The detection of mycobacterial DNA sequences in uncultured clinical specimens with cloned Mycobacterium tuberculosis DNA as probes

Comparison of fixatives and fixation time for PCR detection of Mycobacterium in zebrafish Danio rerio

Mycobacteriosis is a common disease of laboratory zebrafish Danio rerio. Different infection patterns occur in zebrafish depending on mycobacterial species. Mycobacterium marinum and M. haemophilum produce virulent infections associated with high mortality, whereas M. chelonae is more widespread and is not associated with high mortality. Identification of mycobacterial infections to the species level provides important information for making management decisions. Observation of acid-fast bacilli in histological sections or tissue imprints is the most common diagnostic method for mycobacteriosis in fish, but only allows for diagnosis to the genus level. Mycobacterial culture followed by molecular or biochemical identification is the traditional approach, but DNA of diagnostic value can also be retrieved from paraffin blocks. Here we investigated the type of fixative, time in fixative before processing, species of mycobacteria, and severity of infection as parameters to determine whether the hsp gene PCR assay (primer set HS5F/hsp667R) could detect and amplify mycobacterial DNA from paraffin-embedded zebrafish. Whole zebrafish were experimentally infected with either M. chelonae or M. marinum, and then preserved in 10% neutral buffered formalin or Dietrich's fixative for 3, 7, 21, and 45 d. Subsequently, fish were evaluated by hematoxylin and eosin and Fite's acid-fast stains to detect mycobacteria within granulomatous lesions. The PCR assay was quite effective and obtained PCR product from 75 and 88% of the M. chelonae- and M. marinum-infected fish, respectively. Fixative type, time in fixative, and mycobacterial species showed no statistical relationship with the efficacy of the PCR test.

Evaluation of polymerase chain reaction for detection of Mycobacterium tuberculosis in pleural fluid

OBJECTIVES

Tuberculosis, a reemergent killer, is threatening to assume serious proportions all over the world, particularly in view of the AIDS pandemic. The detection of mycobacterial DNA by polymerase chain reaction (PCR) in clinical samples is a promising approach for the rapid diagnosis of tuberculous infections. The aims of this study were to evaluate PCR for detection of Mycobacterium tuberculosis in pleural fluids and to correlate the results with adenosine deaminase activity (ADA) estimation and acid-fast bacilli (AFB) screening.

METHODS

The sensitivity and specificity of PCR in detection of mycobacterial DNA in 20 samples of tuberculous pleural effusion were evaluated using 40 samples of nontubercular pleural effusion as controls. The results were correlated with the ADA in all 60 pleural fluids. In addition, AFB detection by Ziehl-Neelsen staining on cytospin smears of all pleural fluids was also compared.

RESULTS

Of the 20 samples of tuberculous pleural effusion, mycobacterium could be detected by AFB staining in 4 samples. Fourteen samples were PCR positive. None of the samples from the control group were AFB or PCR positive. The sensitivity of PCR, therefore, was 70.0% with specificity of 100% (positive predictive value, 100%; negative predictive value, 86.95%). The sensitivity of AFB screening was at best 20%. The mean of ADA values in tubercular pleural effusions was 63.21 U/L (SD, 33.01), and the mean in the control samples was 51.1 U/L (SD, 29.71). Taking a cut-off value of 50 U/L, both the sensitivity and specificity of ADA estimation in diagnosing tuberculosis were only 55%.

CONCLUSION

PCR represents a rapid and sensitive method for the detection of mycobacterial DNA in tuberculous pleural effusions. AFB screening has low sensitivity, and ADA estimation has both low sensitivity and specificity. Therefore, when the clinical suspicion is high and smear result is negative, but the signs and symptoms of M tuberculosis are apparent, PCR is the method of choice for identifying the infection.

Development of a polymerase chain reaction dot-blotting system for detecting cutaneous tuberculosis

For a definitive diagnosis of cutaneous tuberculosis the demonstration of mycobacteria is essential, but this is generally not possible in skin lesions. Routinely available techniques have poor sensitivity and are time consuming, therefore, delaying the institution of timely therapy. The high sensitivity and speed of polymerase chain reaction (PCR) for the detection of infectious agents has prompted investigators to use this technique for the detection of Mycobacterium tuberculosis in body fluids such as cerebrospinal fluid or pleural fluid. In the present study, PCR was used to examine punch biopsy specimens from the affected skin of 10 patients with clinical diagnoses of tuberculosis verrucosa cutis, lupus vulgaris, scrofuloderma, papulonecrotic tuberculide and erythema induratum. A control group of 20 patients included individuals having skin manifestations with definite clinical diagnoses other than cutaneous tuberculosis, such as leprosy, fungal mycetoma, chronic bullous disease of childhood and pemphigus vulgaris. The PCR amplified products were dot hybridized with a probe which was random prime labelled with 32P. The results were compared with routine microbiological and histological findings. Among the test group, six of 10 (60%) were positive for M. tuberculosis by PCR, although their histopathology showed non-specific chronic inflammation with no definite diagnosis. Microbiological investigations, including acid-fast bacillus smear and culture, were positive in a single case of scrofuloderma. All patients in the control group were negative by PCR for M. tuberculosis. The data indicate that the combination of dot hybridization with PCR markedly increased the sensitivity and specificity of PCR. This may be a useful tool in the diagnosis of tuberculosis when conventional methods fail.

Diagnostic value of different PCR assays for the detection of mycobacterial DNA in granulomatous lymphadenopathy

Diagnosis of mycobacterial infection is made by assessment of characteristic histological features, staining of acid-fast bacilli, or agar culture. Recent advances in molecular biology have provided alternative approaches for the detection of mycobacteria, but only limited data are available dealing with the comparative evaluation of these methods. In order to determine the diagnostic applicability of polymerase chain reaction (PCR)-based assays, 20 formalin-fixed and paraffin-embedded lymph nodes with bacille Calmette-Guérin (BCG) lymphadenitis were investigated which in Löwenstein Jensen agar culture were either positive or negative (ten cases each); ten lymph nodes with non-specific lymphadenitis served as negative controls. Ziehl-Neelsen staining as well as three different PCR assays (including nested PCR), amplifying a specific sequence of the Mycobacterium tuberculosis complex or sequences of the 65 kD antigen gene, were performed. Positive culture was only obtained from lymph nodes which had been surgically removed within 20 weeks after vaccination (P < 0.001). In contrast to microscopic examination, which yielded no more information than agar culture, PCR detection of mycobacterial DNA was unrelated to culture findings. Combined use of different assays, as well as DNA extraction from at least three paraffin sections from each specimen, resulted in the detection of mycobacterial DNA in all lymph nodes with amplifiable DNA (18 out of 20 cases). Controls remained consistently negative. Thus, the combined use of different PCR assays is proposed as a rapid and sensitive technique for the detection of mycobacterial DNA in formalin-fixed and paraffin-embedded tissue.

Establishment and evaluation of a multiplex polymerase chain reaction for detection of mycobacteria and specific identification of Mycobacterium tuberculosis complex

OBJECTIVE

To establish a multiplex polymerase chain reaction for detection of mycobacteria and specific identification of Mycobacterium tuberculosis complex and to evaluate the test in the diagnosis of tuberculosis.

DESIGN

Three sets of primers were used to amplify 383 bp, 240 bp and 131 bp DNA fragments from the genes encoding the 65 kDa, MPB64 and the 19 kDa proteins of M. tuberculosis in a single reaction tube. Reaction conditions were optimized with respect to the requirement of DMSO, concentration of MgCl2, annealing and denaturation temperatures and number of amplification cycles. Inhibitory activity in clinical samples was identified by amplifying a 500 bp DNA fragment of the phage lambda along with the mycobacterial targets within the same reaction tube. The multiplex PCR was evaluated in differentiating M. tuberculosis complex from other mycobacteria and in the diagnosis of tuberculosis by testing clinical specimens.

RESULTS

Amplification of the 383 bp DNA fragments was specific to the genus Mycobacterium. The 240 bp DNA fragment was amplified from M. tuberculosis complex and M. fortuitum and the 131 bp DNA fragment was amplified from the mycobacteria of M. tuberculosis complex and M. scrofulaceum. All the three bands were amplified only from M. tuberculosis complex. Applicability of the multiplex PCR is demonstrated in differentiating M. tuberculosis complex from other mycobacteria by using standard strains and clinical isolates. The multiplex PCR was also useful in the detection of inhibitory activity and in the identification of M. tuberculosis complex directly in clinical samples.

CONCLUSION

The multiplex PCR established in this study could differentiate M. tuberculosis complex from other mycobacteria. This test may also be helpful in the early and specific diagnosis of tuberculosis.

The ribosomal intergenic spacer region: a target for the PCR based diagnosis of tuberculosis

SETTING

DNA Diagnostics, The National Diagnostics Centre and University College Hospital, Galway, Republic of Ireland.

OBJECTIVE

To investigate the possibility of developing a DNA probe to distinguish the members of the Mycobacterium tuberculosis complex and develop an assay for the detection of M. tuberculosis in sputum.

DESIGN

The ribosomal intergenic spacer regions from the members of the M. tuberculosis complex were sequenced and analysed for the ability of this region to provide sequence diversity for DNA probe development.

RESULTS

The 100% sequence homology in this region precluded the development of a probe to distinguish the individual members of the M. tuberculosis complex. However it was possible to develop a DNA probe that could specifically detect only the members of the M. tuberculosis complex.

CONCLUSION

A specific DNA probe was developed for the detection of the M. tuberculosis complex and its application to M. tuberculosis detection in sputum was demonstrated.

The detection of Mycobacterium tuberculosis in bone marrow aspirate using the polymerase chain reaction

SETTING

Tygerberg Hospital, South Africa.

OBJECTIVE

Bone marrow aspirate and biopsy were obtained from 37 patients who were in-patients at the Tygerberg hospital. The specificity and sensitivity of the polymerase chain reaction (PCR) in the detection of Mycobacterium tuberculosis in bone marrow aspirate was evaluated.

DESIGN

The PCR was compared to standard culture as well as to clinical and bone marrow biopsy data in 24 patients with suspected tuberculosis (TB).

RESULTS

12 of the 24 patients eventually had definite or probable TB and in these 12 patients the detection incidence was 42% for PCR and 25% for culture.

CONCLUSION

This study confirms that it is possible to use PCR to detect M. tuberculosis in bone marrow aspirate material and that this technique is more sensitive than culture methods. The PCR technique has the added advantage of being a rapid test yielding results within 2 days of sampling. Overall sensitivity for the detection of M. tuberculosis in bone marrow aspirate may be improved to 58% [corrected] by using both culture and PCR techniques.

Detection of Mycobacterium tuberculosis in clinical specimens by polymerase chain reaction and Gen-Probe Amplified Mycobacterium Tuberculosis Direct Test

The polymerase chain reaction (PCR) using oligonucleotides based on the repetitive sequence (IS986) of Mycobacterium tuberculosis as a primer and the Gen-Probe Amplified Mycobacterium Tuberculosis Direct Test (MTD), which combines an M. tuberculosis rRNA amplification method with the hybridization protection assay format, were evaluated for detection of M. tuberculosis in clinical samples. The detection limits of these two assay systems based on nucleic acid amplification for cultured M. tuberculosis were less than 10 cells per reaction. A total of 135 sputum specimens were examined by the two assay systems. The PCR and the MTD systems for detection of M. tuberculosis gave overall positivity rates of 84.2% (32 of 38) and 91.9% (34 of 37), respectively, as compared with 71.9% (23 of 32) by smear and 96.9% (31 of 32) by culture in the liquid medium MB-Check. Procedures for sample preparation used in the two methods were different. Although the sensitivities of the PCR and MTD appeared to be similar to that of culture with the MB-Check system, the two methods based on nucleic acid amplification should be very useful for rapid detection of M. tuberculosis infections without the long time required for culture of M. tuberculosis.

Preparation of a specific RNA probe for detection of Mycobacterium paratuberculosis and diagnosis of Johne's disease

A species-specific recombinant clone (F57) was obtained from a genomic library of Mycobacterium paratuberculosis in the transcription vector pGem 3Z. This clone proved to be specific for all mycobacteria tested, including M. avium, and was able to recognize all of the tested M. paratuberculosis strains isolated from animals and humans (patients with Crohn's disease). The F57 insert was sequenced and a segment of 620 bp with a G + C content of 58.9% was identified. Comparison of the sequence with sequences in the EMBL and UGEN data banks revealed the uniqueness of the F57 sequence, which had no resemblance to other known genes.

Use of PCR in routine diagnosis of treated and untreated pulmonary tuberculosis

AIMS

To assess the routine use of a polymerase chain reaction (PCR) assay for the direct detection of Mycobacterium tuberculosis in expectorated sputum specimens.

METHODS

A pair of primers (20-mer) were designed to amplify the 38 kilodalton protein of M tuberculosis. The specificity of the assay was evaluated in 31 M tuberculosis strains, 15 atypical mycobacterium species, and several commensal bacteria of the upper respiratory tract. The assay was subsequently applied to 519 sputum specimens from 85 inpatients of a chest hospital in Hong Kong.

RESULTS

An amplified product of 239 base pairs was found in all M tuberculosis strains, standard strains of M bovis, and M africanum but not in the other bacterial strains tested. For the 51 patients with pulmonary radiographic lesions, the diagnosis of pulmonary tuberculosis was subsequently confirmed by both culture and PCR in 41 of them. Five patients who were treated before admission were positive by PCR alone. All but one patient in the control group (patients with acute exacerbation of chronic obstructive airway diseases) or those with atypical mycobacterial diseases were PCR negative. The PCR remained positive after four weeks of anti-tuberculosis treatment in 29 patients, 16 of whom had become culture negative.

CONCLUSION

This PCR assay is a useful technique for the diagnosis of untreated and recently treated cases of pulmonary tuberculosis.

Detection of Mycobacterium tuberculosis DNA in clinical samples by using a simple lysis method and polymerase chain reaction

We have evaluated the polymerase chain reaction for detection of Mycobacterium tuberculosis in clinical samples from patients with tuberculous infection. Two simple methods for mycobacterial DNA release have been compared: sonication and lysis with nonionic detergents and proteinase K. The more effective method was the enzymatic technique. By using this protocol with 75 specimens we detected M. tuberculosis DNA in all of the samples, whereas only 48 and 71 samples were positive by acid-fast staining and culture, respectively.

Identification of Mycobacterium tuberculosis DNA in a case of lupus vulgaris

A variety of cutaneous lesions are believed to result from the presence of Mycobacterium tuberculosis. Demonstration of M. tuberculosis directly or in culture in some of these eruptions can be difficult. We studied a typical case of lupus vulgaris that had been followed for several years with frequent unrewarding biopsies and cultures to see if M. tuberculosis DNA could be demonstrated in skin biopsy specimens. We used the polymerase chain reaction and a primer/probe set specific for a region in the gene for the 65 kd antigen of M. tuberculosis to search for M. tuberculosis complex DNA. M. tuberculosis complex DNA was demonstrated in archival skin biopsy specimens from the lesion of lupus vulgaris. The polymerase chain reaction and specific primer/probe sequences can be used to demonstrate M. tuberculosis complex DNA in skin lesions. A variety of skin lesions believed to be related to tuberculosis (tuberculids) can be revisited with these techniques and studied for the presence of an infectious agent.

A comparative study of the polymerase chain reaction and conventional procedures for the diagnosis of tuberculous pleural effusion

Preliminary reports by ourselves and others suggest that amplification of mycobacterial DNA by the polymerase chain reaction (PCR) is a sensitive and rapid diagnostic test for tuberculosis. We recently described a PCR assay with a 336 bp repetitive sequence specific for Mycobacterium tuberculosis as the DNA target, which gave encouraging results in culture-positive smear-negative clinical specimens. In the present prospective study of patients with pleural effusions we compared PCR of the pleural fluid with conventional procedures. 84 adult patients with pleural effusions were divided into 4 groups. In group A (44 patients), M. tuberculosis was detected by culture of pleural fluid, pleural biopsy or extrapleural source. In group B (6 patients), tuberculous infection was confirmed by histology (group A excluded). Group C (3 patients) had clinical evidence of tuberculosis. Group D (31 patients) had no evidence of active M. tuberculosis infection. Analysis of the pleural fluid confirmed a sensitivity for PCR of 81%. The sensitivity of pleural fluid culture, culture of pleural biopsy, and histology of biopsy was 52.8%, 69.8% and 77.3% respectively. There were however 7 PCR positive results within group D; 6 of these were in patients with malignant effusions. We conclude that for the diagnosis of M. tuberculosis PCR is more sensitive than laboratory culture as determined by the analysis of pleural fluids. Positive PCR results among patients with malignant effusions may be false-positives or the result of latent tuberculous infections. PCR should remain an investigational procedure until prospective studies in high and low prevalence areas have critically evaluated the specificity of the assay.

Detection of genes in feces by booster polymerase chain reaction

A 321-bp fragment intragenic to the gene ereA carried by Escherichia coli BM2195 was used as a model target to study the conditions under which DNA amplification by booster polymerase chain reaction can be used to detect specific bacterial DNA sequences in fecal specimens. When target E. coli cells were mixed with 41 freshly obtained fecal specimens, the polymerase chain reaction detection limit varied from 4.5 to 7.1 log CFU/g of feces, depending on the individual fecal specimen used to prepare the test sample. These variations were not statistically related to the sex or age of the subject from whom the specimen was obtained. After storage of the samples for 4 weeks at room temperature on swabs or filter papers, no loss in sensitivity was observed.

Detection and identification of mycobacteria by amplification of a segment of the gene coding for the 32-kilodalton protein

A polymerase chain reaction (PCR) assay for the rapid detection of mycobacterial DNA is described. Oligonucleotide primers, derived from the sequence of a gene coding for the 32-kDa antigen of Mycobacterium tuberculosis, amplified DNA from all 28 species of mycobacteria tested. All nonmycobacterial species tested were negative. An oligonucleotide probe hybridized to the PCR products of the strains belonging to the M. tuberculosis complex. This method could detect as little as 50 fg, as tested with purified M. tuberculosis DNA. By this amplification method, 127 sputum specimens were tested, with 7.9% of the specimens proving to be inhibitory in PCR. The sensitivity of detection by PCR compared with that by culture was 55.9%; when the inhibitory specimens were excluded, the sensitivity was 70.4%. The specificity of PCR combined with hybridization was 100%.

Characterization of a DNA probe for detection of Mycobacterium tuberculosis complex in clinical samples by polymerase chain reaction

We cloned and sequenced a DNA fragment from Mycobacterium tuberculosis for use in the identification of members of the M. tuberculosis complex. The DNA probe for culture confirmation had a sensitivity and a specificity of 100%. By using primers developed from this probe, the polymerase chain reaction detected 20 mycobacteria by ethidium bromide staining. This polymerase chain reaction system demonstrated 98% sensitivity and 100% specificity for detection of the M. tuberculosis complex in 200 sputum specimens.

The detection of Mycobacterium tuberculosis in uncultured clinical specimens using the polymerase chain reaction and a non-radioactive DNA probe

A Sal I-Hin dIII restriction fragment from Mycobacterium tuberculosis was found to hybridize specifically with genomic DNA from M. tuberculosis. Primers were designed from the sequence of this fragment and used to amplify uniquely M. tuberculosis-group DNA in a polymerase chain reaction. It is suggested that a combination of these primers and an acetylaminofluorene-labelled probe will prove to be a useful tool for the early diagnosis of tuberculous infections.

New microbial diagnosis

Rapid methods for comprehensive nucleic acid analysis are essential for the progress in basic research. In microbial diagnosis nucleic acid analyses are useful for achieving quick, sensitive results with new dimensions of specificity. As to specificity, hybridisation tests are easily constructed for genus or species specific microbial typing or for the detection of genes accounting for pathogenic properties. Modern sequence analysis allows rapid detection of mutations eg., those conferring antiviral resistance. A new level of sensitivity comparable to that of the conventional enrichment culture is obtainable by enzymatic amplification (PCR) of microbial nucleic acids before detection. PCR-technology has proved particularly useful in the diagnosis of microbial infections when the organisms are impossible or tedious to cultivate. For reliable diagnostic use the performance of in vitro amplification requires extreme care to prevent false positive results owing to carry over problems. In conclusion, nucleic acid analyses are expanding the potential for diagnosing microbial infections and may well replace some conventional diagnostic methods.

Amplification of a species-specific DNA fragment of Mycobacterium tuberculosis and its possible use in diagnosis

In recent work, a species-specific Mycobacterium tuberculosis DNA fragment was cloned and sequenced. On the basis of its nucleotide sequence, two oligonucleotides were synthesized and used as primers for polymerase chain reaction (PCR) amplification. A 396-bp fragment was specifically amplified from the M. tuberculosis genome. No amplification was observed from any of 10 different mycobacterial strains, included those belonging to the M. tuberculosis complex. Neither was this fragment amplified from genomes of humans or different species of clinically important bacteria. The PCR product was detected by dot blot hybridization even when as little as 10 fg of purified M. tuberculosis DNA was used. This amplification method was subsequently used to detect and identify bacilli in different clinical samples, such as sputum, urine, and cerebrospinal fluid. A good correlation was observed between the results obtained with the PCR method that we describe and other diagnostic tests currently used. Thus, PCR amplification of this genomic fragment is proposed as a specific, rapid, and sensitive test for the diagnosis of infection with M. tuberculosis.

Use of DNA amplification for the rapid identification of Mycobacterium bovis

DNA amplification using the polymerase chain reaction technique was evaluated for rapid identification of Mycobacterium bovis. Two oligonucleotide primers of 20 bases in length were constructed to target a region of the gene encoding the M. bovis secretory protein, MPB70. The amplification reaction produced a single product 372 bp in size which was readily detected by agarose gel electrophoresis. All 84 strains of M. bovis tested produced a positive signal in the amplification reaction. In addition all isolates fro the M. tuberculosis complex tested, with the exception of M. microti, gave a single band at 372 bp. No amplified product was detected when 24 other species of mycobacteria and species from four other genera were tested. The sensitivity of the test was such that a single viable cell could be detected in the reaction. This technique provides a simple and extremely sensitive method of identifying isolates of M. bovis and other pathogenic M. tuberculosis complex organisms.

Evaluation of a polymerase chain reaction for the diagnosis of tuberculosis

A polymerase chain reaction for the specific detection of Mycobacterium tuberculosis has been developed and evaluated for clinical applicability. Primers were designed to amplify a 240 base pair region in the MPB 64 protein coding gene (nts 460-700). From among 15 different DNA templates tested (including 10 species of mycobacteria) PCR amplified the DNA from M. tuberculosis complex only, demonstrating its exquisite specificity. Sensitivity studies using serial ten-fold dilutions of M. tuberculosis bacilli determined the limit of detectability to be 10 organisms. A total of 143 clinical specimens were analysed. This consisted of 26 known non-tuberculous specimens (control group) and 117 specimens received at the Tuberculosis Diagnostic Service of AIIMS (test group). None of the specimens in the control group was positive by PCR. Out of 117 specimens in the test group, 19 were culture positive for mycobacteria and 17 of these isolates were identified as M. tuberculosis. All the specimens from which M. tuberculosis was grown were also PCR positive. The remaining two isolates were identified as mycobacteria other than M. tuberculosis and these two specimens were PCR negative. An additional 14 culture negative specimens were PCR positive yielding an overall M. tuberculosis positivity rate of 26.5% (31/117) compared to 14.5% (17/117) by culture. The superior sensitivity of PCR over culture was more evident in non-pulmonary cases where PCR picked up 10 cases in addition to three culture positives out of 69 specimens. On the other hand, out of 48 pulmonary specimens only four cases in addition to 14 culture positives were picked up by PCR.

Direct detection of Mycobacterium tuberculosis in clinical specimens by DNA amplification

A polymerase chain reaction assay was developed for the amplification of a 336-bp repetitive fragment in the chromosome of Mycobacterium tuberculosis. The assay is specific for M. tuberculosis and can be used to detect the amount of DNA present in less than 10 organisms. It was used to demonstrate M. tuberculosis DNA in 14 of 26 clinical specimens (from cerebrospinal fluids, pleural fluid aspirates and biopsies, pericardial fluid aspirates, and an open lung biopsy), and it was shown to be at least as sensitive as conventional culture techniques with these specimens.

The detection of Gardnerella vaginalis DNA sequences in uncultured clinical specimens with cloned G. vaginalis DNA as probes

Cloned Gardnerella vaginalis DNA were selected from a plasmid DNA library constructed with partially restriction endonuclease Hind III-digested genomic DNA of G. vaginalis to serve as DNA probe in detecting G. vaginalis. The level of detection was determined to be approximately 10,000 cells by slot-blot DNA hybridization. This probe DNA will not cross-hybridize with DNA of a number of non-Gardnerella micro-organisms commonly found in female genital tract. The DNA probe-based hybridization test may become a useful tool for the identification of G. vaginalis in uncultured clinical specimens.

New approaches to the diagnosis of tuberculosis in childhood with special reference to neurotuberculosis

Bacteriological diagnosis of tuberculosis in childhood is often unsuccessful owing to the difficulty in obtaining suitable specimens. Many attempts have been made to diagnose tuberculosis immunologically but with very limited success. Positive tuberculin reactions may be the result of nonspecific sensitization while negative reactions occur in undernourished children. Serodiagnostic tests suffer from problems of specificity, even when very specific antigens are used, and are often least helpful in diagnostically difficult cases. Detection of antigen has proved to be of more value, especially with clean specimens such as cerebrospinal and pleural fluids. Detection of specific components of Mycobacterium tuberculosis by linked gas chromatography and mass spectroscopy is very sensitive and specific but the equipment is very costly. Detection of specific DNA sequences of M. tuberculosis in specimens by use of labelled 'DNA probes' is rather insensitive although the sensitivity may be increased greatly by use of the polymerase chain reaction to amplify small amounts of the specific DNA. Non specific indicators of tuberculosis are generally unhelpful although the bromide partition test and assay of the enzyme adenosine deaminase in cerebrospinal fluid appear to be of value in the diagnosis of tuberculous meningitis. More research is required to develop a simple, specific and automated test for tuberculosis in childhood.

Detection and identification of Mycobacterium tuberculosis by DNA amplification

The polymerase chain reaction (PCR) was used to identify mycobacterial DNA sequences in uncultured clinical specimens. Two oligonucleotide primers derived from the sequence of a gene that codes for the 65-kilodalton antigen of Mycobacterium tuberculosis amplified DNA from all 11 species of mycobacteria tested. Amplified DNAs of nontuberculosis mycobacteria were found to be approximately 20 to 40 bases shorter than those from M. tuberculosis and Mycobacterium bovis BCG. DNA equivalent to that present in as few as 40 M. tuberculosis cells either alone or in the presence of DNA equivalent to that in 10(6) human cells could be detected. Results from analysis of cultured bacteria and clinical specimens showed PCR was sensitive and specific both in detecting mycobacteria and in differentiating M. tuberculosis and BCG from other species of mycobacteria. The PCR method with the primers reported here may become a useful tool in the early and rapid detection of mycobacterial infections in uncultured clinical specimens.

Diagnosis of tuberculosis by polymerase chain reaction

For the diagnosis of extrapulmonary tuberculosis in adults and all forms of tubercular infections in children, microscopic and cultural techniques have been shown to be inadequate. Many serological techniques have been employed for non culture diagnosis of tuberculosis. Early promising results have repeatedly given way to subsequent findings of non-specificity. Major mycobacterial antigens have been shown to be heat shock proteins which are highly conserved in nature. DNA probes for tuberculosis are specific but have a sensitivity equivalent to AFB smear examination. Polymerase Chain Reaction (PCR) with its ability to selectively amplify DNA fragments of interest offers a potentially powerful technique for the rapid, specific and sensitive diagnosis of tuberculosis. Samples from partially treated patients could be culture negative but can be detected by PCR.

Specific detection of Mycobacterium tuberculosis complex strains by polymerase chain reaction

During the screening of a Mycobacterium tuberculosis lambda gt-11 gene library with monoclonal antibodies, we detected a recombinant clone, lambda PH7311, which contained a mycobacterial DNA insert that hybridized specifically with DNA of M. tuberculosis complex strains. Part of this insert was sequenced and used for the development of an M. tuberculosis complex-specific polymerase chain reaction (PCR). Only strains belonging to species of the M. tuberculosis complex group contained an amplifiable fragment of 158 base pairs (bp). This fragment was absent in all strains tested belonging to 15 other mycobacterial species. After amplification by PCR and dot blot hybridization with a digoxigenin-labeled oligonucleotide, the limit of detection of purified genomic M. tuberculosis DNA amounted to a quantity corresponding to 20 bacterial cells. By this technique about 10(3) M. tuberculosis bacteria were detectable in sputum. Using PCR, we were also able to detect M. tuberculosis cells in clinical material such as pleural fluid, bronchial washings, and biopsies, and these results were comparable with those obtained by classical bacterial culture. Of 34 M. tuberculosis strains, 5 did not carry the amplifiable 158-bp fragment, which occurs usually as a single copy in the chromosome. Evidence is presented that the 158-bp fragment is located near a repeated sequence in the chromosome. We presume that strains which did not carry the 158-bp fragment have lost a chromosomal segment by a genetic rearrangement induced by the repetitive DNA element.

Genus- and species-specific DNA probes to identify mycobacteria using the polymerase chain reaction

Differential diagnosis of Mycobacterium tuberculosis, M. avium, and other mycobacteria remains a lengthy process. Recently, the use of DNA probes has been proposed as a new approach for a more specific and rapid diagnosis. Here, we report the cloning and sequencing of a genus-specific probe for Mycobacterium and a species-specific M. avium probe. The genus-specific probe hybridizes with DNA from nine ATCC type strains and 13 isolates of mycobacteria but not to non-mycobacterial DNA. In addition, the cloned fragment could also be amplified by polymerase chain reaction (PCR) in DNa of ten different mycobacterial type strains. The M. avium specific probe hybridizes strongly to sequences amplified in M. avium but not other mycobacterial or non-mycobacterial DNA. Amplification of the target sequence by PCR allowed the detection of 1 fg of all mycobacterial DNA tested for the genus-specific probe and 1 fg of M. avium DNA for the species-specific probe.

Sequence analysis and amplification by polymerase chain reaction of a cloned DNA fragment for identification of Mycobacterium tuberculosis

Analysis of the 1,016-base-pair sequence of a putative probe for identification of Mycobacterium tuberculosis revealed two almost identical fragments of 507 and 509 bases. From this sequence two pairs of primers were synthesized (MtbAB and MtbCD), ranging from 18 to 22 nucleotides, for use in polymerase chain reactions (PCRs) with DNA from six reference strains of M. tuberculosis, as well as type strains of M. bovis, M. bovis BCG, M. kansasii, M. avium, M. intracellulare, and M. scrofulaceum. Although there was amplification of DNA from all mycobacterial strains included in the study, when used as probes, a predominant band, fragment CD from M. tuberculosis H37Rv DNA, proved to be more specific for strains of M. tuberculosis than the original probe, pMTb4, was. Amplified fragments from as little as 1 fg of DNA (equivalent to one-fifth of an organism) could be resolved on ethidium bromide-stained gels loaded with a 1/10 volume of PCR. Furthermore, it was possible to amplify specific DNA sequences from frozen M. tuberculosis H37Rv organisms which were thawed prior to PCR.

Rapid diagnosis of tuberculosis by amplification of mycobacterial DNA in clinical samples

A method based on DNA amplification and hybridisation for the rapid detection of Mycobacterium tuberculosis was used to test 35 clinical specimens (sputum, gastric aspirate, abscess aspirate, biopsy sample) from 34 patients in whom tuberculosis was suspected. M tuberculosis was detected in 15 specimens, 2 of which were negative by standard microbiological criteria (microscopy and/or culture). 20 specimens, negative by standard methods, were also negative by the amplification method. M tuberculosis was also detected in peripheral blood samples of 2 of 4 patients with AIDS from whom the organism had been isolated.

Detection and identification of mycobacteria by amplification of mycobacterial DNA

A 383bp segment of the gene coding for the 65kD mycobacterial antigens from Mycobacterium tuberculosis, Mycobacterium bovis, Mycobacterium avium, Mycobacterium paratuberculosis, and Mycobacterium fortuitum was amplified using Taq polymerase and synthetic oligonucleotide primers and the amplified DNAs from four of these species were compared by nucleotide sequencing. Although the gene segments from these species showed considerable similarity, oligonucleotide probes which could distinguish M. tuberculosis/M. bovis, M. avium/M. paratuberculosis and M. fortuitum could be identified. Samples containing 10(6) human cells and serial dilutions of a suspension of intact mycobacteria were prepared, DNA was extracted, the segment of the mycobacterial DNA sequence amplified, and the amplified DNA hybridized with oligonucleotide probes. In two independent experiments, this procedure permitted the detection and identification of less than 100 mycobacteria in the original sample. These results suggest that this approach may prove useful in the early diagnosis of mycobacterial infection.

Detection and quantitation of Anaplasma marginale in carrier cattle by using a nucleic acid probe

Cattle which have recovered from acute infection with Anaplasma marginale, a rickettsial hemoparasite of cattle, frequently remain persistently infected with a low-level parasitemia and serve as reservoirs for disease transmission. To fully understand the role of these carriers in disease prevalence and transmission, it is essential that low levels of parasitemia can be accurately detected and quantitated. We have developed a nucleic acid probe, derived from a portion of a gene encoding a 105,000-molecular-weight surface protein, that can detect A. marginale-infected erythrocytes. The probe is specific for A. marginale and can detect 0.01 ng of genomic DNA and 500 to 1,000 infected erythrocytes in 0.5 ml of blood, which is equivalent to a parasitemia of 0.000025%. This makes the probe at least 4,000 times more sensitive than light microscopy. Hybridization of the probe with treated blood from animals proven to be carriers of anaplasmosis showed that parasitemia levels were highly variable among carriers, ranging from greater than 0.0025 to less than 0.000025%. Parasitemia levels of individual animals on different dates were also variable. These results imply that, at any given time, individuals within a group of cattle may differ significantly in their abilities to transmit disease.