Polymerase chain reaction and other amplification techniques in mycobacteriology

Amplification methods for detection of Mycobacterium tuberculosis, such as polymerase chain reaction (PCR), have undergone much research and development in the last several years. The most common methods for extraction, amplification, and detection of mycobacterial nucleic acid sequences used in "in-house" PCR assays are discussed. A list of commercially prepared PCR and non-PCR amplification assays that should be available soon is included. The pros and cons of "in-house" versus commercial technology and issues of implementation of molecular technology in the clinical laboratory are reviewed.     

Polymerase chain reaction to detect Mycobacterium tuberculosis in histologic specimens

BACKGROUND: Whether acute MS lesions are primarily inflammatory or demyelinative is unresolved. Our study examined acute MS lesions longitudinally by quantitative magnetization transfer (MT), an MRI technique that identifies tissue integrity and destruction. METHODS: Four MS patients were studied by serial MRI including MT, conventional T2-weighted images, and postgadolinium T1-weighted images for 9 to 12 months. In 15 new lesions, the MT ratio (MTR) was calculated retrospectively. RESULTS: In 13 lesions, a marked decrease in the MTR was present early during the first 2 months after the onset of the lesion and was followed by a variable increase. In two other lesions, the MTR progressively declined. CONCLUSIONS: These results suggest that major early structural changes compatible with demyelination and followed by remyelination and gliosis, or by continuous demyelination, occur in new MS lesions. The various MTR profiles provide in vivo confirmation of the current knowledge of the progression in MS lesions. Furthermore, MTR may be used to monitor in vivo drug efficacy in new MS lesions.     

Polymerase chain reaction amplification of Trichomonas vaginalis DNA from Papanicolaou-stained smears

We describe 3 cases of Hodgkin's disease (HD) of unusual suppurative type, which were diagnosed on fine-needle aspirates. The smears were dominated by neutrophils, macrophages, and cellular debris. Only a few large, atypical cells of Hodgkin and Reed-Sternberg type were observed. The differential diagnoses of such smears include infectious mononucleosis, tuberculosis, metastatic lymph node involvement, non-Hodgkin's large-cell anaplastic Ki-1-positive lymphomas, T-cell-rich B-cell lymphomas, and peripheral T-cell lymphomas of mixed type. Immunocytochemistry identified the large atypical cells as CD 30 (BerH2)-positive and negative for CD 45 (LCA) in cytospin material from 2 patients, which allowed a conclusive diagnosis of HD.     

Polymerase chain reaction in liposomes

BACKGROUND: Compartmentalization of biochemical reactions within a spherically closed bilayer is an important step in the molecular evolution of cells. Liposomes are the most suitable structures to model this kind of chemistry. We have used the polymerase chain reaction (PCR) to demonstrate that complex biochemical reactions such as DNA replication can be carried out inside these compartments. RESULTS: We describe the first example of DNA amplification by the PCR occurring inside liposomes composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), or of a mixture of POPC and phosphatidylserine. We show that these liposomes are stable even under the high temperature conditions used for PCR. Although only a very small fraction of liposomes contains all eight different reagents together, a significant amount of DNA is produced which can be observed by polyacrylamide gel electrophoresis. CONCLUSIONS: This work shows that it is possible to carry out complex biochemical reactions within liposomes, which may be germane to the question of the origin of living cells. We have established the parameters and conditions that are critical for carrying out this complex reaction within the liposome compartment.     

Polymerase chain reaction amplification analyses of clonality in T-cell malignancy including peripheral T-cell lymphoma

Clonality in T-cell malignancy was investigated using T-cell receptor (TcR) V beta 1-20 family primers and polymerase chain reaction amplification (PCR) of cDNA prepared from tissue biopsies and blood involved with tumour. Secondary PCR amplification of the VDJ joints of primary PCR products was performed to distinguish clonal from polyclonal products, and clonal V beta gene products were confirmed by direct PCR sequencing in the majority of cases. In eight T-cell malignancies including T-cell acute lymphoblastic leukaemia (T-ALL) and T-cell chronic lymphocytic leukaemia (T-CLL) shown to be clonal by Southern blot analysis, one or two primary PCR products were identified and shown to be clonal. In five cases of peripheral T-cell lymphoma (PTCL) all V beta 1-20 families were identified after primary PCR amplification, and clonal products were identified in two cases after secondary amplification; TcR V beta clonal families could not be demonstrated in the remaining three cases. These data were in agreement with previous Southern blot analysis of these cases, and confirmed the presence of reactive T cells in PTCL as well as providing further evidence for the genotypic heterogeneity of this entity. In the remaining case, a blood lymphocytosis, primary PCR amplification produced predominant TcR V beta 6 and V beta 12 family products, of which the V beta 6 family proved clonal after secondary PCR amplification. There was no evidence for overrepresentation of TCR V beta families by the tumour populations in this study, furthermore the data confirm the involvement of reactive cells in T-cell malignancy and the genetic heterogeneity of PTCL.     

Clinical evaluation of polymerase chain reaction DNA amplification method for the diagnosis of pulmonary tuberculosis in patients with negative acid-fast bacilli smear

The nucleotide sequences of 3 cDNA clones corresponding to entire RNA genome of bean common mosaic virus NL3 strain have been determined. The RNA is 9612 nucleotides long, excluding a 3'-terminal poly(A) tail. A putative start codon located at nucleotide positions 170-172 initiates one large open reading frame that is terminated with a UAA codon at position 9368-9370. The predicted polyprotein has 3066 amino acids and an M(r) of 340.3 kDa. The positions of putative protein cleavage sites have been determined by analogy to consensus sequences in other potyviruses. The nucleotide sequences of the non-translated regions and the predicted amino acid sequences of BCMV NL3, were compared with those of other potyviruses. Comparison of the BCMV NL3 proteins with those of other potyviruses indicated a similar genomic organization, and high percentage of amino acid sequence identity in the cylindrical inclusion protein, nuclear inclusion 'b' protein and coat protein. BCMV NL3 displays the highest amino acid sequence identity with soybean mosaic virus.     

Clinical utility of the polymerase chain reaction in the diagnosis of extrapulmonary tuberculosis

This study examines the diagnostic utility of the polymerase chain reaction (PCR) in 156 patients (five human immunodeficiency virus (HIV) seropositive) suspected of extrapulmonary tuberculosis. The results of PCR in 226 samples from 11 different sites were compared with the results of microscopy and culture. Positive culture results were predicted in 86% of samples by PCR but in only 31% by microscopy. Specificity of PCR was 92%. In cases with culture-proven tuberculosis, PCR identified all 11 microscopy positive cases and 19 of 24 (79%) of the microscopy-negative cases. In four patients, PCR excluded the diagnosis of tuberculosis in microscopy-positive samples, which were later shown to contain mycobacteria other than Mycobacterium tuberculosis or laboratory contaminants. In 20 patients (microscopy, PCR and culture negative) a trial of antituberculous drugs was given, but patients showed no improvement and treatment was stopped. In 17 patients, all culture negative (in nine PCR was positive, three of whom also had positive microscopy) the diagnosis was probable tuberculosis based on clinical findings and response to treatment. This polymerase chain reaction has a much higher sensitivity than microscopy and can facilitate therapeutic decisions for those with suspected extrapulmonary tuberculosis.     

Clinical utility of an amplification test based on ligase chain reaction in pulmonary tuberculosis

We evaluated the sensitivity and specificity of a new semiautomated direct amplification test (DAT), the LCx-MTB, for the diagnosis of pulmonary tuberculosis (TB) and assessed its positive predictive value by focusing on patients with high clinical and radiologic suspicion of pulmonary TB. Respiratory tract specimens from 32 consecutive patients with high suspicion of active pulmonary TB (case patients) and from 204 control patients were cultured for Mycobacterium tuberculosis and tested by LCx-MTB. Sensitivity and specificity of LCx-MTB when compared with culture was, respectively, 80 and 98%. Pulmonary TB was confirmed in the 32 case patients without knowledge of the LCx results: 18 patients were smear- and culture-positive for M. tuberculosis, and all gave at least one specimen that was LCx-positive. Eight patients were smear-negative culture-positive, and seven gave at least one LCx-positive specimen. LCx-MTB was negative in all the specimens obtained from six patients with smear- and culture-negative TB. A positive LCx-MTB result in a smear negative specimen was 100% predictive that at least one of the case patients' specimens would yield M. tuberculosis. As a consequence, knowledge of the LCx-MTB results at the time of specimen collection could have hastened the start of the antituberculosis therapy in three (21%) smear-negative case patients and could have avoided unnecessary invasive diagnostic procedures in four (29%). We conclude that the sensitivity of LCx-MTB in detecting M. tuberculosis DNA in respiratory tract specimens is similar to other DATs, that LCx-MTB is a reliable test for confirmation of TB in smear-positive patients and that LCx-MTB could be beneficial as a diagnostic step in smear-negative patients with a high suspicion of pulmonary TB.     

Polymerase chain reaction amplification of Guthrie card deoxyribonucleic acid: extraction of nucleic acid from filter matrices

BACKGROUND: This study was designed to test the association of Chlamydia pneumoniae infection with asthma in a multi-racial population, after adjustments for several potential confounding variables. METHODS: Antibodies to C pneumoniae were measured by microimmunofluorescence in 123 patients with acute asthma, 1518 control subjects admitted to the same hospital with various non-cardiovascular, non-pulmonary disorders, and 46 patients with severe chronic asthma, including some with "brittle" asthma. Acute infection or reinfection was defined by titres of IgG of > or = 512 or IgM > or = 8 or a fourfold rise in IgG, and previous infection by IgG 64-256 or IgA > or = 8. Logistic regression was used to control for likely confounders, including ethnic origin, age, sex, smoking habit, steroid medication, diabetes mellitus and social deprivation, on antibody levels. RESULTS: Antibody titres consistent with acute C pneumoniae infection were found in 5.7% of patients with acute asthma and 5.7% of control patients, while 14.6% of patients with acute asthma and 12.7% of control patients had titres suggesting previous infection. These two groups did not differ significantly. However, titres suggesting previous infection were found in 34.8% of patients with severe chronic asthma: the difference between this group and the control group was statistically significant with an adjusted odds ratio of 3.99 (95% confidence interval 1.60 to 9.97). CONCLUSIONS: These data raise important questions about the previously demonstrated association of C pneumoniae infection with asthma, and suggest that future studies of this association should give particular attention to the presence or absence of a history of severe chronic asthma.     

Polymerase chain reaction for the detection of Bordetella pertussis in clinical nasopharyngeal aspirates

A PCR procedure for the detection of Bordetella pertussis in nasopharyngeal aspirates (NPAs) was developed with primers derived from the pertussis toxin promoter region. The amplification resulted in a 191-bp PCR product specific for B. pertussis. A total of 681 NPAs collected from children with cough lasting >7 days was evaluated by PCR and culture; 104 aspirates were positive by PCR and 93 by culture. Sixteen cases were positive only by PCR and five culture positive aspirates were negative by PCR. An internal control was included in the assay to monitor the performance of the PCR and to identify possible inhibitory components in clinical samples. The PCR method was more efficient than culture in detecting B. pertussis in samples collected late in the disease, in antibiotic-treated children and in patients with mild disease.     

Polymerase chain reaction (PCR) and its possible applications in diagnosis of infection in ophthalmology

Fecal incontinence resulting from pudendal canal syndrome has been treated by pudendal canal decompression (PCD) with satisfactory results. Considering the possible difficulty in exposing the pudendal canal and nerve by the open method, laparoscopic PCD was practiced in 9 women aged between 37 and 52 years. They were complaining of fecal incontinence; urinary stress incontinence was an additional complaint in 4/9 women. Neurologic, manometric, and EMG studies confirmed the diagnosis of pudendal canal syndrome. For laparoscopic PCD a 1-cm incision lateral to the anal orifice was performed. A balloon dilator was introduced in the ischiorectal fossa (IRF) to create a working space, and CO2 was insufflated. Under the guidance of a laparoscope, the IRF was entered and the inferior rectal nerve identified and followed to the pudendal canal. The latter was split open, releasing the pudendal nerve into the IRF. Fecal control was achieved in 7/9 patients and urinary control in 2/4. Fecal and urinary control were associated with improvement in perianal sensation, rectal neck pressure, EMG of external anal sphincter and levator ani muscle as well as in pudendal nerve terminal motor latency. Two women showed no improvement. Failure is suggested to be due to an advanced pudendal neuropathy. In conclusion, laparoscopic PCD is a simple, easy, and safe procedure. It allows for better exposure of the contents of the IRF than the open procedure, thus avoiding injury of the pudendal nerve and its branches during the performance of the PCD.