Detection and identification of Malassezia species in domestic animals and aquatic birds by PCR-RFLP

The present study aimed at detection and species-level identification of the Malassezia yeasts in domestic animals and aquatic birds by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Samples were collected using tape strips and swabs from 471 animals including 97 horses, 102 cattle, 105 sheep, 20 camels, 60 dogs, 30 cats, 1 hamster, 1 squirrel, 50 aquatic birds and 5 turkeys. Tape-strip samples were examined by direct microscopy. All samples were inoculated on modified Leeming and Notman agar medium. DNA extracted from the yeast colonies was amplified by PCR using primers specific for 26S rDNA. RFLP of the PCR products was performed using Hin6I enzyme, and PCR and RFLP products were visualized by agarose gel electrophoresis. Malassezia yeasts were detected at the following frequencies: 15.46% in horses, 12.74% in cattle, 12.38% in sheep, 28.33% in dogs, 26.66% in cats and 26% in aquatic birds. Eighty colonies of 6 species were isolated: Malassezia globosa 41.25%, Malassezia furfur 22.5%, Malassezia restricta 15%, Malassezia sympodialis 15%, Malassezia pachydermatis 5% and Malassezia slooffiae 1.25%. Therefore different lipophilic Malassezia species are found in a wide diversity of animals and aquatic birds. PCR-RFLP is a suitable technique for identification of different Malassezia species.

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

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

Detection of Aspergillus flavus and A. fumigatus in Bronchoalveolar Lavage Specimens of Hematopoietic Stem Cell Transplants and Hematological Malignancies Patients by Real-Time Polymerase Chain Reaction, Nested PCR and Mycological Assays

BACKGROUND

Pulmonary aspergillosis (PA) is one of the most serious complications in immunocompromised patients, in particular among hematopoietic stem cell transplants (HSCT) and patients with hematological malignancies.

OBJECTIVES

The current study aimed to evaluate the incidence of PA and utility of molecular methods in HSCT and patients with hematological malignancies, four methods including direct examination, culture, nested polymerase chain reaction (PCR) and real-time PCR were performed on bronchoalveolar lavage (BAL) specimens in Tehran, Iran.

PATIENTS AND METHODS

During 16 months, 46 BAL specimens were obtained from individuals with allogeneic HSCT (n = 18) and patients with hematological malignancies (n = 28). Direct wet mounts with 20% potassium hydroxide (KOH) and culture on mycological media were performed. The molecular detection of Aspergillus fumigatus and A. flavus was done by amplifying the conserved sequences of internal transcribed spacer 1 (ITS1) ribosomal DNA by nested-PCR and the β-tubulin gene by TaqMan real-time PCR.

RESULTS

Seven (15.2%) out of 46 specimens were positive in direct examination and showed branched septate hyphae; 11 (23.9%) had positive culture including eight (72.7%) A. flavus and three (27.3%) A. fumigatus; 22 (47.8%) had positive nested-PCR and eight (17.4%) had positive real-time PCR. The incidence of invasive pulmonary aspergillosis (IPA) in these patients included proven IPA in 1 (2.2%), probable IPA in 10 (21.7%), possible IPA in 19 (41.3%) and not IPA in 16 cases (34.8%).

CONCLUSIONS

The incidence of IPA in allogeneic HSCT and patients with hematological malignancies was relatively high and A. flavus was the most common cause of PA. As molecular methods had higher sensitivity, it may be useful as screening methods in HSCT and patients with hematological malignancies, or to determine when empirical antifungal therapy can be withheld.

In vitro susceptibility of dermatomycoses agents to six antifungal drugs and evaluation by fractional inhibitory concentration index of combined effects of amorolfine and itraconazole in dermatophytes

To investigate the antifungal drug susceptibility of fungi responsible for dermatomycoses, minimum inhibition concentration (MIC) tests were performed in 44 strains of dermatophytes, including Trichophyton rubrum, Trichophyton mentagrophytes, Trichophyton verrucosum, Trichophyton tonsurans, Microsporum canis, Microsporum gypseum and Epidermophyton floccosum, with six antifungal drugs (amorolfine, terbinafine, butenafine, ketoconazole, itraconazole and bifonazole) by broth microdilution assay according to Clinical Laboratory Standard Institute protocols. Six possible dermatomycosis-causing non-dermatophytic fungi were also tested. The two major causes of tinea, T. rubrum and T. mentagrophytes, showed significantly different sensitivities to ketoconazole and bifonazole. Clinically derived dermatophytes were sensitive to the six antifungal drugs tested. However, non-dermatophytes, especially Fusarium spp., tended to be resistant to these antifungal drugs. In Trichophyton spp., the MICs of non-azole drugs had narrower distributions than those of azoles. To evaluate the effects of antifungal drug combinations, the fractional inhibitory concentration index was calculated for the combination of amorolfine and itraconazole as representative external and internal drugs for dermatophytes. It was found that this combination had synergistic or additive effects on most dermatophytes, and had no antagonistic effects. The variation in susceptibility of clinically derived fungal isolates indicates that identification of causative fungi is indispensable for appropriately choosing effective antifungal drugs in the early stages of infection. The results of combination assay suggest that multiple drugs with different antifungal mechanisms against growth of dermatophytes should be used to treat refractory dermatomycoses, especially onychomycosis.

A comparative study on morphological versus molecular identification of dermatophyte isolates

OBJECTIVE

Dermatophytes are taxonomically classified in the genera Trichophyton, Microsporum, and Epidermophyton. Pleomorphism, cultural variability, slow growth and sporulation, and the need for additional physiological tests make dermatophytes notoriously difficult to identify. The present study aimed to compare the results of morphological and molecular identification of certain groups of clinical isolates of dermatophytes with a view to evaluating the accuracy of molecular methods.

PATIENTS AND METHODS

For each sample, the ITS1-5.8S-ITS2 rDNA region was amplified using the primers ITS1 and ITS4. PCR products were subjected to restriction fragment length polymorphism (RFLP) analysis using the enzyme MvaI and isolate identification was performed by comparing the electrophoretic RFLP patterns with reference profiles obtained previously. Finally, paired comparative analyses of molecular and conventional methods were performed.

RESULTS

While morphology results from routine daily reports of the laboratories indicated that 18 (6.8%) and 136 (52.10%) of the isolates were T. rubrum and T. interdigitale, respectively, PCR-RFLP results suggested that T. rubrum was the most common etiological agent of ringworm accounting for 94 (36.01%), followed by T. interdigitale accounting for 71 (27.20%). Interestingly, 80.8% out of the 94 isolates identified as T. rubrum by molecular testing had been identified by morphological examination as belonging to different species, such as T. interdigitale (75.5%), E. floccosum (2.1%) and M. canis, T. verrucosum, and T. tonsurans (each 1.06%). Ten strains out of 261 (T. interdigitale, n=8; E. floccosum, n=2) had been defined as unknown species by morphological tests.

CONCLUSION

An unexpected high percent of isolates identified as T. interdigitale by conventional methods were in effect T. rubrum shown by PCR-RFLP, and regarding the necessity of correct identification of dermatophytes recovered from different clinical forms of the infection, we highly recommend ITS-sequencing or ITS-RFLP of the isolates, particularly for epidemiological research studies.

β-D-Glucan Assay in Diagnosis and Monitoring the Systemic Candidiasis in a Rat Model

BACKGROUND

Determination of β-D-Glucan (BDG) in the serum aids to diagnose the invasive fungal infections. The current study evaluated the diagnostic potential value of BDG assay in monitoring the disease in experimental systemic candidiasis in a rat model. The results can provide a useful preliminary data to improve this approach in developing countries.

OBJECTIVES

The present study aimed to evaluate β-D-Glucan assay in diagnosis and monitoring the systemic candidiasis in a rat model.

MATERIALS AND METHODS

Twenty one rats were infected with 10(6) Candida albicans blastospore per rat. Twelve rats were considered as the negative controls (six immunocompromised rats without infection and six intact rats). During a week, every 24 hours the BDG sera level was determined by both Fungitell and Wako kits. To confirm the systemic infection in each rat, the suspensions of their internal organs were cultivated on agar plates and the number of colony forming units (CFU) of C. albicans was counted.

RESULTS

All the infected rats were positive with BDG tests. An increasing level of BDG was observed during early days after injection. The cutoff value for discrimination of BDG positive sera was obtained from the negative sera by the Fungitell kit. The sensitivity, specificity, positive and negative predictive values assessed for the Fungitell kit were 95%, 66.6%, 90.47% and 80%, respectively. These criteria for those of Wako were 90%, 83.3%, 94.7% and 71.4%, respectively.

CONCLUSIONS

While BDG assay seems to be a sensitive and specific adjunctive tool to diagnose and monitor the experimental systemic candidiasis, it seems that measuring the positive cutoff value in different laboratory conditions is necessary for favorable establishment of these tests.

Molecular characterization of Aspergillus infections in an Iranian educational hospital using RAPD-PCR method

OBJECTIVES

The nosocomial infections by Aspergillus species are associated with constructions and increased dust loads in hospital indoors. Our main object was to find the environmental sources of Aspergillus species causing hospital acquired infections.

MATERIALS AND METHODS

The clinical and environmental samplings were performed during 18 months from spring 2010 to summer 2011 in Imam educational hospital, Urmia, Iran. A morphological diagnosis was performed including microscopic characterization of isolated aspergillus from cultured specimens and polymerase chain reaction - restriction fragment length polymorphism (PCR-RFLP) for the identification in the level of species. Random amplified polymorphic DNA - PCR RAPD-PCR using random primers for rDNA gene was performed to compare Aspergillus isolates of clinical cases with the relevant environmental sources.

RESULTS

Use of RAPD method resulted various differential patterns, so that some Aspergillus isolates from the clinical and hospital indoor were completely matched (matched pairs) and some other Aspergillus isolates were not matched. In the case of matched pairs, Aspergillus niger and A. flavus isolated from broncoalveolar lavage and sinus discharge were relevant to those of air conditioner and walls surfaces, respectively.

CONCLUSION

The hospital sources for the Aspergillus clinical isolates included air condition and walls. RAPD-PCR analysis can play a trivial role to find the hospital sources of Aspergillus clinical isolates.

Development of RFLP-PCR method for the identification of medically important Aspergillus species using single restriction enzyme MwoI

In this study we attempted to modify the PCR-RFLP method using restriction enzyme MwoI for the identification of medically important Aspergillus species. Our subjects included nine standard Aspergillus species and 205 Aspergillus isolates of approved hospital acquired infections and hospital indoor sources. First of all, Aspergillus isolates were identified in the level of species by using morphologic method. A twenty four hours culture was performed for each isolates to harvest Aspergillus mycelia and then genomic DNA was extracted using Phenol-Chloroform method. PCR-RFLP using single restriction enzyme MwoI was performed in ITS regions of rDNA gene. The electrophoresis data were analyzed and compared with those of morphologic identifications. Total of 205 Aspergillus isolates included 153 (75%) environmental and 52 (25%) clinical isolates. A. flavus was the most frequently isolate in our study (55%), followed by A. niger 65(31.7%), A. fumigatus 18(8.7%), A. nidulans and A. parasiticus 2(1% each). MwoI enabled us to discriminate eight medically important Aspergillus species including A. fumigatus, A. niger, A. flavus as the most common isolated species. PCR-RFLP method using the restriction enzyme MwoI is a rapid and reliable test for identification of at least the most medically important Aspergillus species.

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

We investigated the resolving power of the beta tubulin protein-coding gene (BT2) for systematic study of dermatophyte fungi. Initially, 144 standard and clinical strains belonging to 26 species in the genera Trichophyton, Microsporum, and Epidermophyton were identified by internal transcribe spacer (ITS) sequencing. Subsequently, BT2 was partially amplified in all strains, and sequence analysis performed after construction of a BT2 database that showed length ranged from approximately 723 (T. ajelloi) to 808 nucleotides (M. persicolor) in different species. Intraspecific sequence variation was found in some species, but T. tonsurans, T. equinum, T. concentricum, T. verrucosum, T. rubrum, T. violaceum, T. eriotrephon, E. floccosum, M. canis, M. ferrugineum, and M. audouinii were invariant. The sequences were found to be relatively conserved among different strains of the same species. The species with the closest resemblance were Arthroderma benhamiae and T. concentricum and T. tonsurans and T. equinum with 100% and 99.8% identity, respectively; the most distant species were M. persicolor and M. amazonicum. The dendrogram obtained from BT2 topology was almost compatible with the species concept based on ITS sequencing, and similar clades and species were distinguished in the BT2 tree. Here, beta tubulin was characterized in a wide range of dermatophytes in order to assess intra- and interspecies variation and resolution and was found to be a taxonomically valuable gene.

Morphological and Genotypic Variations among the Species of the Subgenus Adlerius (Diptera: Psychodidae, Phlebotomus) in Iran

BACKGROUND

Female sand flies of subgenus Adlerius are considered as probable vectors of visceral leishmaniasis in Iran. The objective of this study was to determine the morphological and genotypic variations in the populations of this subgenus in the country.

METHODS

Sand flies collected using sticky traps from 17 provinces during 2008-2010. The morphometric measurements were conducted with an Ocular Micrometer. Data was analyzed by SPSS. The Cytb gene was used to estimate population genetic diversity and identify the female specimens. UPGMA phenetic tree was used for DNA haplotypes of Cytb gene.

RESULTS

Six species of subgenus Adlerius identified from which one species, P. (Adlerius) kabulensis, is new record. The identification key is provided for males. Results revealed the molecular systematic in the species of subgenus Adlerius and determine the relationship of three females of P. comatus, P. balcanicus and P. halepensis.

CONCLUSION

The positions of three females and the males in the UPGMA tree are correct and the similarities among them confirm our results. The branches of each species are not genetically distinct which justify the overlapping morphological characters among them. Molecular sequencing of Cytb-mtDNA haplotypes can be used for female identification for different species of subgenus Adlerius in Iran.

Heterogeneity of the internal transcribed spacer region in Leishmania tropica isolates from southern Iran

Most of cutaneous leishmaniasis cases occur in only 7 countries, including Iran. Leishmania tropica is the main cause of anthroponotic cutaneous leishmaniasis in Iran. In order to study the heterogeneity and phylogeny of L. tropica in southern Iran, a total of 61 isolates were obtained from Bam district and the cities Kerman and Shiraz. The internal transcribed spacer (ITS) from the ribosomal DNA locus was amplified and then analysed by sequencing. Analysis of the ITS sequences showed four haplotypes in the isolates, including 3 haplotypes among the 58 isolates from the south eastern region, including Bam district and Kerman city, and 2 haplotypes among the 3 isolates from Shiraz city. The results showed a monophyletic structure for the south eastern population. In comparison to GenBank sequences of L. tropica from different countries, most of the southeast Iranian and Indian isolates are comprised in one cluster, while isolates from other countries and few other Iranian isolates group in a different cluster. Analysis of ITS sequences of south eastern L. tropica showed a homogeneous population which could be the basis for other molecular epidemiology studies using more discriminative markers and tracing possible changes in the population structure of L. tropica.

Incidence of pulmonary aspergillosis and correlation of conventional diagnostic methods with nested PCR and real-time PCR assay using BAL fluid in intensive care unit patients

BACKGROUND

Although the incidence of invasive aspergillosis in the intensive care unit (ICU) is scarce, it has emerged as major problems in critically ill patients. In this study, the incidence of pulmonary aspergillosis (PA) in ICU patients has evaluated and direct microscopy and culture has compared with nested polymerase chain reaction (PCR) and real-time PCR for detection of Aspergillus fumigatus and A. flavus in bronchoalveolar lavage (BAL) samples of the patients.

METHODS

Thirty BAL samples obtained from ICU patients during a 16-month period were subjected to direct examinations on 20% potassium hydroxide (KOH) and culture on two culture media. Nested PCR targeting internal transcribed spacer ribosomal DNA and TaqMan real-time PCR assay targeting β-tubulin gene were used for the detection of A. fumigatus and A. flavus.

RESULTS

Of 30 patients, 60% were men and 40% were women. The diagnosis of invasive PA was probable in 1 (3%), possible in 11 (37%), and not IPA in 18 (60%). Nine samples were positive in nested PCR including seven samples by A. flavus and two by A. fumigatus specific primers. The lowest amount of DNA that TaqMan real-time PCR could detect was ≥40 copy numbers. Only one of the samples had a positive result of A. flavus real-time PCR with Ct value of 37.5.

CONCLUSIONS

Although a significant number of specimens were positive in nested PCR, results of this study showed that establishment of a correlation between the conventional methods with nested PCR and real-time PCR needs more data confirmed by a prospective study with a larger sample group.

Restriction analysis of β-tubulin gene for differentiation of the common pathogenic dermatophytes

BACKGROUND

Identification of dermatophytes at the species level, relying on macro- and microscopic properties of the colonies is time-consuming, questioned in many circumstances, and requires considerable expertise. In this study, we examined the potency of a new genetic marker, β-tubulin (BT2) gene, for differentiation of dermatophytes in an in silico and experimental restriction fragment length polymorphism (RFLP) profile.

METHODS

The BT2 sequences of dermatophyte species were retrieved from GenBank and analyzed using bioinformatics softwares to choose suitable restriction enzyme(s). Forty reference culture collections and 100 clinical isolates were PCR-amplified using the primers T1 and Bt2b and consequently subjected to virtual RFLP analysis. The dermatophytes were identified according to specific lengths of bands in agarose gel electrophoresis.

RESULTS

After digestion of partially amplified β-tubulin gene with the restriction enzyme FatI, three dermatophyte species, that is, Microsporum gypseum, M. canis, and Trichophyton verrucosum yielded unique restriction maps while the remaining species including T. interdigitale, T. rubrum, T. tonsurans, T. schoenleinii, and T. violaceum, were identified by further restriction digestion by Alw21I, MwoI, and HpyCH4V endonucleases. The length of RFLP products was same as of those expected by computer analysis.

CONCLUSION

The two-step BT2 restriction mapping used in this study is an effective tool for reliable differentiation of the clinically relevant species of dermatophytes.

Rapid monitoring of Pseudomonas aeruginosa in hospital water systems: a key priority in prevention of nosocomial infection

Pseudomonas aeruginosa has emerged as a major pathogen in nosocomial infections. Biofilm formation allows the microorganism to persist in hospital water systems for extended periods, which have been associated with nosocomial infections. The aim of this study was to evaluate the frequency of P. aeruginosa colonization of hospital tap waters by nested PCR assay. A total of 44 water samples were collected from 11 hospitals and analyzed for the presence of Pseudomonas spp. and P. aeruginosa by specific primer sets of 16S rRNA gene. Some physicochemical parameters and heterotrophic plate count (HPC) of samples for possible association with P. aeruginosa contamination were also determined. The nested PCR revealed 32% of the water samples being positive for P. aeruginosa. From the 11 hospitals surveyed, 82% (9 of 11) of the hospitals water systems were positive for P. aeruginosa. No correlation was seen between the presence of P. aeruginosa and HPC as well as physicochemical parameters. Identification of contaminated sources could be a key priority in waterborne nosocomial infections. PCR assay was used in the study provides simple, rapid, and reliable identification of P. aeruginosa in hospital water systems, which could eliminate the infections of P. aeruginosa through implementation of immediate control measures.

Investigation of Double-Band Electrophoretic Pattern of ITS-rDNA Region in Iranian Isolates of Leishmania tropica

BACKGROUND

Leishmania tropica is a genetically divergent species. Amplification of entire internal transcribed spacer (ITS) region of L. tropica isolates obtained from Bam district, one of the well known focus of anthroponotic cutaneous leishmaniasis (ACL) in Iran, revealed a double-band pattern in agarose gel electrophoresis. This study explains how this pattern occurs.

METHODS

Twenty seven L. tropica smear preparations were collected from Bam district, south east Iran, and eight L. major and one L. infantum smear preparations were gathered from Shiraz, south west Iran. Furthermore one L. major and one L. infantum cultured standard strains were tested using entire ITS-PCR to survey their electrophoretic pattern. The ITS sequences of L. tropica, L. major, and L. infantum already deposited in GenBank were analyzed. Analysis of GenBank sequences of L. tropica revealed two groups of sequences based on length size, one group having a 100 bp gap. Therefore, a new reverse primer namely LITS-MG was designed to exclude this gap in PCR products.

RESULTS

Whole ITS fragment amplification resulted in a double-band pattern in all L. tropica cases, while a sharp single band was observed for L. infantum and L. major isolates. This result was corresponding to the result obtained from in silico analysis of GenBank sequences. Use of LITS-MG primer was expectedly resulted in a single band including ITS1, 5.8s and partial ITS2 product for L. tropica which is appropriate for following molecular studies such as sequencing or restriction analysis.

CONCLUSION

Sequences analysis of GenBank L. tropica sequences and following practical laboratory tests revealed at least two alleles in L. tropica which were confirmed in Bam isolates. This especial double-band pattern is because of a 100 bp fragment difference within ITS-rDNA alleles.

Candida species in cutaneous candidiasis patients in the Guilan province in Iran; identified by PCR-RFLP method

Due to the epidemiological alteration in distribution of Candida species as well as significant increasing trend of either intrinsic or acquired in resistance of some of these fungi, the precise identification of Candida species is necessary for effective antifungal therapy and also for prevention of nosocomial infections. PCR-RFLP method is indicated to be a reliable, rapid and simple technique which is able to differentiate the Candida species. In the present study, we applied this method to evaluate the distribution of Candida species in patients affected with cutaneous candidiasis in the Guilan province. 896 clinical cutaneous samples were collected from different parts of skin and nail of suspected patients referred to clinical centers all over the Guilan province during 24 months. Samples were examined directly with 15% KOH and cultured on fungal specific media. Genomic DNA was extracted and the restriction enzyme Msp1 was applied for polymorphism analysis. Totally, 47 yeast strains were successfully isolated from different clinical samples and identified by conventional as well as PCR-RFLP methods. The results indicated that Candida albicans (36.17%) was the most frequent species followed by C. parapsilosis (25.53%), C. tropicalis (19.14%), C. guilliermondii (14.89%), C. famata (2.12%) and C. krusei (2.12%). Female finger nails were the most common location to be affected by Candida species. In conclusion, PCR-RFLP method was successfully used for recognition of clinical Candida species within the Guilan province and obtained results revealed C. albicans as the predominant causative agent of cutaneous candidiasis. However, distribution of other Candida species did not completely consist with the reported distribution of Candida species in other parts of Iran with different climate to the Guilan province.

In-vitro Activity of 10 Antifungal Agents against 320 Dermatophyte Strains Using Microdilution Method in Tehran

Dermatophyte fungi are the etiologic agents of skin infections commonly referred to as ringworm. These infections are not dangerous but as a chronic cutaneous infections they may be difficult to treat and can also cause physical discomfort for patients. They are considered important as a public health problem as well. No information is available regarding the efficacy of antifungal agents against dermatophytes in Tehran. Therefore, in this study we evaluated the efficacy of 10 systemic and topical antifungal medications using CLSI broth microdilution method (M38-A). The antifungal agents used included griseofulvin, terbinafine, itraconazole, ketoconazole, fluconazole, voriconazole, clotrimazole, ciclopirox olamine, amorolfine and naftifine.Fifteen different species of dermatophytes which were mostly clinical isolates were used as follows; T. mentagrophytes, T. rubrum, E. floccosum, M. canis, T. verrucosum, T. tonsurans, M. gypseum, T. violaceum, M. ferruginum, M. fulvum, T. schoenleinii, M. racemosum, T. erinacei, T. eriotrephon and Arthroderma benhamiae. The mean number of fungi particles (conidia) inoculated was 1.25 ×10⁴ CFU/mL. Results were read after 7 days of incubation at 28 °C. According to the obtained results,itraconazole and terbinafine showed the lowest and fluconazole had the greatest MIC values for the most fungi tested. Based on the results, it is necessary to do more research and design a reliable standard method for determination of antifungal susceptibility to choose proper antibiotics with fewer side effects and decrease antifungal resistance and risk of treatment failure.

Ultraviolet irradiation: An effective inactivation method of Aspergillus spp. in water for the control of waterborne nosocomial aspergillosis

Invasive aspergillosis is the second most common cause of nosocomial fungal infections and occurring mainly by Aspergillus fumigatus, Aspergillus flavus, and Aspergillus niger. There is evidence that nosocomial aspergillosis may be waterborne. This study was conducted to evaluate the ultraviolet (UV) irradiation efficiency in terms of inactivating the most important Aspergillus species in water since these are potential sources for nosocomial aspergillosis. A continuous flow UV reactor which could be used as a point-of-use (POU) system was used to survey Aspergillus inactivation by UV irradiation. The inactivation efficiency of UV fluence (4.15-25 mJ/cm(2)) was measured by determination of fungal density in water before and after radiation. Because turbidity and iron concentration are two major water quality factors impacting UV disinfection effectiveness, the potential influence of these factors on UV inactivation of Aspergillus spp. was also measured. The 4 log inactivation for A. fumigatus, A. niger and A. flavus at a density of 1000 cfu/ml was achieved at UV fluences of 12.45 mJ/cm(2), 16.6 mJ/cm(2) and 20.75 mJ/cm(2), respectively. The inactivation efficiency for lower density (100 cfu/ml) was the same as for the higher density except for A. flavus. The removal efficiency of Aspergillus spp. was decreased by increasing the turbidity and iron concentration. UV disinfection could effectively inactivate Aspergillus spores from water and eliminate potential exposure of high-risk patients to fungal aerosols by installation of POU UV systems.

First case of disseminated phaeohyphomycosis in an immunocompetent individual due to Alternaria malorum

A 27-year-old Iranian, previously healthy male presented with sub-cutaneous necrotic lesions with a localized dermatosis affecting the anterior chest, neck and face. These lesions consisted of singular, well-defined verrucous plaques which gradually developed and disseminated over time. The dermatosis was followed by the development of necrotic swollen lesions localized on the hard palate. The patient did not recall any history of trauma or puncture at any of the sites of infection. While histopathological examination of periodic acid-Schiff (PAS) stained material revealed irregular, unbranched, septate hyphae, direct examination (KOH 10%) of lesion samples demonstrated the presence of septate indistinct brownish hyphae. Alternaria malorum was isolated (CBS 126589) and its identity was confirmed by sequencing of the internal transcribed spacer (ITS rDNA). Since the palate lesion reoccurred after 10 years and the patient's condition did not improve with amphotericin B combination therapy, the lesion was surgical excised and he underwent antifungal therapy with amphotericin B and itraconazole. There was no dehiscence or fistula formation or any evidence of relapse of fungal infection during a one year follow-up and the patient was successfully cured. In vitro antifungal susceptibility tests revealed that the MIC values for those antifungals employed in this case were amphotericin B (0.125 μg/ml), fluconazole (32 μg/ml), itraconazole (0.125 μg/ml), voriconazole (1 μg/ml), and posaconazole (0.063 μg/ml). The MECs for caspofungin and anidulafungin were 0.25 μg/ml and 0.016 μg/ml, respectively. However, treatment of A. malorum infections with the latter agents remains to be evaluated.

Mycological Microscopic and Culture Examination of 400 Bronchoalveolar Lavage (BAL) Samples

BACKGROUND

The frequency of invasive opportunistic mycoses has increased significantly over the past decades especially in immunocompromised patients. Invasive aspergillosis (IA) has become a major cause of morbidity and mortality among these patients. As bronchoalveolar lavage (BAL) fluid samples are generally useful specimens in the diagnosis of invasive pulmonary aspergillosis (IPA), this study was designed to evaluate the incidence of fungal elements in at-risk patients by direct microscopy and culture of BAL samples.

METHODS

In a 16-month period, 400 BAL samples were obtained from several groups of different patients with pulmonary and respiratory disorders and examined by using both direct microscopy and culture.

RESULTS

Of the 400 samples, 16 (4%) were positive direct examination with branching septate hyphae and 46 (11.5%) were positive culture: 25 (54%) Aspergillus flavus, 6 (13%) A. fumigatus, 5 (10.9%) A. niger, 1 (2.2%) A. terreus, 3 (6.5%) Penicillium spp. and 6 (13%) mixed A. flavus/A. niger. A. flavus was the most common cause of Aspergillus infection or colonization. Bone marrow transplant (BMT) recipients were the most susceptible group to fungal infection and/or colonization.

CONCLUSION

Among Aspergillus species, A. flavus was the most common isolate in both infections and colonization in Iran. More studies are needed to clarify the epidemiological aspect of aspergillosis in Iran.

A case report of tinea pedis caused by Trichosporon faecale in Iran

Trichosporon species are known as the causative agents of cutaneous infections and are involved in systemic, localized, as well as disseminated mycoses particularly in immunocompromised patients. Here we report a case of tinea pedis infection caused by Trichosporon faecale in a healthy 29-year-old woman in the north of Iran. Macroscopic and microscopic characteristics using direct examination as well as culture method revealed the causative agent as Trichosporon species. Molecular analysis of the internal transcribed spacer region validated the initial result and indicated that this case of tinea pedis was caused by T. faecale. The patient was recovered after treatment with topical myconazole accompanied with oral fluconazole.

Use of Single-enzyme PCR-restriction Digestion Barcode Targeting the Internal Transcribed Spacers (ITS rDNA) to Identify Dermatophyte Species

BACKGROUND

Dermatophytes are the most common causative agents of superficial mycoses. Species identification of these fungi is important from therapeutic and epidemiological point of wive. Traditional approaches for identification of dermatophytes at the species level, relying on macroscopic and microscopic features of the colonies, usually are time-consuming and unreliable in many circumstances. Recently a broad varieties of rapid and accurate DNA-based techniques were successfuly utilized for species delineation of dermatophytes.

METHODS

The ITS1-5.8S-ITS2 region of rDNA from various reference strains of dermatophyte species were amplified using the universal fungal primers ITS1 and ITS4.The PCR products were digested by a single restriction enzyme, MvaI. The enzyme was evaluated in both in silico and practical PCR-RFLP assay to find the exact differentiating restriction profiles for each species. To validate the standardized PCR-RFLP system, all tested strains were subjected to sequencing and sequence analysis.

RESULTS

The obtained RFLP patterns were specific for many species including T. interdigitale, T. rubrum, T. violaceum, M. persicolor, M. audouinii, M. nanum (A. obtusum) and E. floccosum but were similar for some closely related species such as M. canis / M. ferrugineum. Sequencing of the ITS1-5.8S-ITS2 fragment from all type strains affirmed the RFLP findings.

CONCLUSION

It was practically revealed that the ITS-PCR followed by MvaI-RFLP is a useful and reliable schema for identification and differentiation of several pathogenic species and can be used for rapid screening of even closely related species of dermatophytes in clinical and epidemiological settings.

Sequence Analysis of the Second Internal Transcribed Spacer (ITS2) Region of rDNA for Species Identification of Trichostrongylus Nematodes Isolated From Domestic Livestock in Iran

BACKGROUND

Infectivity of herbivores with Trichostrongylus nematodes is widespread in many countries, having a major economic impact on breeding, survivability, and productivity of domestic livestock. This study was carried out on Trichostrongylus species isolated from domestic livestock in order to develop an easy-to-perform method for species identification.

METHODS

Trichostrongylus isolates were collected from sheep, goat, cattle, and buffaloes in Khuzestan Province, southwest Iran. Primary species identification was carried out based on morphological characterization of male worms. PCR amplification of ITS2-rDNA region was performed on genomic DNA and the products were sequenced. Phylogenetic analysis of the nucleotide sequence data was conducted employing Bayesian Inference approach. Consequently, a restriction fragment length polymorphism (RFLP) profile was designed to differentiate Trichostrongylus species.

RESULTS

A consensus sequence of 238 nucleotides was deposited in the GenBank for Iranian isolates of Trichostrongylus species including T. colubriformis, T. capricola, T. probolurus and T. vitrinus. The designated RFLP using restriction enzyme TasI could readily differentiate among species having different ITS2 sequence. The molecular analysis was in concordance with morphological findings.

CONCLUSION

Phylogenetic analysis indicated a close relationship among the sequences obtained in this study and reference sequence of relevant species. ITS2-RFLP with TasI is recommended for molecular differentiation of common Trichostrongylus species.

Morphological and morphometrical description of trichostrongylus species isolated from domestic ruminants in khuzestan province, southwest iran

BACKGROUNDS

Genus Trichostrongylus (Nematoda: Trichostrongylidae) is one of the most important zoonotic nematodes with wide geographic distribution in the world. The purpose of the present study was to describe morphological and morphometrical characteristics of male Trichostrongylus species, currently prevalent in domestic ruminants of Khuzestan Province, southwest Iran.

METHODS

Gastro-intestinal organs of 1600 sheep, goats, cattle, and buffalos, slaughtered in Khuzestan Province, southwest Iran, were examined for infectivity with Trichostrongylus species. For examination and measurements of helminthes, Azo-carmine staining was performed, followed by camera lucida drawings of morphological characters and measurements of morphometrical criteria with a calibrated microscope. Using valid nematodes systematic keys, almost all the parasites were identified at the level of species.

RESULTS

Overall, 114 animals were found infected with at least one species of Trichostrongylus. Considering morphological characteristics of male Trichostrongylus, six species were identified including T. colubriformis, T. vitrinus, T. probolorus, T. capricola, T. longispicularis and Trichostrongylus sp.

CONCLUSION

Although, compared to the previous decades, currently Trichostrongylus is much less prevalent in the domestic ruminants of the study area, but still different species occur in these animals.

Molecular Diagnosis of Strongyloides stercoralis Infection by PCR Detection of Specific DNA in Human Stool Samples

BACKGROUND

Strongyloidiasis is mostly an asymptomatic infection and diagnosis of latent infections is difficult due to limitations of current parasitological and serological methods. This study was conducted to set up a PCR-based method for molecular diagnosis of Strongyloides stercoralis infection by detection of copro-DNA in stool samples.

METHODS

A total of 782 fresh stool samples were collected and examined by agar plate culture. Among those sixteen stool samples, which confirmed to be infected with S. stercoralis were examined as positive control to set up each single and nested PCR, using two primer sets designing to amplify partial ribosomal DNA of S. stercoralis genome. Since, single PCR method yielded higher efficacy in detecting positive samples, in the second step, 30 stool samples, which found negative for S. stercoralis by agar plate culture of single stool sample, were examined by single PCR. Data analysis was performed using McNemar's χ(2) test, with consideration of a P-value of <0.05 as indication of significant difference.

RESULTS

In amplification of DNA extracted from stool samples, single PCR detected S. stercoralis DNA target in all 16 positive samples, while nested PCR amplified DNA in only 75% of samples. In the second step, single PCR amplified S. stercoralis extracted DNA in 5 out of 30 samples which were negative by coproculture.

CONCLUSION

Single PCR method amplifying a short (100bp) target represented more efficacies for detection of S. stercoralis in faecal examination compared to agar plate culture and nested PCR, which amplified longer target.

Differentiation of Candida glabrata, C. nivariensis and C. bracarensis based on fragment length polymorphism of ITS1 and ITS2 and restriction fragment length polymorphism of ITS and D1/D2 regions in rDNA

Different molecular methods for the discrimination of Candida glabrata, C. bracarensis and C. nivariensis were evaluated and the prevalence of these species among Danish blood isolates investigated. Control strains were used to determine fragment length polymorphism in the ITS1, ITS2, ITS1-5.8S-ITS2 regions and in the D1/D2 domain of 26S rDNA using primers designed for this study. A total of 133 blood isolates previously identified as C. glabrata were examined by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and the peptide nucleic acid-fluorescent in situ hybridization (PNA-FISH) method. The size of ITS1 allowed differentiation between C. glabrata (483), C. nivariensis (361) and C. bracarensis (385), whereas the ITS2 region was of similar size in C. nivariensis (417) and C. glabrata (418). Sequence analysis of the ITS region suggested that many restriction enzymes were suitable for RFLP differentiation of the species. Enzymatic digestion of the D1/D2 domain with TatI produced unique band sizes for each of the three species. PCR-RFLP and PNA-FISH were in agreement for all of the isolates tested. None of the 133 Danish blood isolates were C. nivariensis or C. bracarensis. Fragment size polymorphism of ITS1 and RFLP of the D1/D2 domain or the ITS region are useful methods for the differentiation of the species within the C. glabrata group. C. bracarensis and C. nivariensis are rare among Danish C. glabrata blood isolates.

Preliminary Identification and Typing of Pathogenic and Toxigenic Fusarium Species Using Restriction Digestion of ITS1-5.8S rDNA-ITS2 Region

BACKGROUND

Fusarium species are capable of causing a wide range of crop plants infections as well as uncommon human infections. Many species of the genus produce mycotoxins, which are responsible for acute or chronic diseases in animals and humans. Identification of Fusaria to the species level is necessary for biological, epidemiological, pathological, and toxicological purposes. In this study, we undertook a computer-based analysis of ITS1-5.8SrDNA-ITS2 in 192 GenBank sequences from 36 Fusarium species to achieve data for establishing a molecular method for specie-specific identification.

METHODS

Sequence data and 610 restriction enzymes were analyzed for choosing RFLP profiles, and subsequently designed and validated a PCR-restriction enzyme system for identification and typing of species. DNA extracted from 32 reference strains of 16 species were amplified using ITS1 and ITS4 universal primers followed by sequencing and restriction enzyme digestion of PCR products.

RESULTS

The following 3 restriction enzymes TasI, ItaI and CfoI provide the best discriminatory power. Using ITS1 and ITS4 primers a product of approximately 550bp was observed for all Fusarium strains, as expected regarding the sequence analyses. After RFLP of the PCR products, some species were definitely identified by the method and some strains had different patterns in same species.

CONCLUSION

Our profile has potential not only for identification of species, but also for genotyping of strains. On the other hand, some Fusarium species were 100% identical in their ITS-5.8SrDNA-ITS2 sequences, therefore differentiation of these species is impossible regarding this target alone. ITS-PCR-RFLP method might be useful for preliminary differentiation and typing of most common Fusarium species.

Leishmania species: detection and identification by nested PCR assay from skin samples of rodent reservoirs

Many rodent species act as reservoir hosts of zoonotic cutaneous leishmaniasis in endemic areas. In the present study a simple and reliable assay based on nested PCR was developed for the detection and identification of Leishmania parasites from rodent skin samples. We designed Leishmania-specific primers that successfully amplified ITS regions of Leishmania major, Leishmania gerbilli and Leishmania turanica using nested PCR. Out of 95 field collected Rhombomys opimus, 21 were positive by microscopic examination and 48 by nested PCR. The percentage of gerbils infected with L. major, L. gerbilli and L. turanica was 3.2%, 1.1% and 27.4%, respectively. In 15.8% of the rodents, we found mixed natural infections by L. major and L. turanica, 1.1% by L. major and L. gerbilli, and 2.1% by the three species. We concluded that this method is simple and reliable for detecting and identifying Leishmania species circulating in rodent populations.

Sequence analysis of cox1 and nad1 genes in Echinococcus granulosus G3 genotype in camels (Camelus dromedarius) from central Iran

Nineteen hydatid cyst isolates collected from camels in central Iran were subjected to sequences analysis of mitochondrial cytochrome c oxidase subunit 1 (cox1) and NADH dehydrogenase subunit 1 (nad1) genes. A consensus sequence obtained containing 366 nucleotides for cox1 and 471 nucleotides for nad1 genes. Overall, the camel isolates indicated five different sequences in cox1 and nine in nad1 genes. The sequences analysis indicated that 26.3%, 42.1%, and 31.6% of isolates belonging to G1, G3, and G6 genotypes of Echinococcus granulosus, respectively. The isolates with G3 genotype indicated one cox1 sequence having 100% homology with reference G3 sequence (AN: M84663) and two different nad1 sequences, one having 100% homology with reference G3 sequence (AN: AJ237634) and the other with a silent mutation (G to A) in position 279. The presence of G3 genotype (buffalo strain) of E. granulosus as dominant genotype in camels is emphasized. As G3 genotype has formerly been reported in human, the epidemiological role of camels is warranted in future surveys.

Dynamics of Leishmania infection rates in Rhombomys opimus (Rodentia: Gerbillinae) population of an endemic focus of zoonotic cutaneous leishmaniasis in Iran

Zoonotic cutaneous leishmaniasis (ZCL) due to Leishmania major is a great public health problem in the Old World. Leishmania major is widely distributed in populations of rodents in arid and savannah regions. In this study, seasonal variation of natural infection with Leishmania parasites in Rhombomys opimus (Rodentia: Gerbillinae) population of an endemic focus of ZCL in Iran was monitored. The study was conducted from October 2007 to October 2008 in the central part of the country. Nested polymerase chain reaction (PCR) assay was used for the detection and identification of Leishmania parasites, and the results were confirmed by PCR-restriction fragment length polymorphism (RFLP). The results showed that Leishmania infection rate was 55.8% (29 out of 52 gerbils) using nested PCR. The highest and lowest Leishmania infection rates were observed in fall and summer, respectively. Gerbils that were found to be infected only with L. major were 5.8%, and that with Leishmania turanica were 23.1%. A mixed natural infection was seen in the rodents with L. major and L. turanica (21.2%), with L. major and L. gerbilli (1.9%), and with all the three species (3.9%). Leishmania major infection alone was seen in fall and winter whereas mixed infection of L. major and L. turanica was observed in all seasons except in summer. Leishmania turanica infection was observed throughout the year. It is concluded that L. major, L. gerbilli, and L. turanica circulate in the population of R. opimus in central part of Iran. Leishmania major infection is usually accompanied by L. turanica in naturally infected gerbils with the highest rate in fall. It is recommended that the role of L. turanica in the epidemiology and transmission of ZCL should be reconsidered.

Molecular epizootiology of rodent leishmaniasis in a hyperendemic area of iran

BACKGROUND

Zoonotic cutaneous leishmaniasis (ZCL) is an expanding disease and public health problem in Iran. In the current study, natural Leishmania infection rate and seasonal fluctuation of the infection in Rhombomys opimus population of a hyperendemic focus of ZCL in Iran was investigated.

METHODS

The study was conducted from October 2006 to October 2008 in Esfahan Province, central part of Iran. An extensive sampling of rodents using Sherman traps was done in different seasons. Nested PCR assay was used for detection and identification of Leishmania species and the results were confirmed using PCR-RFLP.

RESULTS

Leishmania infection rate was 58.6% (34 of 58) using nested PCR. 44.8% of the gerbils were infected only with L. turanica and 1.7% with L. gerbilli alone. A mixed natural infection with L. major and L. turanica was seen in 12.1% of the rodents. L. major infection alone was not seen in R. opimus population in the study area. The highest and lowest Leishmania infection rates were observed in fall and spring respectively. L. turanica infection was observed throughout the year whereas mixed infections with L. major and L. turanica was not seen in spring.

CONCLUSION

It is concluded that in the study area, L. major, L. gerbilli and L. turanica circulate in the population of R. opimus. Leishmania major infection usually accompanied by L. turanica in naturally infected gerbils with the highest rate in fall. It is recommended that the role of L. turanica in the epidemiology and transmission of ZCL be revisited.

Molecular screening for Candida orthopsilosis and Candida metapsilosis among Danish Candida parapsilosis group blood culture isolates: proposal of a new RFLP profile for differentiation

Candida orthopsilosis and Candida metapsilosis are recently described species phenotypically indistinguishable from Candida parapsilosis . We evaluated phenotyping and molecular methods for the detection of these species among 79 unique blood culture isolates of the C. parapsilosis group obtained during the years 2004-2008. The isolates were screened by PCR amplification of the secondary alcohol dehydrogenase-encoding gene ( SADH) followed by digestion with the restriction enzyme Ban I, using C. parapsilosis ATCC 22019, C. orthopsilosis ATCC 96139 and C. metapsilosis ATCC 96144 as controls. Isolates with RFLP patterns distinct from C. parapsilosis were characterized by sequence analysis of the ITS1-ITS2, 26S rRNA (D1/D2) and SADH regions. Restriction patterns for the 3 species with each of 610 restriction enzymes were predicted in silico using 12 available sequences. By PCR-RFLP of the SADH gene alone, four isolates (5.1 %) had a pattern identical to the C. orthopsilosis reference strain. Sequence analysis of SADH and ITS (internal transcribed spacer) regions identified two of these isolates as C. metapsilosis. These results were confirmed by creating a phylogenetic tree based on concatenated sequences of SADH, ITS and 26S rRNA gene sequence regions. Optimal differentiation between C. parapsilosis, C. metapsilosis and C. orthopsilosis was predicted using digestion with NlaIII, producing discriminatory band sizes of: 131 and 505 bp; 74, 288 and 348 bp; and 131, 217 and 288 bp, respectively. This was confirmed using the reference strains and 79 clinical isolates. In conclusion, reliable discrimination was obtained by PCR-RFLP profile analysis of the SADH gene after digestion with NlaIII but not with BanI. C. metapsilosis and C. orthopsilosis are involved in a small but significant number of invasive infections in Denmark.

Identification and differentiation of Fasciola hepatica and Fasciola gigantica using a simple PCR-restriction enzyme method

Accurate morphological differentiation between the liver fluke species Fasciola hepatica and Fasciola gigantica is difficult. We evaluated PCR-restriction enzyme profiles of internal transcribed spacer 1 (ITS1) that could aid in their identification. Fifty F. hepatica and 30 F. gigantica specimens were collected from different hosts in three provinces of Iran. For DNA extraction, we crushed fragments of the worms between two glass slides as a new method to break down the cells. DNA from the crushed materials was then extracted with a conventional phenol-chloroform method and with the newly developed technique, commercial FTA cards. A primer pair was selected to amplify a 463-bp region of the ITS1 sequence. After sequencing 14 samples and in silico analysis, cutting sites of all known enzymes were predicted and TasI was selected as the enzyme that yielded the most informative profile. Crushing produced enough DNA for PCR amplification with both the phenol-chloroform and commercial FTA card method. The DNA extracted from all samples was successfully amplified and yielded a single sharp band of the expected size. Digestion of PCR products with TasI allowed us to distinguish the two species. In all samples, molecular identification was consistent with morphological identification. Our PCR-restriction enzyme profile is a simple, rapid and reliable method for differentiating F. hepatica and F. gigantica, and can be used for diagnostic and epidemiological purposes.

A case of fatal strongyloidiasis in a patient with chronic lymphocytic leukemia and molecular characterization of the isolate

Strongyloides stercoralis is a human intestinal parasite which may lead to complicated strongyloidiasis in immunocompromised. Here, a case of complicated strongyloidiasis in a patient with chronic lymphocytic leukemia is reported. Presence of numerous S. stercoralis larvae in feces and sputum confirmed the diagnosis of hyperinfection syndrome in this patient. Following recovery of filariform larvae from agar plate culture of the stool, the isolate was characterized for the ITS1 region of ribosomal DNA gene by nested-PCR and sequencing. Albendazole therapy did not have cure effects; and just at the beginning of taking ivermectin, the patient died. The most important clue to prevent such fatal consequences is early diagnosis and proper treatment.

Molecular analysis of Malassezia species isolated from hospitalized neonates

Malassezia species are a part of the skin microflora of neonates. Under certain circumstances, they can cause diseases ranging from simple pustulosis to lifethreatening fungemia in newborn infants. Little information is available about the epidemiology of Malassezia species in neonates. In the present study, we successfully isolated Malassezia yeasts from 68.7% of hospitalized neonates. Using the polymerase chain reaction-restriction fragment length polymorphism method (PCR-RFPL), M. furfur (88.06%) was identified as the most isolated species, followed in frequency by M. globosa (10.48%), M. obtusa (0.73%), and M. slooffiae (0.73%). Among the variables studied, only a longer stay in the ward resulted in a higher colonization rate. Using multiple logistic regression, only the type of hospital and ward had some effects on the colonization rate. Our results supported the hypothesis that neonates acquire Malassezia flora through direct contact with their mothers or hospital personnel.

A one-enzyme PCR-RFLP assay for identification of six medically important Candida species

Early identification of Candida isolates to the species level is necessary for effective antifungal therapy, and can also facilitate control of hospital infections. Phenotype-based methods for identifying Candida species are often difficult and time-consuming. Molecular biological techniques provide a useful alternative approach. In the present study, the ITS1-5.8S-ITS2 regions of fungal rRNA genes were amplified with universal primers in 20 standard strains. Digestion of the PCR products with one restriction enzyme, MspI, allowed discrimination of medically important Candida species, including C. albicans, C. glabrata, C. parapsilosis, C. tropicalis, C. krusei, and C. guilliermondii. Using this method, we successfully identified 137 clinical isolates of Candida. Among them, C. albicans was identified as the most common species, followed by C. parapsilosis, C. tropicalis, C. glabrata, C. krusei, and C. guilliermondii. This method is a simple, rapid, and cost-effective method for differentiation between species that is applicable in clinical laboratories.

Rapid identification of Trichophyton tonsurans by specific PCR based on DNA sequences of nuclear ribosomal internal transcribed spacer (ITS) 1 region

BACKGROUND

Trichophyton tonsurans, a dermatophyte implicated in an international epidemic of tinea capitis, was also found to be responsible for infecting wrestling and Judo athletes nationwide in Japan since 2001.

OBJECTIVE

A rapid and highly accurate means of identifying this pathogen has been required to control the infection. We have developed a T. tonsurans-specific PCR method based on the DNA sequences of the nuclear ribosomal internal transcribed spacer 1 region.

SUBJECTS

Eighteen species of six genera of standard strains and 75 strains of clinically isolated Trichophyton species were used in this study.

METHODS

A T. tonsurans-specific PCR primer pair (tonsF1 and tonsR1) was designed on the nuclear ribosomal internal transcribed spacer 1 region, located between 18S and 5.8S rDNA. Fungal DNA was extracted from the colonies grown on culture plates, and the specificity of the PCR primers was tested.

RESULTS

The specific PCR product was amplified from the standard strain of T. tonsurans and from five strains isolated from black dot ringworms, but there was no band from the 70 clinical isolates of other Trichophyton species. This T. tonsurans-specific PCR method was able to detect 10 pg of T. tonsurans genomic DNA with ethidium bromide staining.

CONCLUSIONS

A PCR identification system specific for T. tonsurans is rapid, sensitive, and specific.

Differentiation of Candida albicans and Candida dubliniensis using a single-enzyme PCR-RFLP method

Candida dubliniensis is a novel Candida spp. that is similar to Candida albicans with respect to several phenotypic characteristics. However, they differ from each other with respect to epidemiology, pathogenesis, and the rapid development of resistance to fluconazole. In the present study, we used a single-enzyme PCR-restriction fragment length polymorphism (RFLP) technique to differentiate C. dubliniensis from C. albicans. The amplified ITS region of C. dubliniensis was digested once using the enzyme B1nI, whereas that of C. albicans remained intact. All standard strains tested were identified successfully by this method. None of 140 clinical isolates identified morphologically as C. albicans were recognized as C. dubliniensis based on their PCR-RFLP pattern. Our PCR-RFLP method easily differentiated C. dubliniensis from C. albicans, and this result was also demonstrated with standard strains.

A simple PCR-RFLP method for identification and differentiation of 11 Malassezia species

A PCR-RFLP method targeted toward 26S rDNA and with 2 restriction enzymes, CfoI and BstF51, was developed to identify 11 Malassezia species. Not only type and standard strains but also 13 clinical isolates were identified successfully in this study. The results of identifications were confirmed by DNA sequencing.