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Memórias do Instituto Oswaldo Cruz
Fundação Oswaldo Cruz, Fiocruz
ISSN: 1678-8060 EISSN: 1678-8060
Vol. 96, Num. 8, 2001, pp. 1137-1139
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Untitled Document
Mem Inst Oswaldo Cruz, Rio de
Janeiro, Vol. 96(8) 2001, pp. 1137-1139
SHORT COMMUNICATION
Inhibition of the Polymerase
Chain Reaction by Sputum Samples from Tuberculosis Patients After Processing
Using a Silica-guanidiniumthiocyanate DNA Isolation Procedure
Philip Suffys/+, Patricia Rosa Vanderborght,
Patricia Barros dos Santos, Leticia Almeida Pinto Correa, Yolanda Bravin*, Afranio
Lineu Kritski**
Laboratório de Biologia Molecular e Diagnóstico
de Doenças Infecciosas, Departamento de Bioquímica e Biologia
Molecular, Instituto Oswaldo Cruz-Fiocruz, Av. Brasil 4365, 21045-900 Rio de
Janeiro, RJ, Brasil *Laboratório Central Noel Nutels, Secretaria Estadual
de Saúde do Rio de Janeiro, Rio de Janeiro, RJ, Brasil **Unidade de Pesquisa
em Tuberculose, Hospital Universitário Clementino Fraga Filho, UFRJ,
Rio de Janeiro, RJ, Brasil
+Corresponding author. Fax: +55-21-2270.9997. E-mail: psuffys@gene.dbbm.fiocruz.br
Received 23 February 2001
Accepted 19 June 2001
Code Number: oc01218
With the objective to evaluate PCR-mediated
detection of Mycobacterium tuberculosis DNA as a diagnostic procedure
for diagnosis of tuberculosis in individuals attending ambulatory services in
Primary Health Units of the City Tuberculosis Program in Rio de Janeiro, Brazil,
their sputum samples were collected and treated with a DNA extraction procedure
using silica-guanidiniumthiocyanate. This procedure has been described to be
highly efficient for extraction of different kind of nucleic acids from bacteria
and clinical samples. Upon comparing PCR results with the number of acid-fast
bacilli, no direct relation was observed between the number of bacilli present
in the sample and PCR positivity. Part of the processed samples was therefore
spiked with pure DNA of M. tuberculosis and inhibition of the PCR reaction
was verified in 22 out of 36 (61%) of the samples, demonstrating that the extraction
procedure as originally described should not be used for PCR analysis of sputum
samples.
Key words: PCR - sputum - tuberculosis - silica-guanidiniumthiocyanate
- inhibition
In 1995, 94,870 new cases of tuberculosis (TB)
were reported in Brazil, being 76,840 pulmonary TB; the incidence of the disease
was 58.2/100.000 (Ruffino Netto 1999). The situation is more severe in big cities
like São Paulo and Rio de Janeiro, where co-infection with HIV and multi-drug
resistant strains of Mycobacterium tuberculosis complicates efficient
use of general control programs. Rapid diagnosis and adequate treatment of TB
is the most efficient way to avoid spread of TB. During the last couple of years,
several studies were performed to compare recently developed commercial and
"in house" PCR systems with conventional diagnostic procedures such
as detection of acid-fast bacilli by microscopy, culture and X-ray (Eing et
al. 1998, Tortoli et al. 1999). In general, because of their high speed, sensitivity
and specificity, nucleic acid amplification systems are promising diagnostic
tools; however, double blind studies have shown that the use of "in house"
PCR as a routine procedure for diagnosis of TB is still controversial (Noordhoek
et al. 1994, 1996, Suffys et al. 2000). More studies are needed to evaluate
the sensitivity of the methods on paucibacillary material and for evaluation
of feasibility and cost-effectiveness when used as a routine procedure in TB
control programs, especially in developing countries (Roos et al. 1998).
One of the bottle necks of PCR for diagnostic
purpose is the extraction of parasite DNA from clinical samples (Noordhoek et
al. 1994). During the last decade, several methods have been published, including
a very promising procedure using guanidiniumthiocyanate (GuSCN) for isolation
of different types of nucleic acids from cell-rich sources and pathogenic bacteria
(Boom et al. 1990). For evaluation of PCR as a diagnostic procedure of pulmonary
TB in individuals attended at 14 ambulatory services in Rio de Janeiro, sputum
samples were collected locally, stored at 4°C for a maximum of 4 days and
further processed at the State Reference Laboratoroy (Central Laboratory Noel
Nutels-Lacen, RJ). The laboratory methods for processing cultures and smears
as well as for the identification of mycobacteria were standard procedures (Kent
& Kubica 1985). Briefly, an aliquot of 8-10 ml of sputum was processed using
using NaOH-N-acetyl-L-cysteine, resuspended in 2.5 ml phosphate-buffered saline
and a fraction was processed according to Boom et al. (1990), slightly modified.
Briefly, 0.2 ml of the sample was added to 0.2 ml of 0.1 mm glass beads (Biospec
products, Bartlesville, OK, USA) and 0.9 ml of L6 lysis buffer (Boom et al.
1990), vortexed during 10 min, submitted to two cycles of heat shock (5 min
65°C and 5 min -170°C) after which 40 µl of celite were added
and the solution mixed gently at room temperature during 30 min. Supernatant
was discarded and the pellet was washed twice with 1 ml of L2 buffer (Boom et
al. 1990), twice with 1 ml of 70% ethanol, once with 1 ml of acetone and the
pellet air dried at 56°C during 10 min. Nucleic acids were eluted in 0.1
ml TE buffer (10 mM Tris, 1 mM EDTA, pH 8.0) during 10 min at 56°C and stored
at -20°C until further use. Amplification was performed on 5 µl of
the sample in a 25 µl PCR reaction using primers 5'-CCTGCGA GCGTAGGCGTCGG
and 5'-TTGCTCGATCGC GTCGAGGA, flanking a 178 bp fragment of the insertion sequence
IS6110 of M. tuberculosis (Suffys et al. 2000) and detection of the amplification
product was performed on agarose gel after staining with ethidium bromide.
From the 183 sputum samples obtained from individuals
with clinical and radiological diagnosis of pulmonary TB, 80 (44%) had positive
PCR; when comparing PCR results with the number of bacilli observed on smears
(acid fast bacilli - AFB -, +, ++ or +++), 35 (30%) of the 116 samples that
were AFB -, 29 (69%) of the 42 samples that were BAAR +, 10 (77%) of 13 samples
that were AFB ++ and 6 (50%) out of 12 samples that were AFB +++ were PCR positive,
demonstrating that PCR positivity was not directly related to the number of
bacilli present in the sample. Ninety AFB - samples had culture results: 58%
was culture positive and positive PCR was observed in 48% of these, against
18% in AFB -, culture-samples. This demonstrates that M. tuberculosis
DNA is detected more frequently in culture positive samples (p = 0.0037).
Because of the low PCR sensitivity in samples
that had positive AFB (45 out of 67; 67%), deterioration of the parasites DNA
during processing or inhibition of the PCR reaction was suspected. To verify
inhibition, processed sputum samples were spiked with pure DNA of M. tuberculosis
in the following way: purified DNA was added to the PCR mix to a final concentration
of 10 ng/ml and 36 samples were submitted to PCR in the presence of this DNA;
inhibition was evaluated by comparing the intensity of the amplified product
of the samples with three reactions with no clinical sample added. The three
control samples had identical PCR product yield and diminished or negative PCR
reaction was observed 22 samples (61%): 8 out of 17 AFB-, 4 out of 7 AFB +,
3 out of 3 AFB ++ and 7 out of 9 AFB +++, demonstrating that inhibition of the
PCR reaction is occurring in a significant number of sputum samples. No attempts
were made to further evaluate the influence between the volume ratio of sample
and reaction mixture on PCR inhibition.
Several studies have used the GuSCN protocol
for processing of clinical samples but few concentrated on sputum samples from
TB patients. Although better results were obtained when comparing to other extraction
protocols (Brisson-Noel et al. 1991, Noordhoek et al. 1994), these studies expressed
results as PCR positivity of samples with clinically confirmed TB and did not
verify inhibitors. While our study was underway, low amplification signals of
cytomegalovirus (CMV) DNA in cerebrospinal fluid (CSF) and urine specimens processed
with GuSCN was reported (Boom et al. 1999). Detailed analysis revealed that
an inhibitor of DNA-modifying enzymes is introduced into the samples during
the extraction procedures and coeluted with nucleic acids during the last step.
This was not observed upon processing serum, suggesting that a silica particle-derived
inhibitor can apparently be neutralized by a serum component and possibly by
factors present in other tissues; addition of alpha-casein to the L6 lysis buffer
prevented inhibition of PCR from CSF and urine specimens (Boom et al. 1999).
Forbes and Hicks (1996) detected interference of PCR in 52% of respiratory specimens
using an internal control; addition of bovine serum albumin was able to override
the presence of interfering substances. We conclude from our observations that
the GuCSN procedure should not be used on sputum samples without addition of
internal controls or spiking experiments to verify false negative results. Sputum
is one of the most frequently used sample for diagnosis of pulmonary TB and
76% of TB cases in Rio de Janeiro have the pulmonary form of the disease, demonstrating
the importance of further studies to evaluate whether substances such as alpha-casein
and BSA, known to enhance Taq polymerase activity, will improve PCR yield in
sputum samples, after processing with GuCSN or other DNA extraction protocols.
ACKNOWLEDGEMENTS
To Guida Vasconcelos Barrera, coordinator of
the City Tuberculosis Control Program of Rio de Janeiro City; to Oscar Berro
(director) and personnel of the State Reference Laboratory (Lacen) of Rio de
Janeiro and to the health care professionals at the different Primary Health
Units that participated in this project
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This study was supported by CNPq, process 35
04 77/ 95.7 and Pronex.
Copyright 2001 Instituto Oswaldo
Cruz - Fiocruz.
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