Relevance of commercial amplification methods for direct detection of Mycobacterium tuberculosis complex in clinical samples

Comparison of targeted next-generation sequencing and the Xpert MTB/RIF assay for detection of Mycobacterium tuberculosis in clinical isolates and sputum specimens

Targeted next-generation sequencing (tNGS) can be used to perform Mycobacterium tuberculosis (MTB) complex-specific amplification or target capture directly from sputum samples, yielding simultaneous coverage of many genes and DNA regions associated with antimicrobial resistance (AMR). Performance comparisons of tNGS and another molecular testing tool, Xpert MTB/rifampicin (RIF), have been empirical. Here, using a dilution series of a RIF-resistant clinical isolate of MTB, we found that tNGS had a slightly lower limit of bacterial detection (102 CFU/mL) compared with Xpert MTB/RIF (103 CFU/mL) in culture medium. However, the minimum detection limit of the rpoB S450L mutation in this isolate was significantly lower with tNGS (102 CFU/mL) than with Xpert MTB/RIF (106 CFU/mL). Sputum samples collected from 129 suspected pulmonary tuberculosis patients were also prospectively studied with the clinical diagnosis as a reference, revealing that the sensitivity of tNGS (48.6%) was higher than those of culture (46.8%), Xpert MTB/RIF (39.4%), and smear microscopy (34.9%) testing. Notably, AMR analysis of 56 MTB-positive samples as determined by tNGS revealed high mutation frequencies of 96.4%, 35.7%, 26.8%, and 19.6% in the following AMR-associated genes: rrs, rpoB, katG, and pncA, respectively. The findings of this study provide theoretical support for the differential clinical application of tNGS and Xpert MTB/RIF and suggest that tNGS has greater application value in tuberculosis drug resistance monitoring and prevention.IMPORTANCETargeted next-generation sequencing (tNGS) can be used to perform Mycobacterium tuberculosis (MTB) complex-specific amplification or target capture directly from sputum samples, yielding simultaneous coverage of genes and DNA regions associated with antimicrobial resistance (AMR). Performance comparisons of tNGS and Xpert MTB/rifampicin (RIF) have been empirical. The Xpert MTB/RIF assay is a commercial system that uses the nucleic acid amplification detection method for rapid (2 hours) diagnosis of tuberculosis (TB). The cost of the tNGS and Xpert MTB/RIF assays in this study was similar, at USD 98 and USD 70-104 per sample, respectively, but the time required for tNGS (3 days) was much longer than that required for the Xpert MTB/RIF assay. However, tNGS yielded more accurate results and a larger number of AMR-associated gene mutations, which compensated for the extra time and highlighted the greater application value of tNGS in TB drug resistance monitoring and prevention.

Detection of Mycobacterial DNA in Human Bone Marrow

Bone marrow is a cell-rich tissue of the reticuloendothelial system essential in the homeostasis and accurate functioning of hematopoiesis and of the immune system; moreover, it is also rich in lipids because it contains marrow adipocytes. This work aimed to evaluate the detection of mycobacterial DNA in human bone marrow as a tool to understand the complex pathology caused by the main pathogen Mycobacterium tuberculosis (Mtb). Formalin-fixed paraffin-embedded human bone marrow samples were studied using both conventional PCR + hybridization and in situ PCR to figure out the cell distribution of the targeted DNA. Samples were retrospectively collected from HIV+ patients with microbiologically proved mycobacterial infection and from subjects without evidence of infection. Mycobacterium avium (Mav) as well as Mtb DNA was detected in both settings, including tissues with and without granulomas. We detected DNA from both mycobacterial species, using in situ PCR, inside bone marrow macrophages. Other cell types, including adipocytes, showed positive signals only for Mtb DNA. This result suggested, for the first time, that marrow adipocytes could constitute an ideal reservoir for the persistence of Mtb, allowing the bacilli to establish long-lasting latent infection within a suitable lipid environment. This fact might differentiate pathogenic behavior of non-specialized pathogens such as Mav from that of specialized pathogens such as Mtb.

Innovations in Molecular Identification of Mycobacterium tuberculosis

Tuberculosis (TB) continues to be a significant public health concern on a global scale. Quick and precise identification of Mycobacterium tuberculosis (MTB) in symptomatic patients is pivotal for worldwide TB eradication initiatives. As an infectious disorder induced by MTB, it remains a critical threat to public health, particularly in poor countries, due to an inadequate diagnostic research laboratory. There is a need for a persistent incentive to reduce response time for effective diagnosis and control of TB infection, which is a benefit that molecular techniques provide over traditional methods. Although there is a tremendous overall prevalence of TB and a relatively poor probability of case identification worldwide. Common screening techniques have focused on tests that have many fundamental shortcomings. Due to the development of antibiotic-resistant Mycobacterium strains, TB is one of the leading contributors to fatalities. It is now possible to examine TB using molecular detection techniques, which are faster and more cost-effective than previous methods, such as standard culture procedures to test and verify antibiotic resistance in patients with TB. Whole genome sequencing (WGS), faster nucleic acid amplification tests, has made it easier to diagnose and treat TB more quickly. This article addresses the genetic approaches for detecting Mycobacterium tuberculosis complex (MTBC) in clinical specimens as well as antibiotic resistance in mycobacterium and discusses the practical limitations of using these methods.

Performance of Mali's biosafety level 3 laboratory in the external quality assessment in preparedness of laboratory accreditation and support to clinical trials

Background:

The external quality assessment (EQA) or external quality control is an evaluation conducted by a certified external organization to inquire about the quality of the results provided by a laboratory. The primary role of EQA is to verify the accuracy of laboratory results. This is essential in research because research data should be published in international peer-reviewed journals, and laboratory results must be repeatable. In 2007, the University Clinical Research Center (UCRC’s) biosafety level 3 (BSL-3) laboratory joined the EQA program with the College of American Pathologists in acid-fast staining and culture and identification of mycobacteria as per laboratory accreditation preparedness. Thus, after 11 years of participation, the goal of our study was to evaluate the performance of our laboratory during the different interlaboratory surveys.

Methods:

We conducted a descriptive retrospective study to evaluate the results of UCRC mycobacteriology laboratory from surveys conducted during 2007 and 2017.

Results:

Of the 22 evaluations, the laboratory had satisfactory (100% of concordance results) in 18 (81.8%) and good (80% of concordance results) in 4 (18.2%). Overall, the laboratory was above the commended/accepted limits of 75%.

Conclusion:

So far, UCRC’s BSL-3 performed well during the first 11 years of survey participation, and efforts should be deployed to maintain this high quality in the preparedness for laboratory accreditation and support to clinical trials.

Multiplex Real-Time PCR-shortTUB Assay for Detection of the Mycobacterium tuberculosis Complex in Smear-Negative Clinical Samples with Low Mycobacterial Loads

Tuberculosis (TB) remains a major health problem worldwide. Control of TB requires rapid, accurate diagnosis of active disease. However, extrapulmonary TB is very difficult to diagnose because the clinical specimens have very low bacterial loads. Several molecular methods involving direct detection of the Mycobacterium tuberculosis complex (MTBC) have emerged in recent years. Real-time PCR amplification simultaneously combines the amplification and detection of candidate sequences by using fluorescent probes (mainly TaqMan or Molecular Beacons) in automated systems. The multiplex real-time PCR-short assay is performed using locked nucleic acid (LNA) probes (length, 8 to 9 nucleotides) in combination with CodUNG to detect multiple pathogens in clinical samples. In this study, we evaluated the performance of this novel multiplex assay for detecting the MTBC in comparison with that of the conventional culture-based method. The multiplex real-time PCR-short_TUB assay targets two genes, whiB3 (redox-responsive transcriptional regulator) and pstS1 (phosphate-specific transporter), yielding limits of detection (LOD) of 10 copies and 100 copies, respectively, and amplification efficiencies of 92% and 99.7%, respectively. A total of 94 extrapulmonary samples and pulmonary samples with low mycobacterial loads (all smear negative; 75 MTBC culture positive) were analyzed using the test, yielding an overall sensitivity of 88% and a specificity of 95%. For pleural fluid and tissues/biopsy specimens, the sensitivity was 83% and 85%, respectively. In summary, this technique could be implemented in routine clinical microbiology testing to reduce the overall turnaround time for MTBC detection and may therefore be a useful tool for the diagnosis of extrapulmonary tuberculosis and diagnosis using pulmonary samples with low mycobacterial loads.

Comparative evaluation of Xpert MTB/RIF and the new Xpert MTB/RIF ultra with respiratory and extra-pulmonary specimens for tuberculosis case detection in a low incidence setting

BACKGROUND

The Xpert MTB/RIF assay (Xpert) is an automated molecular test for the detection of tuberculosis and rifampin resistance (RIF-R), but it lacks sensitivity in smear-negative samples and some limitations in determination of RIF-R have also been reported. The new Xpert MTB/RIF Ultra (Ultra) was developed to overcome these limitations. We aimed to compare Ultra and Xpert diagnostic accuracy setting culture and drug susceptibility testing as reference standards.

METHODS

A retrospective analysis was performed on 359 consecutive, respiratory (269) and extrapulmonary (90) specimens collected from 340 patients investigated for TB along a two-year period. Patients presenting at primary health-care centres and hospitals were recruited on the basis of symptoms and abnormal X-ray imaging. One-hundred seventy-four subjects were identified to have active tuberculosis by culture and 2 were MDR.

FINDINGS

Sensitivities of Ultra and Xpert were 87% and 75% for the 48 individuals with smear-negative and culture-positive respiratory TB (difference of 12%, 95% CI 3 to 21); 95% and 72% for the 40 individuals with smear-negative and culture-positive extrapulmonary disease (22%, 95% CI 10 to 34); and 95% and 86%, respectively, across all 174 individuals with culture-positive samples (8.5%, 95% CI 4.5 to 12.5). Specificities of Ultra and Xpert for tuberculosis case detection were 98% and 100% (-2.0%, 95% CI -4.3 to +0.3). Ultra and Xpert performed equal in detecting RIF-R.

INTERPRETATION

Sensitivity of Ultra was superior to that of Xpert in all categories of clinical samples. However, improved sensitivity was associated with a modest reduction in specificity.

Advances in the molecular diagnosis of tuberculosis: From probes to genomes

Tuberculosis, disease caused by Mycobacterium tuberculosis, is currently the leading cause of death by a single infectious agent worldwide. Early, rapid and accurate identification of M. tuberculosis and the determination of drug susceptibility is essential for the treatment and management of this disease. Tuberculosis diagnosis is mainly based on chest radiography, smear microscopy and bacteriological culture. Smear microscopy has variable sensitivity, mainly in patients co-infected with the human immunodeficiency virus (HIV). Conventional culture for M. tuberculosis isolation, identification and drug susceptibility testing requires several weeks owning to the slow growth of M. tuberculosis. The delay in the time to results drives the prolongation of potentially inappropriate antituberculosis therapy contributing to the emergence of drug resistance, reducing treatment options and increasing treatment duration and associated costs, resulting in increased mortality and morbidity. For these reasons, novel diagnostic methods are need for timely identification of M. tuberculosis and determination of the antibiotic susceptibility profile of the infecting strain. Molecular methods offer enhanced sensitivity and specificity, early detection and the capacity to detect mixed infections. These technologies have improved turnaround time, cost effectiveness and are amenable for point-of-care testing. However, although these methods produce results within hours from sample collection, the phenotypic susceptibility testing is still needed for the determination of drug susceptibility and quantify the susceptibility levels of a given strain towards individual antibiotics. This review presents the history, advances and forthcoming promises in the molecular diagnosis of tuberculosis. An overview on the general principles, diagnostic value and the main advantages and disadvantages of the molecular methods used for the detection and identification of M. tuberculosis and its associated disease, is provided. It will be also discussed how the current phenotypic methods should be used in combination with the genotypic methods for rapid antituberculosis susceptibility testing.

Paradigm for diagnosing mycobacterial disease: direct detection and differentiation of Mycobacterium tuberculosis complex and non-tuberculous mycobacteria in clinical specimens using multiplex real-time PCR

AIMS

Mycobacterium tuberculosis and non-tuberculous mycobacteria (NTM) are clinically different, and the rapid detection and differentiation of M. tuberculosis complex (MTBC) and NTM is crucial for patient management and infection control. Given the slow growth of most pathogenic mycobacteria, nucleic acid amplification assays are excellent tools for direct identification of mycobacteria in clinical specimens. Recently, a multiplex real-time PCR assay was developed that can directly detect 20 mycobacterial species in clinical specimens. Here, we evaluated the diagnostic performance of the assay for diagnosing mycobacterial disease under routine laboratory conditions.

METHODS

A total of 3334 specimens collected from 1437 patients suspected of tuberculosis infection were subjected to acid-fast bacilli staining, conventional culture and the multiplex real-time PCR assay. To evaluate the sensitivity and specificity of the assay, the overall diagnosis of tuberculosis was defined by positive culture plus medical history, and the 2007 American Thoracic Society and Infectious Disease Society of America diagnostic criteria for NTM disease were applied.

RESULTS

The sensitivity, specificity, positive predictive value and negative predictive value were 87.5%, 99.6%, 96.1% and 98.5%, respectively, for the detection of MTBC isolates and 53.3%, 99.9%, 95.2%, and 98.9%, respectively, for detecting NTM isolates.

CONCLUSIONS

Thus, the assay can correctly differentiate between MTBC and NTM isolates in clinical specimens and would be a useful tool for the rapid differentiation of tuberculosis and NTM disease, despite its limited sensitivity for the diagnosis of NTM disease.

Practice Guidelines for Clinical Microbiology Laboratories: Mycobacteria

Mycobacteria are the causative organisms for diseases such as tuberculosis (TB), leprosy, Buruli ulcer, and pulmonary nontuberculous mycobacterial disease, to name the most important ones. In 2015, globally, almost 10 million people developed TB, and almost half a million patients suffered from its multidrug-resistant form. In 2016, a total of 9,287 new TB cases were reported in the United States. In 2015, there were 174,608 new case of leprosy worldwide. India, Brazil, and Indonesia reported the most leprosy cases. In 2015, the World Health Organization reported 2,037 new cases of Buruli ulcer, with most cases being reported in Africa. Pulmonary nontuberculous mycobacterial disease is an emerging public health challenge. The U.S. National Institutes of Health reported an increase from 20 to 47 cases/100,000 persons (or 8.2% per year) of pulmonary nontuberculous mycobacterial disease among adults aged 65 years or older throughout the United States, with 181,037 national annual cases estimated in 2014. This review describes contemporary methods for the laboratory diagnosis of mycobacterial diseases. Furthermore, the review considers the ever-changing health care delivery system and stresses the laboratory's need to adjust and embrace molecular technologies to provide shorter turnaround times and a higher quality of care for the patients who we serve.

Performance of a molecular assay to detect Mycobacterium tuberculosis complex DNA in clinical specimens: multicenter study in Brazil

BACKGROUND

In high tuberculosis (TB) burden countries, there are few data on the performance of new molecular commercialised assays developed locally.

OBJECTIVE

To evaluate the performance of a new molecular commercialised assay for TB diagnosis (Detect-TB) in three laboratories.

METHODS

A total of 302 sputum samples from an equal number of patients with presumptive diagnosis of pulmonary tuberculosis (PTB) were submitted for routine smear microscopy, culture, and Detect-TB assay at three different sites in Brazil (the cities of Caxias do Sul, São Paulo and Canoas).

FINDINGS

Seventy four (24.7%) TB cases were diagnosed (65 bacteriologically confirmed). When compared to smear microscopy/culture results, the overall sensitivity and specificity of Detect-TB assay was 84.6% (CI 95%; 73.7-91.6) and 93.1% (CI 95%; 89.1-95.8), respectively. When compared to bacteriological and clinical diagnostic criteria, the sensitivity and specificity of Detect-TB assay was 74.3% (CI 95%; 63.3-82.9) and 92.9% (CI 95%; 88.7-95.6), respectively. Among the three sites - Caxias do Sul, São Paulo and Canoas - the sensitivity and specificity were respectively 94.7% and 97.8%; 71.4% and 93.9%, 82.1% and 88.9%.

MAIN CONCLUSIONS

These findings suggest that the Detect-TB assay could be applied routinely in reference laboratories across different regions in Brazil.

Rapid culture-based detection of living mycobacteria using microchannel electrical impedance spectroscopy (m-EIS)

Background

Multiple techniques exist for detecting Mycobacteria, each having its own advantages and drawbacks. Among them, automated culture-based systems like the BACTEC-MGIT™ are popular because they are inexpensive, reliable and highly accurate. However, they have a relatively long “time-to-detection” (TTD). Hence, a method that retains the reliability and low-cost of the MGIT system, while reducing TTD would be highly desirable.

Methods

Living bacterial cells possess a membrane potential, on account of which they store charge when subjected to an AC-field. This charge storage (bulk capacitance) can be estimated using impedance measurements at multiple frequencies. An increase in the number of living cells during culture is reflected in an increase in bulk capacitance, and this forms the basis of our detection. M. bovis BCG and M. smegmatis suspensions with differing initial loads are cultured in MGIT media supplemented with OADC and Middlebrook 7H9 media respectively, electrical “scans” taken at regular intervals and the bulk capacitance estimated from the scans. Bulk capacitance estimates at later time-points are statistically compared to the suspension’s baseline value. A statistically significant increase is assumed to indicate the presence of proliferating mycobacteria.

Results

Our TTDs were 60 and 36 h for M. bovis BCG and 20 and 9 h for M. smegmatis with initial loads of 1000 CFU/ml and 100,000 CFU/ml respectively. The corresponding TTDs for the commercial BACTEC MGIT 960 system were 131 and 84.6 h for M. bovis BCG and 41.7 and 12 h for M smegmatis, respectively.

Conclusion

Our culture-based detection method using multi-frequency impedance measurements is capable of detecting mycobacteria faster than current commercial systems.

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.

Mycobacteria

The immunocompromised host is at increased risk of Mycobacterium tuberculosis complex and nontuberculous mycobacteria infection. Although Mycobacterium tuberculosis complex is a significant mycobacterial pathogen, nontuberculous mycobacteria causes substantial disease in those with suppressed immune responses. Mycobacterial infections can cause significant morbidity and mortality in this patient population, and rapid identification and susceptibility testing of the mycobacterial species is paramount to patient management and outcomes. Mycobacterial diagnostics has undergone some significant advances in the last two decades with immunodiagnostics (interferon gamma release assay), microscopy (light-emitting diode), culture (automated broth-based systems), identification (direct PCR, sequencing and matrix-assisted laser-desorption ionization–time of flight mass spectrometry) and susceptibility testing (molecular detection of drug resistance from direct specimens or positive cultures). Employing the most rapid and sensitive methods in the mycobacterial laboratory will have a tremendous impact on patient care and, in the case of Mycobacterium tuberculosis complex, in the control of tuberculosis.

Pulmonary Tuberculosis Diagnosis: Where We Are?

In recent years, in spite of medical advancement, tuberculosis (TB) remains a worldwide health problem. Although many laboratory methods have been developed to expedite the diagnosis of TB, delays in diagnosis remain a major problem in the clinical practice. Because of the slow growth rate of the causative agent Mycobacterium tuberculosis, isolation, identification, and drug susceptibility testing of this organism and other clinically important mycobacteria can take several weeks or longer. During the past several years, many methods have been developed for direct detection, species identification, and drug susceptibility testing of TB. A good understanding of the effectiveness and practical limitations of these methods is important to improve diagnosis. This review summarizes the currently-used advances in nonmolecular and molecular diagnostics.

Diagnosis of active tuberculosis disease: From microscopy to molecular techniques

Methods used for the laboratory diagnosis of tuberculosis are continually evolving in order to achieve more rapid, less expensive, and accurate results. Acid-fast staining and culture for mycobacteria remain at the core of any diagnostic algorithm. Following growth in culture, molecular technologies such as nucleic acid hybridization probes, MALDI-TOF MS, and DNA sequencing may be used for definitive species identification. Nucleic acid amplification methods allow for the direct detection of Mycobacterium tuberculosis complex within respiratory specimens without relying on culture growth, leading to more rapid diagnoses and appropriate patient care.

Early detection of Mycobacterium tuberculosis complex in BACTEC MGIT cultures using nucleic acid amplification

We evaluated the application of nucleic acid amplification (NAA) in liquid cultures for the early detection of Mycobacterium tuberculosis. The Cobas TaqMan MTB test, IS6110 real-time PCR, and hsp65 PCR-restriction fragment length polymorphism (RFLP) analysis were used to detect BACTEC MGIT 960 (MGIT) cultures on days 3, 5, 7, and 14. The procedure was initially tested with a reference strain, H37Rv (ATCC 27294). Subsequently, 200 clinical specimens, including 150 Acid Fast bacillus (AFB) smear-positive and 50 AFB smear-negative samples, were examined. The Cobas TaqMan MTB test and IS6110-based PCR analysis were able to detect M. tuberculosis after 1 day when the inoculum of H37Rv was >3 x 10(-2) CFU/ml. After a 5-day incubation in the MGIT system, all three NAA assays had a positive detection regardless of the inoculum size. After a 1-day incubation of the clinical specimens in the MGIT system, the sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) for the Cobas TaqMan MTB assay were 70.2%, 100%, 100%, and 82.3% respectively. For IS6110-based PCR analysis, these values were 63.1%, 100%, 100%, and 78.9%, and were 88.1%, 100%, 100%, and 92.1% respectively for hsp65 PCR-RFLP analysis. After a 3-day incubation, the specificity and PPV were 100% for all three NAA tests; the Cobas TaqMan MTB assay had the best sensitivity (97.6%) and NPV (98.3%). The sensitivity, specificity, PPV, and NPV for conventional culture analysis were 98.8%, 100%, 100%, and 99.1%. Thus, NAA may be useful for the early detection of M. tuberculosis after 3 days in MGIT.

Detection of Mycobacterium tuberculosis in extrapulmonary biopsy samples using PCR targeting IS6110, rpoB, and nested-rpoB PCR Cloning

Present study was aimed to examine the diagnostic utility of polymerase chain reaction (PCR) and nested PCR techniques for the detection of Mycobacterium tuberculosis (MTB) DNA in samples from patients with extra pulmonary tuberculosis (EPTB). In total 80 formalin-fixed, paraffin-embedded (FFPE) samples comprising 70 samples with definite diagnosis of EPTB and 10 samples from known non- EPTB on the basis of histopathology examination, were included in the study. PCR amplification targeting IS6110, rpoB gene and nested PCR targeting the rpoB gene were performed on the extracted DNAs from 80 FFPE samples. The strong positive samples were directly sequenced. For negative samples and those with weak band in nested-rpoB PCR, TA cloning was performed by cloning the products into the plasmid vector with subsequent sequencing. The 95% confidence intervals (CI) for the estimates of sensitivity and specificity were calculated for each method. Fourteen (20%), 34 (48.6%), and 60 (85.7%) of the 70 positive samples confirmed by histopathology, were positive by rpoB-PCR, IS6110-PCR, and nested-rpoB PCR, respectively. By performing TA cloning on samples that yielded weak (n = 8) or negative results (n = 10) in the PCR methods, we were able to improve their quality for later sequencing. All samples with weak band and 7 out of 10 negative samples, showed strong positive results after cloning. So nested-rpoB PCR cloning revealed positivity in 67 out of 70 confirmed samples (95.7%). The sensitivity of these combination methods was calculated as 95.7% in comparison with histopathology examination. The CI for sensitivity of the PCR methods were calculated as 11.39-31.27% for rpoB-PCR, 36.44-60.83% for IS6110- PCR, 75.29-92.93% for nested-rpoB PCR, and 87.98-99.11% for nested-rpoB PCR cloning. The 10 true EPTB negative samples by histopathology, were negative by all tested methods including cloning and were used to calculate the specificity of the applied methods. The CI for 100% specificity of each PCR method were calculated as 69.15-100%. Our results indicated that nested-rpoB PCR combined with TA cloning and sequencing is a preferred method for the detection of MTB DNA in EPTB samples with high sensitivity and specificity which confirm the histopathology results.

Rapid detection of Mycobacterium tuberculosis using a novel ultrafast chip-type real-time polymerase chain reaction system

BACKGROUND

NBS LabChip G2-3 is a novel, ultrafast, chip-type portable real-time polymerase chain reaction (PCR) system. We evaluated the clinical usefulness of this system in detecting pulmonary TB and assessed its diagnostic performance compared with a conventional tube-type PCR system.

METHODS

A total of 247 sputum samples were collected from patients suspected of having pulmonary TB. After the decontamination process, these samples were examined by fluorescence staining for acid-fast bacilli, cultures with both solid and liquid media, and real-time PCR with the NBS LabChip and a conventional tube-type system. The diagnostic accuracy of the NBS LabChip system and the agreement between the two assays were evaluated.

RESULTS

Considering mycobacterial culture results as a gold standard, the overall sensitivity and specificity of the NBS LabChip was 83.8% (95% CI, 73.8%-91.1%) and 94.0% (95% CI, 89.3%-97.1%), respectively. For the detection of TB from the smear-positive samples, the sensitivity and specificity of the NBS LabChip was 96.0% (95% CI, 86.3%-99.5%) and 83.3% (95% CI, 72.3%-95.7%), respectively. For the smear-negative samples, the sensitivity and specificity of the NBS LabChip was 63.3% (95% CI, 43.9%-80.1%) and 95.0% (95% CI, 90.4%-97.8%), respectively. There were no significant differences in the sensitivity and specificity between the NBS LabChip and a conventional tube-type system, although the NBS LabChip shortened the PCR time (27 min for 45 cycles).

CONCLUSIONS

The NBS LabChip G2-3 system has potential as an ultrafast, cost-effective diagnostic tool for pulmonary TB with high sensitivity and specificity.

Standardization of a TaqMan-based real-time PCR for the detection of Mycobacterium tuberculosis-complex in human sputum

Real-time polymerase chain reaction (qPCR) was optimized for detecting Mycobacterium tuberculosis in sputum. Sputum was collected from patients (N = 112) with suspected pulmonary tuberculosis, tested by smear microscopy, decontaminated, and split into equal aliquots that were cultured in Löwenstein-Jensen medium and tested by qPCR for the small mobile genetic element IS6110. The human ERV3 sequence was used as an internal control. 3 of 112 (3%) qPCR failed. For the remaining 109 samples, qPCR diagnosed tuberculosis in 79 of 84 patients with culture-proven tuberculosis, and sensitivity was greater than microscopy (94% versus 76%, respectively, P < 0.05). The qPCR sensitivity was similar (P = 0.9) for smear-positive (94%, 60 of 64) and smear-negative (95%, 19 of 20) samples. The qPCR was negative for 24 of 25 of the sputa with negative microscopy and culture (diagnostic specificity 96%). The qPCR had 99.5% sensitivity and specificity for 211 quality control samples including 84 non-tuberculosis mycobacteria. The qPCR cost ∼5US$ per sample and provided same-day results compared with 2-6 weeks for culture.

In house reverse membrane hybridisation assay versus GenoType MTBDRplus and their performance to detect mutations in the genes rpoB, katG and inhA

Drug-resistant tuberculosis (TB) threatens global TB control and is a major public health concern in several countries. We therefore developed a multiplex assay (LINE-TB/MDR) that is able to identify the most frequent mutations related to rifampicin (RMP) and isoniazid (INH) resistance. The assay is based on multiplex polymerase chain reaction, membrane hybridisation and colorimetric detection targeting of rpoB and katG genes, as well as the inhA promoter, which are all known to carry specific mutations associated with multidrug-resistant TB (MDR-TB). The assay was validated on a reference panel of 108 M. tuberculosis isolates that were characterised by the proportion method and by DNA sequencing of the targets. When comparing the performance of LINE-TB/MDR with DNA sequencing, the sensitivity, specificity and agreement were 100%, 100% and 100%, respectively, for RMP and 77.6%, 90.6% and 88.9%, respectively, for INH. Using drug sensibility testing as a reference standard, the performance of LINE-TB/MDR regarding sensitivity, specificity and agreement was 100%, 100% and 100% (95%), respectively, for RMP and 77%, 100% and 88.7% (82.2-95.1), respectively, for INH. LINE-TB/MDR was compared with GenoType MTBDRplus for 65 isolates, resulting in an agreement of 93.6% (86.7-97.5) for RIF and 87.4% (84.3-96.2) for INH. LINE-TB/MDR warrants further clinical validation and may be an affordable alternative for MDR-TB diagnosis.

Molecular methods for detection of invasive fungal infections and mycobacteria and their clinical significance in hematopoietic stem cell transplantation

Infection remains an important source of morbidity and mortality in patients who undergo hematopoietic stem cell transplantation (HSCT). In the immune reconstitution period after transplantation, HSCT recipients are most likely to have bacterial or fungal infections. Invasive fungal infections (IFIs) and mycobacterial infections (MBIs) are among the complications of HSCT, with high morbidity and mortality rates. Early diagnosis of both is crucial in order to manipulate the disease and to avoid fulminant outcomes. This chapter reviews the current knowledge on the molecular diagnosis of IFIs and MBIs in HSCT recipients, describing two different polymerase chain reaction (PCR)-based methods, one commercial (qPCR, Roche) and one in-house IS6110-based protocol.

Comparison of the Xpert MTB/RIF and Cobas TaqMan MTB assays for detection of Mycobacterium tuberculosis in respiratory specimens

The Xpert MTB/RIF assay (Cepheid, Sunnyvale, CA) is a fully automated, cartridge-based real-time PCR assay designed to detect Mycobacterium tuberculosis and rifampin resistance within 2 h. The performance of the Xpert assay has been evaluated in various clinical settings. However, there are few data comparing the Xpert assay to the Cobas TaqMan MTB test (Roche Diagnostics, Basel, Switzerland), one of the most widely utilized molecular assays for M. tuberculosis detection. In this prospective study, 320 consecutive respiratory specimens were processed simultaneously using acid-fast bacillus (AFB) staining, mycobacterial cultures with both solid and liquid media, and the Cobas and Xpert assays. The Xpert assay was performed with direct respiratory specimens, while the Cobas assay was done with decontaminated concentrated specimens. Based on the culture as a reference method, the overall sensitivities of the Cobas and Xpert assays were 71.4% and 67.9%, respectively. When AFB smear results were taken into consideration, the sensitivities of the Cobas assay for smear-positive and -negative specimens were 87% and 54%, while those of the Xpert assay were 67% and 69%, respectively. The Cobas assay showed 100% specificity and 100% positive predictive value (PPV) regardless of smear results, while the Xpert assay showed 100% specificity and 100% PPV for smear-positive specimens but 98% specificity and 60% PPV for smear-negative specimens. In conclusion, the Xpert assay showed performance that was slightly inferior to that of the Cobas assay but seems useful for the rapid detection of M. tuberculosis, considering that it was performed without laborious and time-consuming decontamination and concentration procedures.

Evaluation of Cobas TaqMan MTB for direct detection of the Mycobacterium tuberculosis complex in comparison with Cobas Amplicor MTB

The Roche Cobas Amplicor MTB assay, recently replaced by the Roche Cobas TaqMan MTB assay, was one of the first commercially available assays for detection of the Mycobacterium tuberculosis complex based on nucleic acid amplification. We reported previously on the limited specificity of the Cobas Amplicor MTB assay, in particular for positive samples with an optical density at 660 nm (OD660) of <2.0. Using a selected set of respiratory samples, which were scored as false positive by the Cobas Amplicor test, we demonstrate here that the specificity of the Cobas TaqMan assay is significantly improved. In addition, our study of a set of 133 clinical samples revealed that the Cobas TaqMan MTB assay showed significantly less PCR inhibition than the Cobas Amplicor test. An overall concordance of 98.2% was observed between the two assays. In a subsequent prospective study, we evaluated the performance of the Roche Cobas TaqMan MTB assay on 1,143 clinical specimens, including respiratory (n = 838) and nonrespiratory (n = 305) specimens. Using culture as the gold standard, we found a sensitivity of 88.4% and a specificity of 98.8% for the 838 respiratory specimens, compared to a sensitivity of 63.6% and a specificity of 94.6% for the 305 nonrespiratory specimens. We conclude that the Cobas TaqMan MTB assay is a significantly improved tool for the direct detection of M. tuberculosis DNA in clinical specimens.

Integrating the Xpert MTB/RIF assay into a diagnostic workflow for rapid detection of Mycobacterium tuberculosis in a low-prevalence area

The Xpert MTB/RIF assay is a rapid and fully automated real-time PCR assay. The performance of the Xpert MTB/RIF assay as a primary screening test for urgent clinical specimens was evaluated during a 2-year period. The results showed that replacing smear microscopy with the Xpert MTB/RIF assay facilitates laboratory handling and improves the sensitivity and specificity of Mycobacterium tuberculosis detection.

Detonation nanodiamonds for rapid detection of clinical isolates of Mycobacterium tuberculosis complex in broth culture media

Routinely used molecular diagnostic methods for mycobacterium identification are expensive and time-consuming. To tackle this problem, we develop a method to streamline identification of Mycobacterium tuberculosis complex (MTBC) in broth culture media by using detonation nanodiamonds (DNDs) as a platform to effectively capture the antigen secreted by MTBC which is cultured in BACTEC MGIT 960, followed by the analysis of matrix-assisted laser desorption/ionization mass spectrometry (MALDI-TOF MS). The 5 nm DNDs can capture the MTBC secretory antigen without albumin interference. With on diamond digestion, we confirm the DND captured antigen is cell filtrate protein 10 (CFP-10) because its Mascot analysis shows a score of 68. The dot blotting method further verifies a positive reaction with anti-CFP-10, indicating that CFP-10 is secreted in the medium of mycobacterium growth indicator tube (MGIT) and captured by DNDs. The minimal CFP-10 protein detection limit was 0.09 μg/mL. Furthermore, our approach can avoid the false-positive identification of MTBC by immunological methods due to cross-reactivity. Five hundred consecutive clinical specimens subjected to routine mycobacteria identification in hospital were used in this study, and the sensitivity of our method is 100% and the specificity is 98%. The analysis of each MTBC sample from culture solution can be finished within 1 h and thus shortens the turnaround time of MTBC identification of gold standard culture methods. In sum, DND MALDI-TOF MS for the detection of MTBC is rapid, specific, safe, reliable, and inexpensive.

Characterization of Mycobacterium tuberculosis isolated from cancer patients with suspected tuberculosis infection in Egypt: identification, prevalence, risk factors and resistance pattern

Data are sparse on Mycobacterium tuberculosis infection among patients with cancer in Egypt. We sought to detect the presence of tuberculosis (TB) disease among patients with malignant conditions and suspected TB and to study the main risk factors. Also, we compared different diagnostic procedures and detected the antimicrobial susceptibility of M. tuberculosis isolates against rifampin and isoniazid. One hundred patients were included in this study, all of them had malignant conditions and were suspected by the clinicians of having TB. Identification of M. tuberculosis in different specimens was performed by smear microscopy, followed by Lowenstein-Jensen medium and Mycobacterium growth indicator tube (MGIT) cultures and artus(®) real-time PCR. In addition, an indirect MGIT anti-TB susceptibility test was carried out against rifampin and isoniazid. A total of 76% of studied cases were found to be TB positive. The frequencies of TB-positive cases in the bronchogenic, haematological and solid tumour malignancy groups were 21%, 25% and 30%, respectively. Significant differences between pulmonary and extrapulmonary TB in different malignancy groups were recorded. Real-time PCR showed the highest overall diagnostic efficiency. Multidrug-resistance of M. tuberculosis to both rifampin and isoniazid was detected in 28.6% of examined isolates. Infection in cancer patients with TB was significantly more often recorded among elderly patients and those suffering from poverty. Pulmonary TB is more common than extrapulmonary TB in patients with malignancy. Real-time PCR is the most accurate and rapid method for TB diagnosis. MGIT-rifampin resistance may be used as a reliable marker for detection of multidrug-resistant TB. Diagnosis and instituting treatment course for active or latent TB infection are crucial before starting anticancer therapy.

Evaluation of real-time polymerase chain reaction for detection of the 16S ribosomal RNA gene of Mycobacterium tuberculosis and the diagnosis of cervical tuberculous lymphadenitis in a country with a high tuberculosis incidence

BACKGROUND

Tuberculous lymphadenitis (TBL) is the most common form of extrapulmonary tuberculosis. Currently, the standard diagnostic test for TBL is culture, which takes more than several weeks to yield results. We studied a real-time polymerase chain reaction (PCR) for rapid detection of Mycobacterium tuberculosis in cervical lymph node specimens obtained from patients in a country where the tuberculosis incidence is high.

METHODS

Patients with cervical lymphadenopathy were prospectively enrolled between April 2009 and March 2010. Clinical specimens obtained through fine-needle aspiration (FNA) and excisional biopsy were tested for M. tuberculosis by the COBAS TaqMan MTB Test, a real-time PCR assay for detecting the 16S ribosomal RNA gene of M. tuberculosis. Mycobacterial culture and histopathological findings from tissue biopsy specimens were used as a reference standard for sensitivity and specificity calculations.

RESULTS

Of 73 patients, 41 received a diagnosis of TBL. For biopsy specimens, the sensitivity of real-time PCR was 63.4%, and the specificity was 96.9%. For FNA specimens, the sensitivity was 17.1%, and the specificity was 100%. The sensitivity of real-time PCR of biopsy specimens was comparable to that of tissue culture but significant lower than that of histopathological examination (P < .01).

CONCLUSIONS

Real-time PCR did not increase the yield for rapid diagnosis of TBL.

Colorimetric microwell plate reverse-hybridization assay for Mycobacterium tuberculosis detection

Direct smear examination using Ziehl-Neelsen staining for pulmonary tuberculosis (PTB) diagnosis is inexpensive and easy to use, but has the major limitation of low sensitivity. Rapid molecular methods are becoming more widely available in centralized laboratories, but they depend on timely reporting of results and strict quality assurance obtainable only from costly commercial kits available in high burden nations. This study describes a pre-commercial colorimetric method, Detect-TB, for detecting Mycobacterium tuberculosis DNA in which an oligonucleotide probe is fixed onto wells of microwell plates and hybridized with biotinylated polymerase chain reaction amplification products derived from clinical samples. The probe is capable of hybridising with the IS6110 insertion element and was used to specifically recognise the M. tuberculosis complex. When combined with an improved silica-based DNA extraction method, the sensitivity of the test was 50 colony-forming units of the M. tuberculosis reference strain H37Rv. The results that were in agreement with reference detection methods were observed in 95.2% (453/476) of samples included in the analysis. Sensitivity and specificity for 301 induced sputum samples and 175 spontaneous sputum samples were 85% and 98%, and 94% and 100%, respectively. This colorimetric method showed similar specificity to that described for commercially available kits and may provide an important contribution for PTB diagnosis.

Combination of molecular assay and clinical evaluation for early confirmation of tuberculosis cases

The cost-effectiveness of the ProbeTec ET Direct TB assay (DTB) was compared with that of culture for detection of Mycobacterium tuberculosis complex in 361 acid-fast stain-positive respiratory specimens. The overall sensitivity, specificity, positive predictive value and negative predictive value of DTB were 97.7%, 86.6%, 87.2% and 97.6%, respectively. When clinical evaluation was added to DTB, the specificity and positive predictive value of DTB increased to 94.7% and 95.4%, respectively. Treatment costs of $133,521 would have been saved in this cohort if DTB, instead of culture results, had been used to eliminate 'false-positive' smear results.

[Bacteriological tests for tuberculosis]

This review describes current developments for the bacteriological diagnosis of active tuberculosis. It deals mainly with molecular methods, describing their performance and how they can be integrated into more traditional diagnostic approaches. At present, microscopic examination and culture are still essential for the diagnosis of TB and to guide therapeutic decisions. Nucleic acid amplification and line probe assays speed up the identification and susceptibility testing of mycobacteria in AFB smear positive specimens or in culture. They are also efficient for comparison of M. tuberculosis strains with each other (genotyping). On the other hand, at present, molecular tests are not applicable for diagnosis in smear negative specimens and even less so for diagnosis of culture-negative tuberculosis. The use of serology for antibody/antigen detection is not useful and it is not appropriate to assays based on the release of interferon-γ release as they are currently available. Notable progress has been made but more sensitive diagnostic tests for TB are still urgently needed.

Laboratory diagnosis of tuberculosis in resource-poor countries: challenges and opportunities

With an estimated 9.4 million new cases globally, tuberculosis (TB) continues to be a major public health concern. Eighty percent of all cases worldwide occur in 22 high-burden, mainly resource-poor settings. This devastating impact of tuberculosis on vulnerable populations is also driven by its deadly synergy with HIV. Therefore, building capacity and enhancing universal access to rapid and accurate laboratory diagnostics are necessary to control TB and HIV-TB coinfections in resource-limited countries. The present review describes several new and established methods as well as the issues and challenges associated with implementing quality tuberculosis laboratory services in such countries. Recently, the WHO has endorsed some of these novel methods, and they have been made available at discounted prices for procurement by the public health sector of high-burden countries. In addition, international and national laboratory partners and donors are currently evaluating other new diagnostics that will allow further and more rapid testing in point-of-care settings. While some techniques are simple, others have complex requirements, and therefore, it is important to carefully determine how to link these new tests and incorporate them within a country's national diagnostic algorithm. Finally, the successful implementation of these methods is dependent on key partnerships in the international laboratory community and ensuring that adequate quality assurance programs are inherent in each country's laboratory network.

Advances in rapid diagnosis of tuberculosis disease and anti-tuberculous drug resistance

Rapid diagnosis of tuberculosis (TB) and multidrug-resistant (resistance to at least rifampin and isoniazid) Mycobacterium tuberculosis (MDR-TB) is one of the cornerstones for global TB control as it allows early epidemiological and therapeutic interventions. The slow growth of the tubercle bacillus is the greatest obstacle to rapid diagnosis of the disease. However, considerable progress has recently been made in developing novel diagnostic tools, especially molecular methods (commercial and 'in-house'), for direct detection in clinical specimens. These methods, based on nucleic acid amplification (NAA) of different targets, aim to identify the M. tuberculosis complex and detect the specific chromosome mutations that are most frequently associated with phenotypic resistance to multiple drugs. In general, commercial methods are recommended since they have a better level of standardization, reproducibility and automation. Although some aspects such as cost-efficiency and the appropriate setting for the implementation of these techniques are not yet well established, organizations such as the WHO are strongly supporting the implementation and universal use of these new molecular methods. This chapter summarizes current knowledge and the available molecular methods for rapid diagnosis of TB and anti-tuberculous drug resistance in clinical microbiology laboratories.

Comparison of the Xpert MTB/RIF test with an IS6110-TaqMan real-time PCR assay for direct detection of Mycobacterium tuberculosis in respiratory and nonrespiratory specimens

The sensitivities of the Xpert MTB/RIF test and an in-house IS6110-based real-time PCR using TaqMan probes (IS6110-TaqMan assay) for the detection of Mycobacterium tuberculosis complex (MTBC) DNA were compared by use of 117 clinical specimens (97 culture positive and 20 culture negative for MTBC) that were frozen in sediment. The 97 clinical specimens included 60 respiratory and 37 nonrespiratory specimens distributed into 36 smear-positive and 61 smear-negative specimens. Among the 97 culture-positive specimens, 4 had rifampin-resistant isolates. Both methods were highly specific and exhibited excellent sensitivity (100%) with smear-positive specimens. The sensitivity of the Xpert MTB/RIF test with the whole smear-negative specimens was more reduced than that of the IS6110-TaqMan assay (48 versus 69%, P = 0.005). Both methods exhibited similar sensitivities with smear-negative respiratory specimens, but the Xpert MTB/RIF test had lower sensitivity with smear-negative nonrespiratory specimens than the IS6110-TaqMan assay (37 versus 71%, P = 0.013). Finally, the sensitivities of the Xpert MTB/RIF test and the IS6110-TaqMan assay were 79% and 84%, respectively, with respiratory specimens and 53% and 78%, respectively (P = 0.013), with nonrespiratory specimens. The Xpert MTB/RIF test correctly detected the rifampin resistance in smear-positive specimens but not in the one smear-negative specimen. The Xpert MTB/RIF test is a simple rapid method well adapted to a routine laboratory that appeared to be as sensitive as the IS6110-TaqMan assay with respiratory specimens but less sensitive with paucibacillary specimens, such as smear-negative nonrespiratory specimens.

Evaluation of the Cobas TaqMan MTB test for direct detection of Mycobacterium tuberculosis complex in respiratory specimens

The Cobas TaqMan MTB test, based on real-time PCR technology, was evaluated for direct detection of Mycobacterium tuberculosis complex (MTBC) in respiratory specimens. A total of 1,093 samples from 446 patients, including 118 acid-fast smear-positive and 975 acid-fast smear-negative specimens, were investigated. Diagnostic cultures performed with 7H11 agar, Löwenstein-Jensen medium, and the Bactec MGIT 960 system were considered the reference methods. When discrepant results between the Cobas TaqMan MTB test and culture occurred, additional results from the BD MGIT TBc identification test and the GenoType Mycobacterium CM test performed on growth-positive and acid-fast-stain-positive MGIT tubes and review of the patient's medical history were used for discrepancy analysis. The overall sensitivity, specificity, positive predictive value, and negative predictive value for the Cobas TaqMan MTB test were 91.5%, 98.7%, 91.5%, and 98.7%, respectively. In general, the performance of the new Cobas TaqMan MTB test was comparable to that of the replaced Cobas Amplicor MTB system. The most prominent feature of the new system was its extraordinarily high sensitivity (79.5%) for detecting MTBC in smear-negative specimens; out of 44 smear-negative but culture-positive specimens, 35 were positive by the new system. The Cobas TaqMan MTB assay, including DNA extraction, can be completed within 3 h.

Evaluation of Cobas TaqMan MTB PCR for detection of Mycobacterium tuberculosis

Nucleic acid-based amplification tests allow the rapid detection of Mycobacterium tuberculosis. Recently, a real-time PCR assay for M. tuberculosis complex, the Cobas TaqMan MTB test (Roche Diagnostics, Basel, Switzerland), was introduced. We performed a prospective study to evaluate the diagnostic performance of the Cobas TaqMan MTB test system. A total of 406 specimens collected from 247 patients were simultaneously tested by conventional culture, Cobas Amplicor MTB PCR, and TaqMan MTB PCR. The cross-reactivity with other Mycobacterium species and the detection limit were also evaluated. Among 406 specimens, a total of 24 specimens (5.9%) were culture positive: 14 specimens were positive by both TaqMan and Amplicor MTB PCRs, while 5 specimens were positive by only TaqMan PCR. The remaining five specimens were negative by both PCR methods. Seven specimens with negative culture results were positive by TaqMan PCR, but five of these were negative by Amplicor MTB PCR. The sensitivity, specificity, and positive (PPV) and negative (NPV) predictive values were 79.1%, 98.2%, 73.1%, and 98.7% for TaqMan and 58.3%, 99.5%, 87.5%, and 97.4% for the Amplicor MTB PCR test, respectively. There was no cross-reactivity with M. tuberculosis and nontuberculous mycobacterial species. The detection limit for the Cobas TaqMan MTB PCR test was 4.0 copies/μl. The Cobas TaqMan MTB PCR test showed higher sensitivity for detection of the M. tuberculosis complex without disturbing the specificity and NPV than the Amplicor MTB PCR test.

Detection and identification of Mycobacterium spp. in clinical specimens by combining the Roche Cobas Amplicor Mycobacterium tuberculosis assay with Mycobacterium genus detection and nucleic acid sequencing

We have recently developed a PCR assay for detection of Mycobacterium spp. at the genus level based on the Cobas Amplicor platform. The sensitivities for smear-positive and smear-negative specimens were found to be 100% and 47.9%, respectively. The specificity was 97.7%, the positive predictive value 84.6%, and the negative predictive value 93.1%. In a follow-up study, we have systematically evaluated the Mycobacterium genus assay in parallel with the Cobas Amplicor Mycobacterium tuberculosis assay on 2,169 clinical specimens, including respiratory and nonrespiratory specimens. Based on the genus assay, nontuberculous mycobacteria were readily detected and identified to the species level by PCR-mediated sequencing. In addition, our data point to a limited specificity of the Cobas Amplicor M. tuberculosis assay.

Evaluation of the GenoType Mycobacteria Direct assay for direct detection of the Mycobacterium tuberculosis complex obtained from sputum samples

An increase in the prevalence of tuberculosis (TB) in recent years has accelerated the search for novel tools for the rapid diagnosis of TB infection. This study evaluated the GenoType Mycobacteria Direct (GTMD) assay (Hain Lifescience) for direct detection of the Mycobacterium tuberculosis complex (MTBC) from sputum samples and compared it with conventional methods. The GTMD test is a commercial assay produced using strip techniques and works based on a nucleic acid sequence-based amplification technique. This test allows 23S rRNA amplification-based detection of MTBC, Mycobacterium avium, Mycobacterium intracellulare, Mycobacterium kansasii and Mycobacterium malmoense directly from decontaminated clinical samples within 6 h. In the present study, 115 sputum samples were processed to detect acid-fast bacilli (AFB) using two microscopy methods (carbol fuchsin and fluorescent staining), two culture methods [Löwenstein-Jensen (LJ) and BACTEC 12B media] and the GTMD test. The results showed that 86 of the samples were positive by direct microscopy, 84 were positive by BACTEC 12B culture, 73 were positive by LJ culture and 95 were positive by the GTMD test. All of the isolates turned out to be MTBC. Moreover, the sensitivity and specificity of the GTMD test for MTBC in patients were 97 and 58 %, respectively, taking the culture combination as the gold standard. When the test was compared with culture of samples from anti-TB-treated patients, the sensitivity and specificity for the test were 100 and 15 %, respectively. Low specificity in treated people might arise from depressed proliferation of AFB. As the two methods target the same living bacilli, the difference is obviously notable. When the culture results and clinical findings of the patients were evaluated together (true-positive specimens), the sensitivity and specificity values of the GTMD test for all patients were 97 and 90 %, respectively. However, both of these values increased to 100 % for the patients receiving anti-TB treatment. These results implied that, to determine whether the patient's sputum contains living AFB, more sensitive techniques should be employed during the follow-up of the patients. These observations suggest that the GTMD method can be useful for early diagnosis of clinically and radiologically suspicious TB cases where smears are negative for Mycobacterium. In addition, the use of a GTMD test in smear-positive cases is helpful and practical in order to identify MTBC quickly. This allows more rapid treatment decisions and infection control precautions.

Routine using pattern and performance of diagnostic tests for tuberculosis on a university hospital

INTRODUCTION

Nucleic acid amplification tests to detect Mycobacterium tuberculosis in clinical specimens are used increasingly as a laboratory tool. We aimed to investigate the routine using pattern and the effects on therapeutic decision of diagnostic tests for tuberculosis in our hospital.

METHODS

In this descriptive study, we investigated retrospectively the routine using pattern and the effects on therapeutic decision of diagnostic tests for tuberculosis. Patients with discordant results were clinically evaluated retrospectively by a chest physician. Samples were tested for the presence of M. tuberculosis by a smear technique, M. tuberculosis culture growth technique (Löwenstein-Jensen and/or BACTEC-960), and IS6110 polymerase chain reaction (PCR).

RESULTS

Culture positivity was 7.2% (83 of 1159 patients). In total, 198 (62.4%) were tested with PCR, acid-fast bacilli, and culture. On the basis of culture results as a gold standard, sensitivity, specificity, positive predictive value, and negative predictive value of PCR were 46%, 89%, 23%, and 93.5%, respectively.

CONCLUSIONS

Selection of appropriate patients for further testing and exclusion of low-risk patients from microbiologic testing by experienced clinicians may help to optimize the positive predictive value of PCR.

Multicenter evaluation of a transcription-reverse transcription concerted assay for rapid detection of mycobacterium tuberculosis complex in clinical specimens

A European multicenter study was performed to evaluate the performance of a new method, based on the transcription-reverse transcription concerted reaction (TRC-2), which enabled one-step amplification and real-time detection of the Mycobacterium tuberculosis 16S rRNA target directly in clinical specimens. A total of 633 respiratory and nonrespiratory specimens were tested, and the results were compared with those from smears and cultures. A total of 129 patients (Paris center) were followed up in order to evaluate the clinical performance of TRC-2. By using M. tuberculosis complex strains to inoculate sterile sputa, the detection limit of TRC-2 was found to be 30 to 50 CFU/ml. A total of 548 respiratory specimens and 59 extrapulmonary specimens were assessable. For pulmonary specimens, the sensitivities of TRC-2 and acid-fast smear were 86.8% and 50.4%, respectively (P = 0.002). The specificities were 97.5% and 100%, respectively. For extrapulmonary specimens, the sensitivities of TRC-2 and acid-fast smear were 83.3% and 8.3% (P < 0.0001), and the specificities were 95.8% and 100%, respectively. Fifteen of 129 patients were diagnosed with pulmonary tuberculosis (TB). The sensitivities of culture and TRC-2 were 80% (12/15) and 86.7% (13/15) (P = 0.16), and the specificities were 100% and 93.9%, respectively. Based on an 11.6% incidence of TB in our population, the positive predictive values of TRC-2 and culture were 81.3% and 100%, respectively, and the negative predictive values were 98.2% and 97.4%, respectively. These results demonstrated that detection of M. tuberculosis complex in clinical specimens by TRC-2 with ready-to-use reagents was an efficient and rapid method for the diagnosis of pulmonary and extrapulmonary TB.

Recent advances in diagnostic microbiology

The past decade has seen a surge in the development of a variety of molecular diagnostics designed to rapidly identify or characterize medically important microorganisms. We briefly review important advances in molecular microbiology, and then discuss specific assays that have been implemented in clinical microbiology laboratories throughout the country. We also discuss emerging methods and technologies that will soon be more widely used for the prompt and accurate detection of the agents of infectious diseases.

Non-tuberculous mycobacterial infections

Non-tuberculous mycobacteria (NTM) are ubiquitous environmental organisms in contrast to those belonging to the M. tuberculosi complex (MTB). NTM infects and causes disease only in hosts with local or general predisposing factors. Lung infection following inhalation of NTM is the most common NTM disease but soft tissue infections may occur in connection with contaminated trauma or surgery. Microbiological diagnosis is obtained by microscopy for acid-fast bacteria (AFB) on secretions or biopsies, and by culture on special media. With the high specificity of MTB- polymerase chain reaction (PCR), a positive AFB smear combined with negative MTB-PCR denotes infection with NTM. Sophisticated species diagnosis of cultured NTM is attained by various molecular methods, where 16S rDNA-sequencing remains the gold standard. The panorama of infection with different rapidly growing (RGM) or slowly growing mycobacteria (SGM) in Sweden is described. Sensitivity testing in vitro to antimycobacterial drugs against NTM does not always preclude the in vivo efficacy. Standard antimycobacterial treatment regimens have been defined for infection with several NTM species. Sensitivity testing should be performed in selected cases only, as in case of relapse or suspected development of resistance of the NTM strain. The spectrum of disease caused by NTM species that display a very low pathogenic potential is likely to widen over time as severe immunosuppression will continue to be prevalent in several patient categories.

Pleural fluid ADA, IgA‐ELISA and PCR sensitivities for the diagnosis of pleural tuberculosis

The diagnosis of pleural tuberculosis (pTB) is difficult, and more sensitive and specific techniques are needed. In the period August 1998 to November 2002, we evaluated 132 patients with a pleural effusion submitted to a thoracentesis and pleural biopsy in a tertiary care hospital in Rio de Janeiro, Brazil. Three tests were performed and compared in the pleural fluid: ADA activity measurement, IgA-ELISA for two combined specific Mycobacterium tuberculosis antigens, and polymerase chain reaction (PCR) for detection of M. tuberculosis DNA. Ninety-five patients (72%) were given a final diagnosis of pTB. Overall histopathologic sensitivity was 77%. The sensitivities of pleural fluid culture and AFB smear were 42% and 1%, respectively. Twenty-one (22%) additional patients had a clinical diagnosis of pTB. Median follow-up time of all TB patients after the completion of antituberculous treatment was 13 months. Sensitivities of ADA, IgA-ELISA and PCR were 91%, 78% and 82%, while specificities were 93%, 96% and 85%, respectively. Only ADA sensitivity was significantly higher than the histopathologic examination (McNemar chi2 test; p = 0.002) and also significantly higher than ELISA (p = 0.049), but not higher than PCR (p = 0.143). We conclude that the routine use of ADA activity measurement in pleural fluid can obviate the need for a pleural biopsy in the initial diagnostic approach to pleural effusions, while IgA-ELISA and PCR techniques, potentially more specific tests, need further refinement to improve their accuracy.