2.1 Study design
This was a prospective cohort study in patients with megaesophagus with nonreactive or inconclusive serology for CD monitored by the Study Group on Chagas Disease (GEDoCh), University of Campinas (UNICAMP) – Brazil. Following explanations, participants signed an informed consent form. The study was approved by the Research Ethics Committee of UNICAMP (process no. 779/2007). All procedures complied with the guidelines and standards for research with human beings, as provided in Resolution No. 466/2012 of the Brazilian National Health Council and the principles of the Declaration of Helsinki, to safeguard the rights and well-being of the participants.
2.2 Sampling
Group I (experimental group): 26 adult patients of both sexes, diagnosed with megaesophagus and with nonreactive or inconclusive serology for CD;
Group II (control group): 33 adult patients of both sexes, diagnosed with megaesophagus and with reactive and positive serology for CD.
2.3 Biological material
Peripheral blood samples were collected intravenously at the same time for serological, blood culture and molecular testing. For the serological tests, 4.0 ml of peripheral blood was collected in vacuum tubes with clot activator, which were processed in a clinical analysis laboratory at UNICAMP. The enzyme-linked immunosorbent assay (ELISA) and indirect immunofluorescence (IFI) methods were performed following the guidelines of the II Brazilian Consensus on Chagas Disease (2), which recommends the performance of two tests with different methods for the diagnosis of CD.
For blood culture (BC), five vacuum tubes containing EDTA were collected, resulting in 20 ml of peripheral blood. These tubes were centrifuged at 3,500 rpm for 10 min at 4°C. Then, the plasma was discarded, and the remaining red blood cells and buffy coat were washed in liver infusion tryptose (LIT) culture medium and transferred to Falcon® tubes. They were centrifuged again, and all new supernatant was transferred to a sixth Falcon® tube. LIT was added to the remaining parts until the volume reached 10 ml. Therefore, six tubes of BC were obtained from each participant, which were kept in an oven at 28°C. The reading was performed by ordinary optical microscopy once a fortnight until positive results or 150 days of incubation had been reached.
Molecular testing involved the performance of qualitative PCR, targeting the Sat-DNA and kDNA of T. cruzi and quantitative PCR (qPCR). A 4.0 ml volume of peripheral blood was collected in a vacuum tube containing EDTA. For genetic material isolation, the blood sample was centrifuged at 3,500 rpm for 15 minutes at a temperature of 4°C, and a buffy coat was obtained. The High Pure PCR Template Preparation kit (Roche)® was used, following the manufacturer’s recommendations. After extraction, the genetic material was stored at −20°C until use for the molecular reactions.
2.4 Gene amplification
The integrity of the extracted genetic material was verified by amplification of the human β-globin gene. For this amplification, 400 ng of DNA, 50 mM of KCl, 10 mM of Tris-HCl pH 8.4, 2.5 mM of MgCl2, 200 mM of dNTPs, 0.1 mM of each oligonucleotide and 2 U of Taq DNA polymerase were added to microcentrifuge tubes. P3/P5 oligonucleotides were used for the first reaction, and P5/109 was used for the second (Table 1). The reactions were carried out under the following conditions: 1st cycle of 5 min at 94°C, followed by 35 cycles of 1 min at 94°C, 1 min at 55°C and 1 min at 72°C. The final extension was performed at 72°C for 7 min. Amplicons found were 365 base pairs (bp).
For amplification of the Sat-DNA gene (Nested-PCR), 1.0 μL of DNA, 50 mM of KCl, 10 mM of Tris-HCl pH 8.4, 2.5 mM of MgCl2, 200 mM of dNTPs, 0.1 mM of each TCZ1/TCZ2 oligonucleotide and 2 U of Taq DNA polymerase were added to microcentrifuge tubes, up to a final volume of 20 μl. For the second reaction, 1.0 μl of the previously amplified product was used as a template, with alterations for the concentration of 2.8 mM MgCl2 and for TCZ3/TCZ4 oligonucleotides. The amplicon was 149 bp (Table 1). The amplification cycles were differentiated for the two reactions. Both were preceded by initial denaturation at 94°C for 5 min, and the final extension was performed at 72°C for 7 min. In the first reaction, the first 5 cycles were 94°C for 1 min, 60°C for 1 min, and 72°C for 1 min and 30 s. The next 25 cycles were 94°C for 1 min, 65°C for 1 min, and 72°C for 1 min and 30 s. In the second reaction, 25 cycles were performed under the following conditions: 94°C for 40 s; 55°C for 40 s; and 72°C for 1 min.
For amplification of the kDNA gene (Nested-PCR), 1.0 μL of DNA, 50 mM of KCl, 10 mM of Tris-HCl pH 8.4, 4 mM of MgCl2, 200 mM of dNTPs, 0.1 mM of each S67/S35 oligonucleotide and 2 U of Taq DNA polymerase were added to microcentrifuge tubes for a final volume of 30 μl. For the second reaction, 1.0 μl of the previously product was amplified, and S35/S36 oligonucleotides were used (Table 1). The amplicon was 330 bp. The amplification cycles were differentiated for the two reactions. Both were preceded by initial denaturation at 94°C for 5 min, and the final extension was performed at 72°C for 7 min. In the first reaction, 35 cycles were used: 94°C for 1 min; 56°C for 1 min; and 72°C for 1 min. In the second reaction, 35 cycles were performed under the following conditions: denaturation: 94°C for 30 s; 63°C for 45 s; and 72°C for 1 min.
For absolute amplification (qPCR), the points of the standard curve were obtained from counting in a Neubauer chamber of trypomastigote forms of T. cruzi originating from BC, with the concentration adjusted to 107 parasites/ml. A blood sample from an individual without CD was contaminated with the known concentration, and from this aliquot, gene isolation was performed with the High Pure PCR Template Preparation kit (Roche®). Then, serial dilutions (10X) of the genetic material were made at concentrations from 106 to 10−2 parasites/ml. These diluted points were used in triplicate to build the standard curve of the qPCR.
For the real-time amplification reaction, TaqMan® Universal Master Mix with UNG (Applied Biosystems) 1X, 500 nM of each oligonucleotide (Cruzi 1/Cruzi 2), 200 nM of the probe (Cruzi 3) and RNaseP (Applied Biosystems) 0.1X and 5 µL of DNA were added to a microcentrifuge tube for a final volume of 50 μl. All points used for building the standard curve (106 to 10−2 parasites/ml) were amplified in triplicate, and DNA from clinical samples was amplified in duplicate.
The qPCR was performed in Rotor-Gene 6000 (Corbett Life Science) equipment under the following conditions: first cycle of 2 min at 50°C, second cycle of 10 min at 95°C cycling (45 times): 15 s at 95°C and 60 s at 58°C. To avoid carryover contamination, the TaqMan® Universal Master Mix kit containing AmpErase® UNG was used. The recombinant UNG enzyme is capable of degrading preamplified DNA fragments, preventing their reamplification and consequent false-positive results. The human RNaseP gene was used as an internal control for the amplification reaction. The absence of contaminants in the reagents was ensured by the use of an NTC sample, which did not contain the target sequence. Real-time absolute quantification data were generated by Rotor-Gene 1.7.87 software.
Table 1. Nucleotide sequence of genes for each gene amplification.
Gene
|
Denomination
|
Nucleotide sequence
|
Identification
|
β-globin
|
P3
P5
109
|
5’AGACAGAGAAGACTCTTG 3’
5’TCATTCGTCTGTTTCCCATTC3’
5’CCCTTCCTATGACATGAACTTAACCAT 3’
|
PMID: 2999980
|
Sat-DNA
|
TCZ1
TCZ2
TCZ3
TCZ4
|
5’CGAGCTCTTGCCCACACGGGTGCT3’
5’CCTCCAAGCAGCGGATAGTTCAGG3’
5’TGCTGCA(G/C)TCGGCTGATCGTTTTCGA3’
5’CA(A/G)G(C/G)TTGTTTGGTGTCCAGTGTTGTGA3’
|
PMID: 2504769
PMID: 8644910
|
kDNA
|
S67
S35
S36
|
5’TGGTTTTGGGAGGGG(C/G)(G/C)(T/G)TCAA(A/C)TTTT3’
5’AGTACGTAGAG(T/G)GGGCATGTAATAAA3’
5’GGGTTCGATTGGGGTTGGTGdT3’
|
PMID: 20169193
PMID: 2565018
|
qPCR
|
Cruzi 1 (forward)
Cruzi 2 (reverse)
Cruzi 3 (probe)
|
5′-AST CGG CTG ATC GTT TTC GA-3 ′ (S = G ou C)
5′-AAT TCC TCC AAG CAG CGG ATA-3 ′
5′-6-FAM-CAC ACA CTG GAC ACC AA-BBQ quencher-3 '
|
PMC3019106
|
2.5. Statistics
A descriptive analysis was used with the presentation of frequency tables for categorical variables. To compare proportions, the chi-square test or Fisher’s exact test was used when necessary. To compare proportions evaluated by the two methods, McNemar’s test was used. As a measure of agreement between the methods, the kappa coefficient was applied. The magnitude of the coefficient is defined as follows: values greater than or equal to 0.75 indicate excellent agreement, values between 0.75 and 0.40 indicate good agreement and values below or equal to 0.40 indicate no agreement. The significance level adopted for the statistical tests was 5%.