Practical strategies for performance optimization of the enhanced gen-probe amplified mycobacterium tuberculosis direct test

Recent advances in surface enhanced Raman spectroscopy for bacterial pathogen identifications

BACKGROUND

The rapid and reliable detection of pathogenic bacteria at an early stage is a highly significant research field for public health. However, most traditional approaches for pathogen identification are time-consuming and labour-intensive, which may cause physicians making inappropriate treatment decisions based on an incomplete diagnosis of patients with unknown infections, leading to increased morbidity and mortality. Therefore, novel methods are constantly required to face the emerging challenges of bacterial detection and identification. In particular, Raman spectroscopy (RS) is becoming an attractive method for rapid and accurate detection of bacterial pathogens in recent years, among which the newly developed surface-enhanced Raman spectroscopy (SERS) shows the most promising potential.

AIM OF REVIEW

Recent advances in pathogen detection and diagnosis of bacterial infections were discussed with focuses on the development of the SERS approaches and its applications in complex clinical settings.

KEY SCIENTIFIC CONCEPTS OF REVIEW

The current review describes bacterial classification using surface enhanced Raman spectroscopy (SERS) for developing a rapid and more accurate method for the identification of bacterial pathogens in clinical diagnosis. The initial part of this review gives a brief overview of the mechanism of SERS technology and development of the SERS approach to detect bacterial pathogens in complex samples. The development of the label-based and label-free SERS strategies and several novel SERS-compatible technologies in clinical applications, as well as the analytical procedures and examples of chemometric methods for SERS, are introduced. The computational challenges of pre-processing spectra and the highlights of the limitations and perspectives of the SERS technique are also discussed.Taken together, this systematic review provides an overall summary of the SERS technique and its application potential for direct bacterial diagnosis in clinical samples such as blood, urine and sputum, etc.

Official American Thoracic Society/Infectious Diseases Society of America/Centers for Disease Control and Prevention Clinical Practice Guidelines: Diagnosis of Tuberculosis in Adults and Children

BACKGROUND

Individuals infected with Mycobacterium tuberculosis (Mtb) may develop symptoms and signs of disease (tuberculosis disease) or may have no clinical evidence of disease (latent tuberculosis infection [LTBI]). Tuberculosis disease is a leading cause of infectious disease morbidity and mortality worldwide, yet many questions related to its diagnosis remain.

METHODS

A task force supported by the American Thoracic Society, Centers for Disease Control and Prevention, and Infectious Diseases Society of America searched, selected, and synthesized relevant evidence. The evidence was then used as the basis for recommendations about the diagnosis of tuberculosis disease and LTBI in adults and children. The recommendations were formulated, written, and graded using the Grading, Recommendations, Assessment, Development and Evaluation (GRADE) approach.

RESULTS

Twenty-three evidence-based recommendations about diagnostic testing for latent tuberculosis infection, pulmonary tuberculosis, and extrapulmonary tuberculosis are provided. Six of the recommendations are strong, whereas the remaining 17 are conditional.

CONCLUSIONS

These guidelines are not intended to impose a standard of care. They provide the basis for rational decisions in the diagnosis of tuberculosis in the context of the existing evidence. No guidelines can take into account all of the often compelling unique individual clinical circumstances.

Evaluation of three rapid assays for Mycobacterium tuberculosis complex detection in a comprehensive hospital from West China

OBJECTIVES

To assess the capacity of rapid and accurate confirmation of the Mycobacterium tuberculosis complex (MTBC) in a Chinese clinical laboratory.

DESIGN AND METHODS

This prospective study investigated three rapid assays, the Amplified Mycobacterium Tuberculosis Direct (MTD) test, real-time PCR, and acid-fast bacilli (AFB) smear, for direct detection of MTBC in a large consecutive series of different clinical specimens. Performance parameters were estimated and compared overall and for separate specimen categories using a combined reference gold standard.

RESULTS

The overall sensitivities were similar for MTD and real-time PCR (62.26% vs. 58.49%), significantly higher than those of AFB smear (31.13%). Among three assays, MTD had a satisfactory sensitivity in respiratory specimen (73.33%) and a nearly perfect detection for smear-positive samples (96.97%). Real-time PCR showed a high positive rate (58.97%) in regard to nonrespiratory specimen. A combination of molecular assays with conventional methods reached marked additive diagnostic values (sensitivity up to 76.42%), higher than each method individually. All detection systems showed excellent specificities (>96.00%).

CONCLUSIONS

The present study indicated that our lab had a moderate diagnostic performance for tuberculosis. Quality guarantee for specimen pretreatment, as well as combination analysis, will enable these assays to better incorporate into the routine laboratory workflow in China.

Molecular epidemiology of Mycobacterium abscessus infections in a subtropical chronic ventilatory setting

The aim of this study was to investigate the high level of pulmonary Mycobacterium abscessus infections and implement a surveillance programme among 43 ventilator-dependent patients, 15 with pulmonary M. abscessus infections, in a hospital long-term respiratory care ward (RCW) in central Taiwan. M. abscessus isolates were obtained from 35 patients in the RCW of hospital A, 6 patients in the RCWs of another three hospitals (B, C and D), and from 4 water sources in two of the hospitals (A and B). Strains were characterized by methods including hsp65 PCR-RFLP and PFGE. The patients were followed-up by chest X-ray for 1 year. All clinical isolates were type I and II, and belonged to ten distinct clusters of PFGE patterns. Five clinical strains in two hospitals belonged to a single cluster, whilst four clinical strains in the other two hospitals belonged to a single unique cluster. The strains from hospital A fell into nine clusters and were distinct from the strains isolated from the water supply. Patients infected with type I strains showed a significantly more rapid progression of disease. The number of different strains involved suggested either that there had been a polyclonal outbreak or that a high level of endemic infections was present in the RCW of hospital A. This and the lack of homology between the clinical and environmental isolates from hospital A raised the possibility that pulmonary M. abscessus infections may have been spread by the movement of patients between RCWs, a routine practice in Taiwan's integrated delivery system.

Clinical evaluation of TRCRapid M.TB for detection of Mycobacterium tuberculosis complex in respiratory and nonrespiratory specimens

The rapid and accurate diagnosis of tuberculosis is crucial to providing optimal treatment and reducing the spread of infection. We evaluated respiratory and nonrespiratory clinical specimens using a new automated Mycobacterium tuberculosis complex (MTBC) rRNA detection kit (TRCRapid M.TB; Tosoh Bioscience, Tokyo, Japan), which is based on the transcription-reverse transcription concerted reaction (TRC). TRC enables the rapid and completely homogeneous real-time monitoring of isothermal RNA sequence amplification without any postamplification procedures. The results were compared with those obtained by M. tuberculosis culture. A total of 1,155 respiratory specimens and 420 nonrespiratory specimens collected from 1,282 patients were investigated. Of the 45 specimens culture positive for MTBC, 42 were TRC positive, and of the 1,530 specimens culture negative for MTBC, 1,523 were TRC negative. Compared to the results of culture, the overall sensitivity and specificity of TRC were 96.6% and 99.9%, respectively, for respiratory specimens and 87.5% and 98.5%, respectively, for nonrespiratory specimens. The sensitivities of TRC were 100% for smear-positive respiratory and nonrespiratory specimens, 88.9% for smear-negative respiratory specimens, and 80% for smear-negative nonrespiratory specimens. No significant differences in test performance between respiratory and nonrespiratory specimens were observed. The TRC method proved to be clinically useful for the rapid identification of MTBC in respiratory and nonrespiratory specimens and in both smear-positive and smear-negative samples.

False-negative results obtained with the Gen-Probe Amplified Mycobacterium tuberculosis direct test caused by unrecognized inhibition of the amplification reaction

The Gen-Probe Amplified Mycobacterium tuberculosis direct test is widely used in the diagnosis of tuberculosis. Specimens may contain amplification inhibitors, potentially leading to false-negative results if unrecognized. We report a failure to detect inhibition, despite adherence to the inhibition testing guidelines provided on the label, and recommend changes.

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.

Cost-effectiveness of different strategies for amplified Mycobacterium tuberculosis direct testing for cases of pulmonary tuberculosis

We conducted a decision analysis to assess and compare four algorithms for amplified Mycobacterium tuberculosis direct (MTD) testing of respiratory specimens in terms of cost-effectiveness. The most cost-effective strategy was one in which smear-positive specimens but not smear-negative specimens were diluted prior to MTD testing.

PCR colorimetric dot-blot assay and clinical pretest probability for diagnosis of Pulmonary Tuberculosis in smear-negative patients

BACKGROUND

Smear-negative pulmonary tuberculosis (SNPTB) accounts for 30% of Pulmonary Tuberculosis (PTB) cases reported annually in developing nations. Polymerase chain reaction (PCR) may provide an alternative for the rapid detection of Mycobacterium tuberculosis (MTB); however little data are available regarding the clinical utility of PCR in SNPTB, in a setting with a high burden of TB/HIV co-infection.

METHODS

To evaluate the performance of the PCR dot-blot in parallel with pretest probability (Clinical Suspicion) in patients suspected of having SNPTB, a prospective study of 213 individuals with clinical and radiological suspicion of SNPTB was carried out from May 2003 to May 2004, in a TB/HIV reference hospital. Respiratory specialists estimated the pretest probability of active disease into high, intermediate, low categories. Expectorated sputum was examined by direct microscopy (Ziehl-Neelsen staining), culture (Lowenstein Jensen) and PCR dot-blot. Gold standard was based on culture positivity combined with the clinical definition of PTB.

RESULTS

In smear-negative and HIV subjects, active PTB was diagnosed in 28.4% (43/151) and 42.2% (19/45), respectively. In the high, intermediate and low pretest probability categories active PTB was diagnosed in 67.4% (31/46), 24% (6/25), 7.5% (6/80), respectively. PCR had sensitivity of 65% (CI 95%: 50%-78%) and specificity of 83% (CI 95%: 75%-89%). There was no difference in the sensitivity of PCR in relation to HIV status. PCR sensitivity and specificity among non-previously TB treated and those treated in the past were, respectively: 69%, 43%, 85% and 80%. The high pretest probability, when used as a diagnostic test, had sensitivity of 72% (CI 95%:57%-84%) and specificity of 86% (CI 95%:78%-92%). Using the PCR dot-blot in parallel with high pretest probability as a diagnostic test, sensitivity, specificity, positive and negative predictive values were: 90%, 71%, 75%, and 88%, respectively. Among non-previously TB treated and HIV subjects, this approach had sensitivity, specificity, positive and negative predictive values of 91%, 79%, 81%, 90%, and 90%, 65%, 72%, 88%, respectively.

CONCLUSION

PCR dot-blot associated with a high clinical suspicion may provide an important contribution to the diagnosis of SNPTB mainly in patients that have not been previously treated attended at a TB/HIV reference hospital.

Specimen dilution improves sensitivity of the amplified Mycobacterium tuberculosis direct test for smear microscopy-positive respiratory specimens

Specimen dilution has been proposed as a strategy to minimize amplified Mycobacterium tuberculosis direct (MTD) test inhibition (N. Pollock, J. Westerling, and A. Sloutsky, Am. J. Clin. Pathol. 126:142-147, 2006; A. Sloutsky, L. L. Han, and B. G. Werner, J. Clin. Microbiol. 42:1547-1551, 2004). We evaluated the impact of respiratory specimen dilution on MTD test accuracy in a public health laboratory. The difference in MTD test sensitivity between the dilution and conventional methods was 15.9% (P = 0.001) for smear microscopy-positive specimens and -3.6% (P = 0.38) for smear microscopy-negative specimens.

[Systemic granulomatosis of infectious origin]

PURPOSE

Granulomatous diseases are defined by specific histological features, following the local recruitment of macrophages and lymphocytes. Many infections can lead to the development of granuloma.

CURRENT KNOWLEDGE AND KEY POINTS

Microorganisms responsible for granuloma include mainly mycobacteria, many viral and fungal species, as well as schistosoma in endemic areas. Nevertheless, almost all microorganisms can lead to granuloma, especially if their clearance needs macrophages pathway. New immunosuppressive drugs such as tumor necrosis factor antagonists are associated with a high risk of infectious granulomatous complications. All patients with granuloma must be carefully screened to find a potential underlying infection, since an immunosuppressive therapy could be otherwise considered. We here review the general diagnostic process with a specific glance to the main organs.

FUTURE PROSPECTS AND PROJECTS

Without clinical or epidemiological clue, diagnosis can be very tedious. New molecular tools now assist classical microbiological and histological techniques. Their specificity and sensitivity have recently been better characterized, and their use will probably increase in the near future for the diagnosis of infectious granuloma. They may also lead to discover new infectious aetiologies of granulomatous diseases formerly considered as idiopathic. We describe here the main microorganisms that can be responsible for granuloma, with a specific focus on the use of new diagnostic tools.

Use of the amplified mycobacterium tuberculosis direct test in a public health laboratory: test performance and impact on clinical care

BACKGROUND

The Amplified Mycobacterium tuberculosis Direct Test (MTD; Gen-Probe; San Diego, CA) is a nucleic-acid amplification test for rapid pulmonary tuberculosis (PTB) diagnosis. In a routine public health setting, test accuracy and impact on clinical decisions are unknown.

METHODS

Retrospectively, we evaluated MTD accuracy and impact on clinical decisions in a public health setting. To estimate MTD accuracy, mycobacterial culture was used as the "gold standard." To evaluate MTD impact on clinical decisions, concordance of clinician presumptive diagnosis (at time of MTD and smear availability) and definitive diagnosis, and duration of nonindicated tuberculosis therapy were determined for smear-positive PTB suspects in a period of MTD availability (MTD group) and a prior period of MTD nonavailability (non-MTD group).

RESULTS

A total of 1,151 respiratory specimens from 638 PTB suspects were analyzed. MTD sensitivity, specificity, positive predictive value, and negative predictive value were 91.7%, 98.7%, 96.7%, and 96.5% overall, respectively; and 98.7%, 97.8%, 98.7%, and 97.8% for smear-positive patients; and 62.2%, 98.9%, 85.2%, and 96.1% for smear-negative patients. In the MTD group, concordance between definitive and clinician presumptive diagnoses was 78% (95% confidence interval [CI], 64 to 88%), similar to that for the non-MTD group (79%; 95% CI, 68.4 to 89.6%). However, concordance between definitive diagnosis and the MTD test was 98% (95% CI, 94.1 to 100%). Median duration of nonindicated tuberculosis treatment was 6 days for the MTD group vs 31 days for the non-MTD group (p = 0.002).

CONCLUSION

In this public health setting, MTD was accurate and rapidly detected more than half of the smear-negative PTB cases. For smear-positive PTB suspects, MTD had excellent concordance with definitive diagnosis, but clinicians often inappropriately initiated TB therapy despite a negative MTD result.

[Performances of the "Amplified Mycobacterium tuberculosis Direct Test" in respiratory and non-respiratory specimens]

From March 1998 to December 2004, 3641 specimens (2427 respiratory samples and 1214 non-respiratory samples) collected from 2079 patients, were tested using the "Gen-Probe Amplified Mycobacterium tuberculosis Direct Test" (AMTD). After decontamination procedure every sample was testing by AMTD and by culture on solid and liquid media. The "Gold-standard" was considered by the combination of culture results and clinical diagnosis. Respiratory tuberculosis was present in 9.7% (127 patients), and non-respiratory tuberculosis was present in 18.9% (170 patients, mostly originated from Africa). Among the 2427 respiratory samples (197 culture positive samples, 211 AMTD positive) 225 corresponded to tuberculosis; for the 1214 non-respiratory samples (184 culture positive samples, 213 AMTD positive) 231 corresponded to tuberculosis. After resolving the discordant results, the sensitivity, specificity, positive and negative predictive values were 93.8, 100, 100, 99.4% respectively for respiratory samples and 92.2, 99.9, 99.5, 98% for non respiratory samples.

Nucleic acid-based methods for the detection of bacterial pathogens: Present and future considerations for the clinical laboratory

BACKGROUND

Recent advances in nucleic acid-based methods to detect bacteria offer increased sensitivity and specificity over traditional microbiological techniques. The potential benefit of nucleic acid-based testing to the clinical laboratory is reduced time to diagnosis, high throughput, and accurate and reliable results.

METHODS

Several PCR and hybridization tests are commercially available for specific organism detection. Furthermore, hundreds of nucleic acid-based bacterial detection tests have been published in the literature and could be adapted for use in the clinical setting. Contamination potential, lack of standardization or validation for some assays, complex interpretation of results, and increased cost are possible limitations of these tests, however, and must be carefully considered before implementing them in the clinical laboratory.

CONCLUSIONS

A major area of advancement in nucleic acid-based assay development has been for specific and broad-range detection of bacterial pathogens.

The diagnosis of tuberculosis

Diagnostic testing for tuberculosis has remained unchanged for nearly a century, but newer technologies hold the promise of a true revolution in tuberculosis diagnostics. New tests may well supplant the tuberculin skin test in diagnosing latent tuberculosis infection in much of the world. Tests such as the nucleic acid amplification assays allow more rapid and accurate diagnosing of pulmonary and extrapulmonary tuberculosis. The appropriate and affordable use of any of these tests depends on the setting in which they are employed.

Identification of Mycobacterium species by secA1 sequences

We describe a novel molecular method for the differentiation and identification of 29 mycobacterial species. The target is the secA1 gene that codes for the essential protein SecA1, a key component of the major pathway of protein secretion across the cytoplasmic membrane. A 700-bp region of the secA1 gene was amplified and sequenced from 47 American Type Culture Collection strains of 29 Mycobacterium species as well as from 59 clinical isolates. Sequence variability in the amplified segment of the secA1 gene allowed the differentiation of all species except for the members of the Mycobacterium tuberculosis (MTB) complex, which had identical sequences. A range of 83.3 to 100% interspecies similarity was observed. All species could also be differentiated by their amino acid sequences as deduced from the sequenced region of the secA1 gene, with the exception of the MTB complex. Partial sequences of secA1 from clinical isolates belonging to nine frequently isolated species of mycobacteria revealed a very high intraspecies similarity at the DNA level (typically >99%; range, 96.0 to 100%); all clinical isolates were correctly identified. Comparison of the deduced 233-amino-acid sequences among clinical isolates of the same species showed between 99.6 and 100% similarity. To our knowledge, this is the first time a secretion-related gene has been used for the identification of the species within a bacterial genus.

New method for detection of Mycobacterium tuberculosis Direct Test inhibitors in clinical specimens

Existing protocols for the detection of Mycobacterium tuberculosis Direct Test (MDT) inhibitors require substantial quantities of specimen and cannot distinguish Mycobacterium tuberculosis complex from other mycobacteria if inhibitors are present. We describe a preliminary evaluation of a simple and practical protocol for MTD inhibitor testing that circumvents these difficulties.