Enumeration of tubercle bacilli in sputum of patients with pulmonary tuberculosis

Microfluidic systems for infectious disease diagnostics

Microorganisms, encompassing both uni- and multicellular entities, exhibit remarkable diversity as omnipresent life forms in nature. They play a pivotal role by supplying essential components for sustaining biological processes across diverse ecosystems, including higher host organisms. The complex interactions within the human gut microbiota are crucial for metabolic functions, immune responses, and biochemical signalling, particularly through the gut-brain axis. Viruses also play important roles in biological processes, for example by increasing genetic diversity through horizontal gene transfer when replicating inside living cells. On the other hand, infection of the human body by microbiological agents may lead to severe physiological disorders and diseases. Infectious diseases pose a significant burden on global healthcare systems, characterized by substantial variations in the epidemiological landscape. Fast spreading antibiotic resistance or uncontrolled outbreaks of communicable diseases are major challenges at present. Furthermore, delivering field-proven point-of-care diagnostic tools to the most severely affected populations in low-resource settings is particularly important and challenging. New paradigms and technological approaches enabling rapid and informed disease management need to be implemented. In this respect, infectious disease diagnostics taking advantage of microfluidic systems combined with integrated biosensor-based pathogen detection offers a host of innovative and promising solutions. In this review, we aim to outline recent activities and progress in the development of microfluidic diagnostic tools. Our literature research mainly covers the last 5 years. We will follow a classification scheme based on the human body systems primarily involved at the clinical level or on specific pathogen transmission modes. Important diseases, such as tuberculosis and malaria, will be addressed more extensively.

Rapid Diagnosis of Drug-Resistant Tuberculosis-Opportunities and Challenges

Global tuberculosis (TB) eradication is undermined by increasing prevalence of emerging resistance to available drugs, fuelling ongoing demand for more complex diagnostic and treatment strategies. Early detection of TB drug resistance coupled with therapeutic decision making guided by rapid characterisation of pre-treatment and treatment emergent resistance remains the most effective strategy for averting Drug-Resistant TB (DR-TB) transmission, reducing DR-TB associated mortality, and improving patient outcomes. Solid- and liquid-based mycobacterial culture methods remain the gold standard for Mycobacterium tuberculosis (MTB) detection and drug susceptibility testing (DST). Unfortunately, delays to result return, and associated technical challenges from requirements for specialised resource and capacity, have limited DST use and availability in many high TB burden resource-limited countries. There is increasing availability of a variety of rapid nucleic acid-based diagnostic assays with adequate sensitivity and specificity to detect gene mutations associated with resistance to one or more drugs. While a few of these assays produce comprehensive calls for resistance to several first- and second-line drugs, there is still no endorsed genotypic drug susceptibility test assay for bedaquiline, pretomanid, and delamanid. The global implementation of regimens comprising these novel drugs in the absence of rapid phenotypic drug resistance profiling has generated a new set of diagnostic challenges and heralded a return to culture-based phenotypic DST. In this review, we describe the available tools for rapid diagnosis of drug-resistant tuberculosis and discuss the associated opportunities and challenges.

New Insights into Biomarkers for Evaluating Therapy Efficacy in Pulmonary Tuberculosis: A Narrative Review

Evaluating therapy efficacy is crucial for patients with tuberculosis (TB), especially those with drug-resistant tuberculosis (DR-TB). The World Health Organization currently recommends sputum smear and culture as the standard methods for evaluating pulmonary tuberculosis (PTB) therapy efficacy. However, these approaches have limitations including low sensitivity, lengthy culture periods, and susceptibility to contamination. There is an urgent need for dependable biomarkers to evaluate therapy efficacy in patients with PTB. Numerous new biomarkers of Mycobacterium tuberculosis (MTB) and the host have been used in recent studies to evaluate PTB therapy efficacy. A systematic review and update of these biomarkers can facilitate the discovery of novel biomarkers and assessment models, as well as provide a solid scientific basis for alternative indicators of evaluating therapy efficacy. In this review we summarize the recent advancements and limitations of biomarkers used to monitor therapy efficacy, highlighting the importance of utilizing a combination of biomarkers. Although some biomarkers have potential in evaluating the efficacy of therapy in patients with PTB, they also have some limitations. Further research, validation, and optimization are required to identify the most reliable and effective alternative biomarkers and apply them to clinical practice.

Time-to-detection in culture of Mycobacterium tuberculosis: performance for assessing index cases contact-positivity

OBJECTIVES

Time-to-detection (TTD) in culture on liquid media is inversely correlated to bacillary load and should be a contributing factor for assessing tuberculosis transmission. We wanted to assess if TTD was a better alternative than smear status to estimate transmission risk.

METHODS

From October 2015 to June 2022, we retrospectively studied a cohort of index cases (IC) with pulmonary tuberculosis (tuberculosis disease [TD]) from which samples were culture-positive before treatment. We studied the correlation between TTD and contact-positivity (CP) of IC contacts: CP was defined as CP = 1 (CP group) in case of TD or latent tuberculosis infection (LTI) in at least one screened contact of an IC, and CP = 0 otherwise (contact-negativity [CN] group). Univariate and multivariable analyses (logistic regression) were done.

RESULTS

Of the 185 IC, 122 were included, generating 846 contact cases of which 705 were assessed. A transmission event (LTI or TD) was identified in 193 contact cases (transmission rate: 27%). At day 9, 66% and 35% of the IC had their sample positive in culture for CP and CN groups, respectively. Age and TTD ≤9 days were independent criteria of CP (odds ratio 0.97, confidence interval [0.95-0.98], P = 0.002 and odds ratio 3.52, confidence interval [1.59-7.83], P = 0.001, respectively).

CONCLUSION

TTD was a more discriminating parameter than smear status to evaluate the transmission risk of an IC with pulmonary tuberculosis. Therefore, TTD should be considered in the contact-screening strategy around an IC.

Initial immune response after exposure to Mycobacterium tuberculosis or to SARS-COV-2: similarities and differences

Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb) and Coronavirus disease-2019 (COVID-19), whose etiologic agent is severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), are currently the two deadliest infectious diseases in humans, which together have caused about more than 11 million deaths worldwide in the past 3 years. TB and COVID-19 share several aspects including the droplet- and aerosol-borne transmissibility, the lungs as primary target, some symptoms, and diagnostic tools. However, these two infectious diseases differ in other aspects as their incubation period, immune cells involved, persistence and the immunopathological response. In this review, we highlight the similarities and differences between TB and COVID-19 focusing on the innate and adaptive immune response induced after the exposure to Mtb and SARS-CoV-2 and the pathological pathways linking the two infections. Moreover, we provide a brief overview of the immune response in case of TB-COVID-19 co-infection highlighting the similarities and differences of each individual infection. A comprehensive understanding of the immune response involved in TB and COVID-19 is of utmost importance for the design of effective therapeutic strategies and vaccines for both diseases.

Analytical performances of the Xpert MTB/RIF assay using stool specimens to improve the diagnosis of pulmonary tuberculosis in Burkina Faso, a tuberculosis endemic country

Timely diagnosis of Pulmonary Tuberculosis (PTB) is associated with good prognosis, but remains difficult in primary healthcare facilities and particularly in children and patients living with HIV. The aim of this study was to compare the GeneXpert ® MTB/RIF assay (Xpert) performed using a stool sample (3-5 g) and using the first Respiratory Tract Sample (RTS; i.e., sputum, bronchoalveolar or gastric aspirate; as normally done) concomitantly collected from 119 patients with suspected PTB to improve PTB diagnosis in Burkina Faso, a high tuberculosis burden country with limited resources. Overall, microbiological, microscopic and molecular analysis of the 119 first RTS and 119 stool specimens led to Mycobacterium tuberculosis complex detection in 28 patients (23 positive RTS cultures and 5 negative RTS cultures-RTS Xpert positive). When using the 28 clinical confirmed cases as reference standard, the sensitivities of the stool-based and RTS-based Xpert assays were not different (24/28, 85.7%, versus 26/28, 92.86%; p > 0.30), and 22 results were fully concordant. Considering the first RTS culture as the gold standard, the sensitivities of the stool-based and RTS-based Xpert assays to detect PTB in patients with positive RTS culture were 100% (23/23) and 91.3% (21/23), respectively (p >0.05). The stool-based Xpert assay specificity for excluding PTB was 99% (95/96) (compared with 95%, 91/96, when using RTS) and its negative and positive predictive values were 100% (95/95) and 96% (23/24), respectively. Compared with the 23 positive RTS cultures, the incremental yield rates of the RTS-based and stool-based Xpert assays were 4.2% (5/119) and 0.84% (1/119), respectively. Overall, our findings support using the stool-based Xpert assay as an alternative method for earlier PTB diagnosis, when RTS are difficult to obtain.

Adolescent tuberculosis in the ICU

TB is a major concern in the paediatric age group, especially in India. More than 3.33 lakh children between 0 and 14 years of age are affected by TB. Adolescent tuberculosis has been a neglected area and this age group accounts for about 800,000 cases of tuberculosis (TB) cases every year. Information regarding adolescent tuberculosis patient requiring ICU admission/care is very scanty (unlike adult tuberculosis), and the authors believe that the mode of ICU presentation and challenges in adolescents would almost be the same as in adults, although the outcome is generally expected to be better in the adolescent population in view of lesser comorbidities when compared to adults. ARDS, multiorgan dysfunction and meningitis are the most common reasons for admission to ICU. Critically ill patients with TB carry a high mortality and the increased mortality is likely due to multiorgan dysfunction, nosocomial infections and sepsis. Advanced disease with chronic undernourishment influences not just morbidity but mortality as well. Further, the heavy financial burden incurred for ICU care in TB patients with poor expected outcome is a major concern since TB occurs predominantly in low socio-economic populations.

Diagnosis of Chest Wall Tuberculosis Using Fine Needle Aspiration: A Single-Center Experience

Introduction

Minimally invasive diagnosis of chest wall tuberculosis remains a challenge. Fine needle aspiration (FNA) is a simple and safe method of sampling. However, previous studies have shown that conventional tuberculosis tests had poor diagnostic performance in the needle aspirates. With the popularization of molecular detection application, the value of FNA in the diagnosis of chest wall tuberculosis needs to be reevaluated.

Methods

We retrospectively studied patients with suspected chest wall tuberculosis at admission who underwent FNA for diagnosis and reported the diagnostic efficacy of acid-fast bacilli smear, mycobacterial culture, cytology and Xpert MTB/RIF (GeneXpert) when testing FNA specimens. A composite reference standard (CRS) was used as the diagnostic gold standard for this study.

Results

Among 89 included FNA specimens, acid-fast bacilli smear, mycobacterial culture, and GeneXpert were positive in 15 (16.85%), 23 (25.8%), and 61 (68.5%), respectively. Thirty-nine (43.8%) had cytologic features suggestive of tuberculosis. According to CRS, 75 (84.3%) cases were categorized as chest wall tuberculosis, 14 (15.7%) were not diagnosed with tuberculosis. Using CRS as the gold standard, acid-fast bacilli smear, mycobacterial culture, cytology and GeneXpert exhibited sensitivity of 20%, 30.7%, 52% and 81.3%, respectively. Specificity in these four tests was found to be 100%. Sensitivity of GeneXpert was significantly higher than that of smear, culture and cytology, X ₂=66.3, p<0.001.

Conclusion

GeneXpert achieved higher sensitivity as compared to cytology and conventional TB tests in the chest wall FNA specimens. The implementation of GeneXpert may increase the diagnostic efficacy of FNA in the diagnosis of chest wall TB.

Frequent Suboptimal Thermocycler Ramp Rate Usage Negatively Impacts GenoType MTBDRsl VER 2.0 Performance for Second-Line Drug-Resistant Tuberculosis Diagnosis

Strengthening second-line drug-resistant tuberculosis (TB) detection is a priority. GenoType MTBDRplus VER 2.0 performance is reduced with non-recommended ramp rate usage (temperature change speed between PCR cycles); however, ramp rate's effect on GenoType MTBDRsl VER 2.0 (MTBDRsl) performance, is unknown. Fifty-two Xpert MTB/RIF Ultra-positive rifampicin-resistant smear-negative sputa and a Mycobacterium tuberculosis dilution series were tested at a manufacturer-recommended (2.2°C/second) or suboptimal (4.0°C/second) ramp rate. M. tuberculosis-complex-DNA positivity, indeterminates, fluoroquinolone- and second-line injectable-resistance accuracy, banding differences, and, separately, inter-reader variability were assessed. Five (39%) of 13 re-surveyed laboratories did not use the manufacturer-recommended ramp rate. On sputum, 2.2°C/second improved indeterminates versus 4.0°C/second (0 of 52 versus 7 of 51; P = 0.006), incorrect drug-class diagnostic calls (0 of 104 versus 6 of 102; P = 0.013), and incorrect banding calls (0 of 1300 versus 54 of 1275; P < 0.001). Similarly, 2.2°C/second improved valid results [(52 of 52 versus 41 of 51; +21% (P = 0.001)] and banding call inter-reader variability [34 of 1300 (3%) versus 52 of 1300 (4%); P = 0.030]. At the suboptimal ramp rate, false-resistance and false-susceptible calls resulted from wild-type band absence rather than mutant band appearance, resulting in misclassification of moxifloxacin resistance level from high-to-low. Suboptimal ramp rate contributes to poor MTBDRsl performance. Laboratories must ensure that the manufacturer-recommended ramp rate is used.

Utility of monocyte parameters in diagnosing Sputum Smear Negative Pulmonary TB

Background - Smear-negative TB (SNTB) may remain undetected for a long duration and new bio-markers are needed for diagnosis. Our study investigated monocyte parameters in this regard.

Thirty cases each of SNTB, sputum positive cases and healthy controls were included. Full blood count and immune-phenotyping for ‘monocyte parameters’ by flow cytometry were performed using CD45, CD16, CD14, CD64 and HLA-DR The percentage of monocyte subsets and MFI of CD64 and HLA- DR noted and data statistically compared.

The monocyte to lymphocyte ratio, percentage of intermediate monocytes, expression of CD64 on total as well as intermediate monocytes were significantly elevated in cases with SNTB as compared to healthy controls (p value, 0.07, 0.07, 0.001, 0.001 respectively). The cut off value for MFI CD64 on total and intermediate monocyte was >18 and >19.6 respectively.

Thus monocyte parameters can serve as useful biomarkers for diagnosing tuberculosis in the sputum negative group.

Reduction of blood C-reactive protein concentration complements the resolution of sputum bacillary load in patients on anti-tuberculosis therapy

Background

Tuberculosis (TB) is a difficult-to-treat disease requiring the combination of four antibiotics for a minimum of 6 months. Rapid and quantitative biomarkers to monitor treatment response are urgently needed for individual patient management and clinical trials. C-reactive protein (CRP) is often used clinically as a rapid marker of inflammation caused by infection. We assessed the relationship of TB bacillary load and CRP as biomarkers of treatment response.

Methods

Xpert MTB/RIF-confirmed pulmonary TB cases were enrolled for treatment response assessment in Mozambique. Treatment response was measured using the Tuberculosis Molecular Bacterial Load Assay (TB-MBLA) in comparison with standard-of-care Mycobacterium Growth Indicator Tube (MGIT) culture at baseline and at weeks 1, 2, 4, 8, 12, 17, and 26 of treatment. Blood CRP concentration was measured at baseline, week 8, and week 26. Treatment response was defined as increase in MGIT culture time to positivity (TTP), and reduction in TB-MBLA-measured bacillary load and blood CRP concentration.

Results

Out of the 81 screened presumptive TB cases, 69 were enrolled for 6-month treatment follow-up resulting in 94% treatment completion rate. Four participants did not complete TB treatment and 22 participants had missing CRP or TB-MBLA results and were excluded from TB-MBLA-CRP analysis. The remaining 43 participants-median age, 31 years old [interquartile range (IQR): 18-56]; 70% (30/43) male; and 70% (30/43) infected with HIV-were considered for analysis. Culture TTP and bacillary load were inversely correlated, Spearman's r = -0.67, p < 0.0001. Resolution of sputum bacillary load concurred with reduction of blood CRP, r = 0.70, p < 0.0001. At baseline, bacillary load had a median (IQR) of 6.4 (5.5-7.2), which reduced to 2.4 (0.0-2.9) and 0.0 (0.0-0.0) log₁₀ CFU/ml at months 2 and 6 of treatment, respectively. Correspondingly, blood CRP reduced from 1.9 (1.6-2.1) at baseline to 1.3 (0.9-1.7) and 0.4 (0.1-0.8) log₁₀ mg/dl at months 2 and 6 of treatment, respectively. CRP reduction trialed bacteriological resolution at a rate of -0.06 log₁₀ mg/dl compared to a bacillary load of 0.23 log₁₀ CFU/ml per week. Consequently, 14 (33%) and 37 (88%) patients had reduced CRP to normal concentration and bacillary load to zero by the end of treatment, respectively. Pre-treatment CRP concentration and bacillary load, and resolution during treatment were slightly lower in HIV co-infected patients but not significantly different from HIV-uninfected TB patients.

Conclusion

TB-MBLA-measured bacillary load and blood CRP complement each other in response to anti-TB therapy. Slow CRP reduction probably reflects residual TB bacilli in the lung not expectorated in sputum. Combining both measures can improve the accuracy of these biomarkers for monitoring TB treatment response and shorten turnaround time since the results of both assays could be available in 24 h.

Controlling Droplet Marangoni Flows to Improve Microscopy-Based TB Diagnosis

In developing countries, the most common diagnostic method for tuberculosis (TB) is microscopic examination sputum smears. Current assessment requires time-intensive inspection across the microscope slide area, and this contributes to its poor diagnostic sensitivity of ≈50%. Spatially concentrating TB bacteria in a smaller area is one potential approach to improve visual detection and potentially increase sensitivity. We hypothesized that a combination of magnetic concentration and induced droplet Marangoni flow would spatially concentrate Mycobacterium tuberculosis on the slide surface by preferential deposition of beads and TB–bead complexes in the center of an evaporating droplet. To this end, slide substrate and droplet solvent thermal conductivities and solvent surface tension, variables known to impact microfluidic flow patterns in evaporating droplets, were varied to select the most appropriate slide surface coating. Optimization in a model system used goniometry, optical coherence tomography, and microscope images of the final deposition pattern to observe the droplet flows and maximize central deposition of 1 μm fluorescent polystyrene particles and 200 nm nanoparticles (NPs) in 2 μL droplets. Rain-X^® polysiloxane glass coating was identified as the best substrate material, with a PBS-Tween droplet solvent. The use of smaller, 200 nm magnetic NPs instead of larger 1 μm beads allowed for bright field imaging of bacteria. Using these optimized components, we compared standard smear methods to the Marangoni-based spatial concentration system, which was paired with magnetic enrichment using iron oxide NPs, isolating M. bovis BCG (BCG) from samples containing 0 and 10³ to 10⁶ bacilli/mL. Compared to standard smear preparation, paired analysis demonstrated a combined volumetric and spatial sample enrichment of 100-fold. With further refinement, this magnetic/Marangoni flow concentration approach is expected to improve whole-pathogen microscopy-based diagnosis of TB and other infectious diseases.

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.

Mycobacterium tuberculosis clinical isolates carry mutational signatures of host immune environments

Mycobacterium tuberculosis (Mtb) infection results in a spectrum of clinical and histopathologic manifestations. It has been proposed that the environmental and immune pressures associated with different contexts of infection have different consequences for the associated bacterial populations, affecting drug susceptibility and the emergence of resistance. However, there is little concrete evidence for this model. We prospectively collected sputum samples from 18 newly diagnosed and treatment-naïve patients with tuberculosis and sequenced 795 colony-derived Mtb isolates. Mutant accumulation rates varied considerably between different bacilli isolated from the same individual, and where high rates of mutation were observed, the mutational spectrum was consistent with reactive oxygen species-induced mutagenesis. Elevated bacterial mutation rates were identified in isolates from HIV-negative but not HIV-positive individuals, suggesting that they were immune-driven. These results support the model that mutagenesis of Mtb in vivo is modulated by the host environment, which could drive the emergence of variants associated with drug resistance in a host-dependent manner.

Sensor-as-a-Service: Convergence of Sensor Analytic Point Solutions (SNAPS) and Pay-A-Penny-Per-Use (PAPPU) Paradigm as a Catalyst for Democratization of Healthcare in Underserved Communities

In this manuscript, we discuss relevant socioeconomic factors for developing and implementing sensor analytic point solutions (SNAPS) as point-of-care tools to serve impoverished communities. The distinct economic, environmental, cultural, and ethical paradigms that affect economically disadvantaged users add complexity to the process of technology development and deployment beyond the science and engineering issues. We begin by contextualizing the environmental burden of disease in select low-income regions around the world, including environmental hazards at work, home, and the broader community environment, where SNAPS may be helpful in the prevention and mitigation of human exposure to harmful biological vectors and chemical agents. We offer examples of SNAPS designed for economically disadvantaged users, specifically for supporting decision-making in cases of tuberculosis (TB) infection and mercury exposure. We follow-up by discussing the economic challenges that are involved in the phased implementation of diagnostic tools in low-income markets and describe a micropayment-based systems-as-a-service approach (pay-a-penny-per-use-PAPPU), which may be catalytic for the adoption of low-end, low-margin, low-research, and the development SNAPS. Finally, we provide some insights into the social and ethical considerations for the assimilation of SNAPS to improve health outcomes in marginalized communities.

Nanoparticle-Based Biosensing Assay for Universally Accessible Low-Cost TB Detection with Comparable Sensitivity as Culture

Tuberculosis (TB) is the leading cause of death globally, surpassing HIV. Furthermore, multidrug-resistant and extensively drug-resistant TB have become global public health threats. Care of TB patients starts with quality, accessible, and affordable diagnosis. The study presents a novel technique called nanoparticle-based colorimetric biosensing assay (NCBA) based on the principles of magnetically activated cell enrichment. A total of 1108 sputum samples were subjected to sputum smear microscopy (SSM), NCBA, and standard culture. SSM and NCBA were completed in 20 min; culture was completed in 8 weeks. Results show that NCBA has matching sensitivity of 100.0% and specificity of 99.7% compared to the gold standard culture method at a cost of $0.50/test based on Peruvian conditions. Sputum smear microscopy has 63.87% sensitivity compared to culture. NCBA has the potential of being used in local health clinics as it only requires a microscope that is widely available in many rural areas. Because NCBA could detect low levels of bacterial load comparable to culture, it could be used for rapid and early TB-onset detection. The gain in time is critical as TB is airborne and highly infectious, minimizing contact exposure. Early detection could lead to early treatment, while the patient’s immune system is still high. The low cost makes NCBA affordable and accessible to those who need them the most.

Modeling and Simulation of Pretomanid Pharmacodynamics in Pulmonary Tuberculosis Patients

Pretomanid (PA-824) is a nitroimidazole in clinical testing for the treatment of tuberculosis. A population pharmacodynamic model for pretomanid was developed using a Bayesian analysis of efficacy data from two early bactericidal activity (EBA) studies, PA-824-CL-007 and PA-824-CL-010, conducted in Cape Town, South Africa. The two studies included 122 adult male and female participants with newly diagnosed pulmonary tuberculosis who received once daily oral pretomanid doses of either 50, 100, 150, 200, 600, 1,000, or 1,200 mg for 14 days. The structural model described capacity-limited growth and saturable drug-induced bacterial killing with separate rate equations for sputum solid culture colony forming unit (CFU) counts and liquid culture time to positivity (TTP) that were linked through a time constant. The posterior population geometric means and interindividual variability percent coefficients of variation were, respectively; 0.152±0.013 log₁₀ CFU/mL sputum/day and 54%±6% for the maximum kill rate constant, 20.4±1.0 h and 20.8%±0.1% for the time constant of proportionality between the CFU and TTP rate equations, and 770±140 ng/mL and 48%±17% for the pretomanid half-maximum effect plasma concentration. Model simulations showed once daily pretomanid at 100 mg, 200 mg, and 300 mg, attained 58%, 73%, and 80%, respectively, of an expected maximum 14-day EBA of 0.136 log₁₀CFU/mL sputum/day. These results establish a pretomanid exposure-efficacy relationship with dual outcomes for CFU counts and TTP, and with potential applications to dose optimization of pretomanid-containing regimens.

Activity of a Long-Acting Injectable Bedaquiline Formulation in a Paucibacillary Mouse Model of Latent Tuberculosis Infection

The potent antituberculosis activity and long half-life of bedaquiline make it an attractive candidate for use in long-acting/extended-release formulations for the treatment of latent tuberculosis infection (LTBI). Our objective was to evaluate a long-acting injectable (LAI) bedaquiline formulation in a validated paucibacillary mouse model of LTBI.

The potent antituberculosis activity and long half-life of bedaquiline make it an attractive candidate for use in long-acting/extended-release formulations for the treatment of latent tuberculosis infection (LTBI). Our objective was to evaluate a long-acting injectable (LAI) bedaquiline formulation in a validated paucibacillary mouse model of LTBI. Following immunization with Mycobacterium bovis rBCG30, BALB/c mice were challenged by aerosol infection with M. tuberculosis H37Rv. Treatment began 13 weeks after challenge infection with one of the following regimens: an untreated negative-control regimen; positive-control regimens of daily rifampin (10 mg/kg of body weight), once-weekly rifapentine (15 mg/kg) and isoniazid (50 mg/kg), or daily bedaquiline (25 mg/kg); test regimens of one, two, or three monthly doses of LAI bedaquiline at 160 mg/dose (B_LAI-160); and test regimens of daily bedaquiline at 2.67 mg/kg (B_2.67), 5.33 mg/kg (B_5.33), or 8 mg/kg (B₈) to deliver the same total amount of bedaquiline as one, two, or three doses of B_LAI-160, respectively. All drugs were administered orally, except for B_LAI-160 (intramuscular injection). The primary outcome was the decline in M. tuberculosis lung CFU counts during 12 weeks of treatment. The negative- and positive-control regimens performed as expected. One, two, and three doses of B_LAI-160 resulted in decreases of 2.9, 3.2, and 3.5 log₁₀ CFU/lung, respectively, by week 12. Daily oral dosing with B_2.67, B_5.33, and B₈ decreased lung CFU counts by 1.6, 2.8, and 4.1 log₁₀, respectively. One dose of B_LAI-160 exhibited activity for at least 12 weeks. The sustained activity of B_LAI-160 indicates that it shows promise as a short-course LTBI treatment requiring few patient encounters to ensure treatment completion.

[Respiratory isolation in suspected tuberculosis with negative direct sputum examination]

Airborne isolation is the main confinement measure used to limit human-to-human transmission of tuberculosis. If implemented early, precisely as soon as the patient is clinically diagnosed with tuberculosis, this measure will protect the population, particularly the health workers who are exposed. A patient suspected of being infected with tuberculosis can create a difficult situation if microbiological examination of his respiratory secretions is negative. This is a complex laboratory technique and sensitivity varies from one test to another. Thus, a false negative result is possible; meaning that a patient can have positive results on a microbiological culture performed later. This patient would still have low, but not no, contagiousness as long as a treatment has not been initiated. This situation can extend the period of respiratory isolation while further diagnostic investigations are carried out. This extended isolation can reduce the quality of health care delivered and patients can show signs of depression and anxiety. The use in routine clinical investigation of gene amplification tools should allow a rethinking of respiratory isolation rules. These tools, which are very sensitive and with a short reporting time, could drastically reduce the duration of respiratory isolation for patients suspected of being infected with tuberculosis.

Diagnostic value of bronchoalveolar lavage in the subset of patients with negative sputum/smear and mycobacterial culture and a suspicion of pulmonary tuberculosis

BACKGROUND

The diagnostic value of bronchoalveolar lavage in patients with negative sputum/smear for tuberculous bacilli has been well studied. However, its value in the subset of patients with both negative sputum/smear and culture is seldom reported.

METHODS

A retrospective study of patients referred for diagnostic bronchoscopy for the suspicion of pulmonary tuberculosis during the period from April 1st, 2015 to March 30th, 2016, and who had negative sputum/smear and culture for tuberculous bacilli.

RESULTS

One hundred and ninety patients fulfilled the inclusion criteria. Bronchoalveolar lavage detected further 61/190 (32.1%) pulmonary tuberculosis cases. Bronchoalveolar lavage mycobacterial culture and polymerase chain reaction (positive in 60/190 (31.6%) and 58/190 (30.5%) of patients respectively) provided the highest diagnostic yield, whereas direct smear provided the lowest yield. Bronchoalveolar lavage had a sensitivity of 89.7%, a specificity of 100%, a positive predictive value of 100%, a negative predictive value of 94.6%, and a test accuracy of 96.3% in suspected pulmonary tuberculosis cases with negative sputum/smear and culture. Positive bronchoalveolar lavage yield for tuberculosis was significantly associated with a positive QuantiFERON-TB Gold In-Tube test, positive purified protein derivative skin test, radiological evidence of upper zone abnormality and patient's origin being from the Indian subcontinent.

CONCLUSION

Bronchoalveolar lavage should be pursued as a useful diagnostic tool for suspected pulmonary tuberculosis cases when sputum/smear and culture are negative. Its value is higher in the subset of patients with positive QuantiFERON-TB Gold In-Tube test, positive purified protein derivative skin test, upper zone abnormality on radiograph or being from the Indian subcontinent.

Development of a high sensitivity TaqMan-based PCR assay for the specific detection of Mycobacterium tuberculosis complex in both pulmonary and extrapulmonary specimens

Tuberculosis (TB) causes a heavy health burden worldwide, especially in developing countries. The need for the rapid and accurate diagnosis of TB has not been satisfied, especially for extra-pulmonary specimens or specimens with acid fast stain (AFS)-negative condition. Development and validation of a novel, sensitive and specific assay for diagnosing TB is essential. We developed IS4 primer/probe based on insertion sequence 6110 (IS6110). A qPCR assay was designed for detecting a specific region in IS6110 by BLAST. The IS4 primer/probe concentration, qPCR efficiency and various of PCR additives were evaluated and optimized. Thirty-four species of commonly isolated microorganisms were used for evaluating the analytical specificity. Moreover, 130 clinical specimens were collected for evaluating the performance versus Cobas TaqMan MTB (CTM) assay kit and culture. The amplification efficiencies of IS4 were 99.61% and 102.61% without and with internal control DNA (Bacteriophage Lambda), respectively. Dimethyl sulfoxide outperformed glycerol or BSA for eliciting the most effective amplification and the lowest limit of detection. In evaluating the clinical performance, various specimen types were collected. IS4 demonstrated a high degree of agreement (kappa = 0.71) with CTM. The clinical sensitivity and specificity of IS4 and CTM were 92.11% (35/38), 82.61% (76/92), 84.21% (32/38) and 95.65% (88/92), respectively. The clinical sensitivity and specificity of IS4 were similar for both pulmonary [92.00% (23/25) and 76.92% (30/39), respectively] and extrapulmonary [92.31% (12/13) and 86.79% (46/53), respectively] specimens. Among AFS-negative cases, the clinical sensitivity and specificity remained 90.48% (19/21) and 83.91% (73/87), respectively, with culture as the gold standard. We concluded that IS4, a new primer/probe pair for TaqMan based qPCR assay, was developed, optimized, and validated for the sensitive and specific detection of TB among various specimen types. The performance was not compromised under AFS-negative conditions.

A new DNA sensor system for specific and quantitative detection of mycobacteria

In the current study, we describe a novel DNA sensor system for specific and quantitative detection of mycobacteria, which is the causative agent of tuberculosis. Detection is achieved by using the enzymatic activity of the mycobacterial encoded enzyme topoisomerase IA (TOP1A) as a biomarker. The presented work is the first to describe how the catalytic activities of a member of the type IA family of topoisomerases can be exploited for specific detection of bacteria. The principle for detection relies on a solid support anchored DNA substrate with dual functions namely: (1) the ability to isolate mycobacterial TOP1A from crude samples and (2) the ability to be converted into a closed DNA circle upon reaction with the isolated enzyme. The DNA circle can act as a template for rolling circle amplification generating a tandem repeat product that can be visualized at the single molecule level by fluorescent labelling. This reaction scheme ensures specific, sensitive, and quantitative detection of the mycobacteria TOP1A biomarker as demonstrated by the use of purified mycobacterial TOP1A and extracts from an array of non-mycobacteria and mycobacteria species. When combined with mycobacteriophage induced lysis as a novel way of effective yet gentle extraction of the cellular content from the model Mycobacterium smegmatis, the DNA sensor system allowed detection of mycobacteria in small volumes of cell suspensions. Moreover, it was possible to detect M. smegmatis added to human saliva. Depending on the composition of the sample, we were able to detect 0.6 or 0.9 million colony forming units (CFU) per mL of mycobacteria, which is within the range of clinically relevant infection numbers. We, therefore, believe that the presented assay, which relies on techniques that can be adapted to limited resource settings, may be the first step towards the development of a new point-of-care diagnostic test for tuberculosis.

Nanoparticle-Based Biosensing of Tuberculosis, an Affordable and Practical Alternative to Current Methods

Access to community-based point-of-care, low-cost, and sensitive tuberculosis (TB) diagnostics remains an unmet need. Objective: The objective of this study was to combine principles in nanotechnology, TB biology, glycochemistry, and engineering, for the development of a nanoparticle-based colorimetric biosensing assay (NCBA) to quickly and inexpensively detect acid-fast bacilli (AFB) in sputum samples. Methods: In NCBA, the isolation of AFB from sputum samples was accomplished through glycan-coated magnetic nanoparticles (GMNP) interacting with AFB and then using a simple magnet to separate the GMNP-AFB complex. Acid-fastness and cording properties of mycobacteria were utilized to provide visually observable red-stained clumps of bacteria that were surrounded by brown nanoparticles under a light microscope on prepared smears. The NCBA technique was compared against sputum smear microscopy (SSM) and Xpert MTB/RIF in 500 samples from patients that were suspected to have TB. Results: Statistical analysis showed that NCBA had sensitivity and specificity performances in perfect agreement with Xpert MTB/RIF as gold standard for all 500 samples. SSM had a sensitivity of 40% for the same samples. Conclusion: NCBA technique yielded full agreement in terms of sensitivity and specificity with the Xpert MTB/RIF in 500 samples. The method is completed in 10–20 min through a simple process at an estimated cost of $0.10 per test. Implementation of NCBA in rural communities would help to increase case finding and case notification, and would support programs against drug-resistance. Its use at the first point-of-contact by patients in the healthcare system would facilitate quick treatment in a single clinical encounter, thus supporting the global “End TB Strategy” by 2035.

Pre-immigration Screening for Tuberculosis in South Korea: A Comparison of Smear- and Culture-Based Protocols

BACKGROUND

Tuberculosis (TB) is the most important disease screened for upon patient history review during preimmigration medical examinations as performed in South Korea in prospective immigrants to certain Western countries. In 2007, the U.S. Centers for Disease Control and Prevention (CDC) changed the TB screening protocol from a smear-based test to the complete Culture and Directly Observed Therapy Tuberculosis Technical Instructions (CDOT TB TI) for reducing the incidence of TB in foreign-born immigrants.

METHODS

This study evaluated the effect of the revised (as compared with the old) protocol in South Korea.

RESULTS

Of the 40,558 visa applicants, 365 exhibited chest radiographic results suggestive of active or inactive TB, and 351 underwent sputum tests (acid-fast bacilli smear and Mycobacterium tuberculosis culture). To this end, using the CDOT TB TI, 36 subjects (88.8 per 10⁵ of the population) were found to have TB, compared with only seven using the older U.S. CDC technical instruction (TI) (p<0.001). In addition, there were six drug-resistant cases which were identified (16.7 per 10⁵ of the population), two of whom had multidrug-resistance (5.6 per 10⁵ of the population).

CONCLUSION

The culture-based 2007 TI identified a great deal of TB cases current to the individuals tested, as compared to older U.S. CDC TI.

PD-1 Expression on Mycobacterium tuberculosis-Specific CD4 T Cells Is Associated With Bacterial Load in Human Tuberculosis

Persistent antigen stimulation in chronic infections has been associated with antigen-specific T cell dysfunction and upregulation of inhibitory receptors, including programmed cell death protein 1 (PD-1). Pulmonary tuberculosis (TB) disease is characterized by high levels of Mycobacterium tuberculosis (Mtb), yet the relationship between bacterial load, PD-1 expression, and Mtb-specific T cell function in human TB has not been well-defined. Using peripheral blood samples from adults with LTBI and with pulmonary TB disease, we tested the hypothesis that PD-1 expression is associated with bacterial load and functional capacity of Mtb-specific T cell responses. We found that PD-1 was expressed at significantly higher levels on Th1 cytokine-producing Mtb-specific CD4 T cells from patients with smear-positive TB, compared with smear-negative TB and LTBI, which decreased after completion of anti-TB treatment. By contrast, expression of PD-1 on Mtb-specific CD8 T cells was significantly lower than on Mtb-specific CD4 T cells and did not differ by Mtb infection and disease status. In vitro stimulation of PBMC with Mtb antigens demonstrated that PD-1 is induced on proliferating Mtb-specific CD4 T cells and that Th1 cytokine production capacity is preferentially maintained within PD-1⁺ proliferating CD4 T cells, compared with proliferating Mtb-specific CD4 T cells that lack PD-1 expression. Together, these data indicate that expression of PD-1 on Mtb-specific CD4 T cells is indicative of mycobacterial antigen exposure and identifies a population of effector cells with Th1 cytokine production capacity. These studies provide novel insights into the role of the PD-1 pathway in regulating CD4 and CD8 T cell responses in Mtb infection and provide rationale for future studies to evaluate PD-1 expression on antigen-specific CD4 T cells as a potential biomarker for bacterial load and treatment response in human TB.

Widespread use of incorrect PCR ramp rate negatively impacts multidrug-resistant tuberculosis diagnosis (MTBDRplus)

The scale-up of rapid drug resistance testing for TB is a global priority. MTBDRplus is a WHO-endorsed multidrug-resistant (MDR)-TB PCR assay with suboptimal sensitivities and high indeterminate rates on smear-negative specimens. We hypothesised that widespread use of incorrect thermocycler ramp rate (speed of temperature change between cycles) impacts performance. A global sample of 72 laboratories was surveyed. We tested 107 sputa from Xpert MTB/RIF-positive patients and, separately, dilution series of bacilli, both at the manufacturer-recommended ramp rate (2.2 °C/s) and the most frequently reported incorrect ramp rate (4.0 °C/s). Mycobacterium tuberculosis-complex DNA (TUB-band)-detection, indeterminate results, accuracy, and inter-reader variability (dilution series only) were compared. 32 respondents did a median (IQR) of 41 (20-150) assays monthly. 78% used an incorrect ramp rate. On smear-negative sputa, 2.2 °C/s vs. 4.0 °C/s improved TUB-band positivity (42/55 vs. 32/55; p = 0.042) and indeterminate rates (1/42 vs. 5/32; p = 0.039). The actionable results (not TUB-negative or indeterminate; 41/55 vs. 28/55) hence improved by 21% (95% CI: 9-35%). Widespread use of incorrect ramp rate contributes to suboptimal MTBDRplus performance on smear-negative specimens and hence limits clinical utility. The number of diagnoses (and thus the number of smear-negative patients in whom DST is possible) will improve substantially after ramp rate correction.

Pulmonary Tuberculosis: Role of Radiology in Diagnosis and Management

Tuberculosis is a public health problem worldwide, including in the United States-particularly among immunocompromised patients and other high-risk groups. Tuberculosis manifests in active and latent forms. Active disease can occur as primary tuberculosis, developing shortly after infection, or postprimary tuberculosis, developing after a long period of latent infection. Primary tuberculosis occurs most commonly in children and immunocompromised patients, who present with lymphadenopathy, pulmonary consolidation, and pleural effusion. Postprimary tuberculosis may manifest with cavities, consolidations, and centrilobular nodules. Miliary tuberculosis refers to hematogenously disseminated disease that is more commonly seen in immunocompromised patients, who present with miliary lung nodules and multiorgan involvement. The principal means of testing for active tuberculosis is sputum analysis, including smear, culture, and nucleic acid amplification testing. Imaging findings, particularly the presence of cavitation, can affect treatment decisions, such as the duration of therapy. Latent tuberculosis is an asymptomatic infection that can lead to postprimary tuberculosis in the future. Patients who are suspected of having latent tuberculosis may undergo targeted testing with a tuberculin skin test or interferon-γ release assay. Chest radiographs are used to stratify for risk and to assess for asymptomatic active disease. Sequelae of previous tuberculosis that is now inactive manifest characteristically as fibronodular opacities in the apical and upper lung zones. Stability of radiographic findings for 6 months distinguishes inactive from active disease. Nontuberculous mycobacterial disease can sometimes mimic the findings of active tuberculosis, and laboratory confirmation is required to make the distinction. Familiarity with the imaging, clinical, and laboratory features of tuberculosis is important for diagnosis and management. ^©RSNA, 2017.

Comparison of sputum collection methods for tuberculosis diagnosis: a systematic review and pairwise and network meta-analysis

BACKGROUND

The performance of laboratory tests to diagnose pulmonary tuberculosis is dependent on the quality of the sputum sample tested. The relative merits of sputum collection methods to improve tuberculosis diagnosis are poorly characterised. We therefore aimed to investigate the effects of sputum collection methods on tuberculosis diagnosis.

METHODS

We did a systematic review and meta-analysis to investigate whether non-invasive sputum collection methods in people aged at least 12 years improve the diagnostic performance of laboratory testing for pulmonary tuberculosis. We searched PubMed, Google Scholar, ProQuest, Web of Science, CINAHL, and Embase up to April 14, 2017, to identify relevant experimental, case-control, or cohort studies. We analysed data by pairwise meta-analyses with a random-effects model and by network meta-analysis. All diagnostic performance data were calculated at the sputum-sample level, except where authors only reported data at the individual patient-level. Heterogeneity was assessed, with potential causes identified by logistic meta-regression.

FINDINGS

We identified 23 eligible studies published between 1959 and 2017, involving 8967 participants who provided 19 252 sputum samples. Brief, on-demand spot sputum collection was the main reference standard. Pooled sputum collection increased tuberculosis diagnosis by microscopy (odds ratio [OR] 1·6, 95% CI 1·3-1·9, p<0·0001) or culture (1·7, 1·2-2·4, p=0·01). Providing instructions to the patient before sputum collection, during observed collection, or together with physiotherapy assistance increased diagnostic performance by microscopy (OR 1·6, 95% CI 1·3-2·0, p<0·0001). Collecting early morning sputum did not significantly increase diagnostic performance of microscopy (OR 1·5, 95% CI 0·9-2·6, p=0·2) or culture (1·4, 0·9-2·4, p=0·2). Network meta-analysis confirmed these findings, and revealed that both pooled and instructed spot sputum collections were similarly effective techniques for increasing the diagnostic performance of microscopy.

INTERPRETATION

Tuberculosis diagnoses were substantially increased by either pooled collection or by providing instruction on how to produce a sputum sample taken at any time of the day. Both interventions had a similar effect to that reported for the introduction of new, expensive laboratory tests, and therefore warrant further exploration in the drive to end the global tuberculosis epidemic.

FUNDING

Wellcome Trust, Joint Global Health Trials consortium, Innovation For Health and Development, and Bill & Melinda Gates Foundation.

Mycobacterial Cultures Contain Cell Size and Density Specific Sub-populations of Cells with Significant Differential Susceptibility to Antibiotics, Oxidative and Nitrite Stress

The present study shows the existence of two specific sub-populations of Mycobacterium smegmatis and Mycobacterium tuberculosis cells differing in size and density, in the mid-log phase (MLP) cultures, with significant differential susceptibility to antibiotic, oxidative, and nitrite stress. One of these sub-populations (~10% of the total population), contained short-sized cells (SCs) generated through highly-deviated asymmetric cell division (ACD) of normal/long-sized mother cells and symmetric cell divisions (SCD) of short-sized mother cells. The other sub-population (~90% of the total population) contained normal/long-sized cells (NCs). The SCs were acid-fast stainable and heat-susceptible, and contained high density of membrane vesicles (MVs, known to be lipid-rich) on their surface, while the NCs possessed negligible density of MVs on the surface, as revealed by scanning and transmission electron microscopy. Percoll density gradient fractionation of MLP cultures showed the SCs-enriched fraction (SCF) at lower density (probably indicating lipid-richness) and the NCs-enriched fraction (NCF) at higher density of percoll fractions. While live cell imaging showed that the SCs and the NCs could grow and divide to form colony on agarose pads, the SCF, and NCF cells could independently regenerate MLP populations in liquid and solid media, indicating their full genomic content and population regeneration potential. CFU based assays showed the SCF cells to be significantly more susceptible than NCF cells to a range of concentrations of rifampicin and isoniazid (antibiotic stress), H2O2 (oxidative stress),and acidified NaNO2 (nitrite stress). Live cell imaging showed significantly higher susceptibility of the SCs of SC-NC sister daughter cell pairs, formed from highly-deviated ACD of normal/long-sized mother cells, to rifampicin and H2O2, as compared to the sister daughter NCs, irrespective of their comparable growth rates. The SC-SC sister daughter cell pairs, formed from the SCDs of short-sized mother cells and having comparable growth rates, always showed comparable stress-susceptibility. These observations and the presence of M. tuberculosis SCs and NCs in pulmonary tuberculosis patients' sputum earlier reported by us imply a physiological role for the SCs and the NCs under the stress conditions. The plausible reasons for the higher stress susceptibility of SCs and lower stress susceptibility of NCs are discussed.

De-isolation of patients with pulmonary tuberculosis after start of treatment - clear, unequivocal guidelines are missing

The study review guidelines on isolation of patients with tuberculosis, TB, from the World Health Organization, WHO, Centers for Disease Control and Prevention, CDC, and the European Center for Disease Control, ECDC. The review found that unequivocal guidelines for removing patients out of negative-pressure isolation and de-isolation patients from either single rooms or isolation at home is needed. Studies show that the time of effective treatment is the key parameter to follow to determine if patients are contagious to others or not. This means that standard treatment of multi-drug resistant, MDR, TB will not result in the patient being non-infectious. Thus it is important right from the time of diagnosis to know if the patient is infected with MDR TB or not. Thus the early use of molecular techniques to reveal drug susceptibility is important. Clear guidelines stating if patient with microscopy negative sputum no matter infected with fully susceptible or MDR TB, no matter HIV positive or not is needed.

Challenges in the clinical assessment of novel tuberculosis drugs

To tackle the global TB epidemic effectively, novel treatment strategies are critically needed to shorten the duration of TB therapy and treat drug-resistant TB. Drug development for TB, stymied for decades, has enjoyed a renaissance over the past several years. However, the development of new TB regimens is hindered by the limitations in our understanding and use of preclinical models; the paucity of accurate, early surrogate markers of cure, and challenges in untangling the individual contributions of drugs to multidrug regimens in a complex, multi-compartment disease. Lack of profit motive, advocacy, and imagination has contributed mightily to the dearth of drugs we have on the shelf to treat this ancient disease. Areas that will speed the development of new regimens for TB include novel murine and in vitro pharmacodynamics models, clinical endpoints that are not culture-based, innovative clinical trial designs, and an infusion of much-needed funding.

Analytical and Clinical Evaluation of the Epistem Genedrive Assay for Detection of Mycobacterium tuberculosis

The Epistem Genedrive assay rapidly detects the Mycobacterium tuberculosis omplex from sputum and is currently available for clinical use. However, the analytical and clinical performance of this test has not been fully evaluated. The analytical limit of detection (LOD) of the Genedrive PCR amplification was tested with genomic DNA; the performance of the complete (sample processing plus amplification) system was tested by spiking M. tuberculosismc(2)6030 cells into distilled water andM. tuberculosis-negative sputum. Specificity was tested using common respiratory pathogens and nontuberculosis mycobacteria. A clinical evaluation enrolled adults with suspected pulmonary tuberculosis, obtained three sputum samples from each participant, and compared the accuracy of the Gene drive to that of the Xpert MTB/RIF assay using M. tuberculosiscultures as the reference standard. The Genedrive assay had an LOD of 1 pg/μl (100 genomic DNA copies/reaction). The LODs of the system were 2.5 × 10(4)CFU/ml and 2.5 × 10(5)CFU/ml for cells spiked into water and sputum, respectively. False-positiverpoBprobe signals were observed in 3/32 (9.4%) of the negative controls and also in few samples containing Mycobacterium abscessus,Mycobacterium gordonae, o rMycobacterium thermoresistibile In the clinical study, among 336 analyzed participants, the overall sensitivities for the tuberculosis case detection of Gene drive, Xpert, and smear microscopy were 45.4% (95% confidence interval [CI], 35.2% to 55.8%), 91.8% (95% CI, 84.4% to 96.4%), and 77.3% (95% CI, 67.7% to 85.2%), respectively. The sensitivities of Gene drive and Xpert for the detection of smear-microscopy-negative tuberculosis were 0% (95% CI, 0% to 15.4%) and 68.2% (95% CI, 45.1% to 86.1%), respectively. The Genedrive assay did not meet performance standards recommended by the World Health Organization for a smear microscopy replacement tuberculosis test. Epistem is working on modifications to improve the assay.

Evaluation of Xpert® MTB/RIF Assay in Induced Sputum and Gastric Lavage Samples from Young Children with Suspected Tuberculosis from the MVA85A TB Vaccine Trial

Objective

Diagnosis of childhood tuberculosis is limited by the paucibacillary respiratory samples obtained from young children with pulmonary disease. We aimed to compare accuracy of the Xpert^® MTB/RIF assay, an automated nucleic acid amplification test, between induced sputum and gastric lavage samples from young children in a tuberculosis endemic setting.

Methods

We analyzed standardized diagnostic data from HIV negative children younger than four years of age who were investigated for tuberculosis disease near Cape Town, South Africa [2009–2012]. Two paired, consecutive induced sputa and early morning gastric lavage samples were obtained from children with suspected tuberculosis. Samples underwent Mycobacterial Growth Indicator Tube [MGIT] culture and Xpert MTB/RIF assay. We compared diagnostic yield across samples using the two-sample test of proportions and McNemar’s χ² test; and Wilson’s score method to calculate sensitivity and specificity.

Results

1,020 children were evaluated for tuberculosis during 1,214 admission episodes. Not all children had 4 samples collected. 57 of 4,463[1.3%] and 26 of 4,606[0.6%] samples tested positive for Mycobacterium tuberculosis on MGIT culture and Xpert MTB/RIF assay respectively. 27 of 2,198[1.2%] and 40 of 2,183[1.8%] samples tested positive [on either Xpert MTB/RIF assay or MGIT culture] on induced sputum and gastric lavage samples, respectively. 19/1,028[1.8%] and 33/1,017[3.2%] admission episodes yielded a positive MGIT culture or Xpert MTB/RIF assay from induced sputum and gastric lavage, respectively. Sensitivity of Xpert MTB/RIF assay was 8/30[26.7%; 95% CI: 14.2–44.4] for two induced sputum samples and 7/31[22.6%; 11.4–39.8] [p = 0.711] for two gastric lavage samples. Corresponding specificity was 893/893[100%;99.6–100] and 885/890[99.4%;98.7–99.8] respectively [p = 0.025].

Conclusion

Sensitivity of Xpert MTB/RIF assay was low, compared to MGIT culture, but diagnostic performance of Xpert MTB/RIF did not differ sufficiently between induced sputum and gastric lavage to justify selection of one sampling method over the other, in young children with suspected pulmonary TB.

Trial Registration

ClinicalTrials.gov NCT00953927

Tuberculosis Biomarker Extraction and Isothermal Amplification in an Integrated Diagnostic Device

In this study, we integrated magnetic bead-based sample preparation and isothermal loop mediated amplification (LAMP) of TB in a single tube. Surrogate sputum samples produced by the Program for Appropriate Technology in Health containing inactivated TB bacteria were used to test the diagnostic. In order to test the sample preparation method, samples were lysed, and DNA was manually extracted and eluted into water in the tube. In a thermal cycler, LAMP amplified TB DNA from 103 TB cells/mL of sputum at 53.5 ± 3.3 minutes, 104 cells/mL at 46.3 ± 2.2 minutes, and 105 cells/mL at 41.6 ± 1.9 minutes. Negative control samples did not amplify. Next, sample preparation was combined with in-tubing isothermal LAMP amplification by replacing the water elution chamber with a LAMP reaction chamber. In this intermediate configuration, LAMP amplified 103 cells/mL at 74 ± 10 minutes, 104 cells/mL at 60 ± 9 minutes, and 105 TB cells/mL of sputum at 54 ± 9 minutes. Two of three negative controls did not amplify; one amplified at 100 minutes. In the semi-automated system, DNA was eluted directly into an isothermal reaction solution containing the faster OptiGene DNA polymerase. The low surrogate sputum concentration, 103 TB cells/mL, amplified at 52.8 ± 3.3 minutes, 104 cells/mL at 45.4 ± 11.3 minutes, and 105 cells/mL at 31.8 ± 2.9 minutes. TB negative samples amplified at 66.4 ± 7.4 minutes. This study demonstrated the feasibility of a single tube design for integrating sample preparation and isothermal amplification, which with further development could be useful for point-of-care applications, particularly in a low-resource setting.

Delay in sputum smear conversion and outcomes of smear-positive tuberculosis patients: a retrospective cohort study in Bafoussam, Cameroon

BACKGROUND

In limited resource settings, sputum smear conversion at the end of the intensive phase of tuberculosis treatment is an indicator not only of patients' response to treatment, but also of anti-tuberculosis program performance. The objective of this study was to identify factors associated to sputum smear non-conversion at the end of the intensive phase of treatment, and the effect of smear non-conversion on the outcome of smear-positive pulmonary tuberculosis patients.

METHOD

This retrospective cohort study was carried out on data of patients treated in the Diagnostic and Treatment Centre of Baleng, West-Cameroon from 2006 to 2012. Logistic regression models were used to evaluate the association of socio-demographic and clinical factors with delay in sputum smear conversion, and the association of this delay with treatment outcomes.

RESULT

Out of 1425 smear-positive pulmonary tuberculosis patients treated during the study period, 1286 (90.2%) were included in the analysis. Ninety four (7.3% CI: 6.0- 8.9) patients were identified as non-converted at the end of the intensive phase of treatment. Pre-treatment smears graded 2+ and 3+ were independently associated to delay in smear conversion (p<0.01). Years of treatment ranging from 2009 to 2012 were also associated to delay in smear conversion (p<0.02). Delay in smear conversion was significantly associated to failure [Adjusted Odd Ratio (AOR):12.4 (Confidence Interval: CI 4.0- 39.0)] and death, AOR: 3.6 (CI 1.5- 9.0).

CONCLUSION

Heavy initial bacillary load and treatment years ranging from 2009 to 2012 were associated to sputum smear non-conversion at the end of the intensive phase of TB treatment. Also, delay in smear conversion was associated to unfavorable treatment outcomes. Patients with heavy initial bacillary load should thus be closely monitored and studies done to identify reasons for the high proportion of non-conversion among patients treated between 2009 and 2012.

A Rapid and Sensitive Diagnostic Screening Assay for Detection of Mycobacteria Including Mycobacterium tuberculosis Directly from Sputum without Extraction

We report a novel approach utilising a real-time PCR screening assay targeting a 53 bp tandemly repeated element present at various loci within the Mycobacterium tuberculosis (Mtb) genome. Positive samples were identified within a discriminatory melting curve range of 90–94°C, with results obtained in under one hour directly from decontaminated sputum samples without extraction. A panel of 89 smear-positive sputa were used for analytical validation of the assay with 100% concordance, with sensitivity matching that of culture. Cross reactivity was detected within a narrow range of mycobacteria other than tuberculosis (MOTT) (five sputa, three in silico), with the highest sensitivity within M. avium complex (MAC). A year-long head to head evaluation of the test with the GeneXpert platform was carried out with 104 consecutive samples at the Royal Free Hospital, UK. Receiver operating characteristics (ROC) analysis of the data revealed that the two tests are approximately equivalent in sensitivity, with the area under the curve being 0.85 and 0.80 for the GeneXpert and our assay, respectively, indicating that the test would be a cost effective screen prior to GeneXpert testing.

Relative Versus Absolute Noncontagiousness of Respiratory Tuberculosis on Treatment

Objective:

To assess the validity of current estimates of the noncontagiousness of sputum smear-positive respiratory tuberculosis (TB) on treatment.

Design:

A descriptive analysis of the mycobacteriologic response to treatment.

Setting:

A TB inpatient unit of a Canadian hospital.

Patients:

Thirty-two HIV-seronegative patients with moderate to advanced sputum smear-positive respiratory TB were treated with uninterrupted, directly observed, weight-adjusted isoniazid, rifampin, and pyrazinamide. Each patient's initial isolate was drug susceptible and each patient's sputum mycobacteriology was systematically followed until 3 consecutive sputum smears were negative on 3 separate days.

Results:

The time to smear conversion varied remarkably (range, 8 to 115 days; average, 46 days) and was influenced by sputum sampling frequency. Only 3 patients (9.4%) had smear conversions by 14 days and only 8 (25%) had smear conversions by 21 days, the average time it took for drug susceptibility test results to become available. During the first 21 days of treatment, the semiquantitative sputum smear score decreased rapidly and the time to detection of positive cultures doubled. Within the time to smear conversion, virtually all smear-positive specimens (98%) were culture positive and only 34% of the patients had culture conversions (ie, 3 consecutive negative cultures).

Conclusion:

Current estimates of the noncontagiousness of sputum smear-positive respiratory TB on treatment (for 14 days, for 21 days, or until smear conversion) are estimates of relative noncontagiousness. They do not signal absolute noncontagiousness (culture conversion). Semiquantitative smear and time-to-detection data suggest that respiratory isolation beyond 21 days of optimal treatment should be selective.

Clinical evaluation of tuberculosis viability microscopy for assessing treatment response

Tuberculosis viability microscopy predicted, within 1 hour, quantitative culture results that became available weeks later. Viability microscopy provides promising results for informing decisions concerning drug susceptibility testing, treatment changes, and infection control measures in resource-constrained settings where most tuberculosis occurs.

Background. It is difficult to determine whether early tuberculosis treatment is effective in reducing the infectiousness of patients' sputum, because culture takes weeks and conventional acid-fast sputum microscopy and molecular tests cannot differentiate live from dead tuberculosis.

Methods. To assess treatment response, sputum samples (n = 124) from unselected patients (n = 35) with sputum microscopy–positive tuberculosis were tested pretreatment and after 3, 6, and 9 days of empiric first-line therapy. Tuberculosis quantitative viability microscopy with fluorescein diacetate, quantitative culture, and acid-fast auramine microscopy were all performed in triplicate.

Results. Tuberculosis quantitative viability microscopy predicted quantitative culture results such that 76% of results agreed within ±1 logarithm (r_S = 0.85; P < .0001). In 31 patients with non-multidrug-resistant (MDR) tuberculosis, viability and quantitative culture results approximately halved (both 0.27 log reduction, P < .001) daily. For patients with non-MDR tuberculosis and available data, by treatment day 9 there was a >10-fold reduction in viability in 100% (24/24) of cases and quantitative culture in 95% (19/20) of cases. Four other patients subsequently found to have MDR tuberculosis had no significant changes in viability (P = .4) or quantitative culture (P = .6) results during early treatment. The change in viability and quantitative culture results during early treatment differed significantly between patients with non-MDR tuberculosis and those with MDR tuberculosis (both P < .001). Acid-fast microscopy results changed little during early treatment, and this change was similar for non-MDR tuberculosis vs MDR tuberculosis (P = .6).

Conclusions. Tuberculosis quantitative viability microscopy is a simple test that within 1 hour predicted quantitative culture results that became available weeks later, rapidly indicating whether patients were responding to tuberculosis therapy.

Microscopic examination and smear negative pulmonary tuberculosis in Ethiopia

INTRODUCTION

Tuberculosis causes illness among millions of people each year and ranks as the second leading cause of death from infectious disease worldwide. The aim of this study was to investigate the detection rate of microscopic examination and estimate risk of transmission of TB by smear negative pulmonary TB patients.

METHODS

A cross-sectional study and retrospective data analysis on TB were undertaken in Northwest Shewa, Ethiopia. Microscopic examination, bacterial culture and PCR were performed. The statistical analysis was made by using STATA software version 10.

RESULTS

A total of 92 suspected TB cases was included in the study. Of these, 27.17% (25/92) were positive for microscopic examination and 51% (47/92) for culture. The sensitivity and specificity of microscopic examination with 95% CI were 48.94% (34.08% to 63.93%) and 95.56% (84.82 to 99.33%), respectively. The positive and negative predictive values were 92% (73.93% to 98.78%) and 64.18% (51.53% to 75.53%), respectively. Of 8150 pulmonary TB cases in the retrospective study, 58.9% was smear negative. The proportion of TB-HIV co-infection was 28.66% (96/335).

CONCLUSION

The sensitivity of microscopic examination was 48.94% which was very low. The poor sensitivity of this test together with the advent of HIV/AIDS elevated the prevalence of smear negative pulmonary TB. This in turn increased the risk of TB transmission.

Point-of-care system for detection of Mycobacterium tuberculosis and rifampin resistance in sputum samples

Early detection of Mycobacterium tuberculosis complex (MTBC) and markers conveying drug resistance can have a beneficial impact on preventive public health actions. We describe here a new molecular point-of-care (POC) system, the Genedrive, which is based on simple sample preparation combined with PCR to detect MTBC and simultaneously detect mutation markers in the rpoB gene directly from raw sputum sample. Hybridization probes were used to detect the presence of the key mutations in codons 516, 526, and 531 of the rpoB gene. The sensitivities for MTBC and rpoB detection from sputum samples were assessed using model samples spiked with known numbers of bacteria prepared from liquid cultures of M. tuberculosis. The overall sensitivities were 90.8% (95% confidence interval [CI], 81, 96.5) for MTBC detection and 72.3% (95% CI, 59.8, 82.7) for rpoB detection. For samples containing ≥1,000 CFU/ml, the sensitivities were 100% for MTBC and 85.7% for rpoB detection, while for samples containing ≤100 CFU/ml, the sensitivities were 86.4% and 65.9% for MTBC and rpoB detection, respectively. The specificity was shown to be 100% (95% CI, 83.2, 100) for MTBC and rpoB. The clinical sputum samples were processed using the same protocol and showed good concordance with the data generated from the model. Tuberculosis-infected subjects with smear samples assessed as scanty or negative were detectable by the Genedrive system. In these paucibacillary patients, the performance of the Genedrive system was comparable to that of the GeneXpert assay. The characteristics of the Genedrive platform make it particularly useful for detecting MTBC and rifampin resistance in low-resource settings and for reducing the burden of tuberculosis disease.

Utility of the Xpert MTB/RIF assay for diagnosis of tuberculous meningitis

David Boulware discusses the challenges of diagnosing tuberculous meningitis and the implications of the study by Patel and colleagues using the Xpert MTB/RIF assay for diagnosis. Please see later in the article for the Editors' Summary.

Comparing same day sputum microscopy with conventional sputum microscopy for the diagnosis of tuberculosis--Chhattisgarh, India

BACKGROUND

The World Health Organization (WHO) recommends same day sputum microscopy (spot-spot) in preference to conventional strategy (spot-morning) for the diagnosis of smear positive tuberculosis with the view that completing diagnosis on a single day may be more convenient to the patients and reduce pre-treatment losses to follow-up.

METHODS

We conducted a cross-sectional study in seven selected district level hospitals of Chhattisgarh State, India. During October 2012 - March 2013, two sputum specimens (spot-early morning) were collected from consecutively enrolled adult (≥ 18 years) presumptive TB patients as per current national guidelines. In addition, a second sample was collected (one hour after the collection of first spot sample) from the same patients. All the samples were examined by ziehl-Neelsen (ZN) microscopy. McNemar's test was used to compare statistical differences in the proportion smear positive between the two approaches (spot-spot versus spot-morning).

RESULTS

Of 2551 presumptive TB patients, 69% were male. All patients provided the first spot specimen, 2361 (93%) provided the second spot specimen, and 2435 (96%) provided an early morning specimen. 72% of specimens were mucopurulent in conventional strategy as compared to 60% in same day strategy. The proportion of smear-positive patients diagnosed by same day microscopy was 14%, as compared to 17% by the conventional method (p<0.001). A total of 73 (16.9%) potential cases were missed by the same day method compared to only 2 (0.5%) by the conventional method.

CONCLUSION

Same-day microscopy method missed 17% of smear-positive cases and contrary to prior perception, did not increase the proportion of suspects providing the second sample. These findings call for an urgent need to revisit the WHO recommendation of switching to same-day diagnosis over the current policy.

A new unifying theory of the pathogenesis of tuberculosis

It is set in stone that Mycobacterium tuberculosis is a facultative intracellular bacterial parasite. This axiom drives our knowledge of the host response, the way we design vaccines against the organism by generating protective T cells, and to a lesser extent, the way we try to target anti-microbial drugs. The purpose of this article is to commit total heresy. I believe that M. tuberculosis can equally well be regarded as an extracellular pathogen and may in fact spend a large percentage of its human lung "life-cycle" in this environment. It is of course intracellular as well, but this may well be little more than a brief interlude after infection of a new host during which the bacterium must replicate to increase its chances of transmission and physiologically adapt prior to moving back to an extracellular phase. As a result, by focusing almost completely on just the intracellular phase, we may be making serious strategic errors in the way we try to intervene in this pathogenic process. It is my opinion that when a TB bacillus enters the lungs and starts to reside inside an alveolar macrophage, its central driving force is to switch on a process leading to lung necrosis, since it is only by this process that the local lung tissue can be destroyed and the bacillus can be exhaled and transmitted. I present here a new model of the pathogenesis of the disease that attempts to unify the pathogenic process of infection, disease, persistence [rather than latency], and reactivation.

Risk factors for tuberculosis

The risk of progression from exposure to the tuberculosis bacilli to the development of active disease is a two-stage process governed by both exogenous and endogenous risk factors. Exogenous factors play a key role in accentuating the progression from exposure to infection among which the bacillary load in the sputum and the proximity of an individual to an infectious TB case are key factors. Similarly endogenous factors lead in progression from infection to active TB disease. Along with well-established risk factors (such as human immunodeficiency virus (HIV), malnutrition, and young age), emerging variables such as diabetes, indoor air pollution, alcohol, use of immunosuppressive drugs, and tobacco smoke play a significant role at both the individual and population level. Socioeconomic and behavioral factors are also shown to increase the susceptibility to infection. Specific groups such as health care workers and indigenous population are also at an increased risk of TB infection and disease. This paper summarizes these factors along with health system issues such as the effects of delay in diagnosis of TB in the transmission of the bacilli.