Multicentre quality control study for detection of Mycobacterium tuberculosis in clinical samples by nucleic amplification methods

Rifampicin Resistance Pattern of Mycobacterium tuberculosis Infection in Tertiary Care Hospital Settings

Introduction Mycobacterium tuberculosis (MTB), the causative agent of tuberculosis (TB), continues to pose a significant global health threat, with increasing concerns about antimicrobial resistance (AMR). This study aims to elucidate the AMR patterns of MTB infections in tertiary care hospital settings. Materials and methods A retrospective analysis was conducted on 138 clinical samples collected from patients attending the outpatient ward with clinically suspected MTB infections from November 2022 to April 2023 in a tertiary care hospital, Saveetha Medical College and Hospital. The study focused on the sample isolates collected from various clinical specimens, such as sputum, pus, synovial fluid, wound swabs, and other forms of samples from the patients. The samples were processed and analyzed with routine microbiological confirmation tests using standard laboratory methods such as staining and culture. Further, the samples were subjected to a GeneXpert MTB/RIF assay to assess the resistance to Rifampicin (RIF). The results were interpreted, analyzed using standard statistical methods, and presented. Results The findings revealed marked resistance of the clinical isolate MTB to TIF, with positive and negative results through various peak levels shown by GeneXpert. Out of the 138 samples screened by GeneXpert for resistance, 14 samples were found to be positive (10.14%). Resistance to the first-line drug, namely RIF, was observed in the study, raising concerns about the effectiveness of standard tuberculosis treatment regimens followed in the country. Conclusion This study implies the urgency of monitoring and addressing AMR in MTB infections in tertiary care hospital settings. The emergence of resistance to even the first-line drugs necessitates continuous surveillance, the implementation of appropriate diagnostic strategies, and the development of effective treatment protocols. A comprehensive understanding of the AMR landscape in tuberculosis is crucial for optimizing therapeutic interventions, preventing the spread of drug-resistant strains, and ultimately curbing the global burden of tuberculosis.

Revisiting the methods for detecting Mycobacterium tuberculosis: what has the new millennium brought thus far?

Tuberculosis (TB) affects around 10 million people worldwide in 2019. Approximately 3.4 % of new TB cases are multidrug-resistant. The gold standard method for detecting Mycobacterium tuberculosis, which is the aetiological agent of TB, is still based on microbiological culture procedures, followed by species identification and drug sensitivity testing. Sputum is the most commonly obtained clinical specimen from patients with pulmonary TB. Although smear microscopy is a low-cost and widely used method, its sensitivity is 50-60 %. Thus, owing to the need to improve the performance of current microbiological tests to provide prompt treatment, different methods with varied sensitivity and specificity for TB diagnosis have been developed. Here we discuss the existing methods developed over the past 20 years, including their strengths and weaknesses. In-house and commercial methods have been shown to be promising to achieve rapid diagnosis. Combining methods for mycobacterial detection systems demonstrates a correlation of 100 %. Other assays are useful for the simultaneous detection of M. tuberculosis species and drug-related mutations. Novel approaches have also been employed to rapidly identify and quantify total mycobacteria RNA, including assessments of global gene expression measured in whole blood to identify the risk of TB. Spoligotyping, mass spectrometry and next-generation sequencing are also promising technologies; however, their cost needs to be reduced so that low- and middle-income countries can access them. Because of the large impact of M. tuberculosis infection on public health, the development of new methods in the context of well-designed and -controlled clinical trials might contribute to the improvement of TB infection control.

Trends in Diagnosis for Active Tuberculosis Using Nanomaterials

Background:

Tuberculosis (TB), one of the leading causes of death worldwide, is difficult to diagnose based only on signs and symptoms. Methods for TB detection are continuously being researched to design novel effective clinical tools for the diagnosis of TB.

Objective:

This article reviews the methods to diagnose TB at the latent and active stages and to recognize prospective TB diagnostic methods based on nanomaterials.

Methods:

The current methods for TB diagnosis were reviewed by evaluating their advantages and disadvantages. Furthermore, the trends in TB detection using nanomaterials were discussed regarding their performance capacity for clinical diagnostic applications.

Results:

Current methods such as microscopy, culture, and tuberculin skin test are still being employed to diagnose TB, however, a highly sensitive point of care tool without false results is still needed. The utilization of nanomaterials to detect the specific TB biomarkers with high sensitivity and specificity can provide a possible strategy to rapidly diagnose TB. Although it is challenging for nanodiagnostic platforms to be assessed in clinical trials, active TB diagnosis using nanomaterials is highly expected to achieve clinical significance for regular application. In addition, aspects and future directions in developing the high-efficiency tools to diagnose active TB using advanced nanomaterials are expounded.

Conclusion:

This review suggests that nanomaterials have high potential as rapid, costeffective tools to enhance the diagnostic sensitivity and specificity for the accurate diagnosis, treatment, and prevention of TB. Hence, portable nanobiosensors can be alternative effective tests to be exploited globally after clinical trial execution.

Optimized Lysis-Extraction Method Combined With IS6110-Amplification for Detection of Mycobacterium tuberculosis in Paucibacillary Sputum Specimens

Background: When available, nucleic acid tests (NATs) offer powerful tools to strengthen the potential of tuberculosis (TB) diagnosis assays. The sensitivity of molecular assays is critical for detection of Mycobacterium tuberculosis (MTB) in paucibacillary sputum.

Materials and Methods: The impact of targeting repetitive IS6110 sequences on the PCR sensitivity was evaluated across mycobacterium strains and reference material. Six lysis-extraction protocols were compared. Next, 92 clinical sputum specimens including 62 culture-positive samples were tested and the results were compared to sputum-smear microscopy, culture, and Xpert MTB/RIF test. Finally, the capacity to detect low MTB DNA concentrations was assessed in 40 samples containing <1.5 × 10² copies/ml ex vivo or after dilution.

Results: The lower limit of detection (LOD) using the IS6110 PCR was 107 genome copies/ml (95% CI: 83–130) using MTB H37Rv as a reference strain, versus 741 genome copies/ml (95% CI: 575–1094) using the senX3 PCR. The proportion of recovered MTB DNA after lysis and extraction ranged from 35 to 82%. The Chelex^® method appeared as a more efficient protocol among the six different protocols tested. The sensitivity and specificity in clinical sputum samples were 95.1% (95% CI: 90.7–99.6) and 100% (95% CI: 96.2–100.8), respectively. Among 40 samples with low MTB DNA concentration, 75% tested positive for IS6110 PCR, versus 55% using the Xpert MTB/RIF assay (p = 0.03).

Conclusion: Laboratory assays based on an efficient MTB lysis and DNA extraction protocols combined with amplification of IS6110 repeat sequences appear as a sensitive diagnostic method to detect MTB DNA in sputum with low bacterial load.

Evaluation of molecular detection of extrapulmonary tuberculosis and resistance to rifampicin with GeneXpert® MTB/RIF

OBJECTIVE

We aimed to evaluate the GeneXpert® MTB/RIF test for the diagnosis of extrapulmonary tuberculosis. The test simultaneously detects Mycobacterium tuberculosis complex and resistance to rifampicin.

METHODS

We analyzed 153 clinical samples collected in a tertiary hospital in Sfax, Tunisia, between 2013 and 2014. We performed the GeneXpert® test, a Ziehl-Neelsen and auramine-rhodamine staining, conventional culture on MGIT 960 and LJ media, and we tested the resistance to anti-tuberculosis drugs on MGIT 960 and LJ media for each sample. Diagnosis was based on clinical, radiological, microbiological, pathological, and therapeutic data.

RESULTS

We considered that 59 patients out of 153 presented with tuberculosis. PCR was positive in 50 samples and all of these samples were susceptible to rifampicin. Sensitivity, specificity, positive predictive value, and negative predictive value of the GeneXpert® test were 84.7%, 96.8%, 94.3%, and 91%, respectively, compared with diagnosis. We observed a statistically significant difference between the direct test and the GeneXpert® test, and between culture and the GeneXpert® test. No statistically significant difference was observed between pathological results and the GeneXpert® test. Sensitivity of the GeneXpert® test was 87.5% in biopsies, 80% in pus and abscesses, and 66.7% in biological fluids. All strains were susceptible to rifampicin with culture and GeneXpert® test.

CONCLUSION

The GeneXpert® test helped detect a higher proportion of M. tuberculosis complex. It does not replace conventional diagnostic methods but it is a useful addition to achieve better sensitivity and obtain rapid results.

Multicenter external quality assessment program for PCR detection of Mycobacterium ulcerans in clinical and environmental specimens

BACKGROUND

Mycobacterium ulcerans is the causative agent of Buruli ulcer (BU), a necrotizing disease of the skin, soft tissue and bone. PCR is increasingly used in the diagnosis of BU and in research on the mode of transmission and environmental reservoir of M. ulcerans.

METHODOLOGY/PRINCIPAL FINDINGS

The aim of this study was to evaluate the performance of laboratories in detecting M. ulcerans using molecular tests in clinical and environmental samples by implementing sequential multicenter external quality assessment (EQA) programs. The second round of the clinical EQA program revealed somewhat improved performance.

CONCLUSIONS/SIGNIFICANCE

Ongoing EQA programs remain essential and continued participation in future EQA programs by laboratories involved in the molecular testing of clinical and environmental samples for M. ulcerans for diagnostic and research purposes is strongly encouraged. Broad participation in such EQA programs also benefits the harmonization of quality in the BU research community and enhances the credibility of advances made in solving the transmission enigma of M. ulcerans.

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.

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.

Diagnostic accuracy of in-house PCR for pulmonary tuberculosis in smear-positive patients: meta-analysis and metaregression

In-house PCR (hPCR) could speed differential diagnosis between tuberculosis (TB) and nontuberculous mycobacterial disease in patients with positive smears and pulmonary infiltrates, but its reported accuracy fluctuates across studies. We conducted a systematic review and meta-analysis of hPCR sensitivity and specificity for smear-positive TB diagnosis, using culture as the reference standard. After searching English language studies in MEDLINE and EMBASE, we estimated cumulative accuracy by means of summary receiver operating characteristic analysis. The possible influence of hPCR procedures and study methodological features on accuracy was explored by univariate metaregression, followed by multivariate adjustment of items selected as significant. Thirty-five articles (1991 to 2006) met the inclusion criteria. The pooled estimates of the diagnostic odds ratio, sensitivity, and specificity (random-effect model) were, respectively, 60 (confidence interval [CI], 29 to 123), 0.96 (CI, 0.95 to 0.97), and 0.81 (CI, 0.78 to 0.84), but significant variations (mainly in specificity) limit their clinical applicability. The quality of the reference test, the detection method, and real-time PCR use explained some of the observed heterogeneity. Probably due to the limited study power of our meta-analysis and to the wide differences in both laboratory techniques and methodological quality, only real-time PCR also displayed a positive impact on accuracy in the multivariate model. Currently, hPCR can be confidently used to exclude TB in smear-positive patients, but its low specificity could lead to erroneous initiation of therapy, isolation, and contact investigation. As the inclusion of samples from treated patients could have artificially reduced specificity, future studies should report mycobacterial-culture results for each TB and non-TB sample analyzed.

Reliability of Cobas Amplicor PCR test in detection of Mycobacterium tuberculosis in respiratory and nonorespiratory specimens

Background/Aim. Traditional methods for detection of mycobacteria, such as microscopic examination for the presence of acid-fast bacilli and isolation of the organism by culture, have either a low sensitivity and/or specificity, or take weeks before a definite result is available. Molecular methods, especially those based on nucleic acid amplification, are rapid diagnostic methods which combine high sensitivity and high specificity. The aim of this study was to determine the usefulness of the Cobas Amplicor Mycobacterium tuberculosis polymerase chain reaction (CAPCR) assay in detecting the tuberculosis cause in respiratory and nonrespiratory specimens (compared to culture). Methods. Specimens were decontaminated by the N-acetyl-L-cystein- NaOH method. A 500 ?L aliquot of the processed specimen were used for inoculation of L?wenstein-Jensen (L-J) slants, a drop for acid-fast staining, and 100 ?L for PCR. The Cobas Amplicor PCR was performed according to the manufacturer's instructions. Results. A total of 110 respiratory and 355 nonrespiratory specimens were investigated. After resolving discrepancies by reviewing medical history, overall sensitivity, specificity, and positive and negative predictive values for CA-PCR assay compared to culture, were 83%, 100%, 100%, and 96.8%, respectively. In comparison, they were 50%, 99.7%, 87.5%, and 98%, respectively, for the nonrespiratory specimens. The inhibition rate was 2.8% for respiratory, and 7.6% for nonrespiratory specimens. Conclusion. CA-PCR is a reliable assay that enables specialists to start treatment promptly on a positive test result. Lower value for specificity in a group of nonrespiratory specimens is a consequence of an extremely small number of mycobacteria in some of them.

Clinical evaluation of Gen-Probe's amplified mycobacterium tuberculosis direct test for rapid diagnosis of Mycobacterium tuberculosis in Egyptian children at risk for infection

CONTEXT

Diagnostic detection of tuberculosis (TB) has improved considerably. Available, standardized, nucleic acid-based amplification techniques have been shown to yield reliable results within 4 to 7 hours of sample processing.

OBJECTIVE

To study the diagnostic performance of Gen-Probe's technique for direct detection of Mycobacterium tuberculosis in comparison with BACTEC 460 TB culture for both positive and negative Ziehl-Neelsen smears in Egyptian children at risk for TB infection.

DESIGN

We prospectively evaluated 50 children from families with a positive history of TB. All patients were referred from outpatient clinics of the Mansoura University Children's Hospital, Egypt. The children had a positive tuberculin skin test with an induration diameter of more than 10 mm and had scars from a bacille Calmette-Guérin vaccination within the past 2 years. Three consecutive sputum samples were taken from each patient. The samples were examined to detect M. tuberculosis by means of the Gen-Probe technique, direct smear microscopy, and bacterial culture by BACTEC 460 TB.

RESULTS

Of the 50 cases, 30 (60%) had sputum samples that were positive for TB by BACTEC 460 TB culture, and 29 cases (58%) were positive by the Gen-Probe technique. Sensitivity and specificity of Ziehl-Neelsen smears was 83.3% and 100%, respectively, with overall accuracy of 90%. Sensitivity and specificity of the Gen-Probe technique were 96.7% and 100%, respectively, with overall accuracy of 98%.

CONCLUSIONS

The results of this study suggest that the Gen-Probe technique is an accurate method for rapid detection of M. tuberculosis complexes in respiratory samples from children at risk for TB. It can be used for diagnosis of smear-negative cases that are suspect for TB.

Epidemiological evidence for Mycobacterium avium subspecies paratuberculosis as a cause of Crohn's disease

Mycobacterium avium subspecies paratuberculosis is the causative agent of Johne's disease, a chronic enteritis in ruminants including cattle, sheep, goats, and farmed deer. Recently, this bacterium has received an increasingly wide interest because of a rapidly growing body of scientific evidence which suggests that human infection with this microorganism may be causing some, and possibly all, cases of Crohn's disease. Recent studies have shown that a high percentage of people with Crohn's disease are infected with M. avium subsp. paratuberculosis; whether the association of this bacterium and Crohn's disease is causal or coincidental is not known. Crohn's disease is a gastrointestinal disease in humans with similar histopathological findings to those observed in the paucibacillary form of Johne's disease in cattle. The search for risk factors in Crohn's disease has been frustrating. However, epidemiologists have gathered enough information that points to an association between M. avium subsp. paratuberculosis and Crohn's disease. This paper reviews epidemiological models of disease causation, the major philosophical doctrines about causation, the established epidemiological criteria for causation, and the currently known epidemiological evidence of M. avium subsp. paratuberculosis as a possible cause of Crohn's disease.

Quality control of direct molecular diagnostics for methicillin-resistant Staphylococcus aureus

Ten samples containing various amounts of methicillin-resistant Staphylococcus aureus (MRSA), methicillin-susceptible S. aureus, methicillin-resistant Staphylococcus epidermidis (MRSE), and combinations thereof were distributed to 51 laboratories for molecular diagnostics testing. Samples containing 10(2) to 10(3) MRSA cells were frequently reported to be negative. MRSE samples were scored as negative by all commercial tests but by only two out of three in-house tests.

Multicenter proficiency study for detection of Toxoplasma gondii in amniotic fluid by nucleic acid amplification methods

A proficiency panel was designed to assess the performance of nucleic acid amplification technologies for the detection of Toxoplasma gondii in amniotic fluid.

METHODS

The proficiency panel consisted of five lyophilised coded samples in a range of concentration between 5 to 1000 parasites/ml and a negative control. The distribution also included a questionnaire on the applied methods.

RESULTS

Thirty-three laboratories in 17 countries participated and returned a total of 38 data sets. The percentage of data sets achieving correct results on all panel samples was 42.1%, whereas two or more incorrect or equivocal results were reported for 36.8%. The lowest concentration (5 parasites/ml) was not identified correctly in 15 (39.5%) data sets. False positive results were reported by two laboratories both of which had not included a step in their procedure to rule out contamination. In 32 (84.2%) data sets an "in-house" method was used, and in 6 (15.8%) sets a commercial assay was applied.

CONCLUSIONS

Overall, the results of this study demonstrate the need for improvements in both sensitivity and specificity of molecular detection methods of T. gondii and for the development of international reference materials to help laboratories with the development and validation of their assays.

Evaluation of in situ methods used to detect Mycobacterium avium subsp. paratuberculosis in samples from patients with Crohn's disease

In common with other diagnostic tests, detection of mycobacteria in tissue by microscopic examination is susceptible to spectrum bias. Since Crohn's disease is defined by the absence of detectable pathogenic organisms, the use of in situ techniques to search for Mycobacterium avium subsp. paratuberculosis in Crohn's disease samples requires validation of methods in a paucibacillary setting. To generate paucibacillary infection, C57BL/6 mice were artificially infected with Mycobacterium avium subsp. paratuberculosis strain K10 and M. tuberculosis H37Rv, yielding tissues harboring fewer than one bacillus per oil immersion field. Serial sections of organs were then studied by cell wall-based staining techniques (Ziehl-Neelsen and auramine rhodamine) and nucleic acid-based staining techniques (in situ hybridization [ISH] and indirect in situ PCR [IS PCR]). Microscopic examination and measurement of morphometric parameters of bacilli revealed that for all methods, Mycobacterium avium subsp. paratuberculosis bacilli were observed to be shorter, smaller, and less rod shaped than M. tuberculosis bacilli. Ziehl-Neelsen, auramine rhodamine stains, ISH targeting rRNA, and IS-PCR targeting the IS900 element afforded comparable sensitivities, but for all methods, visualization of individual bacterial forms required magnification x1,000. Auramine rhodamine staining and IS-PCR generated positive signals in negative controls, indicating the nonspecificity of these assays. Together, our results indicate that detection of Mycobacterium avium subsp. paratuberculosis bacilli in tissue requires oil immersion microscopy, that rRNA-ISH provides sensitivity and specificity comparable to those of Ziehl-Neelsen staining, and that the microscopic detection limit for Mycobacterium avium subsp. paratuberculosis in tissue is governed more by bacterial burden than by staining method.

TB in developing countries: diagnosis and treatment

Childhood tuberculosis poses great challenges to the public health manager as well as the pediatrician. While mycobacterial detection and isolation remain the gold standard but has a poor sensitivity for several reasons. The diagnosis of the disease is often based on indirect methods like PPD positivity, radiological features and history of contact. Serology and PCR based diagnostic methods have failed to help a clinician working at the peripheral level. The review shares and discusses the place of the various tests in the diagnosis of tuberculosis. WHO has been propagating the use of intermittent supervised treatment for all cases including children. We discuss the concerns of the pediatricians and share our experience on this therapy.

Newer diagnostics for tuberculosis and multi-drug resistant tuberculosis

PURPOSE OF REVIEW

This article will review some of the recent developments for the rapid diagnosis and detection of drug resistance in tuberculosis.

RECENT FINDINGS

Tuberculosis remains one of the major causes of death from a single infectious agent worldwide. Of great concern for tuberculosis control is the emergence of drug resistance since there is no cure for some multidrug-resistant strains of M. tuberculosis, and there is concern that they may spread around the world, stressing the need for additional control measures such as new diagnostics and better drugs for treatment. Recent advances in molecular biology and a better understanding of the molecular basis of drug resistance have provided new tools for rapid tuberculosis diagnosis. Other non-conventional diagnostic approaches have also been proposed. Nucleic acid amplification techniques, both commercial and in-house, and non-molecular methods are being evaluated. The overall accuracy of most of these tests is promising and some of them can be easily implemented in clinical mycobacteriology laboratories.

SUMMARY

New genotypic and phenotypic methods for rapid diagnosis and detection of drug resistance have been developed and tested both in M. tuberculosis strains as well as in clinical samples. Further controlled evaluations are necessary in high-endemic countries for their eventual implementation in the routine diagnostic systems.

Current evidence on diagnostic accuracy of commercially based nucleic acid amplification tests for the diagnosis of pulmonary tuberculosis

BACKGROUND

Even though commercial nucleic acid amplification tests (NAATs) have become the most frequently used molecular tests for laboratory diagnosis of pulmonary tuberculosis (TB), published studies report variable estimates of their diagnostic accuracy. We analysed the accuracy of commercial NAATs for the diagnosis of pulmonary TB in smear positive and smear negative respiratory samples using culture as a reference standard.

METHODS

English language studies reporting data sufficient for calculating sensitivity and specificity of commercial NAATs on smear positive and/or smear negative respiratory samples were included. Meta-regression was used to analyse associations with reference test quality, the prevalence of TB, sample and test type. Predictive values for different levels of pre-test probability were quantified using Bayes' approach.

RESULTS

Sixty three journal articles published between 1995 and 2004 met the inclusion criteria. Pooled sensitivity and specificity were 0.96 and 0.85 among smear positive samples and 0.66 and 0.98 among smear negative samples. The number of culture media used as reference test, the inclusion of bronchial samples, and the TB prevalence were found to influence the reported accuracy. The test type had no effect on the diagnostic odds ratio but seemed to be correlated with sensitivity or specificity, probably via a threshold effect.

CONCLUSIONS

Commercial NAATs can be confidently used to exclude TB in patients with smear positive samples in which environmental mycobacteria infection is suspected and to confirm TB in a proportion of smear negative cases. The methodological characteristics of primary studies have a considerable effect on the reported diagnostic accuracy.

Recent advances in the diagnosis and management of tuberculosis

PURPOSE OF REVIEW

Tuberculosis (TB) remains one of the leading infectious killers of adults in the world today. This paper will review recent advances and understanding in the epidemiology, diagnosis, and management of TB.

RECENT FINDINGS

Tuberculosis remains a significant global threat, particularly in regions of the world heavily affected by HIV. Diagnosis of TB infection and disease rely on outdated and problematic methods, but newer immunologic and nucleic acid-based techniques are emerging. Treatment of latent TB infection still relies mainly on the use of isoniazid but several treatment-shortening strategies are being studied. Treatment of active disease has advanced little since the introduction of short-course chemotherapy with rifampin, but several new drugs are being developed and studied. Timely initiation of HIV treatment in co-infected patients is increasingly seen as important and strategies for initiating therapy for both diseases are being refined. The existence of immune reconstitution inflammatory reactions is also becoming more widely appreciated. Other populations at risk for TB such as those receiving TNF-alpha antagonists are being recognized and improved screening and control measures implemented.

SUMMARY

The global epidemiology of TB has been shaped in recent decades by HIV, urbanization and poverty. Diagnosis and treatment remain challenging, however, improved screening of at-risk populations and new diagnostic modalities and treatment strategies offer hope to the millions who suffer from tuberculosis.

Sensitivity of the Cobas Amplicor system for detection of Mycobacterium tuberculosis in respiratory and extrapulmonary specimens

The Cobas Amplicor PCR system (CA-PCR) was compared with culture and staining for acid-fast bacilli (AFB) for the early detection of Mycobacterium tuberculosis in respiratory clinical specimens and otherwise normal sterile body fluids. The sensitivity, specificity and positive and negative predictive values of CA-PCR were determined with AFB-positive and AFB-negative specimens. The sensitivity of CA-PCR ranged from 73.6% to 100% for AFB-positive samples, while sputa collected after bronchoscopy were the most useful specimens, with 70% sensitivity and 98.6% specificity among the AFB-negative samples.

A multi-centre pilot proficiency programme to assess the quality of molecular detection of respiratory viruses

Objectives

To assess the quality of molecular detection of respiratory viruses in clinical diagnostic laboratories.

Study design

Respiratory virus proficiency panels were produced from diluted stocks of respiratory viruses provided and tested by four reference laboratories. The panels consisted of strong positive, positive, low positive and negative samples for influenza viruses A and B, respiratory syncytial virus, parainfluenza viruses 1 and 3, adenovirus serotypes 4 and 7, human rhinovirus serotypes 16, 72 and 90, human coronaviruses OC43 and 229E. The panels were sent to 17 participants; results and information on methodology was collected.

Results

All laboratories returned results, of which five submitted complete data sets. So, for analysis all results were combined. Samples were correctly identified by participants in 93.75%, 76.75% and 47.03% for the high positive, positive and low positive samples, respectively. One false positive was reported for all data sets (1.1%). The overall score for all assays using different methodologies was 78.8%. Laboratory performance was not dependant on methodology as all in-house methodologies could achieve optimal results, but dependant on careful optimisation and procedures specific to the laboratory.

Conclusions

The first proficiency panel showed that in general all participants performed well. Although, it also highlights areas for improvement for all participants in order to generate robust results for use in clinical diagnostics.

Comparison of an internally controlled, large-volume LightCycler assay for detection of Mycobacterium tuberculosis in clinical samples with the COBAS AMPLICOR assay

We present a sensitive and specific assay for reliable and flexible detection of members of the Mycobacterium tuberculosis complex (MTBC) in clinical samples. This real-time PCR assay, which uses the LightCycler 2.0 instrument and 100-mul glass capillaries, can provide a result within 1 h after DNA extraction. The primers amplify a 206-bp fragment of the MTBC 16S rRNA gene. The sensor hybridization probe targets a region highly specific to members of the MTBC. The assay also includes a novel type of internal control that monitors the function of the reaction components and can detect potential inhibitors. Template DNA was extracted by the same procedure used for the COBAS AMPLICOR M. tuberculosis assay, so the LightCycler assay could be directly compared to the COBAS AMPLICOR assay. The LightCycler assay was evaluated with 146 clinical samples of various types. Very good agreement (100% sensitivity, 98.6% specificity) could be shown between the LightCycler and COBAS AMPLICOR assays. Specificity was checked with a panel of nontuberculous mycobacteria, as well as a large panel of bacterial and fungal organisms.

Molecular genetic methods for diagnosis and antibiotic resistance detection of mycobacteria from clinical specimens

Mycobacteria comprise a diverse group of bacteria that are widespread in nature, some of which cause significant disease in humans. Members of the Mycobacterium tuberculosis complex (MTBC) are the most important human pathogens of the genus Mycobacterium. Traditional methods for detection and identification of mycobacteria include microscopy, culture and phenotypic tests. These methods either lack sensitivity, specificity, or are time consuming. Advances in the field of molecular biology have provided rapid diagnostic tools that have reduced the turnaround times for detecting MTBC and drug resistance in cultures and directly in clinical specimens from weeks to days. This review discusses the molecular genetic techniques for detecting and identifying MTBC as well as drug resistance of mycobacteria in clinical specimens.