Detection of Mycobacterium tuberculosis directly from spiked human sputum by Q-beta replicase-amplified assay

Rapid method for detecting and differentiating Mycobacterium tuberculosis complex and non-tuberculous mycobacteria in sputum by fluorescence in situ hybridization with DNA probes

OBJECTIVE

In resource-limited tuberculosis-endemic countries, Mycobacterium tuberculosis in sputum is mainly detected by acid-fast bacillus (AFB) staining and the identification of sputum-derived cultures. PCR techniques are practical only in well-resourced laboratories. This study investigated the application of a rapid, simple, and inexpensive fluorescence in situ hybridization (FISH) assay to identify and differentiate M. tuberculosis complex (MTBC) from non-tuberculous mycobacteria (NTM) in sputum.

METHODS

The Mycobacterium/Nocardia Genus (MN Genus)-MTBC FISH assay performed in this study utilizes two different DNA probes labeled with different fluorescent molecules that hybridize respectively with 16S rRNA of the genus Mycobacterium and 23S rRNA of MTBC. The assay was tested on 202 patient sputum samples in Mangaluru, Karnataka State, India. Sputa were first liquefied and bacteria concentrated before performing the FISH assay and parallel culturing and AFB staining. The identities of cultured bacteria from DNA sequencing were compared with FISH assay findings from corresponding sputa.

RESULTS

Of the 202 sputum samples tested, 67 reacted with both MN Genus-specific and MTBC-specific probes, none reacted only with the MTBC-specific probe, and 22 reacted only with the MN Genus-specific probe. The FISH assay yielded results in 2h and had a limit of detection of 2.2×10⁴CFU/ml in sputum spiked with cultured M. tuberculosis. The diagnostic sensitivity, specificity, and positive and negative predictive values of the FISH assay for MTBC in patient sputa were 89.7%, 95.5%, 88.0%, and 92.6%, respectively. NTM were a significant cause of tuberculosis-like infections in Mangaluru.

CONCLUSIONS

The MN Genus-MTBC dual probe fluorescence FISH assay previously applied to cultures can also be utilized in resource-limited tuberculosis-endemic countries for rapidly identifying and differentiating MTBC and NTM in sputum samples.

Facile production and rapid purification of functional recombinant Qβ replicase heterotetramer complex

We describe an improved method for the production of recombinant Qβ replicase heterotetramer. The successful expression of the soluble Qβ RNA polymerase complex depends on the EF-Ts and EF-Tu subunits being co-expressed prior to β-subunit expression. Efficient co-expression requires two different inducible operons to co-ordinate the expression of the heterotrimer. The complete heterotetramer enzyme complex is achieved by production of the recombinant S1-subunit of Qβ replicase in a separate host. This approach represents a facile way for producing and purifying large amounts of soluble and active recombinant Qβ replicase tetramer without the necessity of a His-tag for purification.

Miniaturized bead-beating device to automate full DNA sample preparation processes for gram-positive bacteria

We have developed a miniaturized bead-beating device to automate nucleic acids extraction from Gram-positive bacteria for molecular diagnostics. The microfluidic device was fabricated by sandwiching a monolithic flexible polydimethylsiloxane (PDMS) membrane between two glass wafers (i.e., glass-PDMS-glass), which acted as an actuator for bead collision via its pneumatic vibration without additional lysis equipment. The Gram-positive bacteria, S. aureus and methicillin-resistant S. aureus, were captured on surface-modified glass beads from 1 mL of initial sample solution and in situ lyzed by bead-beating operation. Then, 10 μL or 20 μL of bacterial DNA solution was eluted and amplified successfully by real-time PCR. It was found that liquid volume fraction played a crucial role in determining the cell lysis efficiency in a confined chamber by facilitating membrane deflection and bead motion. The miniaturized bead-beating operation disrupted most of S. aureus within 3 min, which turned out to be as efficient as the conventional benchtop vortexing machine or the enzyme-based lysis technique. The effective cell concentration was significantly enhanced with the reduction of initial sample volume by 50 or 100 times. Combination of such analyte enrichment and in situ bead-beating lysis provided an excellent PCR detection sensitivity amounting to ca. 46 CFU even for the Gram-positive bacteria. The proposed bead-beating microdevice is potentially useful as a nucleic acid extraction method toward a PCR-based sample-to-answer system.

Functional Qbeta replicase genetically fusing essential subunits EF-Ts and EF-Tu with beta-subunit

Qbeta replicase, an RNA-dependent RNA polymerase of RNA coliphage Qbeta, is a heterotetramer composed of a phage-encoded beta-subunit and three host-encoded proteins: the ribosomal protein S1 (alpha-subunit), EF-Tu, and EF-Ts. Several purification methods for Qbeta replicase were described previously. However, in our efforts to improve the production of Qbeta replicase, a substantial amount of the beta-subunit overproduced in Escherichia coli cells was found as insoluble aggregates. In this paper, we describe two kinds of method of producing Qbeta replicase. In one kind, both EF-Tu and EF-Ts subunits were expressed with the beta-subunit, and in the other kind, the beta-subunit was genetically fused with EF-Tu and EF-Ts. The fused protein, a single-chain alpha-less Qbeta replicase, was mostly found in the soluble fraction and could be readily purified. These results pave the way for the large-scale production of the highly purified form of this enzyme.

Direct detection of Mycobacterium tuberculosis in respiratory samples from patients in Scandinavia by polymerase chain reaction

OBJECTIVE: To investigate the use of DNA amplification by the polymerase chain reaction (PCR) for the detection of Mycobacterium tuberculosis directly in human respiratory specimens. METHODS: The PCR assay employed was the Amplicor M. tuberculosis Test (Roche Diagnostics, Switzerland), which uses the 16S rDNA as the target template. Nine hundred and sixty samples from 741 patients in two clinical microbiology laboratories in Norway and Sweden were processed by routine culture analysis and PCR. RESULTS: Of the 56 specimens containing cultivatable M. tuberculosis, 49 (87.5%) were detected by PCR. Among the 904 culture-negative specimens, 897 samples were negative also by PCR and seven (0.8%) were positive by PCR. In comparison with culture, the sensitivity, specificity, and positive and negative predictive values of PCR were 91.7%, 99.6%, 94.2% and 99.4% for laboratory 1 and 80.0%, 98.7%, 76.2% and 99.0% for laboratory 2, respectively. For both laboratories combined the values were 87.5%, 99.2%, 87.5% and 99.2%. CONCLUSIONS: These results indicate that multiple (two or three) respiratory samples from each patients should be tested, to allow sufficient accuracy in detecting M. tuberculosis in the specimens. Still, the labor-intensive format of this test necessitates strong clinical indications and patient prioritization to provide a service feasible within the current limits of routine laboratories.

Sensitive differential detection of genetically related mycobacterial pathogens in archival material

A polymerase chain reaction (PCR) assay targeted to the immunogenic protein MPB64 gene was used to detect members of the Mycobacterium tuberculosis complex, and an outward-primed PCR (OPPCR) designed on the IS6110 element allowed differentiation between Mycobacterium bovis and Mycobacterium tuberculosis. Additionally, the amplification of IS1110 and 16S ribosomal RNA sequences combined with a dot blotting assay were able to differentially detect Mycobacterium avium, Mycobacterium intracellulare, and Mycobacterium paratuberculosis. The validity of the experimental procedure was tested on reference material and formalin-fixed paraffin-embedded samples from patients with tuberculosis, sarcoidosis, or Crohn disease. We demonstrated mycobacterial DNA in 59 of 75 cases with histologic lesions typical of tuberculosis; we detected M tuberculosis and M paratuberculosis in 6 of 25 sarcoidosis cases and in 7 of 20 Crohn disease specimens, respectively. The proposed diagnostic procedure is directly applicable to archival material and allows differentiation of genetically related mycobacterial pathogens in more detail than other molecular methods. It provides a tool for the diagnostic study of tuberculosis, sarcoidosis, and Crohn disease.

Performance of an automated Q-beta replicase amplification assay for Mycobacterium tuberculosis in a clinical trial

We present data from a clinical trial study in which an automated version (Galileo) of a previously described Q-Beta replicase-amplified probe assay (J. S. Shah et al., J. Clin. Microbiol. 33:1435-1441, 1995) was used for the direct detection of Mycobacterium tuberculosis complex in sputum. The assay was designed to target specific regions of 23S rRNA found in M. tuberculosis, Mycobacterium bovis, Mycobacterium africanum, and Mycobacterium microti and had a sensitivity ranging from approximately <10 to 300 CFU. The assay was tested for cross-hybridization by using large numbers (e.g., 10(5)to 10(10) CFU/assay) of 133 other organisms commonly found in respiratory tract samples, including non-M. tuberculosis Mycobacterium spp., other bacteria, fungi, and viruses. All of these competitors tested negative by the assay. Automated assay results for 780 respiratory tract samples (sputum or bronchoalveolar lavage specimens) collected and tested at three trial sites in the United States) were compared with the results of culture and acid-fast microscopy. Aliquots of conventionally digested and decontaminated sputum pellets were heated at 100 degrees C and mechanically disrupted prior to hybridization and background reduction, amplification, and detection in a closed disposable test pack. Pertinent elements of individual patient histories relating to tuberculosis exposure, previous active disease, antituberculosis therapy status, etc., were considered in the resolution of discrepant results for 48 (assay false-positive) samples. Seventy-one of 90 (78.9%) culture-positive samples were positive when tested in the Galileo assay, while 7% of culture-negative samples were assay positive, corresponding to a sensitivity of 79% and a specificity of 93%. Following resolution of discrepant results by chart review, the sensitivity and specificity for the Q-Beta replicase amplification assay with the Galileo analyzer were 84 and 97%, respectively. A total of 69.2% of smear-negative (culture positive) samples were detected by the assay. Ten test packs at a time were automatically processed by the Galileo analyzer without operator intervention following loading of samples. The first result was reported in approximately 3 h, and the last result was available in 6.5 h. To our knowledge, this is the first report of a clinical study with a fully automated amplification probe hybridization assay for the detection of pathogens directly from a clinical specimen.

Gene amplification in the diagnosis of mycobacterial infections

The number of importance of infections caused by Mycobacterium tuberculosis and other mycobacterial species is increasing. Since the detection and identification of mycobacteria by conventional laboratory methods (cultivation, staining, and biochemical tests) is a slow and complex procedure, rapid diagnostic methods are urgently needed. Several amplification methods based on different techniques have been applied in the detection of mycobacteria directly from clinical specimens. Most experience has been obtained from different polymerase chain reaction (PCR) assays and their general performance is good. However, their sensitivity in the analysis of samples containing small amounts of mycobacteria or samples containing inhibitory substances has been low. Furthermore, the risk of false positives caused by contamination is high, and the clinical relevance of the results may be unclear. Thus, these gene amplification techniques are a valuable adjunct to the diagnosis of mycobacteria, but so far they cannot replace conventional microbiological methods.

New directions in diagnostics

BACKGROUND

Infectious diseases are still a significant clinical problem in children, and accurate identification of the causal pathogen plays an important role in clinical management. The availability of an etiologic diagnosis enables the clinician to make appropriate therapeutic decisions and to avoid the indiscriminate use of antibiotics. The availability of a microbiologic diagnosis and the susceptibility profile of the pathogen allows the prompt initiation of suitable antibiotic treatment. However, the usefulness of current culture and identification methods is limited by the time needed and by their sensitivity and specificity. Also some microorganisms are difficult or impossible to grow in the laboratory.

OBJECTIVES

To review the newer and more rapid diagnostic techniques that are becoming available and consider their application in the diagnosis of specific infections.

DISCUSSION

Immunoassays have many advantages and it is hoped that new optical immunoassays will overcome the problems of poor sensitivity. Nucleic acid amplification techniques have enormous potential in the diagnosis of infectious diseases because of their high specificity and sensitivity and the speed with which the results can be obtained. However, there are still a number of difficulties that must be overcome before these methods can be widely adopted for routine testing. These techniques may be particularly relevant for the rapid diagnosis of streptococcal pharyngitis, where throat culture is slow and beset by a number of factors which reduce its accuracy. Polymerase chain reaction methods have been developed for many respiratory pathogens, including Mycoplasma pneumoniae, Chlamydia pneumoniae and Mycobacterium tuberculosis, and are likely to play an increasingly important part in diagnosis. In bacterial meningitis culture is still the gold standard and molecular techniques have not yet been developed to the point where they can be used in routine diagnosis. Nucleic acid techniques are likely to be very valuable in the diagnosis of streptococcal pharyngitis and viral central nervous system infections in the near future.

Detection of Mycobacterium tuberculosis in respiratory specimens by strand displacement amplification of DNA

A total of 294 clinical respiratory specimens, including 75 with culture-positive results, were tested for the presence of Mycobacterium tuberculosis by strand displacement amplification (SDA) of DNA. A region of the IS6110 insertion element and an internal control sequence were amplified and then detected by a chemiluminescence assay. Receiver operator-characteristic curves were used to evaluate three methods for declaring specimens positive for M. tuberculosis. By the preferred method, SDA chemiluminescence results were converted to theoretical numbers of M. tuberculosis organisms. A positive threshold (PT) value, above which 95% of the SDA results were judged to be M. tuberculosis positive (sensitivity = 95%), was found to be 2.4 M. tuberculosis organisms per SDA reaction. The analogous PT value for 95% sensitivity on smear-positive specimens was 3.6 M. tuberculosis organisms per reaction. The PT of 2.4 M. tuberculosis organisms per reaction detected 100% of culture-positive, smear-positive specimens (sensitivity = 100%), while 95% sensitivity was achieved with a PT of 15.5 M. tuberculosis organisms per reaction. Specificities, which were calculated with respect to culture- and smear-negative specimens, ranged from 96% at a PT of 15.5 M. tuberculosis organisms to 84% at a PT of 2.4 M. tuberculosis organisms per reaction. The M. tuberculosis-negative specimens were also segregated according to whether the patients received antituberculosis chemotherapy. SDA specificity ranged from 90% (PT = 2.4 M. tuberculosis organisms) to 98% (PT = 15.5 M. tuberculosis organisms) for the M. tuberculosis-negative specimens from patients who had not received chemotherapy. SDA specificity in the M. tuberculosis-negative specimens from patients who received chemotherapy was lower (85 to 94%). This study represents the first large-scale demonstration of M. tuberculosis detection in clinical sputum specimens by isothermal DNA amplification with SDA.

Q-beta replicase-amplified assay for detection of Mycobacterium tuberculosis directly from clinical specimens

We report the results of a study conducted to evaluate the performance of manual Q-Beta replicase-amplified Mycobacterium tuberculosis complex assay compared with that of culture for detecting M. tuberculosis directly from digested sputum pellets. A total of 261 specimens submitted to three tuberculosis testing laboratories were analyzed. Culture and acid-fast bacillus smear results were provided by the tuberculosis testing laboratories. Of these 261 specimens, 34 (13% prevalence rate) were positive for M. tuberculosis by culture. The samples were digested and decontaminated by the testing laboratories by using their standard digestion and decontamination procedures. An aliquot of the digested and decontaminated pellet was sent to GENE-TRAK. The digested and decontaminated pellet was neutralized by washing it with 0.067 M phosphate buffer (pH 6.8), and the bacteria present in the washed pellet were heat inactivated at 100 degrees C for 15 min. The samples were combined with sample processing buffer containing GuSCN and were treated for 6 min in the GENE-TRAK Sample Processing Instrument to release the nucleic acids. The release rRNA was analyzed in a manual Q-Beta replicase assay format which incorporates elements of sandwich hybridization, reversible target capture, and Q-beta replicase signal amplification technologies. In comparison with culture, the overall assay sensitivity and specificity were 97.1 and 96.5%, respectively. The positive predictive value was 80.5%, and the negative predictive value was 99.5%. After analysis of discrepant results, the assay sensitivity and specificity were 97.3 and 97.8, respectively, and the prevalence rate was 14%. The positive predictive value and the negative predictive value were 87.8 and 99.5%, respectively. The Q-Beta replicase assay is rapid sensitive, semiquantitative, and specific for the direct detection of M. tuberculosis from clinical specimens.