Molecular diagnosis of dermatophyte infections

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.

Rapid and Accurate Diagnosis of Dermatophyte Infections Using the DendrisCHIP® Technology

Dermatophytosis is a superficial fungal infection with an ever-increasing number of patients. Culture-based mycology remains the most commonly used diagnosis, but it takes around four weeks to identify the causative agent. Therefore, routine clinical laboratories need rapid, high throughput, and accurate species-specific analytical methods for diagnosis and therapeutic management. Based on these requirements, we investigated the feasibility of DendrisCHIP® technology as an innovative molecular diagnostic method for the identification of a subset of 13 pathogens potentially responsible for dermatophytosis infections in clinical samples. This technology is based on DNA microarray, which potentially enables the detection and discrimination of several germs in a single sample. A major originality of DendrisCHIP® technology is the use of a decision algorithm for probability presence or absence of pathogens based on machine learning methods. In this study, the diagnosis of dermatophyte infection was carried out on more than 284 isolates by conventional microbial culture and DendrisCHIP®DP, which correspond to the DendrisCHIP® carrying oligoprobes of the targeted pathogens implicated in dermatophytosis. While convergence ranging from 75 to 86% depending on the sampling procedure was obtained with both methods, the DendrisCHIP®DP proved to identify more isolates with pathogens that escaped the culture method. These results were confirmed at 86% by a third method, which was either a specific RT-PCR or genome sequencing. In addition, diagnostic results with DendrisCHIP®DP can be obtained within a day. This faster and more accurate identification of fungal pathogens with DendrisCHIP®DP enables the clinician to quickly and successfully implement appropriate antifungal treatment to prevent the spread and elimination of dermatophyte infection. Taken together, these results demonstrate that this technology is a very promising method for routine diagnosis of dermatophytosis.

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.

Status quo and future perspectives of molecular diagnostics in dermatology

Molecular diagnostics (MDx) has become an indispensable pillar of diagnostics in dermatology. Modern sequencing technologies allow for identification of rare genodermatoses, analysis of somatic mutations in melanoma are prerequisite for targeted therapies, and cutaneous infectious pathogens are quickly detected by PCR and other amplification methods. However, to push innovation in molecular diagnostics and tackle so far unmet clinical needs, research activities need to be bundled and the pipeline from idea to MDx product clearly rolled out. Only then, the requirements for technical validity and clinical utility of novel biomarkers can be fulfilled and the long-term vision of personalized medicine will be realized.

Rapid and Visual RPA-Cas12a Fluorescence Assay for Accurate Detection of Dermatophytes in Cats and Dogs

Dermatophytosis, an infectious disease caused by several fungi, can affect the hair, nails, and/or superficial layers of the skin and is of global significance. The most common dermatophytes in cats and dogs are Microsporum canis and Trichophyton mentagrophytes. Wood’s lamp examination, microscopic identification, and fungal culture are the conventional clinical diagnostic methods, while PCR (Polymerase Chain Reaction) and qPCR (Quantitative PCR) are playing an increasingly important role in the identification of dermatophytes. However, none of these methods could be applied to point-of-care testing (POCT). The recent development of the CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) based diagnostic platform promises a rapid, accurate, and portable diagnostic tool. In this paper, we present a Cas12a-fluorescence assay to detect and differentiate the main dermatophytes in clinical samples with high specificity and sensitivity. The Cas12a-based assay was performed with a combination of recombinase polymerase amplification (RPA). The results could be directly visualized by naked eyes under blue light, and all tested samples were consistent with fungal culture and sequencing results. Compared with traditional methods, the RPA-Cas12a-fluorescence assay requires less time (about 30 min) and less complicated equipment, and the visual changes can be clearly observed with naked eyes, which is suitable for on-site clinical diagnosis.

Tinea Gladiatorum: Epidemiology, Clinical Aspects, and Management

Tinea gladiatorum (TG) is a fungal skin infection that occurs among wrestlers and other contact sport athletes with a varied prevalence rate. The most common causative factor responsible as well for local outbreaks of the infection is an anthropophilic dermatophyte species—Trichophyton tonsurans (T. tonsurans). The purpose of this study was to gather current data about TG, including epidemiology, possible diagnosing methods, clinical features, treatment approaches, and potential prevention techniques. We also performed a systematic review of studies describing TG incidence. The prevalence of the disease varied from 2.4% up to 100%. That wide range of variability forces medical practitioners to update knowledge about TG and points to the fact that it still may be a diagnostic and therapeutic challenge. Spreading awareness among athletes and trainers is one of the most important preventive steps.

A retrospective analysis of the concordance of in-house fungal culture and a commercial quantitative PCR from 16 dermatology referral practices across the USA (2018-2019)

BACKGROUND

Commercial quantitative (q)PCR and fungal culture can be used concurrently or individually to test for dermatophytosis with a reported high sensitivity and specificity.

HYPOTHESIS/OBJECTIVES

The aims of this retrospective study were: (i) to evaluate the concordance of a commercial qPCR with in-house fungal culture for the initial diagnosis of dermatophytosis and for monitoring for mycological cure during treatment in dermatology private practice; and (ii) determine the sensitivity and specificity of qPCR overall, (iii) for initial diagnosis and (iv) for treatment monitoring in dogs and cats.

ANIMALS

Four-hundred and twenty-seven client-owned dogs and 188 client-owned cats.

MATERIALS AND METHODS

Retrospective evaluation of electronic medical records from 615 client-owned dogs and cats presented to 16 dermatology referral practices across the USA from 2018 to 2019. Concordance of qPCR with in-house fungal culture and sensitivity and specificity were determined from 667 paired samples.

RESULTS

qPCR agreed with in-house fungal culture in 63 of 85 positive tests and 571 of 582 negative tests, with an overall sensitivity and specificity of 74.1% [95% confidence interval (CI) 63.5-83.0] and 98.1% (95%CI 96.6-99.0), respectively. qPCR sensitivity and specificity for the initial diagnosis of dermatophytosis and for treatment monitoring were 72.4% (95%CI 59.1-83.3) and 98.7% (95%CI 97.3-99.5), and 77.8% (95%CI 57.7-91.4) and 92.0% (95%CI 80.1-97.8), respectively.

CONCLUSIONS AND CLINICAL RELEVANCE

Compared to in-house fungal culture, qPCR was less sensitive and more specific than reported previously. These findings suggest that a diagnosis of dermatophytosis and determining mycological cure should continue to be based on a combination of complementary diagnostic tests.

Multiplex RT-PCR provides improved diagnosis of skin and nail dermatophyte infections compared to microscopy and culture: a laboratory study and review of the literature

Dermatophytes are the most common cause of superficial mycosis, estimated to affect 20% to 25% of the general population. We assessed the performance of a novel real-time polymerase chain reaction (RT-PCR) multiplex assay for diagnosis of dermatophytosis. To evaluate sensitivity and specificity, 10 known bacteria and 10 known fungi commonly found on skin, as well as 105 samples with culture confirmed dermatophytosis were tested using Dermatophyte and Fungi assay (AusDiagnostics, Sydney, Australia), a novel multiplex assay for diagnosis of dermatophytosis in skin and nail. This was followed by prospective evaluation of 195 clinical samples for dermatophytosis by both conventional methods and RT-PCR. RT-PCR showed almost two-fold higher sensitivity and high specificity in the diagnosis of skin and nail dermatophytosis compared to traditional microscopy and culture. In addition, RT-PCR demonstrated markedly reduced turnaround time from 4 to 6 weeks to 4 to 6 hours and ability for high throughput.

Diagnosis of Onychomycosis: From Conventional Techniques and Dermoscopy to Artificial Intelligence

Onychomycosis is a common fungal nail infection. Accurate diagnosis is critical as onychomycosis is transmissible between humans and impacts patients' quality of life. Combining clinical examination with mycological testing ensures accurate diagnosis. Conventional diagnostic techniques, including potassium hydroxide testing, fungal culture and histopathology of nail clippings, detect fungal species within nails. New diagnostic tools have been developed recently which either improve detection of onychomycosis clinically, including dermoscopy, reflectance confocal microscopy and artificial intelligence, or mycologically, such as molecular assays. Dermoscopy is cost-effective and non-invasive, allowing clinicians to discern microscopic features of onychomycosis and fungal melanonychia. Reflectance confocal microscopy enables clinicians to observe bright filamentous septate hyphae at near histologic resolution by the bedside. Artificial intelligence may prompt patients to seek further assessment for nails that are suspicious for onychomycosis. This review evaluates the current landscape of diagnostic techniques for onychomycosis.

Detection of Dermatophytes from Dermatophytosis-Suspected Cases in Iran, Evaluation of Polymerase Chain Reaction-Sequencing Method

Background

Dermatophytosis is mostly caused by dermatophytes species, and the diagnosis of disease is very important for early treatment. The aim of this study was to identify the commonly dermatophytes species isolated directly from the clinical samples, using the polymerase chain reaction (PCR) and evaluate both conventional and molecular methods.

Materials and Methods

This study was performed on 115 clinical samples. Dermatophyte isolates were initially identified by conventional method and confirmed by the sequencing molecular method. In this study, the molecular technique is implemented directly on clinical samples. Statistical analysis of the information was performed by the SPSS software, and the results were statistically analyzed.

Results

Our findings demonstrated that the most abundant dermatophyte species by PCR-sequencing were Trichophyton mentagrophytes (20%), followed by Trichophyton tonsurans (10%), Trichophyton rubrum (6.7%), T. interdigital (6.7%), Arthroderma otae, and Arthroderma vanbreuseghemii, (3.3%) for each one.

Conclusion

For medical laboratories, routine procedures are still preferred because of their lower cost, and the results are almost the same as the molecular methods. The sensitivity and specificity values for PCR under our laboratory condition were 60% and 87%, respectively. This study shows that molecular results performed better in nails than other samples, by culture results.

Recent trends in rapid diagnostic techniques for dermatophytosis

Dermatophytosis is a common contagious disease of both humans and animals. It is caused by a group of filamentous fungi known as dermatophytes, including several genera and various species. An accurate diagnosis of dermatophytes as a causative agent of a skin lesion requires up to one month of conventional laboratory diagnostics. The conventional gold standard diagnostic method is a direct microscopic examination followed by 3 to 4 weeks of Sabouraud's dextrose agar (SDA) culturing, and it may require further post-culturing identification through biochemical tests or microculture technique application. The laborious, exhaustive, and time-consuming gold standard method was a real challenge facing all dermatologists to achieve a rapid, accurate dermatophytosis diagnosis. Various studies developed more rapid, accurate, reliable, sensitive, and specific diagnostic tools. All developed techniques showed more rapidity than the classical method but variable specificities and sensitivities. An extensive bibliography is included and discussed through this review, showing recent variable dermatophytes diagnostic categories with an illustration of weaknesses, strengths, and prospects.

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.

In Vitro Activity of Antifungal Drugs Against Trichophyton rubrum and Trichophyton mentagrophytes spp. by E-Test Method and Non-supplemented Mueller-Hinton Agar Plates

Trichophyton rubrum and Trichophyton mentagrophytes spp. are two of the most frequently isolated dermatophytes causing dermatophytosis worldwide. Since the incidence of resistance to antifungal agents is increasing, antifungal susceptibility tests are needed to successfully treat dermatophytoses. Most of the methods currently available are complicated, time-consuming and lack of reference procedures. The aim of this work was to establish a simple protocol to test the susceptibility of dermatophytes isolated from clinical samples against five antifungal drugs using E-test and disk diffusion methods. We used the E-test on non-supplemented Mueller-Hinton agar plates to determine the minimum inhibitory concentrations (MICs) of fluconazole, itraconazole, voriconazole and amphotericin B, and disk diffusion method to determine the interpretive MIC of terbinafine. Fifty dermatophytes-10 T. rubrum and 40 T. mentagrophytes spp.-were assessed after only 96 h of colony growth. Terbinafine was the most active antifungal agent with an inhibition diameter greater than 70 mm (sensitivity > 20 mm), followed by voriconazole, itraconazole and amphotericin B with MICs ranging from 0.032 to 0.38 µg/mL, from 0.006 to 0.125 µg/mL and from 0.5 to 1.5 µg/mL, respectively. All isolates were resistant to fluconazole. Collectively, the less laborious E-test and disk diffusion method were shown to be suitable and reliable to determine antifungal sensitivity of dermatophytes. This simple standard protocol could be employed in the routine of clinical laboratories.

Identification of clinical dermatophyte isolates obtained from Iran by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

BACKGROUND AND PURPOSE

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is widely used to discriminate among pathogenic microorganisms in clinical laboratories. The aim of this study was to assess the utility of MALDI-TOF MS in the routine identification of clinical dermatophyte isolates obtained from various geographical regions of Iran.

MATERIALS AND METHODS

A total of 94 isolates, including Trichophyton interdigitale (n=44), T. rubrum (n=40), T. tonsurans (n=4), Microsporum canis (n=4), and Epidermophyton floccosum (n=1), were analyzed in this study. The identity of each isolate was determined by polymerase chani reaction amplification and sequencing of the internal transcribed spacer (ITS) region of nuclear-encoded ribosomal DNA and also MALDI-TOF MS. The obtained data by molecular approach were compared with MALDI-TOF MS.

RESULTS

The MALDI-TOF MS led to the identification of 44 (47%) isolates at the species level by generating the spectral score values of ≥ 2.0. However, there was not sufficient agreement between the results of the molecular-based ITS identification methods and MALDI-TOF MS in the species identification of 16 (17%) isolates. The Bruker Daltonics database was also not able to identify protein spectra related to 12 isolates (13%), including T. interdigitale (n=5), T. rubrum (n=4), M. canis (n=2), and T. tonsurans (n=1).

CONCLUSION

According to the results, the utility of MALDI-TOF MS as a routine diagnostic tool for the accurate and reliable identification of dermatophytes can be justified whenever the protein spectra of a large set of worldwide clinical isolates are included in the commercial libraries. In addition, MALDI-TOF MS can be alternatively used to construct an in-house reference database.

PCR-terminal restriction fragment length polymorphism for direct detection and identification of dermatophytes in veterinary mycology

The biological diagnosis of dermatophytosis in veterinary medicine usually relies on direct microscopic examination and inoculation of the samples on appropriate culture media. However, identification of dermatophytes needs expertise, and cultures which require from days to weeks to be conclusive, may lack of sensitivity because of the quite common overgrowth of contaminants. Here we developed a polymerase chain reaction (PCR) assay based on terminal restriction fragment length polymorphism (TRFLP), which may improve sensitivity of the biological diagnosis and reduce the delay for initiation of treatment. This study was first conducted on pure cultures of various dermatophytes (27 species), yeasts (14 species) and moulds (45 species). After DNA extraction, the internal transcribed spacer (ITS)-28S region of ribosomal DNA was amplified with primers targeting specifically pathogenic dermatophytes, and species of interest were identified by TRFLP with appropriate restriction enzymes. After validation, this assay was applied to veterinary samples and results were compared to those obtained by direct microscopic examination and cultures. All target species were correctly identified, and none of the yeast or mould species was amplified, demonstrating specificity of the assay. Regarding clinical samples, the causative agent was detected by PCR-TRFLP from 97.1% of the samples with both positive direct microscopic examination and cultures. No dermatophytes were detected when both conventional tests were negative. PCR-TRFLP developed here demonstrated to be highly sensitive and specific, allowing rapid detection and direct identification of dermatophytes in veterinary practice. Therefore, this assay is especially suitable for the biological diagnosis of dermatophytosis in different animal species.

A prospective study of the epidemiological and clinical patterns of recurrent dermatophytosis at a tertiary care hospital in India

Background

Recurrent and clinically unresponsive dermatophytosis is being increasingly encountered in our country. It runs a protracted course with exacerbations and remissions. However, there is little information regarding the extent of the problem and the characteristics of recurrent dermatophytosis in published literature.

Aims

We sought to determine the prevalence, risk factors and clinical patterns of recurrent dermatophytosis in our institution. We also investigated the causative dermatophyte species and antifungal susceptibility patterns in these species.

Methods

One hundred and fifty patients with recurrent dermatophytosis attending the outpatient department of the Postgraduate Institute of Medical Education and Research, Chandigarh, India were enrolled in the study conducted from January 2015 to December 2015. A detailed history was obtained in all patients, who were then subjected to a clinical examination and investigations including a wet preparation for direct microscopic examination, fungal culture and antifungal susceptibility tests.

Results

Recurrent dermatophytosis was seen in 9.3% of all patients with dermatophytosis in our study. Trichophyton mentagrophytes was the most common species identified (36 patients, 40%) samples followed by T. rubrum (29 patients, 32.2%). In-vitro antifungal susceptibility testing showed that the range of minimum inhibitory concentrations (MIC) on was lowest for itraconazole (0.015-1), followed by terbinafine (0.015-16), fluconazole (0.03-32) and griseofulvin (0.5-128) in increasing order.

Limitation

A limitation of this study was the absence of a suitable control group (eg. patients with first episode of typical tinea).

Conclusion

Recurrence of dermatophytosis was not explainable on the basis of a high (MIC) alone. Misuse of topical corticosteroids, a high number of familial contacts, poor compliance to treatment over periods of years, and various host factors, seem to have all contributed to this outbreak of dermatophytosis in India.

A survey among dermatologists: diagnostics of superficial fungal infections - what is used and what is needed to initiate therapy and assess efficacy?

BACKGROUND

Superficial fungal infections are common. It is important to confirm the clinical diagnosis by mycological laboratory methods before initiating systemic antifungal treatment, especially as antifungal sensitivity and in vitro susceptibility may differ between different genera and species. For many years, the gold standard for diagnosis of superficial fungal infections has been direct fungal detection in the clinical specimen (microscopy) supplemented by culturing. Lately, newer molecular based methods for fungal identification have been developed.

OBJECTIVE

This study was initiated to focus on the current usage of mycological diagnostics for superficial fungal infections by dermatologists. It was designed to investigate whether it was necessary to differentiate between initial diagnostic tests and those used at treatment follow-up in specific superficial fungal infections.

METHODS

An online questionnaire was distributed among members of the EADV mycology Task Force and other dermatologists with a special interest in mycology and nail disease.

RESULTS

The survey was distributed to 62 dermatologists of whom 38 (61%) completed the whole survey, 7 (11%) partially completed and 17 (27%) did not respond. Nearly, all respondents (82-100%) said that ideally they would use the result of direct microscopy (or histology) combined with a genus/species directed treatment of onychomycosis, dermatophytosis, Candida- and Malassezia-related infections. The majority of the dermatologists used a combination of clinical assessment and direct microscopy for treatment assessment and the viability of the fungus was considered more important at this visit than when initiating the treatment. Molecular based methods were not available for all responders.

CONCLUSION

The available diagnostic methods are heterogeneous and their usage differs between different practices as well as between countries. The survey confirmed that dermatologists find it important to make a mycological diagnosis, particularly prior to starting oral antifungal treatment in order to confirm the diagnose and target the therapy according to genus and species.

Assessment of real-time PCR cycle threshold values in Microsporum canis culture-positive and culture-negative cats in an animal shelter: a field study

Objectives Real-time PCR provides quantitative information, recorded as the cycle threshold (Ct) value, about the number of organisms detected in a diagnostic sample. The Ct value correlates with the number of copies of the target organism in an inversely proportional and exponential relationship. The aim of the study was to determine whether Ct values could be used to distinguish between culture-positive and culture-negative samples. Methods This was a retrospective analysis of Ct values from dermatophyte PCR results in cats with suspicious skin lesions or suspected exposure to dermatophytosis. Results One hundred and thirty-two samples were included. Using culture as the gold standard, 28 were true positives, 12 were false positives and 92 were true negatives. The area under the curve for the pretreatment time point was 96.8% (95% confidence interval [CI] 94.2-99.5) compared with 74.3% (95% CI 52.6-96.0) for pooled data during treatment. Before treatment, a Ct cut-off of <35.7 (approximate DNA count 300) provided a sensitivity of 92.3% and specificity of 95.2%. There was no reliable cut-off Ct value between culture-positive and culture-negative samples during treatment. Ct values prior to treatment differed significantly between the true-positive and false-positive groups ( P = 0.0056). There was a significant difference between the pretreatment and first and second negative culture time points ( P = 0.0002 and P <0.0001, respectively). However, there was substantial overlap between Ct values for true positives and true negatives, and for pre- and intra-treatment time points. Conclusions and relevance Ct values had limited usefulness for distinguishing between culture-positive and culture-negative cases when field study samples were analyzed. In addition, Ct values were less reliable than fungal culture for determining mycological cure.

Comparison of real-time PCR with fungal culture for the diagnosis of Microsporum canis dermatophytosis in shelter cats: a field study

Objectives Fungal culture requires at least 14 days for a final result, compared with 1-3 days for PCR. The study compared a commercial real-time dermatophyte PCR panel with fungal culture in cats in a shelter setting for: (1) diagnosis of Microsporum canis infection; and (2) determination of mycological cure. Methods This was a cross-sectional, observational study of cats with suspicious skin lesions or suspected exposure to dermatophytosis. Hair samples were collected for fungal culture and PCR prior to treatment and at weekly intervals until two negative culture results were obtained. Results One hundred and thirty-two cats were included, of which 28 (21.2%) were culture positive and 104 (78.8%) culture-negative for M canis. PCR correctly identified all culture-positive cats and 92/104 culture negative cats; there were 12 false-positive PCR results. The sensitivity and specificity of PCR were 100% (95% confidence interval [CI] 87.7-100) and 88.5% (95% CI 80.7-93.9), respectively. Data from 17 cats were available for assessment of mycological cure. At the time of the first and second negative fungal cultures, 14/17 (82.4%) and 11/17 (64.7%) tested PCR positive, respectively. Conclusions and relevance PCR showed high sensitivity and specificity for diagnosis of M canis dermatophytosis compared with fungal culture, but was unreliable for identifying mycological cure. False-positive results were relatively common. There were no false-negative PCR results and a negative PCR test was a reliable finding in this study. The ability to rapidly diagnose or rule out dermatophytosis could be a valuable tool to increase life-saving capacity in animal shelters.

Evaluation of multiplex real-time PCR for identifying dermatophytes in clinical samples-A multicentre study

The gold-standard method for dermatophyte identification involves direct microscopy and culture, which have inherent shortcomings. Only few molecular methods have been standardised for routine clinical work. This study aimed to develop and test a platform for identifying the most common dermatophytes in Israel using multiplex real-time polymerase chain reaction (RT-PCR). Specific primers were designed for the multiplex system (LightCycler 480) according to known cultures and validated by reference isolates. The dermatophyte detection rate was compared to smear and culture in 223 clinical samples obtained from a tertiary medical centre. Inconsistencies between methods were evaluated by sequencing. The RT-PCR was further evaluated in 200 community-based samples obtained from a health maintenance organisation and 103 military-personnel-based samples analysed at a central laboratory. In hospital-based clinical samples, complete concordance between methods was observed in 190 samples (85%; Kappa = 0.69). In most cases of non-concordance, sequencing was consistent with RT-PCR results. RT-PCR correctly identified all smear- and culture-positive cases in community and military-personnel samples. The results were available within 4 hours. The multiplex RT-PCR platform is a rapid and efficient method for identifying dermatophyte species in clinical samples and may serve as a first step in the diagnostic algorithm of superficial fungal infections.

Molecular Diagnostic Techniques for Onychomycosis: Validity and Potential Application

BACKGROUND

Diagnosis of onychomycosis requires positive findings by direct microscopy and fungal culture. Fungal culture is slow and difficult, with low yields. We compared two dermatophyte identification methods, one using a real-time polymerase chain reaction (PCR) method, and the other using fungal culture to validate the molecular method.

METHODS

Nail specimens were collected from 149 patients with distal and lateral subungual onychomycosis who were positive for fungal elements by direct microscopy using potassium hydroxide. Each specimen was subjected to the modified real-time PCR assay of Miyajima et al. and fungal culture.

RESULTS

Of 149 specimens, 142 (95.3%) were positive for Trichophyton rubrum or Trichophyton mentagrophytes including Trichophyton interdigitale by PCR, while only 104 (69.8%) were positive by fungal culture performed simultaneously. No specimen was negative by PCR, but positive by culture. All specimens positive for T. rubrum or T. mentagrophytes by culture were also positive by PCR, showing complete concordance for Trichophyton species. The culture of 17 specimens yielded fungi other than T. rubrum or T. mentagrophytes, whereas PCR identified T. rubrum in 11 of these specimens. Among 28 culture-negative specimens, 23 showed T. rubrum and four showed T. mentagrophytes by PCR. PCR allowed more rapid identification of causative fungi (≤2 days vs. ≤28 days).

CONCLUSION

Real-time PCR achieved a higher dermatophyte identification rate and showed complete concordance with conventional culture for two Trichophyton species. Specimens never yielded both T. mentagrophytes and T. rubrum simultaneously, suggesting that mixed infection is uncommon.

Clinical application of a molecular assay for the detection of dermatophytosis and a novel non-invasive sampling technique

The dermatophytoses are the most common superficial fungal infections worldwide. Clinical diagnosis is not reliable as there are many differentials, and laboratory diagnosis is required to gain access to treatment in more severe disease. Traditional diagnostic methods are limited by suboptimal sensitivity, specificity and prolonged turnaround times. Molecular methods are being used increasingly in the diagnostic algorithm in the clinical microbiology laboratory. The aim of this study was to evaluate a real-time polymerase chain reaction (RT-PCR) targeting the chitin synthase 1 gene (CHS1) of dermatophytes for analytical specificity, and to assess its clinical application by comparing it to the current methods of microscopy and culture. We also assessed a novel non-invasive sample collection technique involving adhesive tape impressions of suspected lesions. The PCR was highly specific, being able to discern between cultures of dermatophytes and other microorganisms. It also proved to be more sensitive than traditional methods at detecting dermatophytes in clinical samples. Similar sensitivities were seen on the samples assessed by the adhesive tape technique. An internal control system allowed for the detection of inhibition in certain culture and clinical specimens. This rapid and cost-effective technique could be incorporated into the initial diagnostic algorithm for dermatophytosis in Australian laboratories.

Reappraisal of Conventional Diagnosis for Dermatophytes

Dermatophytoses include a wide variety of diseases involving glabrous skin, nails and hair. These superficial infections are a common cause of consultation in dermatology. In many cases, their diagnosis is not clinically obvious, and mycological analysis therefore is required. Direct microscopic examination of the samples using clearing agents provides a quick response to the clinician and is usually combined with cultures on specific media, which must be used to overcome the growth of contaminating moulds that may hamper the recovery of dermatophytes. Accurate identification of the causative agent (i.e. at the species level), currently based on morphological criteria, is necessary not only to initiate an appropriate treatment but also for setting prophylactic measures. However, conventional methods often lack sensitivity and species identification may require up to 4 weeks if subcultures are needed. Histological analysis, which is considered the "gold standard" for the diagnosis of onychomycoses, is seldom performed, and as direct examination, it does not allow precise identification of the pathogen. Nevertheless, a particular attention to the quality of clinical specimens is warranted. Moreover, the sensitivity of direct examination may be greatly enhanced by the use of fluorochromes such as calcofluor white. Likewise, sensitivity of the cultures could be enhanced by the use of culture media containing antifungal deactivators. With the generalization of molecular identification by gene sequencing or MALDI-TOF mass spectrometry, the contribution of historical biochemical or physiological tests to species identification of atypical isolates is now limited. Nevertheless, despite the recent availability of several PCR-based kits and an extensive literature on molecular methods allowing the detection of fungal DNA or both detection and direct identification of the main dermatophyte species, the biological diagnosis of dermatophytosis in 2016 still relies on both direct examination and cultures of appropriate clinical specimens.

PCR and real-time PCR approaches to the identification of Arthroderma otae species Microsporum canis and Microsporum audouinii/Microsporum ferrugineum

OBJECTIVES

The identification of species in the Arthroderma otae complex is essential to determine the origin of infection and to eliminate the risk of transmission. Microsporum canis is a zoophilic species, whereas Microsporum audouinii and Microsporum ferrugineum are anthropophilic species. In this paper, we propose alternative methods that permit species-specific identification of both anthropophilic and zoophilic members of the A. otae complex METHODS: Two PCR assays were designed based on differences in the DNA fragment encoding β-tubulin and were applied in both traditional and real-time PCR using DNA isolated by rapid method from culture.

RESULT

The two assays presented in this study enable the identification of M. canis and M. audouinii/M. ferrugineum with 100% sensitivity and specificity by both traditional and real-time PCR.

CONCLUSION

We developed a new diagnostic assay using specific primers and both traditional and real-time PCR reactions that can be applied in routine laboratory praxis as well as in epidemiological studies to detect M. canis and M. audouinii/M. ferrugineum DNA from a pure culture.

Species identification of dermatophytes in paraffin-embedded biopsies with a new polymerase chain reaction assay targeting the internal transcribed spacer 2 region and comparison with histopathological features

BACKGROUND

Dermatophytosis is a very common skin infection with a broad clinical spectrum. Biopsies are often used to confirm the diagnosis, especially when the clinical presentation is unusual. Not uncommonly, organisms are hard to find even with periodic acid-Schiff stains. Polymerase chain reaction (PCR) for dermatophytes can be used in such cases.

OBJECTIVES

To test a new PCR assay allowing species identification of dermatophytes on paraffin-embedded biopsies, and to reassess histopathological criteria for diagnosis of dermatophytosis.

METHODS

In total, 121 biopsies of 92 patients with clinical suspicion of tinea were included. In 42 samples the clinical diagnosis had been confirmed histopathologically, and in 79 no fungal elements had been identified. PCRs targeting the internal transcribed spacer (ITS)2 region of dermatophytes were performed on the biopsies with subsequent sequencing. Sections were reassessed for the presence/absence of hyphae/spores, pattern and composition of infiltrate, and epidermal/follicular changes. Patient charts were reviewed for clinical data.

RESULTS

The new ITS2 PCR assay detected 94% of the dermatophyte infections (compared with 79% identified by microscopy). Trichophyton rubrum was the dominant species (89%), and other species identified were Trichophyton verrucosum (2%), Microsporum canis (4%), Epidermophyton floccosum (2%) and Trichophyton interdigitale (4%). In particular, infections with T. interdigitale and manifestations with prominent spongiosis were not diagnosed histologically. Intracorneal neutrophils, which have been emphasized as a histopathological clue to dermatophytosis, were present in only 46% of PCR-positive samples.

CONCLUSIONS

Molecular species identification of dermatophytes via ITS2 PCR can easily be implemented in a routine dermatopathology setting. It is fast and highly specific and improves the sensitivity of histopathological diagnosis of dermatophytosis.

Molecular diagnosis of onychomycosis

Onychomycosis is a frequent cause of nail infections due to dermatophytes. Molds and yeast may also be responsible of these pathologies. Antifungal treatments are frequently given without a mycological diagnosis, partly because of the requisite time for obtaining the biological results. The mycological diagnosis requires a direct microscopic examination and a culture in order to accurately identify the fungal genus and species. Nevertheless, this conventional diagnosis is often time consuming due to the delay of fungal cultures and presents disadvantages that make it not sufficient enough to give a precise and confident response to the clinicians. Therefore additional tests have been developed to help distinguish onychomycosis from other nail disorders. Among them, molecular biology techniques offer modern and rapid tools to improve traditional microbiological diagnosis. In this review, we first present the conventional diagnosis methods for onychomycosis and then we describe the main molecular biology tools and the currently available commercial kits that allow a rapid detection of the pathology.

Accessing indoor fungal contamination using conventional and molecular methods in Portuguese poultries

Epidemiological studies showed increased prevalence of respiratory symptoms and adverse changes in pulmonary function parameters in poultry workers, corroborating the increased exposure to risk factors, such as fungal load and their metabolites. This study aimed to determine the occupational exposure threat due to fungal contamination caused by the toxigenic isolates belonging to the complex of the species of Aspergillus flavus and also isolates from Aspergillus fumigatus species complex. The study was carried out in seven Portuguese poultries, using cultural and molecular methodologies. For conventional/cultural methods, air, surfaces, and litter samples were collected by impaction method using the Millipore Air Sampler. For the molecular analysis, air samples were collected by impinger method using the Coriolis μ air sampler. After DNA extraction, samples were analyzed by real-time PCR using specific primers and probes for toxigenic strains of the Aspergillus flavus complex and for detection of isolates from Aspergillus fumigatus complex. Through conventional methods, and among the Aspergillus genus, different prevalences were detected regarding the presence of Aspergillus flavus and Aspergillus fumigatus species complexes, namely: 74.5 versus 1.0 % in the air samples, 24.0 versus 16.0 % in the surfaces, 0 versus 32.6 % in new litter, and 9.9 versus 15.9 % in used litter. Through molecular biology, we were able to detect the presence of aflatoxigenic strains in pavilions in which Aspergillus flavus did not grow in culture. Aspergillus fumigatus was only found in one indoor air sample by conventional methods. Using molecular methodologies, however, Aspergillus fumigatus complex was detected in seven indoor samples from three different poultry units. The characterization of fungal contamination caused by Aspergillus flavus and Aspergillus fumigatus raises the concern of occupational threat not only due to the detected fungal load but also because of the toxigenic potential of these species.

Matrix-assisted laser desorption ionization-time of flight mass spectrometry: a fundamental shift in the routine practice of clinical microbiology

Within the past decade, clinical microbiology laboratories experienced revolutionary changes in the way in which microorganisms are identified, moving away from slow, traditional microbial identification algorithms toward rapid molecular methods and mass spectrometry (MS). Historically, MS was clinically utilized as a high-complexity method adapted for protein-centered analysis of samples in chemistry and hematology laboratories. Today, matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) MS is adapted for use in microbiology laboratories, where it serves as a paradigm-shifting, rapid, and robust method for accurate microbial identification. Multiple instrument platforms, marketed by well-established manufacturers, are beginning to displace automated phenotypic identification instruments and in some cases genetic sequence-based identification practices. This review summarizes the current position of MALDI-TOF MS in clinical research and in diagnostic clinical microbiology laboratories and serves as a primer to examine the "nuts and bolts" of MALDI-TOF MS, highlighting research associated with sample preparation, spectral analysis, and accuracy. Currently available MALDI-TOF MS hardware and software platforms that support the use of MALDI-TOF with direct and precultured specimens and integration of the technology into the laboratory workflow are also discussed. Finally, this review closes with a prospective view of the future of MALDI-TOF MS in the clinical microbiology laboratory to accelerate diagnosis and microbial identification to improve patient care.

Dermatophyte identification in skin and hair samples using a simple and reliable nested polymerase chain reaction assay

BACKGROUND

Dermatophyte identification in tinea capitis is essential for choosing the appropriate treatment and in tinea infections to identify the possible source. The failure of fungi to grow in cultures frequently occurs, especially in cases of previous antifungal therapy.

OBJECTIVES

To develop a rapid polymerase chain reaction (PCR) sequencing assay for dermatophyte identification in tinea capitis and tinea corporis.

MATERIAL AND METHODS

Fungal DNA was extracted from hair and skin samples that were confirmed to be positive by direct mycological examination. Dermatophytes were identified by the sequence of a 28S ribosomal DNA subunit amplicon generated by nested PCR.

RESULTS

Nested PCR was found to be necessary to obtain amplicons in substantial amounts for dermatophyte identification by sequencing. The results agreed with those of classical mycological identification in 14 of 23, 6 of 10, and 20 of 23 cases of tinea capitis, tinea corporis and tinea pedis, respectively, from which a dermatophyte was obtained in culture. In seven of the 56 cases, another dermatophyte was identified, revealing previous misidentification. A dermatophyte was identified in 12 of 18, three of five, and four of nine cases of tinea capitis, tinea corporis and tinea pedis, respectively, in cases in which no dermatophyte grew in culture.

CONCLUSIONS

Although the gold standard dermatophyte identification from clinical samples remains fungal cultures, the assay developed in the present study is especially suitable for tinea capitis. Improved sensitivity for the identification of dermatophyte species was obtained as it is possible to identify the dermatophyte when the fungus fails to grow in cultures.

PCR test for Microsporum canis identification

Microsporum canis, for which the natural hosts are cats and dogs, is the most prevalent zoophilic agent causing tinea capitis and tinea corporis in humans. We present here a diagnostic PCR test for M. canis, since its detection and species identification is relevant to the choice of treatment and to the understanding of a probable source of infection. An M. canis-specific PCR was evaluated using 130 clinical isolates of dermatophytes (including M. canis [n = 15] and 13 other species), 10 yeast or mold isolates, 12 hair and skin samples from animals with or without experimental M. canis infection, and 35 patient specimens, including seven specimens positive for M. canis and 15 dermatophyte negative samples. All pure cultures, animal specimens and clinical samples with M. canis were detected by the PCR test, whereas none of the other fungal isolates or samples without M. canis was negative. This study indicates that the PCR test for M. canis identification applied directly to patient specimens or animal hair, as well as to clinical isolates had 100% specificity and sensitivity.