1
|
Anton A, Plinet M, Peyret T, Cazaudarré T, Pesant S, Rouquet Y, Tricoteaux MA, Bernier M, Bayette J, Fournier R, Marguerettaz M, Rolland P, Bayol T, Abbaoui N, Berry A, Iriart X, Cassaing S, Chauvin P, Bernard E, Fabre R, François JM. Rapid and Accurate Diagnosis of Dermatophyte Infections Using the DendrisCHIP ® Technology. Diagnostics (Basel) 2023; 13:3430. [PMID: 37998565 PMCID: PMC10670032 DOI: 10.3390/diagnostics13223430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/03/2023] [Accepted: 11/08/2023] [Indexed: 11/25/2023] Open
Abstract
Dermatophytosis is a superficial fungal infection with an ever-increasing number of patients. Culture-based mycology remains the most commonly used diagnosis, but it takes around four weeks to identify the causative agent. Therefore, routine clinical laboratories need rapid, high throughput, and accurate species-specific analytical methods for diagnosis and therapeutic management. Based on these requirements, we investigated the feasibility of DendrisCHIP® technology as an innovative molecular diagnostic method for the identification of a subset of 13 pathogens potentially responsible for dermatophytosis infections in clinical samples. This technology is based on DNA microarray, which potentially enables the detection and discrimination of several germs in a single sample. A major originality of DendrisCHIP® technology is the use of a decision algorithm for probability presence or absence of pathogens based on machine learning methods. In this study, the diagnosis of dermatophyte infection was carried out on more than 284 isolates by conventional microbial culture and DendrisCHIP®DP, which correspond to the DendrisCHIP® carrying oligoprobes of the targeted pathogens implicated in dermatophytosis. While convergence ranging from 75 to 86% depending on the sampling procedure was obtained with both methods, the DendrisCHIP®DP proved to identify more isolates with pathogens that escaped the culture method. These results were confirmed at 86% by a third method, which was either a specific RT-PCR or genome sequencing. In addition, diagnostic results with DendrisCHIP®DP can be obtained within a day. This faster and more accurate identification of fungal pathogens with DendrisCHIP®DP enables the clinician to quickly and successfully implement appropriate antifungal treatment to prevent the spread and elimination of dermatophyte infection. Taken together, these results demonstrate that this technology is a very promising method for routine diagnosis of dermatophytosis.
Collapse
Affiliation(s)
- Aurore Anton
- Dendris SAS, 335 Rue du Chêne Vert, 31670 Labège, France; (M.P.); (T.P.); (T.C.); (S.P.); (E.B.); (R.F.); (J.-M.F.)
| | - Mathilde Plinet
- Dendris SAS, 335 Rue du Chêne Vert, 31670 Labège, France; (M.P.); (T.P.); (T.C.); (S.P.); (E.B.); (R.F.); (J.-M.F.)
| | - Thomas Peyret
- Dendris SAS, 335 Rue du Chêne Vert, 31670 Labège, France; (M.P.); (T.P.); (T.C.); (S.P.); (E.B.); (R.F.); (J.-M.F.)
| | - Thomas Cazaudarré
- Dendris SAS, 335 Rue du Chêne Vert, 31670 Labège, France; (M.P.); (T.P.); (T.C.); (S.P.); (E.B.); (R.F.); (J.-M.F.)
| | - Stéphanie Pesant
- Dendris SAS, 335 Rue du Chêne Vert, 31670 Labège, France; (M.P.); (T.P.); (T.C.); (S.P.); (E.B.); (R.F.); (J.-M.F.)
| | - Yannick Rouquet
- Laboratoire Inovie-CBM, 31000 Toulouse, France; (Y.R.); (M.-A.T.); (M.B.)
| | | | - Matthieu Bernier
- Laboratoire Inovie-CBM, 31000 Toulouse, France; (Y.R.); (M.-A.T.); (M.B.)
| | - Jérémy Bayette
- Laboratoire Inovie-Labosud, 34070 Montpellier, France; (J.B.); (R.F.); (M.M.); (P.R.); (T.B.); (N.A.)
| | - Remi Fournier
- Laboratoire Inovie-Labosud, 34070 Montpellier, France; (J.B.); (R.F.); (M.M.); (P.R.); (T.B.); (N.A.)
| | - Mélanie Marguerettaz
- Laboratoire Inovie-Labosud, 34070 Montpellier, France; (J.B.); (R.F.); (M.M.); (P.R.); (T.B.); (N.A.)
| | - Pierre Rolland
- Laboratoire Inovie-Labosud, 34070 Montpellier, France; (J.B.); (R.F.); (M.M.); (P.R.); (T.B.); (N.A.)
| | - Thibaud Bayol
- Laboratoire Inovie-Labosud, 34070 Montpellier, France; (J.B.); (R.F.); (M.M.); (P.R.); (T.B.); (N.A.)
| | - Nadia Abbaoui
- Laboratoire Inovie-Labosud, 34070 Montpellier, France; (J.B.); (R.F.); (M.M.); (P.R.); (T.B.); (N.A.)
| | - Antoine Berry
- Service de Parasitologie-Mycologie, Centre Hospitalier Universitaire Purpan de Toulouse, Institut Fédératif de biologie (IFB), 31300 Toulouse, France; (A.B.); (X.I.); (S.C.); (P.C.)
- Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), Hôpital Purpan, 31024 Toulouse, France
| | - Xavier Iriart
- Service de Parasitologie-Mycologie, Centre Hospitalier Universitaire Purpan de Toulouse, Institut Fédératif de biologie (IFB), 31300 Toulouse, France; (A.B.); (X.I.); (S.C.); (P.C.)
- Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), Hôpital Purpan, 31024 Toulouse, France
| | - Sophie Cassaing
- Service de Parasitologie-Mycologie, Centre Hospitalier Universitaire Purpan de Toulouse, Institut Fédératif de biologie (IFB), 31300 Toulouse, France; (A.B.); (X.I.); (S.C.); (P.C.)
| | - Pamela Chauvin
- Service de Parasitologie-Mycologie, Centre Hospitalier Universitaire Purpan de Toulouse, Institut Fédératif de biologie (IFB), 31300 Toulouse, France; (A.B.); (X.I.); (S.C.); (P.C.)
| | - Elodie Bernard
- Dendris SAS, 335 Rue du Chêne Vert, 31670 Labège, France; (M.P.); (T.P.); (T.C.); (S.P.); (E.B.); (R.F.); (J.-M.F.)
| | - Richard Fabre
- Dendris SAS, 335 Rue du Chêne Vert, 31670 Labège, France; (M.P.); (T.P.); (T.C.); (S.P.); (E.B.); (R.F.); (J.-M.F.)
| | - Jean-Marie François
- Dendris SAS, 335 Rue du Chêne Vert, 31670 Labège, France; (M.P.); (T.P.); (T.C.); (S.P.); (E.B.); (R.F.); (J.-M.F.)
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, Institut National des Sciences (INSA), 135 Avenue de Rangueil, 31077 Toulouse, France
| |
Collapse
|
2
|
Faramarzi S, Motamedi M, Rezaei-Matehkolaei A, Aboutalebian S, Ansari S, Didehdar M, Bahadoran M, Mirhendi H. A simple multiplex polymerase chain reaction assay for rapid identification of the common pathogenic dermatophytes: Trichophyton interdigitale, Trichophyton rubrum, and Epidermophyton floccosum. Curr Med Mycol 2022; 7:1-7. [PMID: 35028478 PMCID: PMC8740852 DOI: 10.18502/cmm.7.2.7030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 05/22/2021] [Accepted: 06/30/2021] [Indexed: 12/04/2022] Open
Abstract
Background and Purpose: The most common etiological agents of human dermatophytosis in various parts of the world are Trichophyton rubrum, Trichophyton interdigitale, and Epidermophyton floccosum.
The main aim of this study was to design and evaluate a simple and straightforward multiplex polymerase chain reaction (PCR) assay for reliable identification/differentiation of these species
in clinical isolates. Materials and Methods: The reliable sequences of several molecular targets of dermatophytes species were used to design a multiplex PCR for the identification of common pathogenic dermatophytes.
The isolates and clinical specimens examined in this study included seven standard strains of dermatophytes, 101 isolates of dermatophytes and non-dermatophyte molds/yeasts which
had already been identified by sequencing or PCR-restriction fragment length polymorphism (RFLP), and 155 clinical samples from patients suspected of cutaneous mycoses. Results: Species-specific primer pairs for T. rubrum and T. interdigitale/T. mentagrophytes were designed based on the sequence data of the translation elongation factor 1-alpha gene,
and the primers for E. floccosum targeted the specific sequence of the internal transcribed spacer region (ITS). The multiplex PCR successfully
detected T. rubrum, T. interdigitale/T. mentagrophytes, and E. floccosum strains that were identified by sequencing or PCR-RFLP. However, the primer pairs selected
for T. interdigitale/T. mentagrophytes cross-reacted with Trichophyton tonsurans. In testing the PCR system directly for clinical samples, the proportion of positive
multiplex PCR was higher than positive culture (68.1% vs. 55.4%, respectively). Conclusion: The multiplex assay could detect three common agents out of several causal agents of dermatophytosis, namely T. rubrum, T. interdigitale, and E. floccosum. Therefore, by adding
pan-dermatophyte primers it can be used as a comprehensive detection/identification test.
Collapse
Affiliation(s)
- Sama Faramarzi
- Department of Medical Parasitology and Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Marjan Motamedi
- Department of Medical Parasitology and Mycology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ali Rezaei-Matehkolaei
- Department of Medical Mycology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Shima Aboutalebian
- Department of Medical Parasitology and Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Saham Ansari
- Department of Medical Parasitology and Mycology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mojtaba Didehdar
- Department of Medical Parasitology and Mycology, School of Medicine, Arak University of Medical Sciences, Arak, Iran
| | - Mehran Bahadoran
- Department of Medical Parasitology and Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Hossein Mirhendi
- Department of Medical Parasitology and Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| |
Collapse
|
3
|
Molecular Characterisation and Phylogenetic Analysis of Dermatophytic Fungi Isolated from Tinea Capitis in Northwest Nigeria Using Sequence of the 28S rRNA. MICROBIOLOGY RESEARCH 2021. [DOI: 10.3390/microbiolres12030046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The detection and identification of fungal DNA from clinical samples is one of the fundamental approaches in biomedicine. The incidence, distribution, and control of dermatophytes has progress significantly and the use of phylogenetic species concepts based on rRNA regions have enhanced the taxonomy of dermatophyte species; however, the use of 28S rDNA genes has certain limitations. This gene has been used in dermatophyte taxonomy with limited enumeration; we appraised the sequence disparity within and among groups of the species, the gene ranking in identification, phylogenetic analysis, and taxonomy of 32 strains of eight dermatophyte species. In this study, a set of primers was adopted to amplify the target followed by a partial sequencing of the rDNA. The utilization of a pairwise nucleotide differentiation, an affinity was observed among eight dermatophyte species, with disparity among species ranging from 0 to 197 base pair (bp). Intra-species bp differences were found within strains of Trichophyton eriotrephon, Trichophyton bullosum, Trichophyton simii (Trichophyton genus), Microsporum audouinii, and Trichophyton tonsurans (Microsporum and Trichophyton genus, respectively); however, only some strains of Trichophyton eriotrephon were found to be invariant having three genotypes. Trichophyton tonsurans exhibited most intra-species variability. The characterization and construction of a phylogenetic tree of 28S rDNA gene on dermatophyte species provide a bedrock of an additional finding of connections between species. However, 28S rRNA capture provides a novel method of effective and sensitive detection of dermatophytes lodged in human skin scale. We report for the first time the emergence of T. eriotrephon, T. bullosum, T. simii, T. benhamiae, and Ctenomyces serratus dermatophytes from Tinea capitis in Nigeria.
Collapse
|
4
|
Hazlianda C, Muis K, Lubis I. A Comparative Study of Polymerase Chain Reaction-Restriction Fragment Length Polymorphism and Fungal Culture for the Evaluation of Fungal Species in Patients with Tinea Cruris. Open Access Maced J Med Sci 2017; 5:844-847. [PMID: 29362607 PMCID: PMC5771283 DOI: 10.3889/oamjms.2017.197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 10/20/2017] [Accepted: 10/21/2017] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND: Tinea cruris is the second most common dermatophytosis in the world and the most common in Indonesia. The conventional laboratory tests for dermatophyte infection are slow and less specific. Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) is a PCR method with the addition of enzyme after amplification, therefore enabling for more specific results. AIM: This study aimed to find whether the PCR-RFLP test could yield the same fungal species result as a fungal culture. METHODS: The specimens were skin scrapings from thirty-one patients suspected tinea cruris. The tools and materials that were used were Sabaroud’s dextrose agar media, primer ITS 1 and ITS 4 and MvaI. RESULTS: The equation percentage of the test result species between PCR-RFLP and fungal culture was 50% of 12 subjects whose the test results were both positive from the fungal culture and PCR-RFLP. The percentage of the test result with fungal culture the fungal species were found, but in the PCR-RFLP test which the fungal species was not found, the percentage was 50% of 12 subjects which the test results were both positive as fungi from the culture and PCR-RFLP test. CONCLUSIONS: The species from PCR-RFLP examination was the same with the fungal culture.
Collapse
Affiliation(s)
- Cut Hazlianda
- Universitas Sumatera Utara, Fakultas Kedokteran, Dermatology and Venereology, Medan, Indonesia
| | - Kamaliah Muis
- Universitas Sumatera Utara, Fakultas Kedokteran, Dermatology and Venereology, Medan, Indonesia
| | - Isma Lubis
- Universitas Sumatera Utara, Fakultas Kedokteran, Dermatology and Venereology, Medan, Indonesia
| |
Collapse
|
5
|
Koc AN, Atalay MA, Inci M, Sariguzel FM, Sav H. Identification and molecular epidemiology of dermatophyte isolates by repetitive-sequence-PCR-based DNA fingerprinting using the DiversiLab system in Turkey. Mycoses 2017; 60:348-354. [PMID: 28220547 DOI: 10.1111/myc.12602] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 01/04/2017] [Accepted: 01/04/2017] [Indexed: 11/27/2022]
Abstract
Dermatophyte species, isolation and identification in clinical samples are still difficult and take a long time. The identification and molecular epidemiology of dermatophytes commonly isolated in a clinical laboratory in Turkey by repetitive sequence-based PCR (rep-PCR) were assessed by comparing the results with those of reference identification. A total of 44 dermatophytes isolated from various clinical specimens of 20 patients with superficial mycoses in Kayseri and 24 patients in Hatay were studied. The identification of dermatophyte isolates was based on the reference identification and rep-PCR using the DiversiLab System (BioMerieux). The genotyping of dermatophyte isolates from different patients was determined by rep-PCR. In the identification of dermatophyte isolates, agreement between rep-PCR and conventional methods was 87.8 % ( 36 of 41). The dermatophyte strains belonged to four clones (A -D) which were determined by the use of rep-PCR. The dermatophyte strains in Clone B, D showed identical patterns with respect to the region. In conclusion, rep-PCR appears to be useful for evaluation of the identification and clonal relationships between Trichophyton rubrum species complex and Trichophyton mentagrophytes species complex isolates. The similarity and diversity of these isolates may be assessed according to different regions by rep-PCR.
Collapse
Affiliation(s)
- A Nedret Koc
- Department of Microbiology, Erciyes University Medical Faculty, Kayseri, Turkey
| | - Mustafa A Atalay
- Department of Microbiology, Erciyes University Medical Faculty, Kayseri, Turkey
| | - Melek Inci
- Department of Medical Microbiology, School of Medicine, Mustafa Kemal University, Hatay, Turkey
| | - Fatma M Sariguzel
- Department of Microbiology, Kayseri Research and Training Hospital, Kayseri, Turkey
| | - Hafize Sav
- Department of Microbiology, Cerrahpaşa Medical Faculty, İstanbul, Turkey
| |
Collapse
|
6
|
Yo A, Yamamoto M, Nakayama T, Ishikawa J, Makimura K. Detection and identification of Trichophyton tonsurans from clinical isolates and hairbrush samples by loop-mediated isothermal amplification system. J Dermatol 2016; 43:1037-43. [PMID: 26892741 DOI: 10.1111/1346-8138.13303] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 12/17/2015] [Indexed: 11/27/2022]
Abstract
Since the 1990s, there have been reports of the spread of dermatophytosis caused by Trichophyton tonsurans among contact sports athletes in several countries, including Japan. This study was performed to develop a loop-mediated isothermal amplification (LAMP) system for rapid and accurate detection and identification of T. tonsurans from clinical isolates or hairbrush samples for diagnosis and to prevent the spread of infection. A specific primer set was prepared by comparing the whole genome sequence of T. tonsurans with those of six other closely related dermatophytes. After confirming the sensitivity and specificity of this system, LAMP assay was performed using 37 clinical samples obtained from three healthy volunteers and 24 judo athletes. A total of 155 fungal isolates (56 strains of various standard fungi, 96 identified T. tonsurans isolates, three hairbrush-cultured isolates from judo athletes) and 37 hairbrush samples (34 samples from 24 judo athletes, and three samples from three healthy volunteers) were used for culture and LAMP assay, respectively. The assay showed no cross-reactivity to standard strains other than T. tonsurans. The detection limit was 100 copies of DNA template per tube. All of the 96 T. tonsurans isolates were amplified, and all samples from healthy volunteers showed negative results. Four of the 34 hairbrush samples obtained from judo athletes showed positive results in LAMP assay, and two of the four were positive in both culture and LAMP assay. We developed a rapid LAMP system with high specificity and sensitivity for diagnosis of T. tonsurans infection.
Collapse
Affiliation(s)
- Ayaka Yo
- Laboratory of Space and Environmental Medicine, Graduate School of Medicine, Teikyo University, Tokyo, Japan
| | - Mikachi Yamamoto
- Department of Pediatrics, Teikyo University School of Medicine Hospital, Tokyo, Japan
| | - Takako Nakayama
- Laboratory of Space and Environmental Medicine, Graduate School of Medicine, Teikyo University, Tokyo, Japan
| | - Jun Ishikawa
- Department of Bioactive Molecules, National Institute of Infectious Diseases, Tokyo, Japan
| | - Koichi Makimura
- Laboratory of Space and Environmental Medicine, Graduate School of Medicine, Teikyo University, Tokyo, Japan
| |
Collapse
|
7
|
Eckert JC, Ertas B, Falk TM, Metze D, Böer-Auer A. Species identification of dermatophytes in paraffin-embedded biopsies with a new polymerase chain reaction assay targeting the internal transcribed spacer 2 region and comparison with histopathological features. Br J Dermatol 2015; 174:869-77. [PMID: 26556042 DOI: 10.1111/bjd.14281] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/26/2015] [Indexed: 11/30/2022]
Abstract
BACKGROUND Dermatophytosis is a very common skin infection with a broad clinical spectrum. Biopsies are often used to confirm the diagnosis, especially when the clinical presentation is unusual. Not uncommonly, organisms are hard to find even with periodic acid-Schiff stains. Polymerase chain reaction (PCR) for dermatophytes can be used in such cases. OBJECTIVES To test a new PCR assay allowing species identification of dermatophytes on paraffin-embedded biopsies, and to reassess histopathological criteria for diagnosis of dermatophytosis. METHODS In total, 121 biopsies of 92 patients with clinical suspicion of tinea were included. In 42 samples the clinical diagnosis had been confirmed histopathologically, and in 79 no fungal elements had been identified. PCRs targeting the internal transcribed spacer (ITS)2 region of dermatophytes were performed on the biopsies with subsequent sequencing. Sections were reassessed for the presence/absence of hyphae/spores, pattern and composition of infiltrate, and epidermal/follicular changes. Patient charts were reviewed for clinical data. RESULTS The new ITS2 PCR assay detected 94% of the dermatophyte infections (compared with 79% identified by microscopy). Trichophyton rubrum was the dominant species (89%), and other species identified were Trichophyton verrucosum (2%), Microsporum canis (4%), Epidermophyton floccosum (2%) and Trichophyton interdigitale (4%). In particular, infections with T. interdigitale and manifestations with prominent spongiosis were not diagnosed histologically. Intracorneal neutrophils, which have been emphasized as a histopathological clue to dermatophytosis, were present in only 46% of PCR-positive samples. CONCLUSIONS Molecular species identification of dermatophytes via ITS2 PCR can easily be implemented in a routine dermatopathology setting. It is fast and highly specific and improves the sensitivity of histopathological diagnosis of dermatophytosis.
Collapse
Affiliation(s)
- J C Eckert
- Dermatologikum Hamburg, Stephansplatz 5, 20354, Hamburg, Germany.,Department of Dermatology, Münster University, Von Esmarch Straße 58, 48149, Münster, Germany
| | - B Ertas
- Dermatologikum Hamburg, Stephansplatz 5, 20354, Hamburg, Germany
| | - T M Falk
- Dermatologikum Hamburg, Stephansplatz 5, 20354, Hamburg, Germany
| | - D Metze
- Department of Dermatology, Münster University, Von Esmarch Straße 58, 48149, Münster, Germany
| | - A Böer-Auer
- Dermatologikum Hamburg, Stephansplatz 5, 20354, Hamburg, Germany
| |
Collapse
|
8
|
Mohammadi R, Abastabar M, Mirhendi H, Badali H, Shadzi S, Chadeganipour M, Pourfathi P, Jalalizand N, Haghani I. Use of Restriction Fragment Length Polymorphism to Rapidly Identify Dermatophyte Species Related to Dermatophytosis. Jundishapur J Microbiol 2015; 8:e17296. [PMID: 26301058 PMCID: PMC4541063 DOI: 10.5812/jjm.8(5)2015.17296] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Revised: 03/30/2014] [Accepted: 04/08/2014] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Dermatophytes are a group of keratinophilic fungi worldwide, which can infect the skin, hair and nails of humans and animals. This genus includes several species that present different features of dermatophytosis. Although, laboratory diagnosis of dermatophytes is based on direct microscopy, biochemical tests and culture, these manners are expensive, time consuming and need skilled staff. Therefore, molecular methods like PCR-RFLP are the beneficial tools for identification, which are rapid and sensitive. Thus, dermatophyte species are able to generate characteristic band patterns on agarose gel electrophoresis using PCR-RFLP technique, which leads to successful identification at the species level within a 5-hour period. OBJECTIVES The purpose of this study was to study inter- and intraspecific genomic variations for identification of clinically important dermatophyte species obtained from clinical specimens in Isfahan, Iran using PCR-RFLP. MATERIALS AND METHODS From March 2011 to August 2012, 135 clinical isolates were collected from infected patients at Isfahan, Iran. ITS1-5.8S-ITS2 region of rDNA was amplified using universal fungal primers. Subsequently, amplified products were digested by the MvaI restriction enzyme. Using discriminating band profiles on agarose gel, dermatophyte species were identified. However, DNA sequencing was used for unidentifiable strains. RESULTS The specimens were obtained from skin scrapings (70.3%), nail (24.4%) and hair (5.1%) clippings. Most patients were between 21 - 30 years and the ratio of male to female was 93/42. Trichophyton interdigitale was the commonest isolate (52.5%) in our findings, followed by Epidermophyton floccosum (24.4%), T. rubrum (16.2%), Microsporum canis (2.2%), T. erinacei (1.4%), T. violaceum (1.4%), T. tonsurans (0.7%) and M. gypseum (0.7%) based on PCR-RFLP. CONCLUSIONS Combination of traditional methods and molecular techniques considerably improves identification of dermatophytes in the species level in clinical laboratories, which can lead to properly antifungal therapy and successful management of infections. However, restriction and specificity and sensitivity should be lowered and increased, respectively, to be useful for a wide variety of clinical applications.
Collapse
Affiliation(s)
- Rasoul Mohammadi
- Department of Medical Parasitology and Mycology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, IR Iran
| | - Mahdi Abastabar
- Department of Medical Mycology and Parasitology, Invasive Fungi Research Center (IFRC), School of Medicine, Mazandaran University of Medical Sciences, Sari, IR Iran
| | - Hossein Mirhendi
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, IR Iran
| | - Hamid Badali
- Department of Medical Mycology and Parasitology, Invasive Fungi Research Center (IFRC), School of Medicine, Mazandaran University of Medical Sciences, Sari, IR Iran
| | - Shahla Shadzi
- Department of Medical Parasitology and Mycology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, IR Iran
| | - Mustafa Chadeganipour
- Department of Medical Parasitology and Mycology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, IR Iran
| | - Parinaz Pourfathi
- Department of Medical Parasitology and Mycology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, IR Iran
| | - Niloufar Jalalizand
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, IR Iran
| | - Iman Haghani
- Department of Medical Mycology and Parasitology, Invasive Fungi Research Center (IFRC), School of Medicine, Mazandaran University of Medical Sciences, Sari, IR Iran
| |
Collapse
|
9
|
Evaluation of a commercial PCR test for the diagnosis of dermatophyte nail infections. J Med Microbiol 2015; 64:25-31. [DOI: 10.1099/jmm.0.079962-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
10
|
Worek M, Kwiatkowska A, Ciesielska A, Jaworski A, Kaplan J, Miedziak B, Deregowska A, Lewinska A, Wnuk M. Identification of dermatophyte species using genomic in situ hybridization (GISH). J Microbiol Methods 2014; 100:32-41. [DOI: 10.1016/j.mimet.2014.02.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 02/22/2014] [Accepted: 02/22/2014] [Indexed: 10/25/2022]
|
11
|
Bergman A, Heimer D, Kondori N, Enroth H. Fast and specific dermatophyte detection by automated DNA extraction and real-time PCR. Clin Microbiol Infect 2013; 19:E205-11. [DOI: 10.1111/1469-0691.12153] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Revised: 12/29/2012] [Accepted: 01/02/2013] [Indexed: 11/29/2022]
|
12
|
Elavarashi E, Kindo AJ, Kalyani J. Optimization of PCR-RFLP Directly from the Skin and Nails in Cases of Dermatophytosis, Targeting the ITS and the 18S Ribosomal DNA Regions. J Clin Diagn Res 2013; 7:646-51. [PMID: 23730638 DOI: 10.7860/jcdr/2013/5363.2873] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Accepted: 01/17/2013] [Indexed: 11/24/2022]
Abstract
PURPOSE A pan fungal primer targeting the Internal Transcribed Spacer (ITS) region and optimization of PCR-RFLP using a dermatophyte specific primer targeted the 18S ribosomal DNA (rDNA) region were performed for the identification of dermatophyte species and strains directly from clinical specimens. MATERIALS AND METHODS One hundred and thirty eight specimens (129 skin scrapings and 9 nail clippings) from clinically suspected cases of dermatophytosis were collected and subjected to direct microscopy and culture. Among them, 66 skin scrapings and 3 nail clippings were processed for genotyping by PCR-RFLP analysis using the Mva I, Hae III and the Dde I restriction enzymes. RESULTS Of the 138 specimens, 81 specimens were positive for dermatophytosis, the most common one being Trichophyton rubrum (47), followed by Trichophyton mentagrophytes (25) and Epidermophyton floccosum (9). Of the 47 T. rubrum isolates, 10 were T. rubrum var. raubitschekii which were identified phenotypically as urease positive and by DNA sequencing. Since they exhibited minor morphological and physiological features, they have currently been synonymized with T. rubrum. Of the 25 T. mentagrophytes isolates, three were Trichophyton interdigitale, which were identified by DNA sequencing. Among the 66 skin specimens smear, culture and PCR showed the presence of dermatophytes in 36 (54.54%), 42 (63.63%) and 47 (71.21%) cases respectively. Among the three nail specimens, only one was found to be positive for dermatophytosis by smear, culture and PCR. CONCLUSION Amplification of the dermatophyte specific primer is appropriate in the identification of dermatophytes directly from the clinical material. PCR targeting the ITS region by using the Mva I and the Dde I enzymes was equally good for the RFLP analysis. However, by using the above three restriction enzymes, no strain variations were detected among the T. rubrum and the T. mentagrophytes strains.
Collapse
Affiliation(s)
- Elangovan Elavarashi
- PhD Research Scholar, Department of Microbiology, Sri Ramachandra University , Chennai, India
| | | | | |
Collapse
|
13
|
Cafarchia C, Gasser RB, Figueredo LA, Weigl S, Danesi P, Capelli G, Otranto D. An improved molecular diagnostic assay for canine and feline dermatophytosis. Med Mycol 2012; 51:136-43. [PMID: 22686247 DOI: 10.3109/13693786.2012.691995] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The few studies attempting to specifically characterize dermatophytes from hair samples of dogs and cats using PCR-based methodology relied on sequence-based analysis of selected genetic markers. The aim of the present investigation was to establish and evaluate a PCR-based approach employing genetic markers of nuclear DNA for the specific detection of dermatophytes on such specimens. Using 183 hair samples, we directly compared the test results of our one-step and nested-PCR assays with those based on conventional microscopy and in vitro culture techniques (using the latter as the reference method). The one step-PCR was highly accurate (AUC > 90) for the testing of samples from dogs, but only moderately accurate (AUC = 78.6) for cats. A nested-PCR was accurate (AUC = 93.6) for samples from cats, and achieved higher specificity (94.1 and 94.4%) and sensitivity (100 and 94.9%) for samples from dogs and cats, respectively. In addition, the nested-PCR allowed the differentiation of Microsporum canis from Trichophyton interdigitale (zoophilic) and geophilic dermatophytes (i.e., Microsporum gypseum or Trichophyton terrestre), which was not possible using the one step-assay. The PCRs evaluated here provide practical tools for diagnostic applications to support clinicians in initiating prompt and targeted chemotherapy of dermatophytoses.
Collapse
Affiliation(s)
- Claudia Cafarchia
- Dipartimento di Sanità Pubblica e Zootecnia, Università degli Studi di Bari, Bari, Italy
| | | | | | | | | | | | | |
Collapse
|
14
|
Abstract
PURPOSE OF REVIEW Recent advances in the molecular diagnostics of dermatophytosis may improve speed, specificities and sensitivities. This review provides an update on the current available molecular techniques for the diagnosis of dermatophytosis. RECENT FINDINGS Molecular diagnostics of dermatophytosis relate to the direct detection of dermatophyte DNA in clinical specimens. Important challenges have been associated with the DNA extraction procedures, which despite improvement still lack consensus, and the fact that phenotypic species classification not always translates into distinct molecular taxonomic entities. Molecular methods are divided into conventional PCR, real-time PCR and post-PCR techniques. The former benefits from simplicity and being less expensive to implement, real-time PCR is less laborious, may enable a broader spectrum of simultaneous species detections and the closed system reduces contamination risk, whereas post-PCR strategies may increase the number of species identified but prolong the turnaround time, and the processing of PCR products increases the laboratory contamination risk. SUMMARY Current molecular methods are on the verge of overcoming most of the early challenges regarding dermatophyte taxonomy, DNA extraction procedures and species specificity, and thus may lead to an increased adoption of such methods. This may point towards a novel consensus in which molecular methods supplement or even replace classical diagnosis of dermatophytosis.
Collapse
|