Beruflich Dokumente
Kultur Dokumente
b
c
Received 8 February 2007; received in revised form 4 May 2007; accepted 29 May 2007
Available online 23 June 2007
Abstract
The aim of this study was to develop a real-time PCR technique to detect Trypanosoma cruzi DNA in blood of chagasic patients.
Analytical sensitivity of the real-time PCR was assessed by two-fold serial dilutions of T. cruzi epimastigotes in seronegative blood
(7.8 down to 0.06 epimastigotes/mL). Clinical sensitivity was tested in 38 blood samples from adult chronic chagasic patients and 1
blood sample from a child with an acute congenital infection. Specificity was assessed with 100 seronegative subjects from endemic
areas, 24 seronegative subjects from non-endemic area and 20 patients with Leishmania infantum-visceral leishmaniosis. Real-time
PCR was designed to amplify a fragment of 166 bp in the satellite DNA of T. cruzi. As internal control of amplification human
RNase P gene was coamplified, and uracil-N-glycosylase (UNG) was added to the reaction to avoid false positives due to PCR
contamination. Samples were also analysed by a previously described nested PCR (N-PCR) that amplifies the same DNA region as
the real-time PCR. Sensitivity of the real-time PCR was 0.8 parasites/mL (50% positive hit rate) and 2 parasites/mL (95% positive
hit rate). None of the seronegative samples was positive by real-time PCR, resulting in 100% specificity. Sixteen out of 39 patients
were positive by real-time PCR (41%). Concordance of results with the N-PCR was 90%. In conclusion, real-time PCR provides
an optimal alternative to N-PCR, with similar sensitivity and higher throughput, and could help determine ongoing parasitaemia in
chagasic patients.
2007 Elsevier B.V. All rights reserved.
Keywords: Trypanosoma cruzi; Real-time PCR; Chagas disease
1. Introduction
Chagas disease is a protozoan infection caused by
Trypanosoma cruzi. The disease is widespread in Central
196
197
Table 1
Primers and probe selected for the T. cruzi nested PCR and for the real-time PCR
PCR
Primer or probe
Sequencea (5 3 )
Nucleotide positionb
Nested
TCZ 1 (forward)
TCZ 2 (reverse)
TCZ 3 (forward)
TCZ 4 (reverse)
CGAGCTCTTGCCCACACGGG
CCTCCAAGCAGCGGATAGTTCAGG
TGCTGCASTCGGCTGATCGTTTTCGA
CARGSTTGTTTGGTGTCCAGTGTGTGA
120
165188
2146
142168
Real-time
Cruzi 1 (forward)
Cruzi 2 (reverse)
Cruzi 3 (probe)
ASTCGGCTGATCGTTTTCGA
AATTCCTCCAAGCAGCGGATA
CACACACTGGACACCAA
2746
172192
143159
a
b
R, A/G; S, C/G.
Nucleotide position in the DNA satellite sequence (GenBank accession no. AY520036).
marrow with the High Pure PCR Template Preparation kit (Roche, Basel, Switzerland), and eluted in
200 L of elution buffer according to the manufacturers instructions. Five microliters of extracted DNA
was amplified in triplicate in both the real-time PCR and
N-PCR.
2.4. Nested PCR assay
The N-PCR assay is based on a previously described
procedure (Marcon et al., 2002) using primers TCZ
1 and TCZ 2 for the first reaction and TCZ 3 and
TCZ 4 for the nested amplification, with some modifications (Table 1). PCR was carried out in 20 L
reaction mixture containing 1.5 mM MgCl2 and 1 U of
RedTaq polymerase (Sigma), with annealing temperatures of 63 C (40 cycles) and 57 C (25 cycles) in the
first and second amplification runs, respectively. The
PCR programs were run on an MJ Research thermocycler (PTC-200), and the 149-nucleotide amplicon was
separated by electrophoresis on 3% agarose gel and visualised by ultraviolet transillumination after staining with
ethidium bromide.
conditions in the PCR mixture were 1 Universal Master Mix with UNG (Applied Biosystems), 0.1 RNase
P detection reagent, 750 nM each T. cruzi primer and
250 nM for the T. cruzi probe in a 20 L reaction. The
samples were amplified in a thermocycler ABI Prism
7700 (Applied Biosystems) with the following PCR conditions: first step (2 min at 50 C), second step (10 min at
95 C) and 45 cycles (15 s at 95 C and 1 min at 58 C). A
sample was considered valid when the internal control
was efficiently amplified, and was considered positive
for T. cruzi when the threshold cycle (Ct) for the T. cruzi
target was <45. The Ct for a given sample is the first
cycle of the PCR reaction where fluorescence is detected
above the baseline. A non-template control was included
in each run as the real-time PCR negative control.
2.5.1. Statistical analysis
The sensitivity of the real-time PCR assay was calculated by PROBIT analysis (SPSS v13, Chicago, IL),
and the 95% and 50% positive hit rates are reported. The
Ct values are expressed as the mean and standard deviation. The coefficient of variation was calculated as the
percentage of the Ct standard deviation divided by its
mean.
198
Table 2
Results for the sensitivity assay for the real-time PCR using two-fold
dilutions of blood sample spiked with a known T. cruzi concentration
Table 3
Description of the positive and discrepant samples in the real-time PCR
and nested PCR in blood from patients with Chagas disease
Parasites/mL
Positive/tested
Sample
Origin
N-PCR
7.81
3.91
1.95
0.98
0.49
0.24
0.12
0.06
24/24
24/24
21/24
17/24
10/24
6/24
4/24
2/24
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
Argentina
Bolivia
Bolivia
Bolivia
Bolivia
Bolivia
Bolivia
Bolivia
Bolivia
Bolivia
Honduras
Bolivia
Bolivia
Bolivia
Bolivia
Bolivia
Bolivia
Spaina
34.63
28.73
32.92
35.48
36.37
39.21
35.43
39.36
36.33
33.50
30.60
39.35
39.22
39.22
35.55
Negative
Negative
14.74b
Positive
Positive
Positive
Positive
Positive
Positive
Positive
Positive
Positive
Positive
Positive
Negative
Positive
Negative
Positive
Positive
Positive
Positive
inferior to 2.8 parasites/mL. The sensitivity of the realtime PCR was similar to that obtained with the N-PCR
assay, which in our hands yields a clear band down to 2
parasites/mL.
As for the quantitative results, the real-time PCR reactions performed in triplicate with 10-fold serial dilutions
of DNA from blood spiked with T. cruzi epimastigotes (106 101 epimastigotes/mL) showed a linear curve
from 105 down to 10 parasites/mL of blood, with a fourlog dynamic range (Fig. 1).
As for the reproducibility of the assay, single-use
aliquots of Control 1 were extracted and amplified in 28
independent runs. Mean Ct values were 33.73 1.68 for
the T. cruzi target and 28.91 1.36 for the human RNase
P gene, for a resulting coefficient of variation of 4.97%
and 4.87%, respectively. We observed no contamination
of the negative controls or non-template controls of the
assay due to carry-over during either the DNA extraction
or the real-time PCR set-up.
3.2. Clinical sensitivity and specicity
Negative samples have been tested to determine the
specificity of the real-time PCR and the new primers
described here. None of the 124 T. cruzi seronegative
a
b
Herein, we describe the development of a new realtime PCR method based on TaqMan technology for the
diagnosis of T. cruzi infection in blood samples. Previously described PCR methods for the diagnosis of
Chagas disease were based on one-step PCR, with or
without hybridisation, or N-PCR followed by gel electrophoresis. Consequently, they were time-consuming
and produced false positive results due to contamination
of the samples by carry-over, or false negative results due
to inhibition in the amplification process, when PCRs
were performed in the absence of parallel amplification
of a human gene as a control.
More recently, some works have described real-time
PCR methods using SybrGreen technology which is
based on incorporation of a fluorescent dye into the
double-strand DNA (Cummings and Tarleton, 2003;
Virreira et al., 2006). We chose to use a TaqMan probe
that better guaranties the specificity of the measured signal.
Our real-time PCR method is based on amplification
of a genomic DNA sequence which had been previously
described as specific for all T. cruzi lineages (Moser et
al., 1989; Virreira et al., 2003). It has been designed
to include a decontamination step and an internal control for the quality of amplification, and results can be
interpreted both qualitatively and, with the appropriate
standard curve, quantitatively. As is shown in our study,
the real-time PCR has a sensitivity similar to that of the
N-PCR, with a concordance in the clinical samples tested
of 90%. Discrepant results between real-time PCR and
N-PCR can be explained by low parasitaemia, probably
below the limit of detection of both PCR techniques.
Indeed, we noted that both samples with a positive realtime PCR but negative N-PCR result presented relatively
late Ct for the real-time technique (39.35 and 39.22,
Table 3), which actually correspond to low parasitaemia
according to our standard curve (Fig. 1). Therefore, sensitivity could be further improved if a larger volume of
blood were processed for DNA extraction. The samples
included in this study are representative of the T. cruziinfected population in a non-endemic area, that is, young
adults in an indeterminate phase of the disease with low
or absent parasitaemia. We must mention that all the
selected patients were diagnosed on serological findings
and had not received any treatment before enrolment
in the study. All patients with Chagas chronic disease
arrived at Spain between 2000 and 2004 and there was
no significant difference in the time spent outside the
endemic area between patients who presented a positive result by PCR (real-time or N-PCR) and those who
presented a negative result. Use of the real-time PCR
in this context will be as a qualitative assay to accompany the serological diagnosis. Although the quantitative
assay is of limited value in the indeterminate phase of
the disease, the true potential of the real-time PCR will
eventually be better recognised in other situations for
which PCR-based techniques have been promoted, such
199
200