methods.

Methods

The study was conducted in Medical Complex, Riyadh and King Saud University. Samples of infected skin, hairs and nails were collected from 112 patients. Diagnosis of skin infections, direct microscopic test, isolation and identification of dermatophytes by conventional and molecular methods were carried out.

Results

The results indicated that the tinea capitis infection had the highest prevalence among the patients (22.3%) while Tinea barbae had the lowest. In this study the identified dermatophyte isolates belong to nine species as Trichophyton violaceum, Trichophyton verrucosum, Trichophyton rubrum, Trichophyton mentagrophytes, Trichophyton schoenleinii, Trichophyton concentricum, Microsporum canis, Microsporum audouinii and Epidermophyton floccosum which cause skin infections were isolated during this study. Non dermatophyte isolates included 5 isolates from Aspergillus spp. 4 isolates from Acremonium potronii and 15 isolates from Candida spp. M. canis were the most common species (25% of isolated dermatophytes). Out of the 52 dermatophyte isolates identified by conventional methods, there were 45 isolates identified by the molecular method.

Conclusions

The results concluded that approximately M. canis caused a quarter of dermatophyte cases, tinea capitis infection was prevalent and the molecular method was more accurate than conventional methods.

Highly discriminatory variable-number tandem-repeat markers for genotyping of Trichophyton interdigitale strains

Trichophyton interdigitale is the second most frequent cause of superficial fungal infections of various parts of the human body. Studying the population structure and genotype differentiation of T. interdigitale strains may lead to significant improvements in clinical practice. The present study aimed to develop and select suitable variable-number tandem-repeat (VNTR) markers for 92 clinical strains of T. interdigitale. On the basis of an analysis of four VNTR markers, four to eight distinct alleles were detected for each marker. The marker with the highest discriminatory power had eight alleles and a D value of 0.802. The combination of all four markers yielded a D value of 0.969 with 29 distinct multilocus genotypes. VNTR typing revealed the genetic diversity of the strains, identifying three populations according to their colonization sites. A correlation between phenotypic characteristics and multilocus genotypes was observed. Seven patients harbored T. interdigitale strains with different genotypes. Typing of clinical T. interdigitale samples by VNTR markers displayed excellent discriminatory power and 100% reproducibility.

[Taxonomic study of clinic isolates of Trichophyton in Rosario, Argentina]

Due to the pleomorphism and cultural variability displayed by species of the genus Trichophyton, the identification methods based solely on morphological features are usually insufficient for their classification. The goal of the present work was to test a set of phenotypic methods in order to identify fungal isolates that belong to the aforementioned genus. These methods were based on a molecular taxonomic technique used as standard. Clinical isolates (56) were used as samples along with 6 reference strains. Macro and micromorphological studies were performed as well as biochemical and physiological tests such as in vitro hair perforation, nutritional requirements in Trichophyton agar media, urease production and growth on bromocresol purple-milk. solids-glucose (BCP-MS-G) agar. Additionally, PCR fingerprinting using the (GACA)4 primer was employed. As a result of the PCR method, specific profiles were observed for Microsporum canis, Epidermophyton floccosum, Trichophyton rubrum and Trichophyton interdigitale. Identical profiles were obtained for Arthroderma benhamiae y Trichophyton erinacei. Of the total number of clinical isolates, 39 matched the T. rubrum profile while 13 corresponded to A. benhamiae and 4 to T. interdigitale. The most useful phenotypic test to differentiate between T. rubrum and T. mentagrophytes complex strains was alkalinization of the BCP-MS-G medium. Phenotypic tests did not allow differentiation among the T. mentagrophytes complex species. On the other hand, the molecular technique allowed characterization of T. rubrum isolates as well as of those observed in our study and included in the T. mentagrophytes complex: T. interdigitale and Trichophyton sp., the anamorph of A. benhamiae.

Microsatellite-primed PCR for intra-species genetic relatedness in Trichophyton ajelloi strains isolated in poland from various soil samples

Trichophyton ajelloi is a geophilic dermatophyte that specializes in the decomposition of native keratin. It exists in soil with a permanent influx of keratin matter. In the present study, two PCR-based methods were used for the identification and intra-species differentiation of T. ajelloi strains isolated from 3 types of soils with different physicochemical properties. The first method, employed for molecular identification, was PCR amplification of the 5.8S rRNA gene and its flanking regions encoding internal transcribed spacers (ITSs), followed by restriction enzyme digestion using endonuclease HinfI. The second method, employed for molecular differentiation, was microsatellite-primed PCR (MSP-PCR) using the repetitive oligonucleotide (GACA)₄. All the T. ajelloi strains were also identified using a traditional culture method. Our results showed that molecular identification using the PCR-restriction fragment length polymorphism (PCR-RFLP) method agreed with the identification made using the traditional approach. On the other hand, PCR-RFLP results showed no strain differentiation, while MSP-PCR using the (GACA)₄ primer identified different varieties among the T. ajelloi strains. The reasons for the intra-species differentiation of T. ajelloi have been discussed.

Comparative study of Microsporum canis isolates by DNA fingerprinting

Microsporum canis is a zoophilic fungus and it is an important agent of dermatophytosis. Cats act as important reservoirs. Clinically, it is too difficult to differentiate dermatophytosis caused by various species, also this fungus loses its morphological characteristics easily because of subculture; so using of rapid and accurate laboratory techniques for identifying the dermatophytes is important, therefore, RAPD-PCR was applied for the differentiation of the isolates. In this study, 10 M. canis isolates were detected in cats, dog, human, fox and rabbit at the Mycology Research Center, Faculty of Veterinary Medicine, University of Tehran. For running the RAPD-PCR, PCR set system and three random primers OPU 15, OPU 13 and OPA 04 were used. Then phylogenetic tree and similarity coefficient table were drawn. The results showed that there were some common bands between M. canis isolates. There were some specific bands for each isolates, as well. Our study showed, despite the typical morphology of the whole isolates, they were placed in different branches in molecular typing.

Rapid detection for rabbit-derived dermatophytes using microsatellite-primed polymerase chain reaction

A method exhibiting high sensitivity, specificity and rapidity to detect pathogenic dermatophytes was developed using microsatellite-primed polymerase chain reaction (PCR) in combination with a clustering method. The DNA fragments of Trichophyton mentagrophyton, Microsporum gypseum and Microsporum canis were amplified by using the primer (GACA)4 to detect the DNA polymorphism fingerprints. Twenty-one clinical strains identified as T. mentagrophyton, M. gypseum or M. canis by morphological methods were distinguished according to the differences of standard stains' bands combined with NTSYS-pc2.10 software. The results showed that there were obvious and direct differences in the bands of the three pathogenic dermatophytes, and the similarity of isolated strains and standard strains were above 90%, in line with the results of morphological identification. The method is more accurate, rapid and simple, which is meaningful for the clinical diagnosis and epidemic research of the dermatophytes.

Molecular epidemiology, phylogeny and evolution of dermatophytes

Dermatophytes are fungi that invade and propagate in the keratinized skin of mammals, including humans, often causing contagious infections. The species of medical concern belong to the genera Microsporum, Trichophyton, Epidermophyton (in their anamorphic state) and Arthroderma (in their telomorphic state), which were traditionally identified based on their morphology and biochemical characters. Nonetheless, limitations linked to the differentiation of closely related agents at species and strains level have been recently overcome by molecular studies. Indeed, an accurate identification of dermatophytes is pivotal for the establishment of effective control and prevention programs as well as for determining the most appropriate and effective antifungal therapies to be applied. This article reviews the DNA techniques and the molecular markers used to identify and to characterize dermatophyte species, as well as aspects of their phylogeny and evolution. The applications of typing molecular strain to both basic and applied research (e.g., taxonomy, ecology, typing of infection, antifungal susceptibility) have also been discussed.

Genetic variability in Microsporum canis isolated from cats, dogs and humans in Brazil

Dermatophytosis caused by Microsporum canis is a heterogeneous disease with variable clinical manifestations. M. canis is a zoophilic dermatophyte and the most frequent fungi isolated from dogs, cats and children in Brazil. The aim of this study was to investigate the genetic variability of M. canis isolates from different animal species using two microsatellite markers, namely, McGT(13) and McGT(17), and to correlate the results with the clinical and epidemiological patient data in Brazil. The study included a global set of 102 M. canis strains, including 37 symptomatic cats, 35 asymptomatic cats, 19 human patients with tinea, 9 asymptomatic dogs and 2 symptomatic dogs. A total of 14 genotypes were identified, and 6 large populations were distinguished. There was no correlation between these multilocus genotypes and the clinical and epidemiological data, including the source, symptomatology, clinical picture, breed, age, sex, living conditions and geographic location. These results demonstrate that the use of microsatellite polymorphisms is a reliable method for the differentiation of M. canis strains. However, we were unable to demonstrate a shared clinical and epidemiological pattern among the same genotype samples.

Development and validation of a microsatellite marker-based method for tracing infections by Microsporum canis

BACKGROUND

Microsporum canis is a dermatophyte fungus harbored by cats and dogs and is frequently transmitted to humans. Molecular tools able to discriminate fungal isolates at the strain level would prove extremely useful for confirming the route of infection, thus contributing to optimization of prophylaxis and hygienic regimens.

OBJECTIVE

To develop and validate a microsatellite marker-based method for use in tracking infections by M. canis.

METHODS

Primers were designed against sequences flanking the microsatellites individuated by a BLAST search using the nucleotide sequence information assembled by the M. canis CBS 113480 genome project. The PCR conditions were standardized and fragment analysis was performed using a genetic analyzer. The resolving power of the markers was investigated on 26 unrelated M. canis strains while the reproducibility of the technique and the stability of the markers were evaluated on a single strain subcultured in time as well as on 36 strains isolated from nine outbreak episodes.

RESULTS

Eight markers were recognized as being the most polymorphic within the set of M. canis strains isolated from unrelated distant hosts, with a total of 22 multilocus genotypes, which corresponded to a genotypic diversity of 97%. Repeated tests on subcultures of M. canis reference strain CBS 113480 always yielded the same results. Identical multilocus genotypes were obtained for all the isolates from each outbreak episode.

CONCLUSION

The high resolving power and reproducibility of the markers that were identified support the potential of these tools to detect sources and routes of infection by M. canis.

Direct detection of five common dermatophyte species in clinical samples using a rapid and sensitive 24-h PCR-ELISA technique open to protocol transfer

Identification of dermatophytes is usually based on morphological characteristics determined by time-consuming microscopic and cultural examinations. An effective PCR-ELISA method has been developed for rapid detection of dermatophyte species directly from clinical specimens within 24 h. Isolated genomic DNA of skin scrapings and nail samples from patients with suspected dermatophyte infections is amplified with species-specific digoxigenin-labelled primers targeting the topoisomerase II gene. The subsequent ELISA procedure with biotin-labelled probes allows a sensitive and specific identification of the five common dermatophytes -Trichophyton rubrum, T. interdigitale, T. violaceum, Microsporum canis and Epidermophyton floccosum. PCR-ELISA, based on the new polyphasic species concept, was assessed using 204 microscopy-positive samples in two university mycological laboratories in Munich and Tübingen, and 316 consecutive specimens - regardless of mycological findings - in a dermatological practice laboratory in Neu-Ulm. One of the five dermatophytes was confirmed by PCR-ELISA in 163 of 204 (79.9%) of the clinical samples from the university hospitals found positive using microscopy. Culture was positive for dermatophytes in 59.8% of the same cases. A significant difference between these two methods could be demonstrated using the McNemar test (P < 0.005). Analysis of specimens from Neu-Ulm confirmed the results in a dermatological practice laboratory as 25.0% of the specimens had positive PCR results, whereas only 7.3% were positive according to culture. Direct DNA isolation from clinical specimens and the PCR-ELISA method employed in this study provide a rapid, reproducible and sensitive tool for detection and discrimination of five major dermatophytes at species level, independent of morphological and biochemical characteristics.

Molecular typing of Epidermophyton floccosum isolated from patients with dermatophytosis by RAPD-PCR

We evaluated the ability of randomly amplified polymorphic DNA (RAPD) to type Epidermophyton floccosum isolates recovered from patients with dermatophytosis originating from different regions of Iran. A total of 13 clinical isolates of E. floccosum obtained from Iranian patients were analyzed by RAPD with 7 arbitrary primers (OPN16, OPD18' OPU15, OPX19, R28, OPA04 and OPAA17). Among the applied primers, OPN16 produced banding patterns from all the isolates. In addition, some of the isolates had very close relation. The phenon line which represented the mean similarities was at the value of 73%. At this level, 4 groups were characterized. Two isolates of a patient had different molecular patterns, suggesting infection transmission from different sources in the case of a single patient. RAPD-PCR provided a rapid and practical tool for identification of E. floccosum isolates, which was independent of morphological characteristics, and enhanced laboratory diagnosis of dermatophytosis.

Evaluation of a PCR melting profile method for intraspecies differentiation of Trichophyton rubrum and Trichophyton interdigitale

In order to identify the source of infections caused by dermatophytes, as well as the pathogen transmission pathway, there is a need to determine methods that allow detailed genetic differentiation of the strains within the dermatophyte genera. In this work, a PCR melting profile (PCR-MP) technique based on the ligation of adaptors and the difference in melting temperatures of DNA restriction fragments was used for the first time for intraspecies genotyping of dermatophytes. Clinical isolates and reference strains of dermatophytes isolated from skin, scalp, toenails and fingernails were used for this study. PCR-MP and random amplification of polymorphic DNA (RAPD) were used to type 11 isolates of Trichophyton rubrum, 40 isolates of Trichophyton interdigitale and 14 isolates of Microsporum canis. The results distinguished five types (containing one subtype) characteristic for T. rubrum and seven types characteristic for T. interdigitale using the PCR-MP technique. Analysis conducted using RAPD revealed five types for T. rubrum and four types for T. interdigitale isolates. No differentiation was observed for the M. canis isolates with either method. These results demonstrate that PCR-MP is a reliable method for the differentiation of T. rubrum and T. interdigitale strains and yields a discriminatory power that is at least equal to that of RAPD.

Single-step PCR using (GACA)4 primer: utility for rapid identification of dermatophyte species and strains

Dermatophytes are fungi that belong to three genera: Epidermophyton, Microsporum, and Trichophyton. Identification of dermatophyte species is essential for appropriate diagnosis and treatment of dermatophytosis. Routine identification depends on macroscopic and microscopic morphology, which is time-consuming and does not identify dermatophyte strains. In this study, two PCR-based methods were compared for their abilities to identify 21 dermatophyte isolates obtained from Egyptian patients to the species and strain levels. The first method employed a two-step method: PCR amplification, using ITS1 and ITS4 as primers, followed by restriction enzyme digestion using the endonuclease MvaI. The second method employed a one-step approach employing the repetitive oligonucleotide (GACA)(4) as a primer. Dermatophyte strains were also identified using a conventional culture method. Our results showed that the conventional culture method identified four species: Microsporum canis, Trichophyton mentagrophytes, Trichophyton rubrum, and Trichophyton violaceum. Moreover, both PCR methods agreed with the diagnosis made using the conventional approach. Furthermore, ITS1/ITS4-based PCR provided no strain differentiation, while (GACA)(4)-based PCR identified different varieties among the T. mentagrophytes isolates. Taken together, our results suggest that (GACA)(4)-based PCR has utility as a simple and rapid method for identification of dermatophyte species as well as utility for differentiation of T. mentagrophytes variants.

Phylogenetic analysis of Trichophyton mentagrophytes human and animal isolates based on MnSOD and ITS sequence comparison

Dermatophytes are keratinophilic fungi able to infect keratinized tissues of human or animal origin. Among them, Trichophyton mentagrophytes is known to be a species complex composed of several species or variants, which occur in both human and animals. Since the T. mentagrophytes complex includes both anthropophilic and zoophilic pathogens, accurate molecular identification is a critical issue for comprehensive understanding of the clinical and epidemiological implications of the genetic heterogeneity of this complex. Here, 41 T. mentagrophytes isolates from either human patients (14 isolates) or animals (27 isolates) with dermatophytosis were prospectively isolated by culture and identified on morphological bases at the University Hospital Centres of Lille and Poitiers, and the Veterinary School of Alfort, respectively. The isolates were differentiated by DNA sequencing of the variable internal transcribed spacer (ITS) regions flanking the 5.8S rDNA, and of the housekeeping gene encoding the manganese-containing superoxide dismutase (MnSOD), an enzyme which is involved in defence against oxidative stress and has previously provided interesting insight into both fungal taxonomy and phylogeny. ITS1-ITS2 regions and MnSOD sequences successfully differentiate between members of the T. mentagrophytes complex and the related species Trichophyton rubrum. Whatever the phylogenetic marker used, members of this complex were classified into two major clades exhibiting a similar topology, with a higher variability when the ITS marker was used. Relationships between ITS/MnSOD sequences and host origin, clinical pattern and phenotypic characteristics (macroscopic and microscopic morphologies) were analysed.

A virulent genotype of Microsporum canis is responsible for the majority of human infections

The zoophilic dermatophyte speciesMicrosporum canisbelongs to theArthroderma otaecomplex and is known to mate with tester strains of that teleomorph species, at least in the laboratory. Human infections are likely to be acquired from the fur of cats, dogs and horses. Epidemiological studies to reveal sources and routes of infection have been hampered by a lack of polymorphic molecular markers. Human cases mainly concern moderately inflammatory tinea corporis and tinea capitis, but, as cases of highly inflammatory ringworm are also observed, the question arises as to whether all lineages ofM. canisare equally virulent to humans. In this study, two microsatellite markers were developed and used to analyse a global set of 101M. canisstrains to reveal patterns of genetic variation and dispersal. Using a Bayesian and a distance approach for structuring theM. canissamples, three populations could be distinguished, with evidence of recombination in one of them (III). This population contained 44 % of the animal isolates and only 9 % of the human strains. Population I, with strictly clonal reproduction (comprising a single multilocus genotype), contained 74 % of the global collection of strains from humans, but only 23 % of the animal strains. From these findings, it was concluded that population differentiation inM. canisis not allopatric, but rather is due to the emergence of a (virulent) genotype that has a high potential to infect the human host. Adaptation of genotypes resulting in a particular clinical manifestation was not evident. Furthermore, isolates from horses did not show a monophyletic clustering.

Fast and sensitive detection of Trichophyton rubrum DNA from the nail samples of patients with onychomycosis by a double-round polymerase chain reaction-based assay

BACKGROUND

Trichophyton rubrum is one of the most frequently isolated pathogens in onychomycosis. Isolation of T. rubrum from nail samples by traditional methods is time-consuming and has a high false-negative rate of detection.

OBJECTIVES

To investigate the detection of T. rubrum in nail samples using DNA detection methods.

METHODS

A total of 62 nail samples from onychomycosis patients with T. rubrum infection were evaluated by culture on Sabouraud's dextrose agar plus chloramphenicol, cycloheximide and gentamicin and compared with genotyping methods utilizing DNA extracted directly from nails. Trichophyton rubrum DNA isolated directly from nails was amplified using two different conserved regions [actin gene and internal transcribed spacer 1 (ITS)] in double-round polymerase chain reaction (PCR) assays.

RESULTS

Forty-eight of 62 (77.4%) samples were potassium hydroxide (KOH) positive, but T. rubrum culture was positive in only 14 of 62 (22.6%) samples. By contrast, direct T. rubrum DNA detection rate was 59.7% (37/62) by actin gene and 45.2% (28/62) by ITS1 region PCR assays corresponding to higher detection frequencies compared with culture with P < 0.001 and < 0.008, respectively. The combined detection of actin and ITS1 was 69.4% (43/62). Interestingly, T. rubrum DNA was detected in 9 out of 14 (64.3%) of KOH- and culture-negative samples. Importantly, 15 culture-negative samples collected from patients undergoing antifungal treatment tested PCR positive using the actin region.

CONCLUSIONS

These results suggest that a direct DNA detection protocol is more sensitive, accurate and faster than traditional culture-based methods. It can be useful to detect T. rubrum in patients undergoing antifungal therapy and who have been reported mycologically cured on the basis of a culture-based method.

Rapid differentiation of species of Botryosphaeriaceae by PCR fingerprinting

The fingerprinting methods referred to as MSP-PCR (microsatellite-primed polymerase chain reaction) and rep-PCR (repetitive-sequence-based polymerase chain reaction) were used to discriminate between species of Botryosphaeriaceae (Fungi, Ascomycota). Several primers were tested with both methods and each primer enabled clear differentiation of all the species tested. Cluster analysis of banding patterns of the isolates corresponded well with known species delineations based on morphology and phylogenetic analysis. The methods described in this paper provide simple and rapid procedures that can be used for routine differentiation of Botryosphaeriaceae isolates at the species level. The two methods are also useful for studying intraspecific variability.

Study of the ITS region in an atypical isolate and comparison with six species of Microsporum

Microsporum species are a frequent cause of cutaneous mycoses in humans. Atypical strains of Microsporum can sometimes be difficult to identify with conventional methods. Recently, we have obtained a Microsporum isolate with atypical morphology and special nutritional requirements (Microsporum CHUS-126-02). As several molecular techniques have been developed for the identification of fungi, we analysed six Microsporum species (M. canis, M. gypseum, M. gallinae, M. nanum, M. ferrugineum and M. persicolor) in order to compare them with our isolate, by using polymerase chain reaction-restriction enzyme analysis (PCR-REA). We studied the nucleotide sequence of the internal transcribed spacer regions from the nuclear DNA encoding for the ribosomal domain. Digestion with MvaI and EcoRI endonucleases obtained specific patterns for M. gypseum, M. gallinae, M. nanum and M. persicolor. Microsporum canis, M. ferrugineum and Microsporum CHUS-126-02 yielded the same patterns. Based on these results and phenotypic criteria, we classified our atypical isolate as M. canis.