Rapid detection and identification of pathogenic mycobacteria by combining radiometric and nucleic acid probe methods

Laboratory Diagnosis and Susceptibility Testing for Mycobacterium tuberculosis

The laboratory, which utilizes some of the most sophisticated and rapidly changing technologies, plays a critical role in the diagnosis of tuberculosis. Some of these tools are being employed in resource-challenged countries for the rapid detection and characterization of Mycobacterium tuberculosis . Foremost, the laboratory defines appropriate specimen criteria for optimal test performance. The direct detection of mycobacteria in the clinical specimen, predominantly done by acid-fast staining, may eventually be replaced by rapid-cycle PCR. The widespread use of the Xpert MTB/RIF (Cepheid) assay, which detects both M. tuberculosis and key genetic determinants of rifampin resistance, is important for the early detection of multidrug-resistant strains. Culture, using both broth and solid media, remains the standard for establishing the laboratory-based diagnosis of tuberculosis. Cultured isolates are identified far less commonly by traditional biochemical profiling and more commonly by molecular methods, such as DNA probes and broad-range PCR with DNA sequencing. Non-nucleic acid-based methods of identification, such as high-performance liquid chromatography and, more recently, matrix-assisted laser desorption/ionization–time of flight mass spectrometry, may also be used for identification. Cultured isolates of M. tuberculosis should be submitted for susceptibility testing according to standard guidelines. The use of broth-based susceptibility testing is recommended to significantly decrease the time to result. Cultured isolates may also be submitted for strain typing for epidemiologic purposes. The use of massive parallel sequencing, also known as next-generation sequencing, promises to continue to this molecular revolution in mycobacteriology, as whole-genome sequencing provides identification, susceptibility, and typing information simultaneously.

Cervical lymphadenopathy due to mycobacterial infection: a diagnostic protocol

Mycobacterial cervical lymphadenopathy is relatively uncommon in the United Kingdom; when cases do occur opportunities for early diagnosis and treatment may be missed. We have reviewed twenty-three cases of mycobacterial cervical lymphadenopathy presenting to an urban general hospital over a four-year period. We discuss the techniques available to aid a diagnosis of mycobacterial disease and suggest a protocol to allow efficient use of these techniques.

Rapid and specific detection of Mycobacterium tuberculosis from acid-fast bacillus smear-positive respiratory specimens and BacT/ALERT MP culture bottles by using fluorogenic probes and real-time PCR

A real-time PCR assay using the LightCycler (LC) instrument for the specific identification of Mycobacterium tuberculosis complex (MTB) was employed to detect organisms in 135 acid-fast bacillus (AFB) smear-positive respiratory specimens and in 232 BacT/ALERT MP (MP) culture bottles of respiratory specimens. The LC PCR assay was directed at the amplification of the internal transcribed spacer region of the Mycobacterium genome with real-time detection using fluorescence resonance energy transfer probes specific for MTB. The results from the respiratory specimens were compared to those from the Amplicor M. tuberculosis PCR test. Specimens from MP culture bottles were analyzed by Accuprobe and conventional identification methods. MTB was cultured from 105 (77.7%) respiratory AFB smear-positive specimens; 103 of these samples were positive by LC PCR and Amplicor PCR. Two samples negative in the LC assay contained rare numbers of organisms; both were positive in the Amplicor assay. Two separate samples negative by Amplicor PCR contained low and moderate numbers of AFB, respectively, and both of these were positive in the LC assay. There were 30 AFB smear-positive respiratory specimens that grew mycobacteria other than tuberculosis (MOTT), and all tested negative in both assays. Of the 231 MP culture bottles, 114 cultures were positive for MTB and all were positive by the LC assay. The remaining 117 culture bottles were negative in the LC assay and grew various MOTT. This real-time MTB assay is sensitive and specific; a result was available within 1 h of having a DNA sample available for testing.

Nontuberculous mycobacteria in the HIV infected patient

The reduction in disseminated NTM infections caused by HAART is one of the success stories in the history of HIV in the developed world. Despite this success, these diseases still occur and may have atypical presentations in patients receiving HAART. Clinicians treating HIV-infected patients must remain familiar with the diagnosis and treatment of these diseases and implement prevention strategies when indicated.

Rapid and specific detection of the Mycobacterium tuberculosis complex using fluorogenic probes andreal-time PCR

A rapid and sensitive strategy for the specific identification of Mycobacterium tuberculosis (TB) was designed and evaluated using crude mycobacterial lysates. The speed of real-time polymerase chain reaction (PCR) was combined with the sensitivity of fluorogenic probes to confirm the presence of mycobacteria as well as specifically identify the presence of members of the mycobacteria tuberculosis complex (MTC) in a single-tube assay. Oligonucleotides were designed to amplify the internal transcribed spacer (ITS) from several mycobacterial species. Specific fluorogenic probes were included in the PCR reaction for the identification of TB as well as Mycobacterium bovia and Mycobacterium africanum in bacterial lysates. The combination of TB-specific fluorogenic probes with real-time PCR formed an approach determined to be fast (less than 40 min), sensitive (less than 800 copies of DNA) and reliable for the specific detection of the MTC. Our data demonstrate the use of real-time PCR and fluorogenic probes in a rapid and sensitive assay to distinguish members of the MTC from other mycobacterial species.

hsp65 PCR-restriction enzyme analysis (PRA) for identification of mycobacteria in the clinical laboratory

More than 70 species of mycobacteria have been defined, and some can cause disease in humans, especially in immunocompromised patients. Species identification in most clinical laboratories is based on phenotypic characteristics and biochemical tests and final results are obtained only after two to four weeks. Quick identification methods, by reducing time for diagnosis, could expedite institution of specific treatment, increasing chances of success. PCR restriction-enzyme analysis (PRA) of the hsp65 gene was used as a rapid method for identification of 103 clinical isolates. Band patterns were interpreted by comparison with published tables and patterns available at an Internet site (http://www.hospvd.ch:8005). Concordant results of PRA and biochemical identification were obtained in 76 out of 83 isolates (91.5%). Results from 20 isolates could not be compared due to inconclusive PRA or biochemical identification. The results of this work showed that PRA could improve identification of mycobacteria in a routine setting because it is accurate, fast, and cheaper than conventional phenotypic identification.

Evaluation of the LiPA MYCOBACTERIA assay for identification of mycobacterial species from BACTEC 12B bottles

The LiPA MYCOBACTERIA (Innogenetics NV, Ghent, Belgium) assay was used to identify mycobacterial isolates using culture fluid from positive BACTEC 12B bottles. The LiPA method involves reverse hybridization of a biotinylated mycobacterial PCR fragment, a 16 to 23S rRNA spacer region, to oligonucleotide probes arranged in lines on a membrane strip, with detection via biotin-streptavidin coupling by a colorimetric system. This system identifies Mycobacterium species and differentiates M. tuberculosis complex, M. avium-M. intracellulare complex, and the following mycobacterial species: M. avium, M. intracellulare, M. kansasii, M. chelonae group, M. gordonae, M. xenopi, and M. scrofulaceum. The mycobacteria were identified in the laboratory by a series of tests, including the Roche AMPLICOR Mycobacterium tuberculosis (MTB) test, the Gen-Probe ACCUPROBE, and a PCR-restriction fragment length polymorphism (PCR-RFLP) analysis of the 65-kDa heat shock protein gene. The LiPA MYCOBACTERIA assay detected 60 mycobacterium isolates from 59 patients. There was complete agreement between LiPA and the laboratory identification tests for 26 M. tuberculosis complex, 9 M. avium, 3 M. intracellulare complex, 3 M. kansasii, 4 M. gordonae, and 5 M. chelonae group (all were M. abscessus) isolates. Three patient samples were LiPA positive for M. avium-M. intracellulare complex, and all were identified as M. intracellulare by the PCR-RFLP analysis. Seven additional mycobacterial species were LiPA positive for Mycobacterium spp. (six were M. fortuitum, and one was M. szulgai). The LiPA MYCOBACTERIA assay was easy to perform, and the interpretation of the positive bands was clear-cut. Following PCR amplification and gel electrophoresis, the LiPA assay was completed within 3 h.

Use of nucleic acid probes for identification of Mycobacterium tuberculosis directly from MB/BacT bottles

The feasibility of using nucleic acid probes directly from positive MB/BacT broth to identify mycobacteria was determined in this study. A total number of 2,727 specimens were cultured into the MB/BacT (Organon Teknika) automated system and on conventional Loweinstein-Jensen (LJ) slants. The Gen-Probe AccuProbe culture identification tests (DNA probes) were used on samples from bottles which were identified as positive for mycobacteria by MB/BacT. Samples of positive MB/BacT broth (0.1 ml) were used directly in the broth culture method for the DNA probes as published by Gen-Probe. Centrifugation of the contents of the bottle was not done prior to probe testing. The number of mycobacteria detected by MB/BacT and LJ was 253 (221 isolates of M. tuberculosis and 32 isolates of mycobacteria other than M. tuberculosis [MOTT]). A total of 96.4% (213 of 221) of the bottles growing M. tuberculosis produced a positive direct DNA probe result for M. tuberculosis complex. One hundred percent (16 of 16) of the bottles growing M. gordonae produced a positive direct DNA probe result for M. gordonae. A total of 3.6% (8 of 221) of the bottles growing M. tuberculosis did not yield a positive direct DNA probe result for M. tuberculosis complex. The testing of subcultures made onto solid media from the positive bottles by AccuProbe identified six of these eight M. tuberculosis isolates. Two (0.9%) M. tuberculosis isolates gave a negative result for the M. tuberculosis probe test applied on the MB/BacT broth and its subculture. The rest of the positive MB/BacT bottles growing MOTT (16 of 32) were negative for M. gordonae, M. avium, M. intracellulare, and M. kansasii probes. The sensitivity and specificity of AccuProbe for the identification of M. tuberculosis and M. gordonae directly from MB/BacT broth were 96.4 and 100% for M. tuberculosis and 100 and 100% for M. gordonae, respectively. The direct testing of positive MB/BacT broth by AccuProbe, without prior centrifugation, allows for the accurate and rapid identification of M. tuberculosis and M. gordonae.

Direct detection of Mycobacterium tuberculosis complex and M. avium complex in tissue specimens from cattle through identification of specific rRNA sequences

Mycobacterium Tuberculosis Direct test and Accuprobe M. avium Complex test, rely on recognition of specific rRNA sequences. The present investigation included sequentially a pre-evaluation study and a study on non-visible lesion tuberculin reactor cattle. As regards the first study, tests were performed on tissue samples from 14 reactors with tuberculous-like lesions and from as many lesion-free non-reactors, using culture findings as a reference. MTD and Accuprobe M. Avium Complex tests proved positive in 12 and 2 reactors respectively. Both tests proved negative in all non-reactors. Data consisted with culture findings. The aim of the second study was to verify the presence of mycobacteria in lymph node and tonsil homogenates from 32 non-visible lesion cattle. MTD and Accuprobe M. avium Complex test proved positive in 10 and 14 subjects respectively; no overlap was found. Our research demonstrates that low to minimal amounts of the main pathogenic mycobacteria can be reliably identified from cattle tissues by commercially available tests, which give simple, more rapid results than conventional techniques.

Early detection of Mycobacterium tuberculosis in BACTEC cultures by ligase chain reaction

The LCx Mycobacterium tuberculosis ligase chain reaction system (Abbott Diagnostic Division, Abbott Park, Ill.) was used to detect M. tuberculosis in 150 consecutive BACTEC vials on the day on which a positive growth index (GI) was recorded. By LCx, M. tuberculosis DNA was detected in BACTEC vials on average 2.6 days before the presence of acid-fast bacilli could be confirmed by microscopic examination. A total of 106 of 108 M. tuberculosis isolates were detected without centrifugation from bottles presenting very low GIs (average, 70; median, 33). No false-positive result was obtained from nontuberculous mycobacteria or from isolates with contaminants.

Diagnostic value of the Amplicor PCR assay for initial diagnosis and assessment of treatment response for pulmonary tuberculosis

We evaluated the Amplicor PCR assay as an initial diagnostic tool on the basis of clinical diagnosis, and assessed this assay as a follow-up test for patients with pulmonary tuberculosis during chemotherapy. Of the 208 specimens from 155 patients who were bacteriologically and/or clinically diagnosed with active tuberculosis before chemotherapy, 144 were Amplicor PCR-positive (sensitivity, 69.2%), which was equal to the results of culturing. Among 89 specimens which showed positive results by smear and culturing, the Amplicor PCR assay detected 87 (97.8%), whereas among 55 specimens which showed smear-negative but culture-positive results, the Amplicor PCR assay detected 46 (83.6 %)(P= 0.003). No false positive results were found in the two systems (specificity, 100%, 120/120). The Amplicor PCR assay was also evaluated as a follow-up test using 926 specimens from 207 patients receiving active tuberculosis chemotherapy. Among 433 specimens which showed Amplicor-PCR positive, 222 (51.3%) were culture-negative. On the other hand, among 233 culture-positive specimens, only 12 (5.2%) were Amplicor PCR-negative. Therefore, this assay is useful for the rapid diagnosis of tuberculosis. The duration of Amplicor PCR-positive after culture-negative conversion was significantly associated with the presence of cavitary lesion, smear-positive specimens before treatment, and smear-positive specimens with negative cultures during chemotherapy.

Contribution of beta-lactamases to beta-lactam susceptibilities of susceptible and multidrug-resistant Mycobacterium tuberculosis clinical isolates

The beta-lactamases in 154 clinical Mycobacterium tuberculosis strains were studied. Susceptibilities to beta-lactam antibiotics, their combination with clavulanate (2:1), and two fluoroquinolones were determined in 24 M. tuberculosis strains susceptible to antimycobacterial drugs and in nine multiresistant strains. All 154 M. tuberculosis isolates showed a single chromosomal beta-lactamase pattern (pI 4.9 and 5.1). M. tuberculosis beta-lactamase hydrolyzes cefotaxime with a maximum rate of 22.5 +/- 2.19 IU/liter (strain 1382). Neither amoxicillin, carbenicillin, cefotaxime, ceftriaxone, nor aztreonam was active alone. Except for aztreonam, beta-lactam combinations with clavulanate produced better antimycobacterial activity.

Diagnosis of pulmonary tuberculosis using PCR assays on sputum collected within 24 hours of hospital admission

There have been few studies evaluating the efficacy of polymerase chain reaction (PCR) testing in front-line clinical practice. We assessed the diagnostic yield of PCR prospectively in a blinded study of patients admitted to rule out tuberculosis and compared PCR results to a culture and clinical diagnosis of tuberculosis. Specimens were sent for routine smear, culture, and PCR analysis. Sputum sediments were submitted for PCR amplification of IS6110 sequences by an in-house assay and also the Roche Amplicor PCR assay targeting 16s ribosomal RNA genes. Eighty-five patients were enrolled: 27 patients had cultures positive for tuberculosis; 12 were smear-positive. PCR by both assays on the first specimen picked up all patients smear-positive on any specimen. A positive PCR on at least one of two specimens collected in the first 24 h was 85 and 74% sensitive and 88 and 93% specific for tuberculosis by the in-house and Roche techniques, respectively. Sensitivity in smear-negative patients was 73 and 53%, respectively. The in-house PCR detected 100% and Roche detected 95% of patients with more than paucibacillary (greater than 20 colonies) tuberculosis. We conclude that PCR may be a useful tool to evaluate patients for tuberculosis within the first hospital day.

Evaluation of a nonradiometric system (BACTEC 9000 MB) for detection of mycobacteria in human clinical samples

This study was carried out to evaluate the rate of recovery and time required for detection of mycobacteria from pulmonary and extrapulmonary human clinical samples, by using a fluorescence-quenching-based oxygen sensor (BACTEC 9000 MB; Becton Dickinson Microbiology Systems, Sparks, Md.). The results were compared with those obtained by microscopy, conventional culture in Lowenstein-Jensen (LJ) medium, and a BACTEC radiometric system (BACTEC 460 TB; Becton Dickinson). Of the 779 clinical samples processed, 364 from pulmonary sites and 415 from extrapulmonary sites, 62 (7.9%) were positive for mycobacterial isolates; of the positive samples, 59 (95.1%) were detected with the fluorescent BACTEC 9000 MB system, 57 (91.9%) were detected with the radiometric system (BACTEC 460 TB), and 43 (69.3%) were detected with LJ conventional culture. The mean times to detection of all mycobacteria with BACTEC 9000 MB and BACTEC 460 TB were similar (10.3 and 10.0 days, respectively). The results obtained indicate that the nonradiometric BACTEC (BACTEC 9000 MB) system is as efficient as Bactec 460 TB and significantly more efficient than LJ for the rapid recovery of mycobacteria from both pulmonary and extrapulmonary clinical specimens. Though the BACTEC 9000 MB system is recommended for respiratory specimens, we demonstrated that it can be successfully used also for recovery of mycobacteria from clinical specimens from various extrapulmonary sites.

Mycobacterium growth indicator tube testing in conjunction with the AccuProbe or the AMPLICOR-PCR assay for detecting and identifying mycobacteria from sputum samples

We have compared the ability of the Mycobacterium Growth Indicator Tube (MGIT) system, a new culture method with an oxygen-sensitive fluorescent sensor, to recover mycobacteria from sputum samples with the abilities of egg-based medium and the Septi-Chek AFB system. We have also assessed the clinical utility of the AccuProbe or the AMPLICOR-PCR assay to directly identify Mycobacterium tuberculosis complex and M. avium-M. intracellulare complex (MAC) from positive MGITs. From 382 sputum samples, 99 isolates of M. tuberculosis complex and 20 isolates of MAC were recovered. The MGIT system had the highest recovery rates for M. tuberculosis complex (97.0%) and MAC (100%), compared to recovery rates of 51.5 and 65.0%, respectively, with the egg-based medium and 81.8 and 85.0%, respectively, with the Septi-Chek AFB system. The shortest recovery times were also achieved with the MGIT system: 16.6 days for M. tuberculosis complex and 12.0 days for MAC, compared to 27.1 and 20.1 days, respectively, with the egg-based medium and 21.4 and 13.2 days, respectively, with the Septi-Chek AFB system. The AccuProbe identified 74 (77.1%) of the 96 M. tuberculosis complex-positive MGITs and 17 (85.0%) of the 20 MAC-positive vials. The AMPLICOR system correctly identified 94 (97.9%) of the 96 M. tuberculosis complex-positive MGITs and all 20 MAC-positive vials. Therefore, the MGIT system used in conjunction with the AMPLICOR system is a rapid and sensitive method for detecting and identifying M. tuberculosis complex and MAC isolates from sputum samples.

Relevance of nucleic acid amplification techniques for diagnosis of respiratory tract infections in the clinical laboratory

Clinical laboratories are increasingly receiving requests to perform nucleic acid amplification tests for the detection of a wide variety of infectious agents. In this paper, the efficiency of nucleic acid amplification techniques for the diagnosis of respiratory tract infections is reviewed. In general, these techniques should be applied only for the detection of microorganisms for which available diagnostic techniques are markedly insensitive or nonexistent or when turnaround times for existing tests (e.g., viral culture) are much longer than those expected with amplification. This is the case for rhinoviruses, coronaviruses, and hantaviruses causing a pulmonary syndrome, Bordetella pertussis, Chlamydia pneumoniae, Mycoplasma pneumoniae, and Coxiella burnetii. For Legionella spp. and fungi, contamination originating from the environment is a limiting factor in interpretation of results, as is the difficulty in differentiating colonization and infection. Detection of these agents in urine or blood by amplification techniques remains to be evaluated. In the clinical setting, there is no need for molecular diagnostic tests for the diagnosis of Pneumocystis carinii. At present, amplification methods for Mycobacterium tuberculosis cannot replace the classical diagnostic techniques, due to their lack of sensitivity and the absence of specific internal controls for the detection of inhibitors of the reaction. Also, the results of interlaboratory comparisons are unsatisfactory. Furthermore, isolates are needed for susceptibility studies. Additional work remains to be done on sample preparation methods, comparison between different amplification methods, and analysis of results. The techniques can be useful for the rapid identification of M. tuberculosis in particular circumstances, as well as the rapid detection of most rifampin-resistant isolates. The introduction of diagnostic amplification techniques into a clinical laboratory implies a level of proficiency for excluding false-positive and false-negative results.

Current perspectives on multidrug-resistant bacteria. Epidemiology and control

Antimicrobial resistance in bacteria has diminished the availability of effective antimicrobial agents. Knowledge of epidemiology, mechanisms of resistance, and new diagnostic modalities can help to identify and treat patients at risk for infection by these organisms. Limited or nonexistent effective microbial therapy underscores the importance of effective preventive and containment measures.

Evaluation of reformulated chemiluminescent DNA probe (AccuProbe) for culture identification of Mycobacterium kansasii

A panel of 104 isolates belonging to the species Mycobacterium kansasii and 78 mycobacterial isolates belonging to other species was tested in parallel with the present commercially available DNA probe (AccuProbe; Gen-Probe) and with a new probe just developed by the same manufacturer. While the old version of the probe confirmed the previously reported low sensitivity (only 59% of the M. kansasii isolates reacted), the new one was 100% sensitive. Only two non-M. kansasii strains, both M. gastri isolates, gave false-positive hybridization results.

Comparison of a biphasic non-radiometric system with Lowenstein-Jensen and Bactec-460 system for recovery of mycobacteria from clinical specimens

SETTING

The resurgence of tuberculosis and the increase of Mycobacterium avium complex infections have renewed interest in developing more efficient systems for isolation of mycobacteria. The Bactec radiometric method enhances the recovery and shortens the detection time of mycobacteria; however, many clinical laboratories are subject to severe restrictions on the utilization of 14C radiolabelled culture media.

OBJECTIVE

To compare the biphasic MB-Check system in the recovery of mycobacteria from clinical specimens with the Bactec-460 system and Lowenstein-Jensen (LJ) medium.

DESIGN

The MB-Check was evaluated for routine use in a clinical laboratory by comparing the rates and times for isolation of mycobacteria from 1840 clinical specimens with results obtained using the other systems. The isolated organisms were identified by standard procedures and specific deoxyribonucleic acid (DNA) probes.

RESULTS

The rate of recovery of all mycobacteria with the MB-Check system was 84.8%, compared to 87.5% for the Bactec-460 system and only 64.2% on LJ. Of the 147 M. tuberculosis isolates recovered by all methods combined, 92.5% were recovered by MB-Check, 87.1% by Bactec and 79.6% on LJ. Of the 109 isolates of nontuberculous mycobacteria (NTM) recovered by all methods combined, 44% were recovered on LJ, 75% by MB-Check and 88% by Bactec (P < 0.001). A combination of the Bactec and MB-Check systems allowed recovery of 99.2% of isolates. The Bactec system showed a faster detection time than the other two methods.

CONCLUSION

The MB-Check and Bactec systems were more efficient than LJ medium for the isolation of both M. tuberculosis and NTM. The performance of the MB-Check system and the ease with which processing, inspection, detection, and isolation can be performed, indicated that the biphasic approach for cultivation of mycobacteria is feasible and practical. The MB-Check system is more suitable than Bactec system for laboratories that have a small number of specimens or in situations where the disposal of radioactive waste is a problem.

Current techniques in mycobacterial detection and speciation

Tuberculosis, a health concern so well controlled in recent decades that eradication seemed imminent, is once again reaching epidemic proportions following the increasing prevalence of AIDS. One important means of curbing this resurgence is a robust method that has the capability of identifying and speciating mycobacterial infections in a matter of days. Classic biochemical techniques, which require 4 to 8 weeks to identify and speciate tuberculosis infections, are in the process of being replaced by newer methods, including BACTEC, gene probes, nucleic acid amplification, amplification of ribosomal RNA, high-performance liquid chromatography, and gas chromatography-mass spectrometry. This review is intended to give the reader a synopsis of the current literature and research on these methods, including reliability, approximate time required for detection and speciation, and clinical utility.

Selective utilization of DNA probes for identification of Mycobacterium species on the basis of cord formation in primary BACTEC 12B cultures

Primary BACTEC 12B cultures with serpentine cords observed in Kinyoun-stained smears were tested with a probe for Mycobacterium tuberculosis complex, while cultures without cords were tested with a probe for M. avium complex. The sensitivity, specificity, and positive and negative predictive values of cording for the presumptive identification of M. tuberculosis were 95, 95, 90, and 98%, respectively. With experience, the selection of a probe for testing of primary BACTEC 12B cultures on the basis of cord formation and history of tuberculosis can provide a rapid and reliable approach to the laboratory diagnosis of tuberculosis.

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.

Pediatric tuberculosis: an update

The incidence of tuberculous infection and disease in children has risen significantly over the last decade. The management of TB has become more complicated by the changing epidemiology of this disease and the emergence of resistant MTB. Many new recommendations have recently been made to address these issues. It is crucial that pediatricians become familiar with this disease again and have a good working knowledge of pediatric TB.

Tuberculosis in the AIDS era

A resurgence of tuberculosis has occurred in recent years in the United States and abroad. Deteriorating public health services, increasing numbers of immigrants from countries of endemicity, and coinfection with the human immunodeficiency virus (HIV) have contributed to the rise in the number of cases diagnosed in the United States. Outbreaks of resistant tuberculosis, which responds poorly to therapy, have occurred in hospitals and other settings, affecting patients and health care workers. This review covers the pathogenesis, epidemiology, clinical presentation, laboratory diagnosis, and treatment of Mycobacterium tuberculosis infection and disease. In addition, public health and hospital infection control strategies are detailed. Newer approaches to epidemiologic investigation, including use of restriction fragment length polymorphism analysis, are discussed. Detailed consideration of the interaction between HIV infection and tuberculosis is given. We also review the latest techniques in laboratory evaluation, including the radiometric culture system, DNA probes, and PCR. Current recommendations for therapy of tuberculosis, including multidrug-resistant tuberculosis, are given. Finally, the special problem of prophylaxis of persons exposed to multidrug-resistant tuberculosis is considered.

Use of a multiplex PCR to detect and identify Mycobacterium avium and M. intracellulare in blood culture fluids of AIDS patients

The presence of mycobacteria in blood culture fluids (BACTEC) of AIDS patients with positive growth indices (GIs, > 20 U) was investigated by using a multiplex PCR to detect and identify members of the genus Mycobacterium, M. avium, M. intracellulare, and M. tuberculosis. Three different methods of extracting mycobacterial DNA from blood culture fluid were compared for use with the multiplex PCR. Mycobacterial cells were pelleted from a small aliquot of blood culture fluid by centrifugation, and the DNA was extracted from cells by heat lysis or a sodium iodide-isopropanol or a phenol-chloroform method. DNAs of different sizes were amplified from a region of the MPB70 gene of M. tuberculosis (372 bp) and from a region of the 16S rRNA gene of members of the genus Mycobacterium (1,030 bp), M. intracellulare (850 bp), or M. avium (180 bp) as a multiplex PCR in a single tube. The amplified DNA products were detected by agarose gel electrophoresis and ethidium bromide staining in all 41 (100%) positive cultures after sodium iodide-isopropanol extraction, in 18 (44%) after heat lysis, and in 5 (12%) after phenol-chloroform extraction. Of the 41 positive cultures, 38 were identified as M. avium and 2 were identified as M. intracellulare by both routine methods and multiplex PCR. The remaining mycobacterium was identified as M. intracellulare by routine methods and as M. avium by the multiplex PCR. Another six blood cultures that were negative for the presence of acid-fast bacilli after Ziehl-Neelson staining were also negative by PCR. The study shows that the multiplex PCR is a useful method for the detection and identification of either M. avium or M. intracellulare in small samples of cultured BACTEC 13A fluid with positive GIs ranging from 21 to 999 U. The average time to positive GI was 18 days (median, 13 days) and ranged between 8 and 42 days. The multiplex PCR may permit cultured mycobacteria to be identified at an earlier stage than the routine methods which have been adapted for use with the BACTEC system. The results also show that the method selected for extracting mycobacterial DNA from blood culture fluids is crucial for providing sensitive and accurate PCR results.

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

We report on a rapid, sensitive, Q-Beta replicase-amplified nucleic acid hybridization assay for the detection of Mycobacterium tuberculosis directly from spiked human sputum. Specimens were processed by either an N-acetyl-L-cysteine-NaOH or a 2% NaOH digestion-decontamination method and then washed to neutralize the pH of the cell pellet. The washed sputum pellets were heated at 100 degrees C to inactivate the M. tuberculosis organisms. The heat-inactivated samples were mechanically lysed at 5,000 rpm for 6 min in the GENE-TRAK Sample Processing Instrument in the presence of zirconium oxide beads and a buffer containing guanidine thiocyanate. The released nucleic acid was subjected to the GENE-TRAK Q-Beta replicase-amplified, dual-capture assay. The assay sensitivity was 10(3) purified rRNA targets or 1 CFU of M. tuberculosis spiked into M. tuberculosis-negative human sputum. There was a low level of noise because of the limitations of performing a signal amplification assay in an open system. High levels of other mycobacterial rRNA (approximately 10(7) organisms), including rRNAs of Mycobacterium avium and Mycobacterium gordonae, did not interfere with the sensitivity of the assay.

Comparison of polymerase chain reaction with standard methods in the diagnosis of Mycobacterium tuberculosis infection

The polymerase chain reaction (PCR) method was evaluated in the detection of Mycobacterium tuberculosis in comparison with direct microscopy and culture procedures including the standard radiometric system (Bactec). Amplified DNA fragments from clinical samples were analyzed by dot-blot and non-radioactive oligonucleotide hybridization techniques or by agarose gel electrophoresis. The results revealed nested PCR to be the method of choice. The combination of three culture methods could detect Mycobacterium tuberculosis in only 79% of PCR-positive cases. The mean time required to achieve a positive culture result was 17 days in contrast to the PCR method requiring only two to three days. The nested PCR assay provided rapid and reliable results allowing a definitive diagnosis particularly in a number of samples which were negative on culture.

Molecular methods: applications for clinical infectious diseases

The application of molecular biology to microbiology has led to a surge of new information about most infectious microorganisms, the pathogenesis of the infections they cause, and the specific microbial antigens involved in the immune response to these infections. The simultaneous application of the same techniques to diagnosis and epidemiology has also shown great promise, but these developments have not yet had a major effect on the routine practice of medicine. For some purposes, direct probe tests perform as well as other available methods. However, for most infections, these methods have not been proven sufficiently sensitive. The latest generation of highly sensitive diagnostics based on the polymerase chain reaction will overcome this technical obstacle and may revolutionize the management of many infections. Difficulties inherent in performing these tests will require special procedures and training in clinical laboratories to ensure that they are performed reliably. Nucleic acid-based methods for epidemiologic typing of microorganisms and for identification of noncultivatable pathogens are particularly useful for analysis of poorly cultivatable, dangerous, or otherwise untypeable microorganisms.

Tuberculosis and acquired immunodeficiency syndrome: a historical perspective on recent developments

The incidence of tuberculosis has increased in recent years, at least in part as a result of the ongoing worldwide epidemic of acquired immunodeficiency syndrome (AIDS). In addition, the occurrence of outbreaks caused by multidrug-resistant Mycobacterium tuberculosis organisms has greatly heightened concern. In retrospect, a number of seminal studies that have appeared during the past decade have helped to define changing concepts concerning the epidemiology, pathogenesis, approaches to preventive care, diagnosis, and treatment of tuberculosis in HIV-infected persons. Such reports have shown that the variable clinical manifestations of tuberculosis in patients with AIDS are greatly influenced by the degree of HIV-induced immunosuppression. Explosive outbreaks of tuberculosis occurring in closed environments have emphasized that patients with AIDS and pulmonary tuberculosis may be highly contagious, especially when diagnosis and implementation of appropriate infection control measures are delayed. The extent to which homelessness and illicit drug use complicate management of tuberculosis have been examined, and the high risk of persons who are both tuberculin-positive and HIV-positive ultimately developing active tuberculosis, unless chemoprophylaxis is completed, has been clearly shown. The utility of sputum smears, bronchoscopy, and newer technologies such as polymerase chain reaction for diagnosis has been examined. The risk of relapse appears to be low when patients with AIDS with drug-sensitive tuberculosis complete appropriate multiple-drug therapy. Recent reports have addressed important hospital infection control, tuberculin testing, and chemoprophylaxis issues. This paper describes this evolution of understanding, focusing on reports that we believe have been conceptually important.

Direct identification of Mycobacterium species in BACTEC 7H12B medium by high-performance liquid chromatography

Primary cultures of mycobacteria grown in BACTEC 7H12B medium (Becton Dickinson and Co., Paramus, N.J.), with and without the addition of oleic acid-albumin-dextrose-catalase (OADC) enrichment (Becton Dickinson and Co., Cockeysville, Md.), were analyzed for their mycolic acid patterns by high-performance liquid chromatography. Of the 126 isolates grown in medium to which OADC was added, 117 (93%) were successfully identified to the species level. The time to identification of Mycobacterium tuberculosis (n = 65) averaged 19 days, and the average time was 21 days for nontuberculosis mycobacteria (n = 52) from initial specimen processing. None of the 10 isolates cultured without OADC were identified. The mycolic acid patterns were considered reliable for identification if the height of the tallest peak in the chromatogram was at least 50% of the internal standard peak height.

Detection and identification of Mycobacterium directly from BACTEC bottles by using a DNA-rRNA probe

Detection and identification of mycobacterial species using DNA-rRNA probes from colonies has been used for some time. Guidelines for probe use with a specific minimum growth index (GI) cutoff from BACTEC 12B bottles or its use with 7H9 broth has not been defined. This study defined this minimum GI guideline. Clinical specimens received during the study period were decontaminated and directly inoculated into BACTEC 12B bottles and appropriate solid media. An initial probe test was performed at a GI reading of > or = 100. An additional probe test was made at GI of > or = 300. A total of 1377 specimens were processed with 98 specimens containing 99 isolates of Mycobacterium. Of these, 82 were M. avium complex (MAC), six were M. tuberculosis (Mtb), and 11 were other species. At a GI of > or = 100, 82% of MAC were detected; at a GI of > or = 300, 89% were detected. All Mtb were detected at a GI of > or = 100. The probes correctly identified all isolates from backup 7H9 broths. There were no false-positive probe results for any of the isolates from either BACTEC 12B or 7H9 media. Therefore, the DNA-rRNA probe test at a GI of > or = 300 saves considerable time (on average, 21 days saved) for the detection and identification of Mtb and MAC. This time saving compares with waiting for the production of colonies while retaining acceptable sensitivity and excellent specificity.

Gas chromatographic whole-cell fatty acid analysis as an aid for the identification of mixed mycobacterial cultures

Gas chromatographic analysis of whole-cell fatty acids, secondary alcohols and mycolic acid cleavage products could be a useful technique in checking mixed mycobacterial cultures. The mixed cultures were confirmed when species-specific compounds of different mycobacterial species were detected in the same chromatogram.

The Mycobacterium avium complex

Mycobacterium avium complex (MAC) disease emerged early in the epidemic of AIDS as one of the common opportunistic infections afflicting human immunodeficiency virus-infected patients. However, only over the past few years has a consensus developed about its significance to the morbidity and mortality of AIDS. M. avium was well known to mycobacteriologists decades before AIDS, and the MAC was known to cause disease, albeit uncommon, in humans and animals. The early interest in the MAC provided a basis for an explosion of studies over the past 10 years largely in response to the role of the MAC in AIDS opportunistic infection. Molecular techniques have been applied to the epidemiology of MAC disease as well as to a better understanding of the genetics of antimicrobial resistance. The interaction of the MAC with the immune system is complex, and putative MAC virulence factors appear to have a direct effect on the components of cellular immunity, including the regulation of cytokine expression and function. There now is compelling evidence that disseminated MAC disease in humans contributes to both a decrease in the quality of life and survival. Disseminated disease most commonly develops late in the course of AIDS as the CD4 cells are depleted below a critical threshold, but new therapies for prophylaxis and treatment offer considerable promise. These new therapeutic modalities are likely to be useful in the treatment of other forms of MAC disease in patients without AIDS. The laboratory diagnosis of MAC disease has focused on the detection of mycobacteria in the blood and tissues, and although the existing methods are largely adequate, there is need for improvement. Indeed, the successful treatment of MAC disease clearly will require an early and rapid detection of the MAC in clinical specimens long before the establishment of the characteristic overwhelming infection of bone marrow, liver, spleen, and other tissue. Also, a standard method of susceptibility testing is of increasing interest and importance as new effective antimicrobial agents are identified and evaluated. Antimicrobial resistance has already emerged as an important problem, and methods for circumventing resistance that use combination therapies are now being studied.

Rapid identification of mycobacteria by the Gen-Probe Accuprobe system

Chemiluminescent acridinium ester-labelled (AE)-DNA probes (Gen-Probe, Inc., San Diego, Calif.) for the identification of Mycobacterium tuberculosis complex (MTBC) and the M. avium-M. intracellulare complex (MAC) were evaluated using 184 mycobacterial isolates cultured in BACTEC 12B vials (Becton Dickinson and Co., Towson, Md.). A 1.5 mL aliquot from BACTEC 12B vials containing acid-fast bacilli and a Growth Index of > 200 was concentrated 15-fold using a centrifugation step prior to performing the test procedure. When 184 mycobacterial isolates were tested (42MTBC/142 nontuberculous mycobacteria) using the AE-MTBC probe, there was 100% sensitivity and specificity when compared with conventional identification procedures. Criteria for using the AE-MAC probe were defined to optimize results whilst minimizing laboratory costs. Ninety-one (64%) of AE-MTBC probe negative isolates failed to meet selection criteria and were not tested. When 51 (36%) of the AE-MTBC-probe negative mycobacterial isolates were tested, the AE-MAC probe was found to be 88% sensitive and 100% specific. The non-isotopic Gen-Probe test is a rapid and practical alternative to current procedures for differentiation of mycobacteria.

Current practices in mycobacteriology: results of a survey of state public health laboratories

Fifty-six state and territorial public health laboratories were surveyed to determine whether currently available rapid methods for the identification and drug susceptibility testing of Mycobacterium tuberculosis were being performed. Forty (71%) laboratories use fluorochrome rather than conventional basic fuchsin stains for screening clinical specimens for acid-fast bacilli. Of the 55 laboratories that routinely culture for mycobacteria, 16 (29%) use the more rapid radiometric methods. Species identification of isolates is done by biochemical tests in 13 (23%) laboratories; 40 (72%) use nucleic acid probes, high-performance liquid chromatography, or the BACTEC p-nitro-alpha-acetylamino-beta-hydroxypropiophenone (NAP) test (rapid tests); 3 laboratories do not perform species identification. Drug susceptibility testing is performed with solid media by 36 of 45 (80%) laboratories, while the more rapid radiometric methods are used by 9 (20%) laboratories. Compared with the laboratories that use conventional methods, laboratories that use rapid methods report results more quickly: for species identification, 43 days (conventional) versus 22 days (rapid); for drug susceptibility testing, 44 days (conventional) versus 31 days (rapid) from specimen processing. Rapid technologies for microscopy and species identification are being used by many, but not all, state and territorial public health laboratories; however, most laboratories do not use the more rapid radiometric methods for routine culture or drug susceptibility testing of mycobacteria. Implementation of such rapid technologies can shorten turnaround times for the laboratory diagnosis of tuberculosis and recognition of drug resistance.

Identification of Mycobacterium avium complex strains belonging to serovars 21-28 by three commercial DNA probe tests

Various reference strains of Mycobacterium avium complex (MAC) belonging to serovars 21-28 were identified by three DNA probe tests, i.e., Gen-Probe, AccuProbe and SNAP tests. All of these DNA probe tests were in agreement for strains identified as M. avium or M. intracellulare. The tested serovar strains involved M. avium, M. intracellulare, MAC reactive only with Probe X of SNAP test ('Probe X-reactive MAC'), M. scrofulaceum reactive with Probe X of SNAP test ('Probe X-reactive M. scrofulaceum'), and typical M. scrofulaceum which did not react with any of the probes. Both reference strains belonging to serovar 21 were M. avium, and none of the other serovars included this species. On the contrary, M. intracellulare was found in serovars 22, 25, 26, and 28. 'Probe X-reactive MAC' were also widely found in serovars 23, 24, 26, 27, and 28, while 'Probe X-reactive M. scrofulaceum' was seen only in serovar 22. These results confirm the usefulness of SNAP test to identify the MAC showing no reactivity to Gen-Probe and AccuProbe.

Typing by DNA probe of mycobacterial species isolated from patients with AIDS

Restriction fragment length polymorphism (RFLP) types of Mycobacterium avium intracellulare and Mycobacterium kansasii isolated from patients with AIDS were examined. We demonstrate that one RFLP type is much more common than others which confirms previous findings. Carriage of individual RFLP types is constant over long periods of time. In addition, we document a disseminated infection in a patient with M. avium intracellulare of three RFLP types.

Detection of Mycobacterium leprae and the potential for monitoring antileprosy drug therapy directly from skin biopsies by PCR

An improved protocol for PCR analysis of Mycobacterium leprae-infected tissues, based on enzymatic lysis, has been developed and used to demonstrate the feasibility of using PCR for detecting M. leprae in routine skin biopsies taken from leprosy patients throughout the clinical spectrum. Of 92 multibacillary patients tested, 99% were PCR-positive using gel electrophoresis or DNA hybridization to detect the amplified product. Similar analysis of paucibacillary patients, in which only one of 27 biopsies had demonstrable AFB microscopically, gave a positivity rate of 74%. No PCR signals were demonstrated from skin biopsies from seven patients with non-leprosy dermatoses and one AIDS patient with a disseminated atypical mycobacteriosis. Evaluation of leprosy patients with antileprosy drug therapy prior to biopsy demonstrated that PCR signals were either greatly diminished or absent after 2 months of continuous antibiotic therapy. PCR was also able to detect the presence of M. leprae in tissues of patients receiving antibacterial therapy when patients were suspected of harbouring drug-resistant M. leprae.