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Journal of Dermatological Science 69 (2013) 229235

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Journal of Dermatological Science


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Rapid real-time diagnostic PCR for Trichophyton rubrum and Trichophyton


mentagrophytes in patients with tinea unguium and tinea pedis using specic
uorescent probes
Yoshiharu Miyajima a, Kazuo Satoh a,b, Takao Uchida c, Tsuyoshi Yamada a, Michiko Abe d,
Shin-ichi Watanabe e, Miho Makimura a, Koichi Makimura a,f,g,*
a
Teikyo University Institute of Medical Mycology and Genome Research Center, Tokyo, Japan
b
Faculty of Medical Technology, Teikyo University, Tokyo, Japan
c
Department of Dermatology, Showa University School of Medicine, Tokyo, Japan
d
Department of Clinical Chemistry, School of Allied Health Science, Kitasato University, Kanagawa, Japan
e
Department of Dermatology, Faculty of Medicine, Teikyo University, Tokyo, Japan
f
Laboratory of Space and Environmental Medicine, Graduate School of Medicine, Teikyo University, Tokyo, Japan
g
General Medical Education Center, Teikyo University, Tokyo, Japan

A R T I C L E I N F O A B S T R A C T

Article history: Background: Trichophyton rubrum and Trichophyton mentagrophytes human-type (synonym, Trichophyton
Received 28 July 2011 interdigitale (anthropophilic)) are major causative pathogens of tinea unguium. For suitable diagnosis
Received in revised form 24 November 2012 and treatment, rapid and accurate identication of etiologic agents in clinical samples using reliable
Accepted 27 November 2012
molecular based method is required.
Objective: For identication of organisms causing tinea unguium, we developed a new real-time
Keywords: polymerase chain reaction (PCR) with a pan-fungal primer set and probe, as well as specic primer sets
Real-time PCR
and probes for T. rubrum and T. mentagrophytes human-type.
Trichophyton rubrum, Trichophyton
Methods: We designed two sets of primers from the internal transcribed spacer 1 (ITS1) region of fungal
mentagrophytes
ribosomal DNA (rDNA) and three quadruple uorescent probes, one for detection wide range pathogenic
fungi and two for classication of T. rubrum and T. mentagrophytes by specic binding to different sites in
the ITS1 region. We investigated the specicity of these primer sets and probes using fungal genomic
DNA, and also examined 42 clinical specimens with our real-time PCR.
Results: The primers and probes specically detected T. rubrum, T. mentagrophytes, and a wide range of
pathogenic fungi. The causative pathogens were identied in 42 nail and skin samples from 32 patients.
The total time required for identication of fungal species in each clinical specimen was about 3 h. The
copy number of each fungal DNA in the clinical specimens was estimated from the intensity of
uorescence simultaneously.
Conclusion: This PCR system is one of the most rapid and sensitive methods available for diagnosing
dermatophytosis, including tinea unguium and tinea pedis.
2012 Japanese Society for Investigative Dermatology. Published by Elsevier Ireland Ltd. All rights
reserved.

1. Introduction etiologic agents are Trichophyton rubrum and Trichophyton


mentagrophytes human-type [3] (synonym, Trichophyton interdi-
Tinea unguium is a dermatophyte infection and is the most gitale (anthropophilic) [4]), although some non-dermatophytes
common supercial mycosis, being detected in more than 10% of have also been reported to cause onychomycosis, including
the general population in all over the world [1,2]. About half of the Candida spp. [5,6], Aspergillus spp. [6], Fusarium spp. [7,8], and
patients with tinea pedis develop tinea unguium. The main others. For effective antifungal treatment, it is important to know
whether the pathogen is a dermatophyte or not because of some
anti-dermatophytic agents are not effective to non-dermato-
phytes. Recently the incidence of onychomycosis has been
* Corresponding author at: Laboratory of Space and Environmental Medicine,
increasing, and it accounts for up to 90% of toenail disorders
Graduate School of Medicine, Teikyo University, 2-11-1 Kaga, Itabashi-ku, Tokyo
173-8605, Japan. Tel.: +81 3 3964 2140; fax: +81 3 3964 8415. and at least 50% of ngernail disorders [1]. Scales from the infected
E-mail address: makimura@med.teikyo-u.ac.jp (K. Makimura). skin and nails of untreated patients spread this infection to other

0923-1811/$36.00 2012 Japanese Society for Investigative Dermatology. Published by Elsevier Ireland Ltd. All rights reserved.
http://dx.doi.org/10.1016/j.jdermsci.2012.11.589
230 Y. Miyajima et al. / Journal of Dermatological Science 69 (2013) 229235

members of their household. Therefore, early diagnosis and reverse: ITS1R), Trichophyton primer set (forward: ITS1F2; reverse:
treatment of individual patients is essential to prevent the spread ITS1R2), specic T. rubrum probe (TR-ITS1V), specic T. menta-
of these infections. grophytes probe (TM-ITS1F), and pan-fungal probe (PF-ITS1N) were
The discrimination of two major etiologic agents, T. rubrum and designed with MEGA4 alignment software [22] and Primer Express
T. mentagrophytes human-type is important to investigate the (Applied Biosystems, CA, USA), based on the upstream and
pathogenesis and clinical features related in each dermatophyte, downstream sequences of the ITS1 region of the ribosomal RNA
also is essential for epidemiological survey for dermatophytoses. gene (rDNA) of major pathogenic fungi (Fig. 1). These primers and
The standard methods for diagnosis of onychomycosis are uorescent probes were synthesized by Applied Biosystems. The
microscopy and culture. Direct microscopic examination is a basic internal control primers and internal control probe were synthe-
method to detect typical fungal elements. This test is still the gold sized by SigmaAldrich (MO, USA).
standard for the diagnosis of fungal infection, but requires skill and
knowledge about the morphological features of fungi. Culture is 2.2. Preparation of genomic DNA
the most important method for mycological diagnosis, but the
culture-positive rate from nail specimens is often not high enough. The 46 fungal strains used in this study are listed in Table 2. All
Generally, the identication achieved by culture of supercial of the strains were maintained in the TIMM culture collection of
samples is less than 40% [9]. Since the isolates may show atypical Teikyo University Institute of Medical Mycology, most of them
features, fungal culture takes several days longer. were isolated from clinical cases or environment in Japan and part
In order to overcome these defects of the classical methods, of them were obtained from international culture collections.
molecular biological techniques based on the polymerase chain Dermatophytes were fully grown on Sabourauds dextrose agar,
reaction (PCR) have been developed [2,1021]. PCR analysis and were prepared by methods introduced by Makimura et al. [3].
becomes popular as the most reliable method for identication The DNA was quantitated with a Quant-iT dsDNA HS Assay Kit and
of pathogenic fungi from clinical specimens. And to establish more Qubit uorometer (Invitrogen, Carlsbad, CA, USA). An amount of
sensitive, more rapid, cheaper, and simpler PCR system for genomic DNA corresponding to one cell (0.3 pg or roughly 100
practical use, several improvements have been attempted ribosomal RNA gene copies at 3040 Mb per genome) was used as
[9,20,21]. a template in the real-time detection system to conrm the
Recently, real-time PCR methods for identication of several spectrum and specicity of each probe.
dermatophytes have been reported [11,12,21,24]. These methods
are useful for identication of part or most of dermatophytes but 2.3. Plasmid DNA preparation
not other non-dermatophytic fungal pathogens that cause tinea
unguium or tinea pedis [17]. Practically quantitative studies are As the positive control for the PCR assay, three plasmids were
also required to determine the threshold between infection and constructed by using a TOPO TA Cloning Kit (Invitrogen, Carlsbad,
contamination of clinical specimens. CA, USA). The ITS1 regions of T. rubrum (T99), T. mentagrophytes
In this study, we designed two primers sets and three different human-type (T7), and Aspergillus fumigatus (TIMM0108) were
sets of probes, based on previous analyses [3,1316], to detect the cloned into the pCR2.1 plasmid. The copy number of each plasmid
etiologic agents of tinea unguium by real-time PCR. Our primers was calculated from the total length of the bases and the DNA
and probes targeted the internal transcribed spacer 1 (ITS1) region concentration.
in order to detect a wide range of pathogenic fungi and the two
major causative dermatophytes, T. rubrum and T. mentagrophytes 2.4. Clinical specimens
human-type. We compared the results of our new PCR analyses
with the ndings obtained by microscopic examination and The clinical samples were 32 nail specimens and 10 skin
culture of 42 clinical specimens. specimens collected from 32 patients of Kawasaki Social Insurance
Hospital (Kanagawa, Japan) between May 16 and August 17, 2005
2. Materials and methods with written informed consent based on the guideline and
agreement of the institutional ethical committee (Table 1). All of
2.1. Design of the probes and primers the subjects visited the dermatological outpatients department
and were diagnosed as the dermatophytoses by direct microscopic
The sequences of the primers and probes used in this study are examinations. Nail specimens from 39 healthy volunteers were
shown in Table 1. The pan-fungal primer set (forward: ITS1F; used as negative controls for the PCR assay.

Table 1
The primers and probes used for real-time PCR.

Primers and probes Sequences

Pan-fungal primers ITS1F 50 -TAACAAGGTTTCCGTAGGTGAACCT-30


ITS1R 50 -TCGCTGCGTTCTTCATCGA-30

Trichophyton primers ITS1F2 50 -SSCCCCATTCTTGTCTACMTYAC-30


ITS1R2 50 -AACGCTCAGACTGACAGCTCTTC-30

Pan-fungal probe PF-ITS1 50 -[NED]-TTYAACAAYGGATCTCT-[NFQ-MGB]-30


T. rubrum probe TR-ITS1 50 -[VIC]-CGCGCTCCCCCTGC-[NFQ-MGB]-30
T. mentagrophytes probe TM-ITS1 50 -[FAM]-CTCTCTTTAGTGGCTAAAC-[NFQ-MGB]-30

Internal control primers MS2-TM3-F 50 -TGCTCGCGGATACCCG-30


MS2-TM3-R 50 -AACTTGCGTTCTCGAGCGAT-30

Internal control probe MS2-TM2-Cy5 50 -[Cy5]-ACCTCGGGTTTCCGTCTTGCTCGT-[BHQ-3]-30

BHQ-3: Black Hole Quencher 3; Cy5: indodicarbocyanine; FAM: 6-carboxyuorescein; MGB: minor groove binder; NED: 20 -chloro-50 -uoro-70 ,80 -fused phenyl-1,4-dichloro-
6-carboxyuorescein; NFQ: non-uorescent quencher; VIC: 4,7,2-trichloro-7-phenyl-6-carboxyuorescein. Nucleotides. M: A or C; S: C or G; Y: C or T.
Y. Miyajima et al. / Journal of Dermatological Science 69 (2013) 229235 231

18S 5.8S 28S


ITS1 rDNA ITS2
rDNA rDNA

TM-ITS1F TR-ITS1V
dermaF
dermaF2 PF-ITS1N
18S 5.8S
ITS1
rDNA rDNA
dermaR2
dermaR
Fig. 1. Hybridization sites of the primers and probes used in this study. Location of the hybridization sites for the primers and probes are shown in the ITS1 region of ribosomal
RNA gene. Arrows; primers, bars with stars; uorescent probes.

Table 2
Specicity of the primers and probes.

Species Strains Pan-fungal primers Trichophyton primers

Pan-fungal T. rubrum T. mentagrophytes T. rubrum T. mentagrophytes


probe probe probe probe probe

Major causative fungi for tinea


Acremonium curvulum NBRC 32242 +    
Arthroderma benhamiae SM103 +    
Arthroderma vanbreuseghemii TIMM2789 +  +  +
Epidermophyton ocosum 514 (Hasegawa) +    
522 (Hasegawa) +    
Microsporum canis TDGS945 +    
TDGS0222 +    
TDGS0223 +    
TDGS0269 +    
Microsporum gypseum TDGS0009 +    
TDGS0012 +    
Scopulariopsis brumptii NBRC 6441 +    
Scopulariopsis brevicaulis NBRC 4843 +    
Scytalidium lignicola NBRC 104988 +    
Trichophyton rubrum T99 + +  + 
T108 + +  + 
421 (Hasegawa) + +  + 
423 (Hasegawa) + +  + 
425 (Hasegawa) + +  + 
426 (Hasegawa) + +  + 
Trichophyton mentagrophytes human-type T7 +  +  +
T9 +  +  +
Trichophyton tonsurans T117 +    
Other pathogenic fungi
Aspergillus avus TIMM0059 +    
TIMM2935 +    
Aspergillus fumigatus JCM10253 +    
TIMM0108 +    
TIMM2920 +    
Aspergillus niger TIMM0113 +    
TIMM2915 +    
Candida albicans ATCC10231 +    
ATCC90028 +    
TIMM1768 +    
Candida glabrata ATCC90030 +    
CBS138 +    
Candida parapsilosis ATCC2209 +    
ATCC90018 +    
Candida tropicalis ATCC750 +    
TLCS S 9/1 +    
Chaetomium globosum TSY-0369 +    
Cryptococcus neoformans ATCC90113 +    
Tjane +    
Exophiala jeanselmei TSY-0396 +    
Fusarium oxysporum TSY-0351 +    
Fusarium solani TSY-0403 +    
Fusarium verticillioides TSY-0219 +    
Paecilomyces variotii TIMM3182 +    
Pseudallescherichia boydii TIMM0886 +    
Rhizopus oryzae TIMM0921 +    
Trichosporon asahii CBS2479 +    

(+): detected and (): not detected.


232 Y. Miyajima et al. / Journal of Dermatological Science 69 (2013) 229235

Fig. 2. Representative amplication curves obtained by real-time PCR. Curves for three independent PCR batches are shown in each of the four plots. Baseline data were
obtained with fewer than 25 cycles. RFU: relative uorescence unit.

2.5. Preparation of DNA templates from clinical specimens For each real-time PCR assay, we used an internal control
template and primers based on the MS2 bacteriophage, as
The 42 nail and skin specimens from 32 patients and 39 nail described by Dreier et al. [23].
specimens from healthy volunteers were stored at 80 8C before
use. Part of each sample was treated with 15% KOH and 40% diethyl 3. Results
sulfoxide for detection of fungal elements by microscopic
examination. Another part of each samples were cultured on 3.1. Specicity of the probes
Sabourauds dextrose agar containing chloramphenicol (0.05%)
with cycloheximide (0.5%) at 25 8C for several days to 2 weeks, and Representative real-time PCR uorescence signal curves for
morphological examination and sequencing were performed. three specic probes and the internal control probe are shown in
For PCR and sequencing analysis, nail and skin samples (approx. Fig. 2. The target ITS1 region of rDNA was successfully amplied
2 mm  2 mm  1 mm, ca. 10 mg) were frozen for 1 h at 150 8C and the amplied fragments could be used for DNA cloning or
or 5 min in liquid nitrogen. Frozen samples were ground in a Multi- sequencing.
beads Shocker (Yasui Kikai, Osaka, Japan) with metal cones for The specicity of the probes for fungal isolates is shown in
3 min. Then the powdered samples were extracted with phenol Table 2. The expected fungi were detected successfully by
chloroform, as described elsewhere [13]. Ethachinmate copreci- different combinations of primer sets and probes. The
pitation reagent (3 mL, Nippon Gene, Tokyo, Japan) was applied to combination of pan-fungal primers and pan-fungal probe
each sample at the beginning of isopropanol precipitation for reacted with DNA from all fungi, but did not react with human
maximum recovery of DNA. DNA (data not shown).
The specic T. rubrum probe reacted specically with T. rubrum,
2.6. Quantitative real-time PCR analysis while the T. mentagrophytes probe reacted specically with T.
mentagrophytes human-type [3]. Arthroderma vanbreuseghemii is a
A class 100 clean work station equipped with HEPA lters and a teleomorph of T. mentagrophytes that has the almost same ITS1
UV lamp (Airtech Japan, Tokyo, Japan) was used during preparation rDNA region sequence as T. mentagrophytes including its human-
for prevention of airborne fungal contamination. The reaction type [3], and it also reacted with the T. mentagrophytes probe.
mixture for real-time PCR consisted of 10 ml of Premix Ex Taq
(Perfect Real Time) (Takara Bio, Shiga, Japan), 0.2 mM each of the 3.2. Minimum detectable DNA copy number
ITS1F and ITS1R (or ITS1F2 and ITS1R2) primer pairs, 0.2 pmol/ml
of TaqMan MGB probes (TR-ITS1V, TM-ITS1F, PF-ITS1N), and 0.4 ml To determine the detection limit of this system, dilutions of
of ROX (tetrapropano-6-carboxyrhodamine) Reference Dye II plasmid DNA were prepared and measured four times by real-
(Takara Bio, Shiga, Japan). The reaction mixture was combined time PCR (Table 3). The results indicated that 50 template rDNA
with 2 ml of DNA extracted from a sample in each well of a 96-well copies was the minimum number for reliable detection by this
MicroAmp plate (Applied Biosystems, CA, USA) and was adjusted system.
to a nal volume of 20 ml with distilled water. Quantitative PCR
and monitoring were done with a 7500 Fast Real-Time PCR System 3.3. Quantitative real-time PCR analysis of clinical samples
(Applied Biosystems, CA, USA). Initial denaturation at 95 8C for 30 s
was followed by 60 cycles of amplication at 95 8C for 6 s and 60 8C Toe nail and skin specimens from 32 patients with tinea pedis
for 30 s. and toe nail samples from 39 healthy volunteers were tested by
Y. Miyajima et al. / Journal of Dermatological Science 69 (2013) 229235 233

Table 3
Detection rate for each primer set and probe combination.a

DNA copies Pan-fungal primers Trichophyton primers

Pan-fungal probe T. rubrum probe T. mentagrophytes probe T. rubrum probe T. mentagrophytes probe

400 100 100 100 100 100


200 100 100 100 100 100
100 100 100 100 100 100
50 100 100 100 100 100
25 100 25 100 100 100
13 100 50 100 75 100
6 75 25 75 25 100
3 75 0 75 0 75
a
Detection rate with four amplications.

microscopy and culture (Table 4). Both microscopic examination the number of rDNA copies in the clinical samples. The amount of
and culture of all samples from the healthy volunteers were DNA found in each nail sample is shown in Table 4 along with the
negative (data not shown). results of other examinations.
DNA extracted from clinical specimens was also tested by our In the nail samples collected from the 39 healthy individuals,
real-time PCR system with positive control plasmids. The fewer than 1500 copies of rDNA were sometimes detected (data
comparative CT method (DDCT method) was used to calculate not shown), suggesting that non-pathogenic fungi could possibly

Table 4
Detection of fungi from clinical specimens.

Pt. no. Specimen Microscopy Culture Pan-fungal primers Trichophyton primers

Pan-fungal T. rubrum T. mentagrophytes T. rubrum probe T. mentagrophytes


probe probe probe probe

1 Nail +  9270 19,800 4590 96,800


2 Nail +  167,000 2910 1,920,000 13,500,000
3 Nail +  22,100 68,100 167,000
4 Nail + Tr 635,000 14,900,000 3,890,000
Skin +  735 2930 11,700
5 Nail + Tr 42,200 5090 2360 606,000 40,400
6 Nail +  142,000 2,790,000 13,000,000
7 Nail + Ca 125,250 1,545,000 4,430,000
8 Nail + Tm 65,400 79,400 16,400 1,520,000 174,000
Skin + Tm 375,000 375,000 1,500,000
9 Nail +  20,600 76,800 1230 322,500
Skin +  46,875 750,000 3,000,000
10 Nail +  27,300 2280 119,100 2520 1,490,000
11 Nail +  13,800 14,700 69,500 35,100
Skin +  2930 2930 23,400
12 Nail + Tr 34,100 44,900 2490 2,490,000 719,000
Skin + Tm 93,750 93,750 375,000
13 Nail +  11,700 3500 28,100 11,700 72,800
Skin + Tm 23,400 23,400 375,000
14 Nail + Tr 10,400 21,000 50,100
15 Nail +  17,700 54,800 306,000
16 Nail +  180 3090 10,900
17 Nail + Tr 5840 125,000 321,000
18 Nail +  16,100 245,000 3,690,000
Skin +  180 735 2925
19 Nail +  501,000 2,790,000 26,100,000
Skin +  188,000 188,000 23,400 1,500,000 1,500,000
20 Nail +  390 690 5510 960
21 Nail + Tr 4,650,000 7,160,000 2,850,000 14,100,000 3,380,000
22 Nail +  429,000 30 5865 46,875
Skin + Tr 360 11,715
23 Nail + Tr 111,000,000 1,520,000,000 60 2,430,000,000
Skin + Tr 46,875 750,000 6,000,000
24 Nail + Tr 1,346,000 23,700,000 76,100,000
25 Nail + Tr 270 9870 180,000
26 Nail + Tr 570,000 14,800,000 45,500,000
27 Nail +  12,400 267,000 105 1,360,000
28 Nail +  1730 2240 44,700
29 Nail + Tr 44,700 1,070,000 13,300,000
30 Nail +  45 5270
31 Nail + Tr 67,500 1,500,000 9,800,000
32 Nail +  939,000 639,000 1,370,000

Numbers represent estimated rDNA copies per reaction. The threshold of this system is 1500 copies/reaction. Identied fungal species; Tr: Trichophyton rubrum, Tm:
Trichophyton mentagrophytes, and Ca: Candida albicans. (+) Fungal elements detected and () culture negative or no PCR amplication.
234 Y. Miyajima et al. / Journal of Dermatological Science 69 (2013) 229235

be present in clinical samples at this level. Accordingly, we set positive controls) can be processed in a single reaction, and testing
1500 copies as the threshold for detection by this PCR method. is completed after 3 h.
In conclusion, this real-time PCR system is a sensitive, reliable,
and rapid method for specic identication of T. rubrum and T.
4. Discussion mentagrophytes. Our system may be useful for large-scale
epidemiological studies and for clinical trials of antifungal
Our three probes with different uorescent dyes allowed therapy.
simultaneous detection of two major pathogenic dermato-
phytes and a wide range of fungi in only 3 h. One hour was Acknowledgement
required for preparation of DNA from clinical samples, 1 h for
setting up the PCR reaction, and 1 h for PCR amplication. We This study was partly supported by Hisamitsu Pharmaceutical
designed specic uorescence probes and primers for T. Co., Inc. (Tokyo, Japan) via a grant (Koichi Makimura).
rubrum and T. mentagrophytes human-type, which allowed
rapid diagnosis of the pathogens causing tinea unguium and References
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