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Burjasot, Valencia, Spain; and 4Departamento de Microbiologı́a y Ecologı́a, Facultad de Farmacia, Universitat de Valencia, Burjasot, Valencia, Spain
c 2006 Federation of European Microbiological Societies FEMS Yeast Res 6 (2006) 1094–1100
Published by Blackwell Publishing Ltd. All rights reserved
Rapid PCR-based test for identifying Candida albicans 1095
Recently, molecular biology-based techniques have been Table 1. Fungal strains used in this study
adapted to the identification of fungal pathogens (McCul- Lane
lough et al., 1995; Elie et al., 1998; Kanbe et al., 2002; Trost in
et al., 2004). In particular, PCR has increasingly been used Strain Origin Fig. 1
for Candida diagnosis, as it is quick, simple, specific, Candida glabrata CECT1448 1
sensitive and reliable (Mannarelli & Kurtzman, 1998; Wa- Candida guilliermondii CECT1021 2
Downloaded from https://academic.oup.com/femsyr/article/6/7/1094/491946 by Semenov Institite for Chemical Physics user on 24 June 2023
hyuningsih et al., 2000; Arancia et al., 2004). To adapt PCR Candida kefyr CECT1436 3
to daily clinical routine, simplification and standardization Candida krusei CECT1433 4
Candida parapsilopsis Clinical isolatew 5
of DNA extraction and PCR amplification is of major
Candida parapsilopsis Clinical isolate 6
importance.
Candida kefyr CECT1018 7
In this article, a PCR-based method for the rapid detec- Candida tropicalis CECT1005 8
tion of C. albicans isolates is described. A simpler DNA Cryptococcus neoformans CECT1078 9
extraction procedure, based on alkali, detergent and heat Kluyveromyces lactis IFO1267z 10
treatment, which was previously described for the recovery Rhodotorula marina CECT1139 11
of Candida DNA, and the use of primers derived from the Saccharomyces cerevisiae CECT1170 12
Schizosaccharomyces pombe CECT1375 13
specific C. albicans pH-regulated KER1 gene, coding for a
Yarrowia lipolytica INAG135668‰ 14
novel lysine/glutamic acid-rich protein with no significant
Candida glabrata Clinical isolate 15
homology to any other known sequences (Galán et al., Candida albicans CECT1675 16
2004), allows C. albicans detection, identification, and Candida albicans SC5314z –
differentiation from all non-albicans Candida species, in- Candida dubliniensis Clinical isolate –
cluding the azole-resistant C. krusei and C. glabrata, and the Colección Española de Cultivos Tipo, Burjasot, Valencia, Spain.
phenotypically related C. dubliniensis, all of which are of w
Servicio de Microbiologı́a, Hospital Universitario la Fe, Valencia, Spain;
clinical and epidemiologic relevance. identity of clinical isolates assayed in this work belonging to the genus
Candida was further checked when required by means of commercial
Materials and methods biochemical and serological tests (see Materials and methods section).
z
Institute of Fermentation, Osaka, Japan.
‰
Institute Nacional Agronomique Paris-Grignon, France.
Organisms and growth conditions z
See reference Gillum et al. (1984).
Fungal strains used in this work are listed in Table 1. Clinical
isolates, of both superficial and systemic origin, were
isolation. The first approach was based on Einsele’s proce-
provided by the Servicio de Microbiologia, Hospital Uni-
dure (Einsele et al., 1997), with several modifications.
versitario la Fe, Valencia, Spain. The C. albicans reference
Briefly, fungal cells were added to 1 mL of leukocyte lysis
strains used in this work as positive controls were CECT
buffer (WCLB) consisting of 10 mM Tris (pH 7.6), 10 mM
1675 and SC5314 (Gillum et al., 1984). Ura1 and Ura null
EDTA (pH 8.0), 50 mM NaCl, 0.2% sodium dodecyl sulfate
mutant strains for KER1 (C1N7 and CAC1; Galán et al.,
(SDS), and 200 mg of proteinase K (Sigma) per mL, and
2004) were used as negative controls throughout this study.
incubated at 65 1C for 1 h (A). In the second extraction
Fungal species were routinely grown on Sabouraud dextrose
procedure, fungal cells were added to 1 mL of WCLB
agar plates (Pronadisa), and YPD solid medium (1% yeast
supplemented with 300 mg of Zymolyase (ICN Biomedicals)
extract, 2% peptone, 2% glucose, 1.5% agar). CHROMagar
and 28 mM b-mercaptoethanol (Sigma), and incubated at
Candida plates (Biocheck) were used for presumptive iden-
37 1C for 45 min (B). The third extraction method involved
tification of Candida species. Definitive identification of all
the addition of the fungal cells to the same suspension as
clinical isolates assayed in this work belonging to the genus
above and incubation at 37 1C for 45 min and at 95 1C for
Candida was performed by means of biochemical methods
5 min (C). In all three cases, cells were pelleted for 5 min at
(using the API 20C AUX system), and confirmed when
5000 g, and 10 mL of the supernatant was used for the PCR
necessary with the Bichrolatex albicans agglutination test
reaction.
(Fumouze, Levallois-Perret, France).
A mechanical disruption method modified from that of
Hee Shin et al. (1997) was also used to extract fungal DNA.
Extraction of fungal DNA
Fresh yeast cells were resuspended in 300 mL of TXTE buffer
Six different fungal DNA extraction methods were tested consisting of 10 mM Tris, 1 mM EDTA and 1% Triton X-
for further comparative analysis. The method giving the 100, final pH 8.0, and transferred to a new Eppendorf tube
best result in the PCR tests was adapted for the DNA containing 200 mL of 425–600-mm glass beads (Sigma). After
extraction of all clinical isolates. In all cases, fungal isolates boiling in a water bath for 15 min, the mixture was vortexed
were cultured on solid YPD at 30 1C for 48 h prior to DNA for 15 min until complete cell breakage. The tubes were then
centrifuged at 10 000 g for 1 min, and the supernatant was denaturation at 94 1C. This first step was followed by 30
stored at 20 1C until it was used for PCR amplification cycles of 40 s of denaturation at 94 1C, 30 s of annealing at
(D). PCR amplifications were also performed directly on 60 1C, and 2 min of primer extension at 72 1C. The last step
intact cells without any DNA purification steps (Maneu included one cycle of 40 s of denaturation and a final
et al., 2000) (E). extension step of 12 min at 72 1C. A 10-mL aliquot of the
Finally, a heat–alkali treatment for fungal DNA purifica- amplified product was analyzed on 0.8% agarose gel and
stained with a 50 mg mL1 ethidium bromide solution.
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tion was applied. Isolated fresh colonies were resuspended in
100 mL of 10 mM NaOH containing 0.5% Tween-20 and Appropriate positive and negative controls were included,
0.5% Nonidet P-40. Cells were then boiled in a water bath and methods to prevent PCR contamination were used
for 10 min and centrifuged at 10 000 g for 15 min. Ten (Kwok & Higuchi, 1989).
microliters from the supernatant was used for each PCR
reaction (F). To check the sensitivity of this method, Southern blot analysis
extractions were performed with different cell suspensions
Twenty micrograms of genomic DNA were digested with
containing different numbers of cells (from 105 to 10 mL1),
BamHI, and fragments were separated by electrophoresis in
previously assessed by microscopy cell counting in a hemo-
agarose gel (0.8%). The gel was stained with ethidium
cytometer chamber.
bromide, and then denatured and neutralized (Sambrook
For Southern blot analysis, the DNA isolation method
et al., 1989). The DNA was transferred to a Hybond nylon
was adapted from Hoffman and Winston (Hoffman &
membrane (Roche) and hybridized with the KER1 probe
Winston, 1987). Briefly, cells were grown to late stationary
after nonradioactive labeling using the Dig DNA Labeling
growth phase in 10 mL of YPD and collected by centrifuga-
and Detection kit (Roche). Hybridization was carried out
tion, and the cell pellets were resuspended in 0.2 mL of
under high-stringency conditions following the manufac-
breaking buffer (2% Triton X-100, 1% SDS, 100 mM NaCl,
turer’s recommendations.
10 mM Tris buffer, pH 8.0, 1 mM EDTA), and 0.2 mL of
phenol/chloroform/isoamyl alcohol (25 : 24 : 1), and 0.2 g of
glass beads was added. This mixture was vortexed, and
Results and discussion
0.2 mL of Tris-EDTA (TE) was added. After centrifugation, In this study, we describe a rapid, simple and reliable PCR
the aqueous phase was transferred to a new Eppendorf tube, system for the definitive identification of C. albicans. In
and 1 mL of ethanol was added to precipitate the DNA. After general, protocols for extraction of DNA of fungal cells are
centrifugation, the pellet was resuspended in 0.4 mL of TE either very time-consuming or give poor yields compared to
buffer and treated with 100 mg of RNase A. DNA was methods of DNA extraction from human cells or viruses.
precipitated again with 0.3 M (final concentration) NaCl, Accordingly, several DNA extraction kits have been devel-
and two volumes of ethanol. The DNA was finally resus- oped (Löffler et al., 1997) in order to optimize and simplify
pended in 50 mL of TE. Samples were stored at 4 1C. the DNA extraction step, prior to PCR applications. How-
ever, low cost per assay is necessary when clinical PCR
applications are required. In this work, a new PCR assay is
Primers and PCR amplification
described that allows the practical application of this tech-
The oligonucleotide primer pair (SC1F, 5 0 -CGGAGATTTTCT nique in daily clinical practice by optimization of the two
CAATAAGGACCAC, and SC1R, 5 0 -AGTCAATCTCTGTC- steps involved, fungal DNA extraction from clinical samples
TCCCCTTGC) was designed using information from gene and the use of a C. albicans-specific probe.
databases and our own sequence for the KER1 gene. These Six different (in-house) DNA extraction methods that are
primers amplify a 670-bp fragment in the KER1 gene of C. relatively easy and quick have been tested. Two methods, D
albicans. The same batch of primers was used throughout the and F, gave positive amplification rates when two different
study. C. albicans reference strains were used, as shown in Table 2.
Amplification reactions were performed in 50-mL aliquots Protocol F, based on alkali, detergent and heat treatment for
of a solution containing 5 mL of 10 PCR buffer, 3.5 mM fungal DNA release, was the method of choice, as it is
MgCl2, 0.2 mM each dNTP, 0.2 mM each primer, and 2.5 U simple, quick and cheap, factors that are fundamental in
of Taq DNA polymerase (Promega). Ten microliters of the clinical routine. The advantages of this method are that it is
extracted DNA was added to the mixture in all cases, but the simpler and quicker than those described previously for the
reactions were performed directly on intact cells without recovery of Candida DNA from clinical isolates; it does not
DNA purification steps, cells being taken directly from the require the use of toxic chemicals (phenol/chloroform,
solid media with a sterile plastic tip and resuspended in the guanidinium thiocyanate) or expensive enzymes (proteinase
PCR mixture. PCR was performed in a thermocycler (Pro- K, Zymolyase); and it avoids the need to perform a time-
gene, Techne) as follows. The first cycle included 3 min of consuming mechanical disruption step. The reproducibility
c 2006 Federation of European Microbiological Societies FEMS Yeast Res 6 (2006) 1094–1100
Published by Blackwell Publishing Ltd. All rights reserved
Rapid PCR-based test for identifying Candida albicans 1097
i
nd
C. araps osis
is
R. ctis ans
ilos
amplification, using two different reference strains of Candida albicans
Y. mbe e
kef mo
K. ofor is
po sia
ca
ns
a
il
m
a
C. abrat
C. raps
c ina
C.n pica
C. uillier
C. abrat
C. polyti
C. rusei
S. erevi
i ca
Amplicons Amplicons
C. yr
tro r
y
r
ma
kef
alb
pa
DNA with with
gl
la
g
p
l
li
C.g
C.
S.
extraction SC5314 CECT1675 St
Method Protocol description Duration strain strain
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A Lysis buffer1Proteinase 90 min 1/3 0/3
K1Heat
B Lysis buffer1Zymolyase 60 min 0/3 1/3
C Lysis 60 min 1/3 2/3
buffer1Zymolyase1Heat
D Glass beads1Heat 40 min 6/6 6/6
E Intact cells – 6/6 3/6 670 bp
F Alkali1Heat 30 min 6/6 6/6
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16
of this procedure was found to be high, and its sensitivity Fig. 1. PCR-generated DNA products deduced from the Candida albi-
was in the same range as that of the other extraction cans KER1 gene. DNA samples from different fungal strains were
methods reported in the literature with which it was obtained by method F (see Material and methods) and amplified by PCR
using primers SCF1 and SCR1. Only the DNA sample from C. albicans
compared. Thus, a concentration between 1000 and
gave positive amplification with the selected pair of primers.
100 cells mL1 in the assay mixture was required to obtain
positive amplicons.
To determine the specificity of these primers (SC1F and (a)
St C. albicans clinical isolates
SC1R), Candida and non-Candida species (Table 1), includ-
ing both clinical isolates and reference strains, were tested.
With the same DNA extraction and PCR protocol, all fungal
strains listed in Table 1 failed to give any PCR amplification 670 bp
product with the SC1F and SC1R primers, except C. albicans
(Fig. 1). Although C. albicans is known to be the most
75
N7
CA
C1
(a)
75
16
14
CT
C1
53
N7
C. dubliniensis
SC
CA
CE
C1
670 bp
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C. albicans
SC5314 (b)
75
16
14
CT
C1
53
N7
C. dubliniensis
SC
CE
CA
C1
3.8 kb
c 2006 Federation of European Microbiological Societies FEMS Yeast Res 6 (2006) 1094–1100
Published by Blackwell Publishing Ltd. All rights reserved
Rapid PCR-based test for identifying Candida albicans 1099
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Kanbe T, Horii T, Arishima T, Ozeki M & Kikuchi A (2002) PCR-
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c 2006 Federation of European Microbiological Societies FEMS Yeast Res 6 (2006) 1094–1100
Published by Blackwell Publishing Ltd. All rights reserved