Identification of Mycobacterium tuberculosis by polymerase chain reaction

devR PCR for the diagnosis of intraocular tuberculosis

PURPOSE

To compare the efficacy of devR and MPB64 PCR in the diagnosis of intraocular tuberculosis.

METHODS

Prospective, nonrandomized study. Seventy-five patients were enrolled in 3 groups. Group A had 25 patients with presumed intraocular tubercular uveitis, group B had 25 controls with specific uveitis other than tubercular uveitis, and group C included 25 non-uveitic negative controls. The undiluted vitreous/aqueous samples were collected and subjected to PCR assay for devR and MPB64 gene sequence of Mycobacterium tuberculosis (MTB) to detect sensitivity and specificity.

RESULTS

devR PCR was positive in 16 (64%) out of 25 patients with presumed tubercular uveitis. MPB64 PCR was positive in 18 (72%) out of 25 patients with presumed tubercular uveitis. The sensitivity and specificity of devR were 64 and 100%, respectively. The sensitivity and specificity of MPB64 PCR were 72 and 100%, respectively.

CONCLUSION

devR PCR is not a better tool than MPB64 PCR for diagnosing intraocular tuberculosis.

MALDI-TOF mass spectrometry tools for bacterial identification in clinical microbiology laboratory

Since the early 1980s, mass spectrometry has emerged as a particularly powerful tool for analysis and characterization of proteins in research. Recently, bacteriologists have focused their attention on the use of mass spectrometry (MS) for bacterial identification, especially Matrix Assisted Laser Desorption Ionization Time-Of-Flight (MALDI-TOF). Moreover, recent publications have evaluated MALDI-TOF in microbiology laboratory for routine use. MALDI-TOF-MS is a rapid, precise, and cost-effective method for identification of intact bacteria, compared to conventional phenotypic techniques or molecular biology. Furthermore, it allows identification of bacteria directly from clinical samples (blood cultures for example). The goal of this review was to update recent data concerning routine identification of microorganisms by MALDI-TOF in the clinical microbiology laboratory.

Comparison of two matrix-assisted laser desorption ionization-time of flight mass spectrometry methods with conventional phenotypic identification for routine identification of bacteria to the species level

Bacterial identification relies primarily on culture-based methodologies requiring 24 h for isolation and an additional 24 to 48 h for species identification. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is an emerging technology newly applied to the problem of bacterial species identification. We evaluated two MALDI-TOF MS systems with 720 consecutively isolated bacterial colonies under routine clinical laboratory conditions. Isolates were analyzed in parallel on both devices, using the manufacturers' default recommendations. We compared MS with conventional biochemical test system identifications. Discordant results were resolved with "gold standard" 16S rRNA gene sequencing. The first MS system (Bruker) gave high-confidence identifications for 680 isolates, of which 674 (99.1%) were correct; the second MS system (Shimadzu) gave high-confidence identifications for 639 isolates, of which 635 (99.4%) were correct. Had MS been used for initial testing and biochemical identification used only in the absence of high-confidence MS identifications, the laboratory would have saved approximately US$5 per isolate in marginal costs and reduced average turnaround time by more than an 8-h shift, with no loss in accuracy. Our data suggest that implementation of MS as a first test strategy for one-step species identification would improve timeliness and reduce isolate identification costs in clinical bacteriology laboratories now.

Development and validation of a modified broad-range 16S rDNA PCR for diagnostic purposes in clinical microbiology

Broad-range PCR followed by sequencing identifies bacterial pathogens, even in challenging settings such as patients receiving antibiotics or infected with fastidious or non-cultivable organisms. The major problem with broad-range PCR is the risk of sample contamination. Risk is present at every step of the procedure, starting from sample collection. Contaminating bacterial DNA may be present not only in laboratory reagents but also at the surface of plastic consumables and containers used for specimen drawing and transport to the diagnostic laboratory. Contaminating DNA is amplified efficiently, leading to false-positive results. Thus, high specificity depends on eliminating such spurious targets, an awkward problem given the abundance of such targets and a highly sensitive method that detects very small numbers of molecules. Several investigators have reported strategies for eliminating the amplification of contaminating DNA sequences. So far, none of these methods has been entirely effective and reproducible. Here we describe a method that uses Exonuclease III (ExoIII) to disable contaminating sequences from acting as templates, while maintaining the high sensitivity of PCR for pathogen DNA. We use this assay in 144 clinical specimens from normally sterile sites, identifying pathogens from 24 (17%). Conventional methods identified pathogens in only four of these specimens, all of which were positive for the same pathogen by PCR. Compared with conventional methods, broad-range PCR with ExoIII pre-treatment of reagents substantially improves the diagnostic yield of bacterial pathogen identification from normally sterile sites.

Rapid diagnosis of tuberculous meningitis: a comparative evaluation of in-house PCR assays involving three mycobacterial DNA sequences, IS6110, MPB-64 and 65 kDa antigen

A PCR was standardized for amplifying three different mycobacterial--IS6110, MPB-64, 65 kDa DNA sequences. A comparative evaluation of the three PCR assays was carried out for the rapid diagnosis of tuberculous meningitis (TBM) using cerebrospinal fluid (CSF) specimens. While the IS6110 PCR was a single-step amplification reaction, the MPB-64 and 65 kDa antigen PCR assays were nested reactions. A total of 176 cerebrospinal fluid (CSF) samples from 176 patients were subjected to amplification of the three different mycobacterial sequences. Amongst them, 45 samples were obtained from confirmed cases of TBM (culture positive) and 56 samples were obtained from clinically suspected cases of TBM which were culture-negative. The remaining 75 CSF samples were categorized under the non-infectious and infectious illness of the central nervous system (CNS). Against a gold standard of culture, a sensitivity of 98% (NPV=99%) and a specificity of 100% (PPV=100%) was observed with the IS6110 PCR. Among the nested PCRs, a sensitivity of 91% (NPV=94%) and a specificity of 91% (PPV=85%) was observed with the MPB-64 assay, while the 65 kDa protocol had an associated sensitivity of 51% (NPV=76%) and a specificity of 92% (PPV=79%). These findings suggest that among the nested PCR assays, the MPB-64 PCR assay was associated with an enhanced degree of sensitivity and was comparable in terms of specificity. Our study also demonstrates that the IS6110 assay, while being a single-step PCR had the advantage of being a rapid test for the diagnosis of TBM, with increased sensitivity and enhanced specificity as compared to the nested PCR protocols.

Rapid bacterial identification using evanescent-waveguide oligonucleotide microarray classification

Bacterial identification relies primarily on culture-based methodologies and requires 48-72 h to deliver results. We developed and used i) a bioinformatics strategy to select oligonucleotide signature probes, ii) a rapid procedure for RNA labelling and hybridization, iii) an evanescent-waveguide oligoarray with exquisite signal/noise performance, and iv) informatics methods for microarray data analysis. Unique 19-mer signature oligonucleotides were selected in the 5'-end of 16s rDNA genes of human pathogenic bacteria. Oligonucleotides spotted onto a Ta(2)O(5)-coated microarray surface were incubated with chemically labelled total bacterial RNA. Rapid hybridization and stringent washings were performed before scanning and analyzing the slide. In the present paper, the eight most abundant bacterial pathogens representing >54% of positive blood cultures were selected. Hierarchical clustering analysis of hybridization data revealed characteristic patterns, even for closely related species. We then evaluated artificial intelligence-based approaches that outperformed conventional threshold-based identification schemes on cognate probes. At this stage, the complete procedure applied to spiked blood cultures was completed in less than 6 h. In conclusion, when coupled to optimal signal detection strategy, microarrays provide bacterial identification within a few hours post-sampling, allowing targeted antimicrobial prescription.

Assessment of possible tuberculous lymphadenopathy by PCR compared to non-molecular methods

Tuberculosis is a major public health problem in India and other developing countries and has formed a lethal partnership with AIDS. It often presents a diagnostic challenge especially when clinical presentation is suggestive but bacteriological proof is lacking. The objective of this study was to compare the various diagnostic techniques in clinically suspected cases of tubercular lymph nodes and to find a suitable, cost-effective but sensitive and specific method for diagnosis. A total of 100 cases were recruited for the study. Fine needle aspiration cytology was done in all cases and the smears prepared were processed for Giemsa, Ziehl-Neelsen's, Kinyoun and Papanicolaou stains. Parts of the aspirated materials were assessed by fluorescent staining, culture and PCR. Seventy-four percent of aspirates were positive by fluorescent stain while only 22% were positive by culture. PCR could be performed in 55 cases, out of which 22 (40%) were positive. When compared to culture, the sensitivity and specificity of PCR were found to be 89.5% and 86.1%, respectively. Fluorescent stain was found to be the most sensitive (81.8%) of the conventional methods but showed poor specificity (28.2%). Interestingly, PCR detected 80% of smear-negative but culture-positive cases.

Rapid diagnosis of mycobacterial infections and quantitation of Mycobacterium tuberculosis load by two real-time calibrated PCR assays

Sensitive and specific techniques to detect and identify Mycobacterium tuberculosis directly in clinical specimens are important for the diagnosis and management of patients with tuberculosis (TB). We developed two real-time PCR assays, based on the IS6110 multicopy element and on the senX3-regX3 intergenic region, which provide a rapid method for the diagnosis of mycobacterial infections. The sensitivity and specificity of both assays were established by using purified DNA from 71 clinical isolates and 121 clinical samples collected from 83 patients, 20 of whom were affected by TB. Both assays are accurate, sensitive, and specific, showing a complementary pattern of Mycobacterium recognition: broader for the IS6110-based assay and restricted to the M. tuberculosis complex for the senX3-regX3-based assay. Moreover, the addition of a synthetic DNA calibrator prior to DNA extraction allowed us to measure the efficiency of DNA recovery and to control for the presence of PCR inhibitors. The mycobacterial burden of the clinical samples, as assessed by direct microscopy, correlates with the M. tuberculosis DNA load measured by the senX3-regX3-based assay. In addition, reduced levels of M. tuberculosis DNA load are present in those patients subjected to successful therapy, suggesting a potential use of this assay for monitoring treatment efficacy. Therefore, these assays represent a fully controlled high-throughput system for the evaluation of mycobacterial burden in clinical specimens.

Idiopathic Hypertrophic Cranial Pachymeningitis Associated With Total Occlusion of the Dural Sinuses-Case Report-

A 44-year-old man presented with a rare case of idiopathic hypertrophic cranial pachymeningitis manifesting as generalized seizure. Neuroimaging and pathological examinations showed the typical features of hypertrophic cranial pachymeningitis. Tuberculosis was a possible cause based on the positive purified protein-derived skin test, but the origin of the disease was not confirmed by further examinations. Cerebral angiography showed total occlusion of the dural sinuses with development of the emissary veins. Histological examination of the dura showed thickening of the fibrous tissue with rare inflammatory cells, suggestive of the extremely long duration of the disease. The diagnosis was idiopathic hypertrophic cranial pachymeningitis, but was treated only with anticonvulsants. The disease did not progress during follow up of 3 years. Idiopathic hypertrophic cranial pachymeningitis may have various causes related to unusual forms of infectious or autoimmune disorders.

Polymerase chain reaction based detection of Mycobacterium tuberculosis in tissues showing granulomatous inflammation without demonstrable acid-fast bacilli

BACKGROUND

Cutaneous tuberculosis is especially difficult to distinguish from other granulomatous dermatoses. We used polymerase chain reaction (PCR) to evaluate the incidence of cutaneous tuberculosis and atypical mycobacterial infection in formalin-fixed, paraffin-embedded tissues with unspecified granulomatous inflammation and negative results for acid-fast bacilli (AFB), and analyzed the pattern of cutaneous tuberculosis in this group of patients.

METHODS

A total of 38 specimens which had been collected from 36 patients and fulfilled the criteria for tissues described above were used in this study. Two different primer pairs targeting the gene encoding for 16S ribosomal RNA (common to all mycobacteria) and the insertion sequence IS6110 (specific for M. tuberculosis complex) were used in the PCR assays. The clinical characteristics, histopathologic findings, and culture results of the patients were also analyzed.

RESULTS

Four specimens were excluded from the analysis due to the lack of internal control testing. Of the remaining 34 specimens, 22 were PCR positive for the 16S rRNA gene. Among them, 18 specimens were PCR positive for both the 16S rRNA gene and IS6110. Cutaneous tuberculosis could be diagnosed in these 18 cases (56.2%). Out of the 18 cases, there were 8 women and 10 men. The age range was 15-77 years (mean: 44.2 years). After reviewing their clinical presentation, 11 cases were considered as tuberculosis verrucosa cutis, 6 cases as lupus vulgaris, and 1 case as erythema induratum. The remaining 4 cases (12.5%) positive only for 16S rRNA gene were considered as possible atypical mycobacteria infection.

CONCLUSIONS

These results show that in paucibacillary form of cutaneous tuberculosis with unclassical clinical and histological presentation, this PCR system provides rapid and sensitive detection of M. tuberculosis DNA in formalin-fixed, paraffin-embedded specimens. Cutaneous tuberculosis represents a significant proportion in specimens showing granulomatous inflammation. In areas like Taiwan, where prevalence of pulmonary tuberculosis is still high, tuberculosis verrucosa cutis and lupus vulgaris are common forms of cutaneous tuberculosis and are seen more frequently than atypical mycobacterial infection.

Assessment of lymph node tuberculosis in northern Germany: a clinical review

AIM OF STUDY

To evaluate patient profiles, diagnostic approaches, and treatment strategies in patients with lymph node tuberculosis.

METHODS

Demographic data, diagnostic findings, and therapies were retrospectively analyzed in 60 patients with lymph node tuberculosis who were hospitalized between 1992 and 1999.

RESULTS

Thirty percent (n = 18) of patients were natives, and 70% were immigrants (n = 42). The cervical lymph nodes were most frequently involved (63.3%), followed by the mediastinal lymph nodes (26.7%) and the axillary lymph nodes (8.3%). All patients (except one patient who was HIV-positive) showed a positive response to tuberculin skin testing. Lymph node excision and fine-needle aspiration (FNA) were similarly effective in obtaining sufficient material for histologic and microbiological analysis. Mycobacterium tuberculosis was identified in 43.3% of patients by microbiological testing, and culture methods showed the highest sensitivity. Despite standard treatment, the initial enlargement of the lymph nodes occurred in 20% of patients and local complications occurred in 10%.

CONCLUSION

Lymph node tuberculosis is still an important issue in developed countries and has to be considered in differential diagnosis. The best approach appears to be a combination of skin testing and FNA. Negative results in the identification of M tuberculosis do not exclude the diagnosis of lymph node tuberculosis.

Comparison of in-house polymerase chain reaction method with the Roche Amplicor technique for detection of Mycobacterium tuberculosis in cytological specimens

Two techniques have been approved by the United States FDA for diagnosis of tuberculosis in smear positive sputa: LCX M. tuberculosis, a ligase chain reaction procedure manufactured by Abbott Laboratories, and Amplicor, a polymerase chain reaction (PCR) procedure manufactured by Roche. However, these commercial methods are expensive and beyond the reach of laboratories in most developing countries. We compared the Roche Amplicor kit with an in-house PCR using a primer set for Mycobacterium tuberculosis/bovis directed at MPB 64 protein gene. It was able to distinguish between M. tuberculosis, M. avium, M. gordonii, M. intracellularae, and M. kansasii. Fifty-seven cytological samples were submitted to the laboratory for molecular diagnosis of M. tuberculosis. Both procedures were run on every sample submitted and the two methods agreed completely. The custom-made method is less expensive than the commercial technique.

Clinical evaluation of Amplicor Mycobacterium detection system for the diagnosis of pulmonary mycobacterial infection using sputum

SETTING

The Amplicor Mycobacterium detection kit was evaluated for the diagnosis of active pulmonary mycobacterial infection using sputum.

OBJECTIVE

To assess the clinical usefulness of the Amplicor Mycobacterium kit for the diagnosis of pulmonary tuberculosis and non-tuberculous mycobacterial infection in the country of medium prevalence.

DESIGN

All the patients were diagnosed with bacterial, histopathological, and clinical 'gold standard'. The sensitivity and specificity for diagnosing clinically active pulmonary tuberculosis and Mycobacterium avium and Mycobacterium intracellulare infections were evaluated comparing Amplicor results and clinical diagnosis.

RESULTS

A total of 1088 sputum specimens were collected from 780 in and out patients. Mycobacteria were recovered from 339 specimens by culture. The sensitivity and specificity of conventional culture method for the diagnosis of pulmonary tuberculosis were 60.2% and 99.8% respectively based on the number of patients. The figures for Amplicor were 61.8% and 97.4% respectively. There was no statistical significant difference between these methods. In rapidity, the Amplicor was significantly superior to the microscopy method in sensitivity.

CONCLUSION

Patients with Amplicor positive and conventional negative result had mostly mycobacteria related diseases. The Amplicor positive result indicated mostly active mycobacterial infection and was clinically useful for rapid diagnosis.

Potential use of Amplicor PCR kit in diagnosing pulmonary tuberculosis from gastric aspirate

Polymerase chain reaction (PCR) detection of mycobacteria from gastric aspirate for the diagnosis of tuberculosis is not fully evaluated up to now. A total of 116 gastric aspirate specimens were collected from patients with suspected pulmonary tuberculosis. The breakdown of diagnosis was 67 pulmonary tuberculosis, 16 nontuberculous mycobacterial infection, 5 extra pulmonary tuberculosis, and 28 other lung diseases. The conventional methods were shown to have a sensitivity of 47.8% and a specificity of 79.6%; on the other hand, Amplicor had 34.9% and 97.0%, respectively. The Amplicor provided a more rapid and specific method for diagnosing tuberculosis and was more useful than the conventional.

Disseminated cutaneous infection with Mycobacterium kansasii: genotyping versus phenotyping

Mycobacterium kansasii is a common and virulent pathogen. However, primary cutaneous M kansasii infection has rarely been reported, totaling to only 34 cases since 1965. This low incidence has not been explained, but probably is due to difficulty in culture or phenotyping. We describe the first reported case of cutaneous M kansasii diagnosed by genotyping, which is based on the DNA extracted from the formalin-fixed and paraffin-embedded tissue.

Erythema induratum associated with tuberculous lymphadenitis: analysis of a case using polymerase chain reactions with different primer pairs to differentiate bacille Calmette-Guérin (BCG) from virulent strains of Mycobacterium tuberculosis complex

We retrospectively analyzed a bacille Calmette-Guérin (BCG) vaccinated female patient who developed erythema induratum in association with tuberculous lymphadenitis. The polymerase chain reaction (PCR) with two pairs of primers was performed. Only one pair was able to detect the myocobacterial DNA from the paraffin-embedded specimen of the erythema induratum (EI) lesion. However, both pairs showed positive results with the tuberculous lymphadenitis specimen. Sequence analysis of the PCR products excluded the possibility of BCG as the potential pathogen. Both lesions responded favorably to antituberculous therapy. Our study attests to the tuberculous nature of EI and demonstrates that BCG vaccination per se does not induce the lesion or interfere with the PCR result. Finally, using at least two pairs of primers targeting different genomic segments and possessing species-identification capability may raise the detection rates and solve some controversies about the nature of tuberculids.

Heteroduplex mobility assay for rapid, sensitive and specific detection of mycobacteria

We report an improved method for the detection and identification of mycobacteria using PCR and the heteroduplex mobility shift assay (HMA). The HMA for detection of mycobacteria was based on the microheterogeneity within the DNA coding sequences for 16S rRNA. A remarkable shift between single-stranded, heteroduplex and homoduplex bands in PAGE was observed among the Mycobacterium spp. tested. The Mycobacteria HMA (MHMA) of amplified PCR products from mycobacteria DNA coding for 16S rDNA derived from culture showed a specific heteroduplexes formed among different Mycobacterium species. Other bacterium species were distinguished from Mycobaterium due to slow migrating heteroduplexes mobility bands observed when M. bovis (BCG), M. avium, or M. fortuitum were used as a standard. The specific heteroduplexes were detected when as little as 1 etag of DNA template was used, although better results were obtained with 5 etag and when PCR products of sample test and mycobacterium standard were mixed at a ratio of 1.8. To correctly evaluate the feasibility of using MHMA to detect and identify mycobacteria, 15 clinical sample patients were tested. All MTB-positive clinical samples were identified by MHMA as well as the negative samples. In addition, MHMA will, in principle, be applicable to the detection and classification of any microorganism showing differences within the 16S rRNA as well as to the identification of new and unrecognized bacterial species.

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.

Length of time to laboratory diagnosis of Mycobacterium tuberculosis infection: comparison of in-house methods with reference laboratory results

OBJECTIVES

To audit the time taken to obtain laboratory confirmation of infection with Mycobacterium tuberculosis using in-house methods of polymerase chain reaction (PCR) and culture and referral to a reference laboratory.

METHODS

Retrospective collection of data from laboratory records covering a period of 1 year.

RESULTS

Median time to microbiological diagnosis of a new infection using the in-house services in addition to the reference laboratory was 22.0 days. Using reference laboratory results alone, median time to diagnosis would have been 61.5 days.

CONCLUSIONS

Development of on-site laboratory facilities to identify Mycobacterium tuberculosis can reduce the time to its identification by almost two-thirds.

PCR based detection of mycobacteria in paraffin wax embedded material routinely processed for morphological examination

BACKGROUND

The incidence of mycobacterial infections has increased during the past five years. A prompt diagnosis is indispensable for initiating appropriate treatment. Because culturing of mycobacteria takes three to six weeks and sensitivity of microscopic detection of acid fast bacilli is low, amplification methods provide promising possibilities. Recently, the polymerase chain reaction (PCR) has been shown to be useful for confirming a mycobacterial infection, especially in cases with unexpected histological findings or lack of suitable material for culturing.

AIMS

To evaluate the impact of PCR based techniques in the detection of mycobacterial infections in uncultured routine histological specimens as an alternative to surgical pathology.

METHODS

Two hundred and twenty nine formalin fixed and paraffin wax embedded samples from 141 patients with clinical or histological suspicion of a mycobacterial infection were investigated using three different PCR assays and Southern blotting. PCR results were compared with histology and culture and the patients' clinical findings.

RESULTS

When using culture as the reference method, the sensitivity for the detection of mycobacteria of the tuberculosis complex was 90%, specificity was 92%, the positive predictive value was 81%, and the negative predictive value was 96%. The sensitivity for the detection of nontuberculous mycobacteria was 100% and specificity was 78%, the positive predictive value was 26%, and the negative predictive value was 100%. The patients' clinical findings supported the PCR positive results, indicating a mycobacterial infection in 11 of 18 initially culture negative cases and in 21 of 35 PCR positive cases without culture results.

CONCLUSIONS

These results indicate that PCR based techniques are sensitive, specific, and rapid methods for the detection of mycobacteria in routinely processed paraffin wax embedded and formalin fixed histological samples.

Multiplex polymerase chain reaction for rapid detection of atypical mycobacteria and Mycobacterium tuberculosis complex

A three-step polymerase chain reaction (PCR) method was developed for the detection and typing of mycobacterial DNA in clinical samples and fixed tissue specimens. The first step was to rule out or prove the presence of DNA of Mycobacterium tuberculosis complex. An amplified fragment from the insertion sequence (IS) 6110 was used for this purpose. Patients negative for IS 6110 were evaluated for a fragment of the 65 kDa-antigen, present in all mycobacteria. In positive patients, a multiplex PCR was performed for M. gordonae, M. avium, M. kansasii, M. fortuitum, and M. malmoense, combined in one PCR run. As another control, to prove mycobacterial DNA, PCR was used for the gene coding for the 16S ribosomal RNA also found in all mycobacteria. Appropriate negative controls were included. Different clinical samples were compared for an efficient amplification of these different mycobacterial DNA fragments. Different mycobacteria can be identified within one day in either unfixed cytologic and bacteriologic samples, or formalin-fixed paraffin-embedded tissue samples. Therefore, this method is a quick, cost efficient, and reliable tool to identify mycobacteria other than the tuberculosis complex.

Accuracy of a polymerase chain reaction-based assay for detection of pneumococcal bacteremia in children

OBJECTIVE

To evaluate the utility of a polymerase chain reaction (PCR)-based assay for identifying pneumococcal DNA in the blood of pediatric patients with suspected bacteremia.

METHODS

Children evaluated at the Children's Hospital of Pittsburgh who were having blood drawn for culture had an additional 2 to 3 mL of blood (from the same sampling) obtained and placed in a sodium citrate tube for PCR processing (study group). The control group for this study consisted of children having blood drawn for biochemical analysis who were afebrile, well-appearing, and had no recent illnesses. Specimens were frozen at -70 degrees C and then batch-processed for PCR-based analyses with the JM201/202-204 primer/probe set. Amplified products were detected after liquid hybridization format wherein a 32P end-labeled probe was annealed to the amplified DNA and visualized by autoradiographic analysis after gel retardation.

RESULTS

Four hundred eighty study group patients and 103 controls had specimens tested by both PCR and blood culture. Twenty-six (5%) patients had a positive blood culture for a pathogenic organism (21 of which were Streptococcus pneumoniae). Twelve (57%) of the 21 patients with blood cultures positive for S pneumoniae also were positive by PCR. In addition, 206 study group patients and 16 controls with negative blood cultures had positive PCR results. A greater proportion of study group patients were PCR-positive/culture-negative than were controls (206/459 vs 16/103).

CONCLUSION

Although this assay currently lacks adequate sensitivity and specificity for clinical use, the high frequency of PCR-positive cases in patients with suspected bacteremia may indicate a greater role for S pneumoniae than had previously been appreciated. Further refinement of this assay as well as the development of a rapid PCR-based assay appears warranted.

Nested polymerase chain reaction for detection of Mycobacterium tuberculosis in solitary pulmonary nodules

BACKGROUND

Differential diagnosis of solitary pulmonary nodules (SPNs) can be difficult in areas, such as Korea, where tuberculosis is endemic. Nested polymerase chain reaction (PCR) is a widely used method to test a very small amount of pathogen and to detect Mycobacterium tuberculosis from fine needle aspirates.

OBJECTIVES

The usefulness of nested PCR for the detection of M tuberculosis from tuberculous SPN and for the differential diagnosis of SPN was evaluated.

METHODS

Thirty-three patients in whom a diagnosis of SPN was made based on a CT scan of the chest were enrolled in this study. Included were 17 malignant and 16 benign SPNs. Nested PCR was carried out for the detection of M tuberculosis by using TB-1, TB-2, TB-28, and TB-29C on fine needle aspirates from the nodule in all 33 cases.

RESULTS

Aspirates from malignant neoplasms, pneumonia, and sequestration were all negative on nested PCR for tuberculosis. One of the three radiologically suspected tuberculous nodules without response to anti-tuberculosis drugs (uncertain) yielded positive results on nested PCR for the detection of M tuberculosis. In contrast, 7 out of 8 (87.5%) aspirates from proven tuberculous nodules showed positive results on nested PCR. Nested PCR could be used to detect M tuberculosis in fine needle aspirates from tuberculous SPNs with good sensitivity (87.5%) and specificity (96.0%).

CONCLUSION

Nested PCR for the detection of M tuberculosis in fine needle aspirates may be useful in the differential diagnosis of SPNs.

Detection of Mycobacterium tuberculosis in formaldehyde solution-fixed, paraffin-embedded tissue by polymerase chain reaction in Pott's disease

STUDY DESIGN

Twenty-five formaldehyde solution-fixed, paraffin-embedded tissue blocks from vertebral biopsy specimen materials with presumptive diagnosis of tuberculous spondylitis and nonspecific vertebral osteomyelitis were studied.

OBJECTIVES

To evaluate the sensitivity and specificity of polymerase chain reaction in detecting Mycobacterium tuberculosis in formaldehyde solution-fixed, paraffin-embedded tissue samples from histologically proved tuberculous spondylitis.

SUMMARY OF BACKGROUND DATA

Diagnosis of a mycobacterial infection is a long and tedious process; because of the slow growth rate of mycobacteria on solid media, identification and antibiotic sensitivity testing can take up to 10 weeks, but the sensitivity of culture can be as low as 50%. Direct microscopy is insensitive because clinical samples may contain only few organisms. Recently, polymerase chain reaction has been applied in the rapid amplification and identification of many organisms, including mycobacteria.

METHODS

The DNAs were extracted from 25 paraffin-embedded tissue blocks. An insertion element IS 6110 (Integrated DNA Tec. Inc., Corrallville, IA), a DNA sequence unique to Mycobacterium complex (M. tuberculosis and the subspecies Mycobacterium bovis), was amplified by polymerase chain reaction. Polymerase chain reaction results were compared with those of Mycobacterium culture, acid-fast bacilli staining, and histologic findings.

RESULTS

Polymerase chain reaction was positive in 18 cases of 19 tuberculous spondylitis. Three of the polymerase chain reaction test results were positive with concomitant negative culture and positive acid-fast bacilli staining. There were six chronic nonspecific infections, and polymerase chain reaction results were negative in five cases; in the single positive case, DNA amplification results remained positive even after three repeated tests.

CONCLUSION

Polymerase chain reaction has a sensitivity of 94.7%, specificity of 83.3%, positive predictive value of 94.7%, and a negative predictive value of 83.3%. Accuracy was calculated as 92%.

Evaluation of polymerase chain reaction for rapid diagnosis of clinically suspected tuberculous meningitis

SETTING

Since conventional bacteriological methods rarely detect Mycobacterium tuberculosis in cerebrospinal fluid (CSF) and are of limited use in the diagnosis of tuberculous meningitis (TBM), clinical features suggestive of TBM supported by indirect evidence such as CSF examination and computerized tomography (CT) of the head have been used for the early diagnosis of TBM.

OBJECTIVE

We evaluated the efficacy of polymerase chain reaction (PCR) in the diagnosis of TBM.

METHODS

Coded CSF samples from 40 patients with TBM and from 49 patients with other neurological disorders were processed. In the absence of a reliable sensitive and specific test for M. tuberculosis in CSF, we used a set of established clinical criteria as the gold standard. Accordingly, the patients were divided into definite, highly probable, probable and possible TBM. The samples were decoded only after completion of the laboratory tests.

RESULTS

PCR was positive in 2/4, 19/20, 13/16 patients with highly probable, probable and possible TBM respectively. None of the samples were positive by conventional bacteriological methods. However, 3/49 CSF samples from non-TBM patients were also found positive by PCR. PCR detected M. tuberculosis genomic DNA in the CSF of 85% of clinically suspected TBM cases and 6.1% of non-tuberculous controls.

CONCLUSION

PCR, along with the suggested clinical criteria, offers a rapid and fairly accurate diagnosis of TBM.

Amplification of residual DNA sequences in sterile bronchoscopes leading to false-positive PCR results

PCR has been used successfully for the direct detection of Mycobacterium tuberculosis in uncultured patient samples. Its potential is hindered by the risk of false-positive results as a result of either amplicon carryover of cross-contamination between patient samples. In the present study, we investigated whether residual amplifiable human or M. tuberculosis DNA could remain in sterile bronchoscopes and potentially be a cause of false-positive PCR results in subsequent patient samples. Sterilized bronchoscopes were flushed with sterile saline, and the collected eluate was submitted for PCR amplification of IS6110 sequences and exon 8 of the human p53 gene. Of a total of 55 washes of sterile bronchoscopes from two institutions, 2 (3.6%) contained amplifiable M. tuberculosis DNA and 11 (20%) contained residual human DNA. These findings indicate that residual DNA can remain in sterilized bronchoscopes and can be a source of false-positive PCR results.

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.

Multiprimer PCR system for differential identification of mycobacteria in clinical samples

A novel multiprimer PCR method with the potential to identify mycobacteria in clinical samples is presented. The assay relies on the simultaneous amplification of three bacterial DNA genomic fragments by using different sets of oligonucleotide primers. The first set of primers amplifies a 506-bp fragment from the gene for the 32-kDa antigen of Mycobacterium tuberculosis, which is present in most of the species belonging to the genus Mycobacterium. The second set of primers amplifies a 984-bp fragment from the IS6110 insertion sequence of the bacteria belonging to the M. tuberculosis complex. The third set of primers, derived from an M. tuberculosis species-specific sequence named MTP40, amplifies a 396-bp genomic fragment. Thus, while the multiprimer system would render three amplification fragments from the M. tuberculosis genome and two fragments from the Mycobacterium bovis genome, a unique amplification fragment would be obtained from nontuberculous mycobacteria. The results obtained, using reference mycobacterial strains and typed clinical isolates, show that the multiprimer PCR method may be a rapid, sensitive, and specific tool for the differential identification of various mycobacterial strains in a single-step assay.

The utility of polymerase chain reaction (PCR) in the diagnosis of pulmonary tuberculosis

A fragment of DNA of 123 bp belonging to insertion sequence IS6110, specific of Mycobacterium tuberculosis complex, was amplified by polymerase chain reaction (PCR) of respiratory samples, for the diagnosis of pulmonary tuberculosis. A total of 314 samples (286 sputum and 28 bronchoalveolar lavages) from 242 patients were evaluated by PCR, and the results were compared with the those obtained by acid-fast-stained smears, culture, and clinical diagnosis. Mycobacterium tuberculosis was detected by PCR in 102 of 105 patients with clinical diagnosis of pulmonary tuberculosis. All smear and culture-positive samples were PCR positive. The sensitivity of PCR, culture, and staining was 97%, 88%, and 65%, respectively, and the specificity was 100% in all cases. In ten patients with old residual lesions, but no active disease, M tuberculosis genome was detected by PCR. In our experience, PCR proved to be a useful method for the rapid diagnosis of pulmonary tuberculosis.

Rapid diagnosis of tuberculous meningitis by polymerase chain reaction assay of cerebrospinal fluid

A polymerase chain reaction (PCR) method for the rapid diagnosis of tuberculous meningitis (TBM) was used to study prospectively 47 cerebrospinal fluid (CSF) samples from 45 patients. Twenty CSF samples were from patients with clinically suspected TBM and another 27 samples came from patients without clinically suspected TBM. Mycobacterial DNA was detected in 15 CSF samples (14 from patients with clinically suspected TBM and 1 from a patient not suspected of having TBM). Of the PCR-positive samples, 4 were also positive for mycobacterial culture. However, 32 PCR-negative samples were all culture-negative. All samples were negative for the acid-fast bacillus by direct smear. The single PCR-positive patient in the clinically unsuspected TBM group was initially diagnosed as suffering from aseptic meningitis on the basis of his clinical features. The mycobacterial culture of his CSF specimen was also positive and a revised diagnosis of an aseptic type of TBM was made. The estimations of specificity and sensitivity in this study were 100% and 70% respectively. The results showed that using a PCR to detect mycobacterial DNA in CSF for the early diagnosis of TBM is not only a rapid but also an accurate method.

Hepatobiliary tuberculosis presenting as a gall bladder tumor

A 64-year-old married female was admitted with a presentation of anorexia, easy fatiguability, skin discoloration, tea-colored urine and weight loss of 1 month's duration. After a series of clinical and laboratory examinations including radiological image studies, a diagnosis of gall bladder tumor was presumed. A final diagnosis of tuberculosis of the liver and gall bladder was established by histopathological examination of tissue specimens obtained during exploratory laparotomy. Hepatobiliary tuberculosis presenting as a gall bladder tumor is rare and no pathognomonic diagnostic characteristics can be relied upon. It is necessary to confirm the diagnosis by histopathology, polymerase chain reaction (PCR), or microbiological studies on biopsy specimens in order to make possible appropriate, early therapy.

Determination of Helicobacter pylori status by reverse transcription-polymerase chain reaction. Comparison with urea breath test

We previously reported the development and the possible application of reverse transcription-polymerase chain reaction (RT-PCR) assay for the detection of H. pylori in gastric mucosal biopsy specimens. In this communication, the application of this assay was assessed by comparing its results from 79 gastric biopsy specimens obtained from 68 patients with the more traditional [13C]urea breath test. When the amplified products were examined, the specificity and sensitivity of this RT-PCR assay were 100% and 47% on agarose gels and 80% and 91% by Southern hybridization, respectively. The specificity and sensitivity of urea breath test were 91% and 96% and were generally superior to RT-PCR (negative predictive value of 94% for UBT and 59-76% for RT-PCR). Although our RT-PCR results compare favorably with other PCR assays applied to gastric biopsy specimens for the detection of H. pylori, the use of this method did not add significantly to currently available noninvasive diagnostic methods.

Diagnosis of tuberculous meningitis confirmed by means of an immunoblot method

In order to define the mycobacterial antigens that may be specifically associated with human tuberculous infection, the cerebrospinal fluid (CSF) specimens of 30 patients with tuberculous meningitis (TBM) and of an equal number of patients with non-tuberculous meningitis (controls) were compared by means of an immunoblot method for detecting antibody to Mycobacterium tuberculosis. In the CSF of controls, mycobacterial antibody was either absent or, when present, was found to react with 27, 30 and 45 KDa antigens of M. tuberculosis. Among patients with TBM, the numbers as well as intensities of the immunostained bands in the nitrocellulose membranes (NCM) were greater than among controls. Furthermore, a unique disease-associated mycobacterial antigen, 35 KDa of M. tuberculosis, was found to react with a specific antibody in the CSF of patients with TBM but was not detected in the CSF of any of the controls. This 35 KDa antigen could be easily identified in the NCM. The immunoblot method showed 100% sensitivity in all the culture-positive patients with TBM. Because of the high degree of specificity as well as sensitivity of the immunoblot method, we consider that this method is of value for confirming the diagnosis of TBM.

Sensitivity and specificity of PCR for detection of Mycobacterium tuberculosis: a blind comparison study among seven laboratories

PCR is, in principle, a simple and rapid test for use in the detection of Mycobacterium tuberculosis. However, virtually no data are available on the reliability and reproducibility of the method. In order to assess the validity of PCR for the detection of mycobacteria in clinical samples, seven laboratories participated in a blinded study of 200 sputum, saliva, and water samples containing either known numbers of Mycobacterium bovis BCG cells or no added organisms. Each laboratory used its own protocol for pretreatment, DNA extraction, and detection of the amplification product. Insertion sequence IS6110 was the target for DNA amplification. Several participating laboratories reported high levels of false-positive PCR results, with rates ranging from 3 to 20% and with one extreme value of 77%. The levels of sensitivity also ranged widely among the different participants. A positive PCR result was reported for 2 to 90% of the samples with 10(3) mycobacteria. Although most participants did include control tests to check the sensitivity and specificity of the PCR, the sequence of operations from sample pretreatment to purification of DNA from bacteria was not always monitored adequately. During these procedures cross-contaminating DNA was introduced and/or bacterial DNA was lost. The results of the study show that the implementation of an effective system for monitoring sensitivity and specificity is required before the PCR can be used reliably in the diagnosis of tuberculosis.

Genetics of tuberculosis

Molecular methods for identifying organisms, strain typing, and determining drug susceptibilities are extremely valuable for pathogens that are impossible to grow on artificial media, slow growing on artificial media, or exceptionally hazardous to grow in a clinical microbiology laboratory. DNA hybridization probes and RFLP analysis are currently being used to facilitate the diagnosis and evaluation of mycobacterial disease. PCR is rapidly progressing to the point at which it will become routine in the clinical microbiology laboratory. LCR clearly has a future role in mycobacteriology but requires further understanding of mycobacterial genetics and physiology. The mycobacteriophage reporter-gene assay is an exciting future option that may allow us to obtain critical treatment related information in a much more timely fashion. The technologies mentioned in this article do not include all of the possibilities for the future; however, it can already be imagined that the isolation, identification, and drug-resistance properties of mycobacteria can be determined directly from clinical specimens and the results made available in a matter of days rather than weeks to months. What about the cost? These are expensive methods currently; however, the cost of conventional culture, drug susceptibility determinations, unnecessary periods of isolation for infection control, delays in recognition of resistant isolates, and deaths before the availability of laboratory information are high prices to pay. Only through further investigation can we clarify the most efficient and cost-effective tuberculosis treatment and control program. The dual epidemics of the human immunodeficiency virus and TB will continue to press the scientific community to develop cost-effective approaches, both for developed and developing nations, to a wide array of pathogens. If we do not characterize existing and future organisms at the molecular level, we will be forced to deal with them on their terms and at their leisure.

Simple method for production of internal control DNA for Mycobacterium tuberculosis polymerase chain reaction assays

A simple method for the production of internal control DNA for two well-established Mycobacterium tuberculosis polymerase chain reaction assays is described. The internal controls were produced from Mycobacterium kansasii DNA with the same primers but at a lower annealing temperature than that used in the standard assays. In both assays, therefore, the internal control DNA has the same primer-binding sequences at the target DNA. One-microgram quantities of internal control DNA which was not contaminated with target DNA could easily be produced by this method. The inclusion of the internal control in the reaction mixture did not affect the efficiency of amplification of the target DNA. The method is simple and rapid and should be adaptable to most M. tuberculosis polymerase chain reaction assays.

Large-scale use of polymerase chain reaction for detection of Mycobacterium tuberculosis in a routine mycobacteriology laboratory

We investigated the use of DNA amplification by the polymerase chain reaction reaction (PCR) for detection of Mycobacterium tuberculosis from clinical specimens. Two-thirds of each sample was processed for smear and culture by standard methods, and one-third was submitted for DNA extraction, amplification of a 317-bp segment within the insertion element IS6110, and detection by agarose gel electrophoresis, hybridization, or both. DNA was prepared from over 5,000 samples, with 623 samples being culture positive for acid-fast bacilli. Of 218 specimens that were identified as M. tuberculosis, 181 (85%) were positive by PCR. In the M. tuberculosis culture-positive group, PCR was positive for 136 of 145 (94%) and 45 of 73 (62%) of the fluorochrome smear-positive and -negative specimens, respectively. Of 948 specimens that were either culture positive for mycobacteria other than M. tuberculosis or culture negative, 937 specimens were negative by PCR and 11 (1%) specimens initially appeared to be false positive for M. tuberculosis. The reason for discrepant results varied; some errors were traced to the presence of an inhibitor in the specimen (7.3% in unselected specimens), nucleic acid contamination, low numbers of organisms in the specimen antituberculosis therapy, and possible low-level nonspecific hybridization. In comparison with culture, the sensitivity, specificity, and positive predictive value were 83.5, 99.0, and 94.2%, respectively, for PCR. When PCR was corrected for DNA contamination, the presence of inhibitor, and culture-negative disease, the values became 86.1, 99.7, and 98.4%, respectively. If the results for multiple specimens submitted from the same patient are considered, no patient who had three of more sputum specimens tested would have been misdiagnosed.

Polymerase chain reaction for diagnosis of infectious diseases

The polymerase chain reaction (PCR) has been utilized and demonstrated to be useful for detecting minute amounts of a wide variety of infectious agents. In such studies, one must keep in mind that the most appropriate conditions for amplification vary with organisms of interest. In this study, PCR was used as a rapid and sensitive method for detecting infectious agents for which three assay systems were devised comprising the method for the amplification of human T cell leukemia virus type I, Mycobacterium tuberculosis and Mycoplasma pneumoniae. The possibility of vertical transmission of human T cell leukemia virus type I through cord blood was demonstrated using cord blood mononuclear cells from carrier mothers of this virus. In the study of Mycobacterium tuberculosis, PCR was shown to be efficient, particularly in detecting this organism in extrapulmonary cases. Evidence of direct invasion into the central nervous system by Mycoplasma pneumoniae and the concomitant occurrence of mycoplasmaemia in the mycoplasmal central nervous system involvement was obtained using PCR. These results validated the potential of PCR in the clinical research of infectious diseases.

Detection of Mycobacterium tuberculosis in clinical samples by two-step polymerase chain reaction and nonisotopic hybridization methods

Detection of Mycobacterium tuberculosis in clinical specimens by the polymerase chain reaction (PCR) was compared with detection by culture. A 317-bp segment within the M. tuberculosis-specific insertion sequence IS6110 was amplified. The detection limit of the PCR assay for cultured mycobacteria was 50 cells per reaction by ethidium bromide-stained agarose gel electrophoresis and 5 cells per reaction by hybridization with an oligonucleotide probe conjugated with either digoxigenin or alkaline phosphatase (AP). This sensitivity was reduced fivefold in sputum specimens seeded with M. tuberculosis. Seventy-six clinical specimens were amplified and examined by the three detection methods. Both the digoxigenin and AP procedures were found to be more sensitive than agarose gel electrophoresis, but they were occasionally associated with a high background. An additional 308 specimens were examined only by agarose gel electrophoresis and the AP procedure. Of 71 specimens found to contain M. tuberculosis, amplified products were detected from 56 (79%) samples by agarose gel electrophoresis and/or the AP procedure. Of the additional 313 specimens that were culture negative for M. tuberculosis, 19 (6%) had amplified products detectable by agarose gel electrophoresis and/or the AP procedure. Compared with culture, PCR showed sensitivities and specificities of 55 and 98%, respectively, for agarose gel electrophoresis and 74 and 95%, respectively, for the AP procedure. Despite this low sensitivity, a rapid positive PCR result was accurate and clinically useful.

Nested amplification protocol for the detection of Mycobacterium tuberculosis

Several methods for rapid diagnosis of tuberculosis have been devised through DNA amplification. However, the chemically strong cell wall of the species, the presumptively low numbers of organisms and their uneven distribution in clinical samples, and the lack of a "gold standard" for diagnosing tuberculosis, have hindered the routine clinical use of this method. In a pediatric patient group, these factors are more perplexing. To circumvent these problems, we made use of nested amplification and developed a standard protocol for extracting DNA from various forms of clinical samples which were suitable to our clinical laboratory. It is our impression that the overall sensitivity, including technical bias accompanying this method, is equal to, or at least greater than, that of culture. Most notably, the rapidity in obtaining results and the simplicity in handling, storage and transfer of samples are the principal advantages of this method.

Detection of Mycobacterium tuberculosis in clinical samples by using polymerase chain reaction and a nonradioactive detection system

A test based on the polymerase chain reaction (PCR) was developed for the detection of the Mycobacterium tuberculosis complex in clinical samples. In this test, a 245-bp sequence of the insertion element IS986 was amplified and detected by agarose gel electrophoresis in the presence of ethidium bromide and by Southern blot and dot blot hybridization by using a 188-bp digoxigenin-labeled probe. We tested clinical specimens from 227 patients suspected of having tuberculosis. These included 102 cerebrospinal fluid, 48 sputum, 18 pleural fluid, 5 bronchoalveolar lavage, 18 blood, 7 pus, 8 bone marrow, and 6 urine samples and 15 tissue biopsy specimens. We also tested sputum samples from 75 patients with diseases other than tuberculosis. Sputum samples were first decontaminated, and all samples were treated with proteinase K-detergent solution to extract the DNA. Part of each sample was spiked with M. tuberculosis to provide a semiquantitative assay and to control for the loss of mycobacteria or interference with the PCR which may cause false-negative results. One femtogram of M. tuberculosis DNA could be detected. PCR was positive for all 32 culture-positive (for M. tuberculosis) and Ziehl-Neelsen staining (ZN)-positive samples, 10 of 12 culture-positive and ZN-negative samples, and all 4 culture-negative and ZN-positive samples. PCR detected M. tuberculosis complex bacteria in 35 of 178 culture- and ZN-negative samples. Clinical data supported the diagnosis of tuberculosis in the majority of the 35 patients from whom those samples were obtained.

Rapid detection of tuberculous and non-tuberculous mycobacteria by polymerase chain reaction amplification of a 162 bp DNA fragment from antigen 85

A polymerase chain reaction (PCR) assay was developed for detection of mycobacteria using amplification of a 162 bp region of the genes coding for the mycobacterial antigen 85 complex. Strains belonging to the Mycobacterium tuberculosis complex were further differentiated from non-tuberculous mycobacteria by hybridization of the PCR derived Southern blot with an internal oligonucleotide probe and washing under stringent conditions. The method allowed rapid and sensitive detection of mycobacterial DNA in uncultured clinical samples. PCR results obtained for Mycobacterium tuberculosis in 206 specimens from 180 untreated patients gave a sensitivity of 93.9% and a specificity of 94.3% compared with the culture. PCR detected DNA from Mycobacterium tuberculosis in seven samples from patients with clinically evident tuberculosis in whom culture was negative. The results suggest that this PCR assay could be used for early and specific diagnosis of tuberculosis.

Use of polymerase chain reaction for early identification of Mycobacterium tuberculosis in positive cultures

AIMS

To develop a readily applicable polymerase chain reaction (PCR) based technique which would permit the identification of Mycobacterium tuberculosis complex isolates from Bactec phials at an earlier stage than currently available methods.

METHODS

Mycobacterial cells cultured in Bactec 12B medium were harvested by centrifugation. The cells were lysed by heating in distilled water. Oligonucleotide primers based on the sequence of the gene coding for the immunogenic protein MPB64 were then used to amplify a 240 base pair fragment of DNA directly from the crude cell lysate. The PCR product was visualised under ultraviolet light following electrophoresis of an aliquot in an agarose gel containing ethidium bromide. The sensitivity of the PCR was adjusted so that about 600 cfu of M tuberculosis gave a positive result. The lowest growth index at which this method of identification might be applied to Bactec phials was determined and a number of routine cultures giving a positive growth index examined.

RESULTS

M tuberculosis was positively identified at the lowest growth index, as determined by the Bactec system. Of 45 routine cultures examined, with growth indexes ranging from 6 to 999, the 15 confirmed by conventional means to contain M tuberculosis were correctly identified from 1 ml of culture medium.

CONCLUSIONS

The method described can be used to identify M tuberculosis isolates cultured in the Bactec system at the earliest detectable rise in growth index. It may therefore allow cultured mycobacteria to be identified at an earlier stage than conventional methods or the commercially available DNA probes adapted for use with the Bactec system.