Fast, simple and highly sensitive double-rounded polymerase chain reaction assay to detect medically relevant fungi in dermatological specimens

Comparing the diagnostic accuracy of PCR-reverse blot hybridization assay and conventional fungus study in superficial fungal infection of the skin: A systematic review

BACKGROUND

In superficial fungal infections, prompt diagnosis and treatment are essential to prevent the spread of infection and minimise the impact on patients' quality of life. Traditional diagnostic methods, such as KOH smear and fungal culture, have limitations in terms of sensitivity and turnaround time. Recently, the PCR-reverse blot hybridization assay (PCR-REBA) has been developed for the direct detection of dermatophyte DNA. However, there is a lack of information assessing the diagnostic accuracy of PCR-REBA.

OBJECTIVES

This systematic review aimed to evaluate the diagnostic accuracy of PCR-REBA in superficial fungal infections compared to conventional and molecular methods.

METHODS

The comprehensive search containing Ovid MEDLINE and Embase databases was conducted on 7 August 2022. Two reviewers independently reviewed the included articles. Quality assessment was performed using the Newcastle-Ottawa Scale tool.

RESULTS

The included studies were conducted in Korea (five studies) and the Netherlands (two studies), all of which were conducted in a single institution. The quality assessment of these studies indicated low risk of bias. When compared to the potassium hydroxide (KOH) smear and fungus culture, the sensitivity of PCR-REBA ranged from 85% to 100%, and the positive predictive values ranged from 58.9% to 100%. When compared to the RT-PCR, the sensitivity of PCR-REBA ranged from 93.3% to 100%, and the positive and negative predictive values were 91.6%-99.6% and 81.0%-89.1%, respectively.

CONCLUSIONS

The PCR-REBA shows promise as a valuable diagnostic tool for dermatophytosis, offering practical and cost-effective benefits.

Effects of Coleus amboinicus L. Essential Oil and Ethanolic Extracts on Planktonic Cells and Biofilm Formation of Microsporum canis Isolated from Feline Dermatophytosis

Microsporum canis is an important zoonotic fungus that causes dermatophytosis in domestic animals and their owners. Domestic cats are the primary reservoir for M. canis. Antifungal drugs frequently produce adverse effects on the host animal, increasing the demand for novel alternative treatments derived from nature. We evaluated the antifungal activity of Coleus amboinicus essential oil (CEO) and ethanolic extracts (CEE) against M. canis in planktonic and biofilm growth. Twelve clinical isolates of M. canis were identified in feline dermatophyte samples. Using GC-MS, 18 compounds were identified in CEO, with carvacrol being the major constituent. HPLC analysis of CEE revealed that it contained rosmarinic acid, apigenin, and caffeic acid. The planktonic growth of all M. canis isolates was inhibited by C. amboinicus extracts. The minimum inhibitory concentration at which ≥50% of the isolates were inhibited (MIC₅₀) was 128 µg/mL (32-256 µg/mL) for both CEO and CEE. The MIC₉₀ values of CEO and CEE were 128 and 256 µg/mL, respectively. CEO at MIC (128 µg/mL) and 2× MIC (256 µg/mL) significantly inhibited the biofilm formation of weak, moderate, and strong biofilm-producing M. canis. CEE at 2× MIC (256 µg/mL) significantly inhibited the biofilm formation of all isolates. Overall, C. amboinicus extracts inhibited planktonic growth and exhibited a significant antibiofilm effect against M. canis. Thus, C. amboinicus is a potential source of natural antifungal compounds.

Current Topics in Dermatophyte Classification and Clinical Diagnosis

Dermatophytes are highly infectious fungi that cause superficial infections in keratinized tissues in humans and animals. This group of fungi is defined by their ability to digest keratin and encompasses a wide range of species. Classification of many of these species has recently changed due to genetic analysis, potentially affecting clinical diagnosis and disease management. In this review, we discuss dermatophyte classification including name changes for medically important species, current and potential diagnostic techniques for detecting dermatophytes, and an in-depth review of Microsporum canis, a prevalent zoonotic dermatophyte. Fungal culture is still considered the “gold standard” for diagnosing dermatophytosis; however, modern molecular assays have overcome the main disadvantages of culture, allowing for tandem use with cultures. Further investigation into novel molecular assays for dermatophytosis is critical, especially for high-density populations where rapid diagnosis is essential for outbreak prevention. A frequently encountered dermatophyte in clinical settings is M. canis, which causes dermatophytosis in humans and cats. M. canis is adapting to its primary host (cats) as one of its mating types (MAT1-2) appears to be going extinct, leading to a loss of sexual reproduction. Investigating M. canis strains around the world can help elucidate the evolutionary trajectory of this fungi.

Development and Analysis of qPCR for the Identification of Arthroconidial Yeasts of the Genus Magnusiomyces

The arthroconidial yeasts Magnusiomyces capitatus and M. clavatus are emerging opportunistic pulmonary pathogens. They are closely related and difficult to distinguish based on morphological and physiological traits. We applied an SYBR^® green-based quantitative PCR (qPCR) assay to identify the species. We analyzed 30 reference strains originating from clinical and environmental sources by targeting the Rpb2 gene encoding the second largest subunit of RNA polymerase II. The qPCR assays were tested by direct identification of M. capitatus and M. clavatus in spiked sputum and household dishwasher swabs, respectively, as models for clinical and environmental samples. The assays were proved to be reliable for species-level identification of both species, with 100% sensitivity and 100% specificity, lowest inter-assay deviations (RSDr ≤ 1.65%, R² values >0.99), detection limit of 10 theoretical copy number of target DNA, and detection cell limit of ≥5000 yeast cells from spiked sputum samples. The developed qPCR assay is a practical molecular approach for the detection of M. capitatus and M. clavatus that can be used as a stand-alone assay or in conjunction with culture-dependent approaches.

Genes Encoding Proteolytic Enzymes Fungalysin and Subtilisin in Dermatophytes of Human and Animal Origin: A Comparative Study

Dermatophytes are among the most successful fungal pathogens in humans, but their virulence mechanisms have not yet been fully characterized. Dermatophytic fungi secrete proteases in vivo, which are responsible for fungal colonization and degradation of the keratinized tissue during infection. In the present study, we used PCR to investigate the presence of genes encoding fungalysins (MEP) and subtilisins (SUB) in three dermatophyte species whose incidence is increasing in Europe: the anthropophilic Trichophyton rubrum (n = 58), zoophilic Microsporum canis (n = 33), and Trichophyton benhamiae (n = 6). MEP2 and SUB4 genes were significantly correlated with T. rubrum; MEP3 and SUB1 were mostly frequently harbored by M. canis; and MEP1, 2, and 4 and SUB3-7 were most frequently harbored by T. benhamiae isolates (p < 0.05). Furthermore, MEP1-5 and SUB1-3 genes were significantly more prevalent among human clinical isolates of M. canis (n = 17) than among asymptomatic cat isolates of M. canis (n = 16; p < 0.05). Unidentified MEP and/or SUB genes in some isolates in the current study may suggest that other gene repertoires may be involved in the degradation of keratin. The presented analysis of the incidence of MEP and SUB virulence genes in three dermatophyte species of diverse origins provides an insight into the host-fungus interaction and dermatophyte pathogenesis.

Mating genotypes and susceptibility profiles of clinical isolates of Candida glabrata from Turkey

The sexual cycle of Candida glabrata is not known; however, genomic evidence is indicative of recombination among subpopulations and the genome harbours genes necessary for undergoing mating and meiosis, which may increase fitness. The relationship between specific mating type-like (MTL) loci and antifungal susceptibility is not well understood in C. glabrata. We investigated different combinations of clinical C. glabrata isolate mating types and their antifungal susceptibility profiles. Allele profiles of the mating genes of 103 clinical C. glabrata isolates were identified, and their antifungal susceptibility to azoles, echinocandins and amphotericin B were compared. The majority (88.3%) of screened isolates harboured the a allele in the locus. The MTL1, MTL2 and MTL3 loci harboured a (88.3%), a (95.1%), and α (71.8%) alleles, respectively. The C. glabrata isolates were susceptible to echinocandins but displayed high minimal inhibitory concentrations (MICs) for azoles. The MIC ranges and MIC90 values of all isolates were 1.0 to ≥64 and 8.0 μg mL^-1 for fluconazole, 0.06 to ≥16.0 and 0.5 μg mL^-1 for voriconazole, 0.06 to ≥16.0 and 1.0 μg mL^-1 for posaconazole, ≤0.015 to 0.06, and 0.03 μg mL^-1 for caspofungin, ≤0.015 to 0.06 and 0.015 μg mL^-1 for anidulafungin and 0.5-2 and 2.0 μg mL^-1 for amphotericin B, respectively. The mating gene alleles of the clinical C. glabrata isolates were not associated with differences in the MICs of the tested antifungals, except for the MTL3 α-allele and echinocandins. The mating genotypes of the clinical C. glabrata isolates had no recognisable common effect on antifungal susceptibility.

Mating type (MAT) locus and possible sexuality of the opportunistic pathogen Exophiala dermatitidis

Sexual reproduction among the black yeasts is generally limited to environmental saprobic species and is rarely observed among opportunists in humans. To date, a complete sexual cycle has not been observed in Exophiala dermatitidis. In this study, we aimed to gain insight into the reproductive mode of E. dermatitidis by characterizing its mating type (MAT) locus, conducting MAT screening of environmental and clinical isolates, examining the expression of the MAT genes and analyzing the virulence of the isolates of different mating types. Similar to other members of the Pezizomycotina, the E. dermatitidis genome harbors a high mobility group (HMG) domain gene (MAT1-2-1) in the vicinity of the SLA2 and APN2 genes. The MAT loci of 74 E. dermatitidis isolates (11 clinical and 63 environmental) were screened by PCR, and the surrounding region was amplified using long-range PCR. Sequencing of the ∼ 12-kb PCR product of a MAT1-1 isolate revealed an α-box gene (MAT1-1-1). The MAT1-1 idiomorph was 3544-bp long and harbored the MAT1-1-1 and MAT1-1-4 genes. The MAT1-2 idiomorph was longer, 3771-bp, and harbored only the MAT1-2-1 gene. This structure suggests a heterothallic reproduction mode. The distribution of MAT among 74 isolates was ∼ 1:1 with a MAT1-1:MAT1-2 ratio of 35:39. RT-PCR analysis indicated that the MAT genes are transcribed. No significant difference was detected in the virulence of isolates representing different mating types using a Galleria mellonella model (P > 0.05). Collectively, E. dermatitidis is the first opportunistic black yeast in which both MAT idiomorphs have been characterized. The occurrence of isolates bearing both idiomorphs, their approximately equal distribution, and the expression of the MAT genes suggest that E. dermatitidis might reproduce sexually.

Screening for Exotic Forest Pathogens to Increase Survey Capacity Using Metagenomics

Anthropogenic activities have a major impact on the global environment. Canada's natural resources are threatened by the spread of fungal pathogens, which is facilitated by agricultural practices and international trade. Fungi are introduced to new environments and sometimes become established, in which case they can cause disease outbreaks resulting in extensive forest decline. Here, we describe how a nationwide sample collection strategy coupled to next-generation sequencing (NGS) (i.e., metagenomics) can achieve fast and comprehensive screening for exotic invasive species. This methodology can help provide guidance to phytopathology stakeholders such as regulatory agencies. Several regulated invasive species were monitored by processing field samples collected over 3 years (2013 to 2015) near high-risk areas across Canada. Fifteen sequencing runs were required on the Ion Torrent platform to process 398 samples that yielded 45 million reads. High-throughput screening of fungal and oomycete operational taxonomic units using customized fungi-specific ribosomal internal transcribed spacer 1 barcoded primers was performed. Likewise, Phytophthora-specific barcoded primers were used to amplify the adenosine triphosphate synthase subunit 9-nicotinamide adenine dinucleotide dehydrogenase subunit 9 spacer. Several Phytophthora spp. were detected by NGS and confirmed by species-specific quantitative polymerase chain reaction (qPCR) assays. The target species Heterobasidion annosum sensu stricto could be detected only through metagenomics. We demonstrated that screening target species using a variety of sampling techniques and NGS-the results of which were validated by qPCR-has the potential to increase survey capacity and detection sensitivity, reduce hands-on time and costs, and assist regulatory agencies to identify ports of entry. Considering that early detection and prevention are the keys in mitigating invasive species damage, our method represents a substantial asset in plant pathology management.

Comparison of the rolling circle amplification and ligase-dependent reaction methods for the identification of opportunistic Exophiala species

We developed two ligase-dependent probe amplification assays based on rolling circle amplification (RCA) and the ligase-dependent reaction (LDR) to differentiate species of Exophiala targeting the rDNA internal transcribed spacer region. We focused on Exophiala dermatitidis and E. phaeomuriformis, two opportunistic inhabitants of indoor wet cells, and further detected E. heteromorpha, E. xenobiotica, and E. crusticola; 57 reference isolates representing the five species were tested. Depending on the RCA probes used, the sensitivity was 100%, and the specificity ranged from 3.7% to 88.6% (median: 46.1%). In contrast, the sensitivity and specificity of the LDR probes targeting the same isolates were 88.6-100% (median: 95.8%) and 95.4-100% (median: 97.7%), respectively. We analyzed 198 additional environmental isolates representing the same Exophiala species. Overall, the sensitivity and specificity of LDR ranged from 89.7% to 100% (median: 94.1%) and from 93.9% to 100% (median: 96.9%), respectively. The assessment of performance and validation of LDR probes using SYBR Green quantitative polymerase chain reaction revealed high reproducibility and an acceptable range limit, in line with the guidelines of the European Network of GMO Laboratories. In conclusion, the LDR assay was more reliable and less expensive than RCA for species-level identification of Exophiala isolates.

Fast identification of dermatophytes by MALDI-TOF/MS using direct transfer of fungal cells on ground steel target plates

Dermatophytes cause human infections limited to keratinised tissues. We showed that the direct transfer method allows reliable identification of non-dermatophytes mould and yeast by MALDI-TOF/MS. We aimed at assessing whether the direct transfer method can be used for dermatophytes and whether an own mass spectra library would be superior to the Bruker library. We used the Bruker Biotyper to build a dermatophyte mass spectra library and assessed its performance by 1/testing a panel of mass spectrum produced with strains genotypically identified and, 2/comparing MALDI-TOF/MS identification to morphology-based methods. Identification of dermatophytes using the Bruker library is poor. Our library provided 97% concordance between ITS sequencing and MALDI-TOF/MS analysis with a panel of 1104 spectra corresponding to 276 strains. Direct transfer method using unpolished target plates allowed proper identification of 85% of dermatophytes clinical isolates most of which were common dermatophytes. A homemade dermatophyte MSP library is a prerequisite for accurate identification of species absent in the Bruker library but it also improves identification of species already listed in the database. The direct deposit method can be used to identify the most commonly found dermatophytes such as T. rubrum and T. interdigitale/mentagrophytes by MALDI-TOF/MS.

Genetic Diversity and Antifungal Susceptibility of Candida parapsilosis Sensu Stricto Isolated from Bloodstream Infections in Turkish Patients

Candida parapsilosis sensu stricto is an emerging cause of hospital-acquired Candida infections, predominantly in southern Europe, South America, and Asia. We investigated the genetic diversity and antifungal susceptibility profile of 170 independent C. parapsilosis sensu stricto strains obtained from patients with candidemia who were treated at the Ege University Hospital in Izmir, Turkey, between 2006 and 2014. The identity of each strain was confirmed via PCR amplification and digestion of the secondary alcohol dehydrogenase-encoding gene. The 24-h geometric mean minimum inhibitory concentrations of the antifungal agents, in increasing order, were as follows: posaconazole, 0.10 µg/mL; voriconazole, 0.21 µg/mL; caspofungin, 0.38 µg/mL; amphotericin B, 0.61 µg/mL; anidulafungin, 0.68 µg/mL; and fluconazole, 2.95 µg/mL. Microsatellite genotyping of the isolates (using fluorescently labeled primers and a panel of four different short-nucleotide repeat fragments) identified 25, 17, 17, and 8 different allelic genotypes at the CP6, B5, CP4, and CP1 locus, respectively. Posaconazole, caspofungin, and amphotericin B showed the greatest in vitro activity of the tested systemic azole, echinocandin, and polyene agents, respectively, and the observed antifungal susceptibility of the isolates was shown to be independent of their isolation source. We obtained a combined discriminatory power of 0.99 with a total of 130 genotypes for 170 isolates tested. Finally, microsatellite profiling analysis confirmed the presence of identical genotype between separate isolates, supporting that effective surveillance and infection-prevention programs are essential to limit the impact of C. parapsilosis sensu stricto on hospitalized patients' health.

Whole-Genome Analysis Illustrates Global Clonal Population Structure of the Ubiquitous Dermatophyte Pathogen Trichophyton rubrum

Dermatophytes include fungal species that infect humans, as well as those that also infect other animals or only grow in the environment. The dermatophyte species Trichophyton rubrum is a frequent cause of skin infection in immunocompetent individuals. While members of the T. rubrum species complex have been further categorized based on various morphologies, their population structure and ability to undergo sexual reproduction are not well understood. In this study, we analyze a large set of T. rubrum and T. interdigitale isolates to examine mating types, evidence of mating, and genetic variation. We find that nearly all isolates of T. rubrum are of a single mating type, and that incubation with T. rubrum "morphotype" megninii isolates of the other mating type failed to induce sexual development. While the region around the mating type locus is characterized by a higher frequency of SNPs compared to other genomic regions, we find that the population is remarkably clonal, with highly conserved gene content, low levels of variation, and little evidence of recombination. These results support a model of recent transition to asexual growth when this species specialized to growth on human hosts.

Sequencing of FKS Hot Spot 1 from Saprochaete capitata To Search for a Relationship to Reduced Echinocandin Susceptibility

Saprochaete capitata, formerly known as Geotrichum capitatum, is an emerging fungal pathogen with low susceptibility to echinocandins. Here, we report the nucleotide sequence of the S. capitata hot spot 1 region of the FKS gene (FKS HS1), which codifies for the catalytic subunit of β-1,3-d-glucan synthase, the target of echinocandins. For that purpose, we first designed degenerated oligonucleotide primers derived from conserved flanking regions of the FKS1 HS1 segment of 12 different fungal species. Interestingly, analysis of the translated FKS HS1 sequences of 12 isolates of S. capitata revealed that all of them exhibited the same F-to-L substitution in a position that is highly related to reduced echinocandin susceptibility.

Paecilomyces variotii peritonitis in a patient on continuous ambulatory peritoneal dialysis

Paecilomyces variotii (P. variotii) is an extremely rare cause of continuous ambulatory peritoneal dialysis (CAPD) peritonitis. When diagnosed, it usually portends poor prognosis. Patient's survival depends on early laboratory diagnosis and proper treatment. We herein report a P. variotii peritonitis in a patient on CAPD which is a quite rare clinical entity. Laboratory diagnosis was confirmed via both morphological analysis and DNA sequencing. Antifungal susceptibility tests were performed and interpreted according to the Clinical Laboratory Standards Institute M38-A2 guidelines. After laboratory diagnosis, the patient was treated succesfully with liposomal amphotericin B and itraconazole combination and the peritoneal catheter was removed. This case is worthy of reporting since P. variotii is an uncommon cause of peritonitis and leads to dilemmas in both laboratory diagnosis and treatment strategies.

Diagnostic performance of molecular and conventional methods for identification of dermatophyte species from clinically infected Arabian horses in Egypt

BACKGROUND

Rapid and accurate identification of dermatophytes is crucial for the effective control of disease outbreaks. Current methods based on culture and microscopic characteristics may require weeks before positive identification is made.

OBJECTIVES

To (i) identify the most common pathogenic dermatophytes affecting Arabian horses; (ii) compare the performance of direct microscopy (DM), culture, PCR using hair samples (PCRhair ) and PCR based on culture isolates (PCRculture ) for the diagnosis of dermatophytosis.

METHODS

Samples of hair and crusts of skin lesions from Arabian horses were collected on a monthly basis by scraping skin of affected horses. Samples were divided into three portions: the first portion was used for microscopic examination, the second for culture and the third portion for PCR amplification of intergenic spacer (ITS) regions.

RESULTS

Out of 200 horses examined, 70 (35%) showed cutaneous lesions characteristic of dermatophytosis. DM revealed that 70.4% were positive for fungal elements and 85.7% were culture positive. The identified species were Microsporum canis, Trichophyton verrucosum, T. mentagrophytes var. mentagrophytes and M. equinum. Among 25 selected samples, 64, 92, 91.3 and 52% were positive for dermatophytes, as determined by DM, culture, PCRculture and PCRhair , respectively.

CONCLUSIONS

The dermatophytes M. canis, T. verrucosum, T. mentagrophytes var. mentagrophytes and M. equinum were the most common cause of dermatophytosis in Arabian horses. Although the number of samples was small, the ITS-based PCR may be a useful diagnostic tool when combined with culture.

Aspergillus terreus infection in a sutureless self-sealing incision made during cataract surgery

Here, we describe a case of keratitis caused by Aspergillus terreus in an 80-year-old immunocompetent woman 1 month after uneventful cataract surgery. The patient presented with decreased visual acuity (20/50) and severe pain in her right eye. Examination revealed a 3.5 × 4.5 mm white-colored deep stromal infiltration located on the temporal corneal tunnel incision. Corneal scraping samples were obtained for cytological and culture examinations. The cinnamon-brown colonies consisting of a dense felt of conidiophores were identified as A. terreus using molecular data. Using CLSI M38-A2 microdilution method, minimum inhibitory concentration values of amphotericin B, itraconazole, voriconazole, and posaconazole were determined to be 2, 1, 0.25, and 1 μg/ml, respectively, and minimum effective concentration values of caspofungin and anidulafungin were ≤0.03 and ≤0.03, respectively, at 48 h for the A. terreus strain. Antifungal therapy was started as topical 1 % voriconazole drops hourly and 5 % natamycin ointment five times a day; however, corneal infection and melting progressed despite the ongoing intensive treatment and visual acuity dropped to the 20/200 level at the end of the first week. Amniotic membrane transplantation was performed to promote corneal healing. Topical medication was tapered and discontinued within 2 months based on the clinical features. The ulcer healed with scarring and vascularization, and visual acuity improved to 20/50. In conclusion, A. terreus is a very uncommon cause of mycotic keratitis and is especially rare after cataract surgery. We suggest that early and accurate diagnosis and appropriate treatment of A. terreus keratitis may have a major impact on preventing severe disease complications.

Black yeast diversity on creosoted railway sleepers changes with ambient climatic conditions

The environmental isolation of opportunistic pathogenic black yeasts, which are responsible for a wide spectrum of human infections, is essential to understanding the ecology of clinical fungi. Extreme outdoor environments polluted with aromatic hydrocarbons support the growth of black yeasts in unlikely places, such as railway sleepers. However, there are limited data concerning the diversity of these fungi growing on polluted railway sleepers. In this investigation, we examined 845 railway sleeper samples, obtained from 11 Turkish cities representing altitudes from 25 to 1,893 m, and inoculated the samples onto mycological media for the isolation of black yeasts. Ninety-four samples (11.1 %) yielded positive results for black yeast, with creosoted oak sleepers having a significantly higher number of isolates than concrete sleepers (p < 0.05). Identification based on the ribosomal DNA (rDNA) internal transcribed spacer region revealed the highest prevalence of Exophiala phaeomuriformis, followed by Exophiala dermatitidis, Exophiala heteromorpha, Exophiala xenobiotica, and Exophiala crusticola. This study revealed that railway sleepers harboring black yeasts were predominantly (>75 %) populated with thermophilic species. We observed that altitude might have a significant effect on species diversity. Briefly, E. phaeomuriformis exhibited growth over a wide altitude range, from 30 to 1,893 m. In contrast, E. dermatitidis had a remarkable aversion to low altitudes and exhibited maximum growth at 1,285 m. In conclusion, we speculate that one can predict what species will be found on railway sleepers and their probability and that species diversity primarily depends on sleeper type and altitude height. We believe that this study can contribute new insights into the ecology of black yeasts on railway sleepers and the railway factors that influence their diversity.

A dynamic distention protocol for whole-organ bladder decellularization: histological and biomechanical characterization of the acellular matrix

A combined physical-chemical protocol for whole full-thickness bladder decellularization is proposed, based on organ cyclic distention through repeated infusion/withdrawal of the decellularization agents through the urethra. The dynamic decellularization was intended to enhance cell removal efficiency, facilitating the delivery of detergents within the inner layers of the tissue and the removal of cell debris. The use of mild chemical detergents (hypotonic solution and non-ionic detergent) was employed to limit adverse effects upon matrix 3D ultrastructure. Inspection of the presence of residual DNA and RNA was carried out on decellularized matrices to verify effective cell removal. Histological investigation was focused on assessing the retention of adequate structural and functional components that regulate the biomechanical behaviour of the acellular tissue. Biomechanical properties were evaluated through uniaxial tensile loading tests of tissue strips and through ex vivo filling cystometry to evaluate the whole-organ mechanical response to a physiological-like loading state. According to our results, a dynamic decellularization protocol of 17 h duration with a 5 ml/min detergent infusion flow rate revealed higher DNA removal efficiency than standard static decellularization, resulting in residual DNA content < 50 ng/mg dry tissue weight. Furthermore, the collagen network and elastic fibres distribution were preserved in the acellular ECM, which exhibited suitable biomechanical properties in the perspective of its future use as an implant for bladder augmentation.

A MALDI-TOF MS procedure for clinical dermatophyte species identification in the routine laboratory

The conventional identification of dermatophytes requires a long turnaround time and highly skilled mycologists. We have recently developed a tandardized matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) assay to routinely identify molds of potential clinical significance. This study objective was to determine if this same assay could also be employed to identify clinical dermatophytes in the routine laboratory setting. The effects of the inclusion of cycloheximide in the culture medium and incubation time were tested after building a reference spectra library that included 48 well-characterized isolates of 17 dermatophyte species. Then these same isolates were prospectively identified using this library. MALDI-TOF MS-based identification was effective regardless of the presence of cycloheximide or incubation time as 130/133 (97.8%) of the clinical isolates were appropriately identified. Two Microsporum canis isolates yielded uninformative spectra and one M. audouinii isolate was misidentified. Since one only requires a small colony for MALDI-TOF MS analysis, accurate identifications were obtained in 3-6 days and, specifically, before the appearance of their characteristic morphological features. Consequently, identification turnaround time was dramatically reduced as compared to that needed for conventional morphological identification. In conclusion, this standardized MALDI-TOF MS-based identification procedure for filamentous fungi effectively identifies clinical dermatophyte isolates and drastically reduces the response times in the routine clinical laboratory.

Dishwashers are a major source of human opportunistic yeast-like fungi in indoor environments in Mersin, Turkey

The natural habitat of opportunistic fungal pathogens is outside of the host; therefore, it is crucial to understand their ecology and routes of transmission. In this study, we investigated the presence of black and filamentous fungi in moist indoor environments in the city of Mersin in subtropical Turkey. In total, 177 private dwellings were screened and 893 samples obtained using cotton swabs and moistened with physiological saline from dishwashers, washing machines, refrigerators, bath-tubs, bathroom walls, and shower heads. These were then inoculated onto malt extract agar supplemented with chloramphenicol, followed by incubation at 37°C. Thirty samples (3.4%) were positive for fungi, which were then identified by sequencing the rDNA internal transcribed spacer region. Exophiala dermatitidis was the most common species (23), followed by E. phaeomuriformis (three), Magnusiomyces capitatus (two), and Candida parapsilosis (two). Genotype A of E. dermatitidis (14) was more prevalent than genotypes B (eight) and C (one) and E. phaeomuriformis was also represented by two genotypes. Our findings suggest that dishwashers are a major indoor niche for thermophilic black yeasts. The occurrence of the opportunistic filamentous fungus M. capitatus in dishwashers is consistent with a recent report.

Massive contamination of Exophiala dermatitidis and E. phaeomuriformis in railway stations in subtropical Turkey

In order to reveal the source of contamination of opportunistic fungi, their natural habitat has to be understood. Black yeast-like fungi are abundant in man-made environments, particularly in those that are rich in toxic hydrocarbons such as railway ties. In this study, we investigated the presence of black fungi on creosote-treated oak railway ties and concrete sleepers stained with petroleum oil. Samples were collected at two central stations in Turkish cities, Mersin and Adana, and from Tarsus town station located between these two. The sample locations had subtropical climates. A total of 570 railway samples, including 320 from oak and 250 from concrete, were collected. Cotton swabs moistened with sterile physiological saline were applied to the ties and inoculated onto malt extract agar followed by incubation at 37 °C. Overall, we recovered 97 black yeast-like fungi (17.0 % positive). Sixty-three fungi (19.7 %) were collected from creosote-treated oak, whereas 34 isolates (13.6 %) were derived from concrete; the difference was significant (P = 0.05). Identification using rDNA internal transcribed spacer revealed Exophiala dermatitidis (57.7 %) and Exophiala phaeomuriformis (42.3 %). This study suggested that hydrocarbons enrich these opportunistic black yeasts. An eventual health risk is discussed.

Epidemiology of dermatophytosis in junior combat and non-combat sports participants

Participation in competitive sports is popular and widely encouraged worldwide. Herein, we investigated 252 male and 67 female sports players, aged 16.4 ± 1.3 years, active in 15 different types of combat (n = 143) and non-combat (n = 176) sports. Of the 319 participants in this study, 11 (3.5%) players, including six wrestlers, four football players and one handball player, all of whom were men, harboured dermatophytic fungi. Briefly, Trichophyton tonsurans was present in three athletes, who were scalp carriers of the fungus. Furthermore, T. rubrum (4), T. interdigitale (3) and Arthroderma simii (1) were recovered from eight participants with tinea inguinalis (4), tinea pedis (2) or both (1). One patient was a trunk carrier of concomitant tinea pedis. All dermatophytic fungi were identified using both direction sequence of the rDNA regions spanning the internal transcribed spacers (ITS1 and ITS2) and 5.8 rRNA gene. Although sports-active individuals are active and sweat more, we observed a low prevalence of dermatophytosis, both in combat (5.2%) and non-combat sports participants (3.4%) (P > 0.05). However, dermatophyte infections require more attention and appropriate management to eradicate the infection and to prevent possible outbreaks. This study also documents the first case of zoophilic A. simii in Turkey.

Successful medical management of recalcitrant Fusarium solani keratitis: molecular identification and susceptibility patterns

Fungal keratitis is a rare but sight-threatening infection of the cornea that may be caused by several fungal pathogens. A delay in diagnosis and inadequate treatment may even lead to loss of the affected eye. Fungal keratitis is often misdiagnosed as bacterial keratitis because isolation and identification of the fungal pathogen is difficult and requires experience, and fungal growth in culture requires time. In this report, a 14-year-old boy with recalcitrant Fusarium solani keratitis, unresponsive to initial therapy, is presented. CLSI M38-A2 in vitro antifungal susceptibility tests demonstrated that only amphotericin B (0.5 μg/ml) had potent activity against F. solani; however, fluconazole (>64 μg/ml), itraconazole (>16 μg/ml), voriconazole (8 μg/ml), and posaconazole (>16 μg/ml) had high minimum inhibitory concentrations. In addition, caspofungin (>16 μg/ml) and anidulafungin (>16 μg/ml) exhibited high minimum effective concentrations. Repeated intrastromal voriconazole injections, topical voriconazole, and caspofungin combined with systemic antifungal agents improved of the corneal lesion with a significant increase in visual acuity. Intrastromal voriconazole injection may be used as an adjunctive treatment method for recalcitrant fungal keratitis with no prominent complications. The intrastromal route could be an effective route of administration of antifungal agents, especially for F. solani keratitis, as in this case. A combination of various antifungal agents administered by different routes prevented loss of the eye.

Identification of infectious agents in onychomycoses by PCR-terminal restriction fragment length polymorphism

A fast and reliable assay for the identification of dermatophyte fungi and nondermatophyte fungi (NDF) in onychomycosis is essential, since NDF are especially difficult to cure using standard treatment. Diagnosis is usually based on both direct microscopic examination of nail scrapings and macroscopic and microscopic identification of the infectious fungus in culture assays. In the last decade, PCR assays have been developed for the direct detection of fungi in nail samples. In this study, we describe a PCR-terminal restriction fragment length polymorphism (TRFLP) assay to directly and routinely identify the infecting fungi in nails. Fungal DNA was easily extracted using a commercial kit after dissolving nail fragments in an Na(2)S solution. Trichophyton spp., as well as 12 NDF, could be unambiguously identified by the specific restriction fragment size of 5'-end-labeled amplified 28S DNA. This assay enables the distinction of different fungal infectious agents and their identification in mixed infections. Infectious agents could be identified in 74% (162/219) of cases in which the culture results were negative. The PCR-TRFLP assay described here is simple and reliable. Furthermore, it has the possibility to be automated and thus routinely applied to the rapid diagnosis of a large number of clinical specimens in dermatology laboratories.

A case of rhinoorbital mucormycosis in a leukemic patient with a literature review from Turkey

Mucormycosis (Zygomycosis) is a rare, invasive, opportunistic fungal infection of the paranasal sinuses, caused by a fungus of the order Mucorales. We report a case of rhinoorbital mucormycosis caused by Rhizopus oryzae in an acute lymphoblastic leukemia patient and review the 79 Mucormycosis cases reported in the last decade from Turkey. In our case, the diagnosis was made with endoscopic appearance, computerized tomography of the paranasal sinuses, and culture of the surgical materials. Following aggressive surgical debridement and parenteral amphotericin B therapy, the patient recovered completely. In Turkish literature, rhinocerebral manifestations were the most common form of the mucormycosis (64 cases), followed by pulmonary form (6 cases). The most common risk factor was hematologic malignancies (32 cases) and diabetes mellitus (32 cases), similar to those reported from the rest of the world. The etiologic agents responsible for the review cases were Rhizopus sp., Mucor spp., Rhizomucor spp., Rhizopus oryzae, Mucor circinelloides, and Lichtheimia corymbifera. Although various treatment modalities were used, amphotericin B was the mainstay of therapy. Mortality rate was found to be 49.4% in review cases. It seems that strong clinical suspicion and early diagnosis, along with aggressive antifungal therapy and endoscopic sinus surgery, have great importance for better prognosis in mucormycosis.

Colonization by Candida in children with cancer, children with cystic fibrosis, and healthy controls

A longitudinal, prospective study was conducted intermittently in Norway, from 1999 to 2008, to investigate the Candida colonization rates and species distributions in the tonsillopharyngeal and faecal flora in: (i) children with cancer; (ii) children with cystic fibrosis (CF); and (iii) healthy children. The effect of antibiotic treatment on Candida colonization was also studied, and we looked for changes in antifungal susceptibility over time within each child and between the different groups of children. In total, 566 tonsillopharyngeal swabs and 545 faecal samples were collected from 45 children with cancer, 37 children with CF, and 71 healthy, age-matched controls. The overall colonization rate with Candida was not significantly higher in the two groups of children undergoing extensive treatment with broad-spectrum antibiotics than in healthy controls. Approximately one-third of the cancer patients had a total lack of Candida colonization or had only one Candida-positive sample, despite multiple samples being taken, treatment with broad-spectrum antibiotics, long hospital stays, and periods with neutropenia. Children with CF had the highest prevalence of Candida albicans. Amoxycillin, azithromycin, third-generation cephalosporins and oral vancomycin resulted in a significantly increased Candida colonization rate. Phenoxymethylpenicillin, second-generation cephalosporins, metronidazole, trimethoprim-sulphamethoxazole, ciprofloxacin, penicillinase-resistant penicillins and inhaled tobramycin or colistin showed minimal effects on the Candida colonization rate. We found no evidence of development of antifungal resistance over time.

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.

Real-time PCR and DNA sequencing for detection and identification of Trichophyton rubrum as a cause of culture negative chronic granulomatous dermatophytosis

A 31-year-old patient presented with a diagnosis of granulomatous dermatophytosis based on the clinical aspect of the lesions and the rare presence of hyphae on direct microscopic examination of clinical material. A chronic evolution and progression of the disease, its resistance to a wide range of antifungal agents, the occasional presence of hyphae on direct examination but consistently negative cultures over a 5-year period prompted the use of amplification-based DNA analyses of several successive swab samples or skin biopsies. DNA was extracted using a combination of two semi-automated DNA isolation methods (FastPrep preparation and NucliSENS lysis magnetic extraction method). Identification relied both on sequence analysis of amplicons after SYBR Green real-time PCR of the panfungal internal transcribed spacer 1 (ITS1) genetic target, as well as the unique amplicon melting curve profile of positive samples. Accordingly, Trichophyton rubrum was unambiguously identified in several clinical samples collected over a 7-month period. This case illustrates the contribution of DNA-based assays applied directly to sample biopsies for identifying causative agents in cases in which fungal pathogens are highly suspected but culture are repeatedly negative. It also pinpoints the benefit of combining semi-automated DNA preparation methods, analysis of ITS1 amplicon melting curve profiles and sequence analysis on repeated skin biopsy samples for unambiguous identification of the causative fungal species.

Identification of pathogenic yeast species by polymerase chain reaction amplification of the RPS0 gene intron fragment

AIMS

This work focuses on the development of a method for the identification of pathogenic yeast. With this aim, we target the nucleotide sequence of the RPS0 gene of pathogenic yeast species with specific PCR primers. PCR analysis was performed with both the genomic DNA, whole cells of clinical isolates of Candida species and clinical samples.

METHODS AND RESULTS

A single pairs of primers, deduced from the nucleotide sequence of the RPS0 gene from pathogenic yeast, were used in PCR analysis performed with both the genomic DNA and whole cells of clinical isolates of Candida species and clinical samples. The primers designed are highly specific for their respective species and produce amplicons of the expected sizes and fail to amplify any DNA fragment from the other species tested. The set of primers was tested successfully for the identification of yeast from colonies, blood cultures and clinical samples. These results indicate that genes containing intron sequences may be useful for designing species-specific primers for the identification of fungal strains by PCR. The sensitivity of the method with genomic DNA was evaluated with decreasing DNA concentrations (200 ng to 1 pg) and different cell amounts (10(7)-10(5) cells).

CONCLUSION

The results obtained show that the amplification of RPS0 sequences may be suitable for the identification of pathogenic and other yeast species.

SIGNIFICANCE AND IMPACT OF THE STUDY

Identification of Candida species using molecular approaches with high discriminatory power is important in determining adequate measures for the interruption of transmission of this yeast. The approach described in this work is based on standard technology, and it is specific, sensitive and does not involve complex and expensive equipment. Furthermore, the method developed in this work not only can be used in eight yeast species, but also provides the basis to design primers for other fungi species of clinical, industrial or environmental interest.