The evaluation of FASTPlaqueTB test for the rapid diagnosis of tuberculosis

Mycobacteriophages in diagnosis and alternative treatment of mycobacterial infections

Antimicrobial resistance is an increasing threat to human populations. The emergence of multidrug-resistant "superbugs" in mycobacterial infections has further complicated the processes of curing patients, thereby resulting in high morbidity and mortality. Early diagnosis and alternative treatment are important for improving the success and cure rates associated with mycobacterial infections and the use of mycobacteriophages is a potentially good option. Since each bacteriophage has its own host range, mycobacteriophages have the capacity to detect specific mycobacterial isolates. The bacteriolysis properties of mycobacteriophages make them more attractive when it comes to treating infectious diseases. In fact, they have been clinically applied in Eastern Europe for several decades. Therefore, mycobacteriophages can also treat mycobacteria infections. This review explores the potential clinical applications of mycobacteriophages, including phage-based diagnosis and phage therapy in mycobacterial infections. Furthermore, this review summarizes the current difficulties in phage therapy, providing insights into new treatment strategies against drug-resistant mycobacteria.

Review of Label-Free Monitoring of Bacteria: From Challenging Practical Applications to Basic Research Perspectives

Novel biosensors already provide a fast way to detect the adhesion of whole bacteria (or parts of them), biofilm formation, and the effect of antibiotics. Moreover, the detection sensitivities of recent sensor technologies are large enough to investigate molecular-scale biological processes. Usually, these measurements can be performed in real time without using labeling. Despite these excellent capabilities summarized in the present work, the application of novel, label-free sensor technologies in basic biological research is still rare; the literature is dominated by heuristic work, mostly monitoring the presence and amount of a given analyte. The aims of this review are (i) to give an overview of the present status of label-free biosensors in bacteria monitoring, and (ii) to summarize potential novel directions with biological relevancies to initiate future development. Optical, mechanical, and electrical sensing technologies are all discussed with their detailed capabilities in bacteria monitoring. In order to review potential future applications of the outlined techniques in bacteria research, we summarize the most important kinetic processes relevant to the adhesion and survival of bacterial cells. These processes are potential targets of kinetic investigations employing modern label-free technologies in order to reveal new fundamental aspects. Resistance to antibacterials and to other antimicrobial agents, the most important biological mechanisms in bacterial adhesion and strategies to control adhesion, as well as bacteria-mammalian host cell interactions are all discussed with key relevancies to the future development and applications of biosensors.

Actinobacteriophages: Genomics, Dynamics, and Applications

Actinobacteriophages are viruses that infect bacterial hosts in the phylum Actinobacteria. More than 17,000 actinobacteriophages have been described and over 3,000 complete genome sequences reported, resulting from large-scale, high-impact, integrated research-education initiatives such as the Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Sciences (SEA-PHAGES) program. Their genomic diversity is enormous; actinobacteriophages comprise many architecturally mosaic genomes with distinct DNA sequences. Their genome diversity is driven by the highly dynamic interactions between phages and their hosts, and prophages can confer a variety of systems that defend against attack by genetically distinct phages; phages can neutralize these defense systems by coding for counter-defense proteins. These phages not only provide insights into diverse and dynamic phage populations but also have provided numerous tools for mycobacterial genetics. A case study using a three-phage cocktail to treat a patient with a drug-resistant Mycobacterium abscessus suggests that phages may have considerable potential for the therapeutic treatment of mycobacterial infections.

Phage Amplification Assay for Detection of Mycobacterial Infection: A Review

An important prerequisite for the effective control, timely diagnosis, and successful treatment of mycobacterial infections in both humans and animals is a rapid, specific, and sensitive detection technique. Culture is still considered the gold standard in the detection of viable mycobacteria; however, mycobacteria are extremely fastidious and slow-growing microorganisms, and therefore cultivation requires a very long incubation period to obtain results. Polymerase Chain Reaction (PCR) methods are also frequently used in the diagnosis of mycobacterial infections, providing faster and more accurate results, but are unable to distinguish between a viable and non-viable microorganism, which results in an inability to determine the success of tuberculosis patient treatment or to differentiate between an active and passive infection of animals. One suitable technique that overcomes these shortcomings mentioned is the phage amplification assay (PA). PA specifically detects viable mycobacteria present in a sample within 48 h using a lytic bacteriophage isolated from the environment. Nowadays, an alternative approach to PA, a commercial kit called Actiphage™, is also employed, providing the result within 6–8 h. In this approach, the bacteriophage is used to lyse mycobacterial cells present in the sample, and the released DNA is subsequently detected by PCR. The objective of this review is to summarize information based on the PA used for detection of mycobacteria significant in both human and veterinary medicine from various kinds of matrices.

Clinical Validation of the QMAC-DST System for Testing the Drug Susceptibility of Mycobacterium tuberculosis to First- and Second-Line Drugs

There is a high demand for novel approaches to counter the various challenges of conventional drug susceptibility testing (DST) for tuberculosis, the most prevalent infectious disease with significant global mortality. The QMAC-DST system was recently developed for rapid DST using image technology to track the growth of single cells of Mycobacterium tuberculosis (MTB). The purpose of this study was to clinically validate the QMAC-DST system compared to conventional DST. In total, 178 MTB isolates recovered from clinical specimens in Asan Medical Center in 2016 were tested by both QMAC-DST and absolute concentration methods using Lowenstein-Jensen media (LJ-DST). Among the isolates, 156 were subjected to DST using BACTEC MGIT 960 SIRE kits (BD, Sparks, MD, United States) (MGIT-DST). The susceptibility/resistance results obtained by QMAC-DST were read against 13 drugs after 7 days of incubation and compared with those of LJ-DST. Based on the gold standard LJ-DST, the agreement rates of QMAC-DST for all drugs were 97.8%, 97.9%, and 97.8% among susceptible, resistant, and total isolates, respectively, while the overall agreement of MGIT-DST tested for 156 isolates against first-line drugs was 95.5%. QMAC-DST showed the highest major error of 6.4% for rifampin, however, it could be corrected by a revised threshold of growth since false-resistant isolates showed grew only half than the true-resistant isolates. The rapid and accurate performance of QMAC-DST warrants ideal phenotypic DST for a wide range of first-line and second-line drugs.

Mycobacterium diagnostics: from the primitive to the promising

The field of clinical microbiology has been revolutionised by genomic and proteomic methods, which have facilitated more rapid diagnosis and characterisation of infection in many cases. In contrast, mycobacteriological evolution has tended to retain the traditional methods of smear microscopy for detection of acid-fast bacilli to indicate mycobacteria, along with culture, and in synergy with more modern molecular methods. Thus, efforts have been focused on reducing the time to diagnosis of infection, while increasing the amount of diagnostic information available, including more definitive speciation, and more rapid susceptibility test results. Although smear microscopy remains a mainstay for the laboratory-based diagnosis of mycobacterial infection, molecular testing has vastly reduced the time needed for identification of Mycobacterium tuberculosis in particular, when compared with traditional culture-based techniques. Molecular methods may also yield antimicrobial susceptibility results through testing for the most common resistance-inducing mutations to some of the antimicrobial agents of choice. However, the diversity of resistance mutations already characterised suggests that these currently-available molecular detection systems should be accompanied by culture-based susceptibility testing. This review compares the efficacy of microscopic, phenotypic, proteomic and genotypic methods available for mycobacterial diagnosis. The diversity of methods currently in use reflects the complexity of this area of diagnostic microbiology.

Phage-based detection of bacterial pathogens

Bacterial pathogens cause significant morbidity and mortality annually to both humans and animals. With the rampant spread of drug resistance and the diminishing effectiveness of current antibiotics, there is a pressing need for effective diagnostics for detection of bacterial pathogens and their drug resistances. Bacteriophages offer several unique opportunities for bacterial detection. This review highlights the means by which bacteriophages have been utilized to achieve and facilitate specific bacterial detection.

Phage-based platforms for the clinical detection of human bacterial pathogens

Bacteriophages (phages) have been utilized for decades as a means for uniquely identifying their target bacteria. Due to their inherent natural specificity, ease of use, and straightforward production, phage possess a number of desirable attributes which makes them particularly suited as bacterial detectors. As a result, extensive research has been conducted into the development of phage, or phage-derived products to expedite the detection of human pathogens. However, very few phage-based diagnostics have transitioned from the research lab into a clinical diagnostic tool. Herein we review the phage-based platforms that are currently used for the detection of Mycobacterium tuberculosis, Yersinia pestis, Bacillus anthracis and Staphylococcus aureus in the clinical field. We briefly describe the disease, the current diagnostic options, and the role phage diagnostics play in identifying the cause of infection, and determining antibiotic susceptibility.

Rapid identification of Mycobacterium tuberculosis complex by a novel hybridization signal amplification method based on self-assembly of DNA-streptavidin nanoparticles

Rapid detection of Mycobacterium tuberculosis complex (MTBC) is a critical step in controlling tuberculosis (TB). In this study, we used IS6110 as the specific identification target to develop a novel hybridization signal amplification method (HSAM) for the rapid and direct detection of MTBC from clinical sputum specimens. This system consists of magnetic bead-linked capture probes for target isolation, dextran-based nanoparticles for amplifying the reporter molecule (biotinylated-FITC), and detection probes (2B-DNA) for binding the nanoparticles. Both the capture and detection probes were specific to the IS6110 target sequence. Our results determined that as few as 10 copies of the IS6110 sequence or 10 M. tuberculosis bacteria could be detected, indicating that the HSAM assay is as sensitive as conventional PCR, and the assay was specific enough to distinguish MTBC from nontuberculosis mycobacteria (NTM). A total of 176 clinical sputum specimens were collected for HSAM evaluation, and the results were compared to those from traditional culture and biochemical identification techniques. This assay had a sensitivity of 88.3%, a specificity of 91.8%, a positive predictive value of 93.8% and a negative predictive value of 84.8% for the detection of MTBC. This technique is highly sensitive and specific, is easy to perform, and does not require any sophisticated detection equipment; thus, this approach has great potential in clinical TB detection and diagnostic applications.

Clinical evaluation of the mycobacteriophage-based assay in rapid detection of Mycobacterium tuberculosis in respiratory specimens

CONTEXT

Search for a cost-effective, rapid and accurate test has renewed interest in mycobacteriophage as a tool in the diagnosis of tuberculosis (TB). There has been no reported data on the performance of phage assay in a high burden, low-resource setting like Kanpur city, India.

AIMS

To assess the sensitivity and specificity of the FASTPlaque TB kit ability to impact the bacillary load in the phage assay and its performance in the sputum smear sample negative cases.

MATERIALS AND METHODS

The study involved a cross-sectional blinded assessment of phage assay using the FASTPlaque TB kit on 68 suspected cases of pulmonary TB against sputum smear microscopy by Ziehl-Neilsen staining and culture by the LJ method.

RESULTS

The sensitivity, specificity and positive and negative predictive values of the phage assay were 90.7, 96, 97.5 and 85.7%, respectively. The assay was negative in all the five specimens growing mycobacteria other than TB. The sensitivity of the phage assay tended to decrease with the bacillary load. Of the smear-negative cases, three were false negative, and all of which were detected by the phage assay. Smear microscopy (three smears per patient) had a sensitivity and specificity of 93 and 64%, respectively.

CONCLUSIONS

The phage assay has the potential clinical utility as a simple means of rapid and accurate detection of live Mycobacterium tuberculosis bacilli; however, its performance has been inconsistent across various studies, which highlights that the assay requires a high degree of quality control demanding infrastructure and its performance is vulnerable to common adversities observed in "out of research" practice settings like storage, transport and cross-contamination.

Multidrug-resistant and extensively drug-resistant Mycobacterium tuberculosis: epidemiology and control

The emergence of multidrug-resistant (MDR)-TB and, more recently, of extensively drug-resistant (XDR)-TB is a real threat to achieve TB control and elimination. Over 400,000 new cases of MDR-TB occur each year and, although their number is currently unknown, XDR cases are recognized in every setting where there has been the capacity to detect them. The long-term vision for the full control of MDR-TB requires the scaling-up of culture and drug-susceptibility testing capacity, which is very limited in disease-endemic countries, and the expanded use of high-technology assays for rapid determination of resistance. MDR cases are treatable and well designed regimens, largely based on second-line anti-TB drugs, can considerably improve cure rates. However, treatment regimens need to be markedly improved through the introduction of less toxic and more powerful drugs, thus reducing duration of treatment and tolerability. This is of utmost importance for XDR-TB cases. The prevalence of MDR-TB and XDR-TB are inversely correlated with the quality of TB control and the proper use of second-line anti-TB drugs. Adherence to proper standards of care and control is imperative and a top priority of all TB control efforts. However, the risk of an uncontrollable epidemic of MDR- and XDR-TB is real considering current levels of financing and commitment to care.

Facing the crisis: improving the diagnosis of tuberculosis in the HIV era

Although the human immunodeficiency virus (HIV) infection pandemic has had a catastrophic impact on tuberculosis (TB) control efforts, especially in sub-Saharan Africa, most of the fundamental concepts reflected in the directly observed treatment, short course (DOTS) strategy still hold true in the HIV era. What has changed, and dramatically, is the importance of speedy and accurate TB diagnosis and the difficulty of achieving this. The disproportionate amount of smear-negative disease in sub-Saharan Africa, which shoulders two-thirds of the global burden of HIV infection and acquired immunodeficiency syndrome, has greatly complicated TB case detection and disease control. Now, 15 years after TB rates began to soar in countries where HIV infection is prevalent, we have learned that the conventional approach -- passively waiting for patients with advanced symptomatic disease to make their way to microscopy centers for diagnosis -- has disastrous consequences. Without better diagnostic tools for TB and effective strategies for their implementation, transmission will not be interrupted, mortality will not be checked, and TB will not be controlled in areas where HIV infection is prevalent. Fortunately, a number of technical opportunities exist for the creation of improved diagnostic tests. Developing and exploiting such tests to support TB control in HIV-infected populations is an urgent priority. A substantial public sector effort is under way to work in partnership with the biotechnology industry to accelerate progress toward that goal. In this article, we will define the need for better TB tests and describe technologies being developed to meet that need.

Diagnosis of tuberculous meningitis: clinical and laboratory parameters

BACKGROUND

Confirming the clinical suspicion of tuberculous meningitis (TBM) has always been problematic. Whilst smear and culture positivity are diagnostic, these tests have low sensitivity. The polymerase chain reaction (PCR) assay has given variable results.

AIM

This study attempted to improve the diagnostic yield by: (a) increasing the cerebrospinal fluid (CSF) volumes; (b) testing the yield from three specimens of CSF assumed to represent lumbar, cervico-thoracic cord, and base of brain CSF samples; (c) undertaking PCR assays using multiple primer sets; and (d) using real-time PCR.

METHOD

Patients suspected of having cranial or spinal meningeal tuberculosis were entered into the study. Three aliquots of CSF were subjected to smear, culture, and conventional and real-time PCR. Three sets of primers - IS6110, MPB64, and PT8/9 - were used. Patients were retrospectively classified into four categories: 'definite TB' (culture positive), 'probable TB' (clinical and other tests suggestive of TB), 'not TB', and 'uncertain diagnosis'.

RESULTS

A total of 68 patients were studied. There were 20 patients classified as definite TB, 24 probable TB, 17 not TB, and seven uncertain diagnosis. Forty-eight of 57 (84.2%) patients tested were HIV seropositive. The IS6110 PCR was positive in 27 patients which included 18/20 culture positive cases, six in the probable TB group, and three in the not TB group. The MPB64 and PT8/9 primers did not increase the yield. Real-time PCR was positive in seven additional patients. Combining the definite and probable TB, the sensitivity of all PCR assays was 70.5% (31/44) and specificity 87.5% (21/24).

CONCLUSION

Targeting multiple sites of the TB genome using conventional PCR did not increase the number of positive cases. Real-time PCR was more sensitive. However, all the current techniques are still too insensitive to confidently exclude the diagnosis on laboratory grounds.

Bacteriophage- based tests for the detection of Mycobacterium tuberculosis in clinical specimens: a systematic review and meta- analysis

Background

Sputum microscopy, the most important conventional test for tuberculosis, is specific in settings with high burden of tuberculosis and low prevalence of non tuberculous mycobacteria. However, the test lacks sensitivity. Although bacteriophage-based tests for tuberculosis have shown promising results, their overall accuracy has not been systematically evaluated.

Methods

We did a systematic review and meta-analysis of published studies to evaluate the accuracy of phage-based tests for the direct detection of M. tuberculosis in clinical specimens. To identify studies, we searched Medline, EMBASE, Web of science and BIOSIS, and contacted authors, experts and test manufacturers. Thirteen studies, all based on phage amplification method, met our inclusion criteria. Overall accuracy was evaluated using forest plots, summary receiver operating (SROC) curves, and subgroup analyses.

Results

The data suggest that phage-based assays have high specificity (range 0.83 to 1.00), but modest and variable sensitivity (range 0.21 to 0.88). The sensitivity ranged between 0.29 and 0.87 among smear-positive, and 0.13 to 0.78 among smear-negative specimens. The specificity ranged between 0.60 and 0.88 among smear-positive and 0.89 to 0.99 among smear-negative specimens. SROC analyses suggest that overall accuracy of phage-based assays is slightly higher than smear microscopy in direct head-to-head comparisons.

Conclusion

Phage-based assays have high specificity but lower and variable sensitivity. Their performance characteristics are similar to sputum microscopy. Phage assays cannot replace conventional diagnostic tests such as microscopy and culture at this time. Further research is required to identify methods that can enhance the sensitivity of phage-based assays without compromising the high specificity.

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.

Childhood tuberculosis and its early diagnosis

Traditional methods for laboratory diagnosis of tuberculosis are unsatisfactory, especially for children, in whose specimens mycobacteria are usually sparse. Recent changes in tuberculosis epidemiology in developed countries, including a large increase in incidence in children from certain ethnic minorities, have prompted interest in newer diagnostic methods. Liquid-based culture detection systems offer improved sensitivity and speed of diagnosis, although the time taken for detection of growth is still upwards of 1 week. Nucleic acid amplification techniques offer more rapid results, but perform best on smear-positive samples; sensitivities may be as low as 50% in smear-negative specimens. Although these newer techniques are widely used in some developed countries, in others, they are not perceived as offering sufficient benefit to justify their routine use. The diagnostic accuracy of mycobacteriophage and serologic methods is insufficient to justify their wide use even in developing countries. Despite recent developments, there is still no panacea for diagnosis of childhood tuberculosis.

A review of tuberculosis: reflections on the past, present and future of a global epidemic disease

Tuberculosis remains the leading cause of death worldwide from a single infectious organism. Approximately 32% of the world's population is infected and an estimated two million people die annually from this treatable disease. Over the past 50 years, with medical treatment and standard public health practices, tuberculosis diminished in developed countries and resulted in a loss of interest and funding for research in improving diagnostic and treatment options. In developing countries, efforts including BCG vaccination have failed to control tuberculosis and the disease continues to spread as the world becomes more globalized. At the same time, multidrug resistant tuberculosis has emerged, challenging even the most advance treatment centers. Better diagnostic techniques, control measures and treatment options are desperately needed but advances require worldwide commitment to battle this age-old disease.