The ancient Tuberculosis in the novel COVID-19 scenario

Abstract Recently, the world has coped with the challenge of the novel SARS-CoV-2 rapid spreading, causing COVID-19. This scenario has overburdened health systems, forced social isolation, and interrupted some services, changing the way how health assistance is provided. The management of chronic infectious diseases such as tuberculosis is a sensitive matter in times when the control strategies are at risk. In this sense, how could a high burden disease such as tuberculosis affect or be affected when combined with the COVID-19 pandemic? Patients with tuberculosis have a social background and lung impairment that represent risks in the pandemic scenario of another widely transmitted respiratory disease. Thus, even with several questions remaining unanswered, research and public policies should be addressed to control the effects of the current highly contagious COVID-19 without forgetting how it will affect the natural progression of patients suffering from tuberculosis.

Bayesian structural equation modeling for post treatment health related quality of life among tuberculosis patients.

BACKGROUND: The use of Bayesian Structural Equation Model (BSEM) to evaluate the impact of TB on self-reported health related quality of life (HRQoL) of TB patients has been not studied. OBJECTIVE: To identify the factors that contribute to the HRQoL of TB patients using BSEM. METHODS: This is a latent variable modeling with Bayesian approach using secondary data. HRQoL data collected after one year from newly diagnosed 436 TB patients who were registered and successfully completed treatment at Government health facilities in Tiruvallur district, south India under the National TB Elimination Programme (NTEP) were used for this analysis. In this study, the four independent latent variables such as physical well-being (PW = PW1-7), mental well-being (MW = MW1-7), social well-being (SW = SW1-4) and habits were considered. The BSEM was constructed using Markov Chain Monte Carlo algorithm for identifying the factors that contribute to the HRQoL of TB patients who completed treatment. RESULTS: Bayesian estimates were obtained using 46,300 observations after convergence and the standardized structural regression estimate of PW, MW, SW on HRQoL were 0.377 (p<0.001), 0.543 (p<0.001) and 0.208 (p<0.001) respectively. The latent variables PW, MW and SW were significantly associated with HRQoL of TB patients. The age was found to be significantly negatively associated with HRQoL of TB patients. CONCLUSIONS: The current study demonstrated the application of BSEM in evaluating HRQoL. This methodology may be used to study precise estimates of HRQoL of TB patients in different time points.

Pró-Fármacos dendriméricos potencialmente ativos em Malária e Tuberculose: Síntese e avaliação da atividade biológica / Dendrimeric prodrugs potentially active in malaria and tuberculosis: Synthesis and evaluation of biological activity

HIV/AIDS, tuberculose, malária e as doenças tropicais negligenciadas representam uma grande preocupação em Saúde em muitas regiões do mundo. Os fármacos disponíveis para o tratamento apresentam diversos problemas, tais como toxicidade e resistência ao parasita. Mesmo com esse triste panorama, o investimento em pesquisa nessa área é, ainda, pouco significativo. Assim, dentre os métodos de modificação molecular para melhorar propriedades farmacêuticas, farmacocinéticas e/ou farmacodinâmica de compostos bioativos destaca-se a latenciação. Já os dendrímeros vêm despertando interesse em aplicações biológicas, principalmente como transportadores de fármacos, além de atuarem como transportadores de genes, imagem em diagnóstico e compostos com ação per se. Face ao exposto e tendo em vista o caráter promissor dos dendrímeros como sistemas de drug delivery, o objetivo deste trabalho foi a síntese de pró-fármacos dendriméricos potencialmente ativos em malária e tuberculose. Os dendrímeros de Bis-MPA (gerações 0, 1 e 2) foram sintetizados pelo grupo do Professor Scott Grayson, da Tulane University (EUA). No Brasil, foram feitas as funcionalizações destes compostos, através do acoplamento do ácido succínico (que funciona como espaçante) e as moléculas ativas. Selecionaram-se as seguintes substâncias: (1) primaquina, com ação antimalárica e (2) isoniazida, de ação nos primeiros estágios da tuberculose. Foram sintetizados os pró-fármacos dendriméricos de isoniazida nas gerações 0 e 1 (G0-Iso e G1-Iso), e primaquina nas gerações 0, 1 e 2 (G0-Pq, G1-Pq e G2Pq). Importante mencionar que os resultados de Ressonância Magnética e Nuclear de 1H e de 13C demostraram as obtenções dos respectivos produtos, porém contendo impurezas. Já a análise do resultado proveniente da espectrometria de massas do composto G0-Iso revelou a presença de um subproduto ciclizado da isonizaida succinoilada (CIso-Suc), o qual pode ser um potencial pró-fármaco ou apresentar atividade per se. Como não se conhece este composto, o laboratório coordenado pela Profas Elizabeth Igne Ferreira e Jeanine Giarolla manifestou interesse em pesquisa-lo, principalmente quanto suas propriedades físico- químicas, bem como quanto à atividade biológica. Assim, utilizando metodologia analítica previamente estabelecida para o G0-Iso, os estudos de estabilidade química da CIso-Suc, em diferentes valores de pH, demonstraram a capacidade da forma ciclizada em se converter no protótipo Iso-Suc, majoritariamente em pH 7,4 e 8,5. Como perspectivas, destaca-se a avaliação da estabilidade enzimática deste potencial derivado. Ressalta-se, ainda, a a avaliação da respectiva atividade antimicobacteriana. Em relação aos pró-fármacos, as necessidades de aprimoramentos das sínteses são, também, evidenciadas. Uma vez sintetizados e caracterizados, estes últimos derivados serão avaliados quanto à atividade biológica. Ademais, estudos computacionais, sobretudo simulações de docking molecular, foram desenvolvidos com intuito de se entender o modo de interação de alguns compostos com alvos biológicos pré-determinados

HIV/AIDS, tuberculosis, malaria and neglected diseases are a major health concern in many regions of the world. The drugs available present various problems, such as toxicity and parasite resistance. Even with this sad outlook, research investment in this area is still insignificant. Among the molecular modification methods to improve the pharmaceutical, pharmacokinetic and/or pharmacodynamic properties we stands out prodrug design. On the other hand, dendrimers are arousing interest in biological applications, mainly as drug carriers, besides gene delivery, diagnostic imaging, as well as acting as compounds with activity per se. Considering that, added to the promising dendrimer drug delivery features, the aim of this study was to synthesize potentially active dendrimer prodrugs in malaria and tuberculosis. Bis-MPA dendrimers (generations 0, 1 and 2) were synthesized by the group of Professor Scott Grayson of Tulane University (USA). Herein in Brazil, the compounds were functionalized by coupling succinic acid (spacer group), as well as the active molecules. We selected the following substances: (1) primaquine, with antimalarial action and (2) isoniazid, acting in the early stages of tuberculosis. Isoniazid dendrimer prodrugs were synthesized generations 0 and 1 (G0-Iso and G1-Iso), and primaquine in generations 0, 1 and 2 (G0-Pq, G1-Pq and G2-Pq). It is important to mention that the results related to Nuclear and Magnetic Resonance 113C showed chemical structures features, however with impurities. Analysis of the mass spectrometry regarding G0-Iso has revealed the presence of a cyclized by-product of succinylated isonized (CIso-Suc), which may be a potential prodrug or may presentactivity itself. Using the analytical methodology performed for G0-Iso, ICso-Suc demonstrated its ability to convert the Iso-Suc prototype at different pH values, especially at pH 7.4 and 8.5. As perspectives, we highlight the determinations of the chemical stability of ICsoSuc at pH 1.5 and 6.0, as well as the evaluation of the enzymatic stability. We will also investigate the respective antimicobacterial activities. Regarding prodrugs, the needs for synthesis enhancements are also necessary. Once synthesized and characterized, these latter derivatives will be evaluated for biological activity. Moreover, computational studies, especially molecular docking simulations, were developed in order to understand the mode of interaction of some compounds with predetermined biological targets

MCMSeq: Bayesian hierarchical modeling of clustered and repeated measures RNA sequencing experiments.

BACKGROUND: As the barriers to incorporating RNA sequencing (RNA-Seq) into biomedical studies continue to decrease, the complexity and size of RNA-Seq experiments are rapidly growing. Paired, longitudinal, and other correlated designs are becoming commonplace, and these studies offer immense potential for understanding how transcriptional changes within an individual over time differ depending on treatment or environmental conditions. While several methods have been proposed for dealing with repeated measures within RNA-Seq analyses, they are either restricted to handling only paired measurements, can only test for differences between two groups, and/or have issues with maintaining nominal false positive and false discovery rates. In this work, we propose a Bayesian hierarchical negative binomial generalized linear mixed model framework that can flexibly model RNA-Seq counts from studies with arbitrarily many repeated observations, can include covariates, and also maintains nominal false positive and false discovery rates in its posterior inference. RESULTS: In simulation studies, we showed that our proposed method (MCMSeq) best combines high statistical power (i.e. sensitivity or recall) with maintenance of nominal false positive and false discovery rates compared the other available strategies, especially at the smaller sample sizes investigated. This behavior was then replicated in an application to real RNA-Seq data where MCMSeq was able to find previously reported genes associated with tuberculosis infection in a cohort with longitudinal measurements. CONCLUSIONS: Failing to account for repeated measurements when analyzing RNA-Seq experiments can result in significantly inflated false positive and false discovery rates. Of the methods we investigated, whether they model RNA-Seq counts directly or worked on transformed values, the Bayesian hierarchical model implemented in the mcmseq R package (available at https://github.com/stop-pre16/mcmseq ) best combined sensitivity and nominal error rate control.

Optimizing hospital distribution across districts to reduce tuberculosis fatalities.

The spatial distributions of diverse facilities are often understood in terms of the optimization of the commute distance or the economic profit. Incorporating more general objective functions into such optimization framework may be useful, helping the policy decisions to meet various social and economic demands. As an example, we consider how hospitals should be distributed to minimize the total fatalities of tuberculosis (TB). The empirical data of Korea shows that the fatality rate of TB in a district decreases with the areal density of hospitals, implying their correlation and the possibility of reducing the nationwide fatalities by adjusting the hospital distribution across districts. Approximating the fatality rate by the probability of a patient not to visit a hospital in her/his residential district for the duration period of TB and evaluating the latter probability in the random-walk framework, we obtain the fatality rate as an exponential function of the hospital density with a characteristic constant related to each district's effective lattice constant estimable empirically. This leads us to the optimal hospital distribution which finds the hospital density in a district to be a logarithmic function of the rescaled patient density. The total fatalities is reduced by 13% with this optimum. The current hospital density deviates from the optimized one in different manners from district to district, which is analyzed in the proposed model framework. The assumptions and limitations of our study are also discussed.

The Lancet Respiratory Medicine Commission: 2019 update: epidemiology, pathogenesis, transmission, diagnosis, and management of multidrug-resistant and incurable tuberculosis.

The Lancet Respiratory Medicine Commission on drug-resistant tuberculosis was published in 2017, which comprehensively reviewed and provided recommendations on various aspects of the disease. Several key new developments regarding drug-resistant tuberculosis are outlined in this Commission Update. The WHO guidelines on treating drug-resistant tuberculosis were updated in 2019 with a reclassification of second line anti-tuberculosis drugs. An injection-free MDR tuberculosis treatment regimen is now recommended. Over the past 3 years, advances in treatment include the recognition of the safety and mortality benefit of bedaquiline, the finding that the 9-11 month injectable-based 'Bangladesh' regimen was non-inferior to longer regimens, and promising interim results of a novel 6 month 3-drug regimen (bedaquiline, pretomanid, and linezolid). Studies of explanted lungs from patients with drug-resistant tuberculosis have shown substantial drug-specific gradients across pulmonary cavities, suggesting that alternative dosing and drug delivery strategies are needed to reduce functional monotherapy at the site of disease. Several controversies are discussed including the optimal route of drug administration, optimal number of drugs constituting a regimen, selection of individual drugs for a regimen, duration of the regimen, and minimal desirable standards of antibiotic stewardship. Newer rapid nucleic acid amplification test platforms, including point-of-care systems that facilitate active case-finding, are discussed. The rapid diagnosis of resistance to other drugs, (notably fluoroquinolones), and detection of resistance by targeted or whole genome sequencing will probably change the diagnostic landscape in the near future.

Efficient Deep Network Architectures for Fast Chest X-Ray Tuberculosis Screening and Visualization.

Automated diagnosis of tuberculosis (TB) from chest X-Rays (CXR) has been tackled with either hand-crafted algorithms or machine learning approaches such as support vector machines (SVMs) and convolutional neural networks (CNNs). Most deep neural network applied to the task of tuberculosis diagnosis have been adapted from natural image classification. These models have a large number of parameters as well as high hardware requirements, which makes them prone to overfitting and harder to deploy in mobile settings. We propose a simple convolutional neural network optimized for the problem which is faster and more efficient than previous models but preserves their accuracy. Moreover, the visualization capabilities of CNNs have not been fully investigated. We test saliency maps and grad-CAMs as tuberculosis visualization methods, and discuss them from a radiological perspective.

Avaliação de biomarcadores para diagnóstico e monitoramento do tratamento da tuberculose pulmonar / Biomarker assessment for diagnosis and monitoring of treatment of pulmonary tuberculosis

INTRODUÇÃO: A tuberculose (TB), doença crônica infecciosa causada por Mycobacterium tuberculosis, é considerada um grave problema de saúde pública no país. A caracterização de antígenos protéicos e/ou lipídios que induzem uma resposta imunológica no hospedeiro, torna-se um importante passo para o desenvolvimento de novas ferramentas de diagnóstico e resposta terapêutica. Dentre os diferentes antígenos, em especial a mammalian cell entry protein 1A (proteína Mce1A), e os fosfolipídios da parede celular do bacilo como a cardiolipina (CL), os fosfatidilinositol (FI), fosfatidilcolina (FC), fosfatidiletanolamina (FE) e o sulfatide (SL), são, em sua maioria altamente imunogênicos, podendo então ser úteis no sorodiagnóstico. Portanto, o objetivo do estudo é avaliar a produção de anticorpos anti- Mce1A...

INTRODUCTION: Tuberculosis (TB), chronic infectious disease caused by Mycobacterium tuberculosis, is still a serious public health problem in the country. The characterization of protein and/or lipids antigens that induce an immune response in the host, it is an important step in the development of new diagnostic tools and monitoring TB treatment response. Among the different antigens, particularly mammalian cell entry protein 1A (Mce1A protein), and phospholipids from the cell wall of bacillus such as cardiolipin (CL), phosphatidylinositol (PI), phosphatidylcholine (PTC), phosphatidylethanolamine (PE) and sulfatide (SL), are highly immunogenic and can be used for improvement of the serodiagnosis. Therefore, the aim of the study is to evaluate the production of anti-Mce1A...

Diagnostic utility of bone marrow examination for the assessment of patients with fever of unknown origin: a 10-year single-centre experience.

Bone marrow (BM) examination is included in the diagnostic algorithm of fever of unknown origin (FUO), although its role is not clearly determined. The purpose of this study was to assess the role of BM studies in patients with FUO. We retrospectively reviewed 45 consecutive patients (25% human immunodeficiency virus-positive) with FUO who underwent a BM study in the University Hospital of Salamanca from 2000 to 2010. We analysed the diagnostic role of BM smears, multiparameter flow cytometry analysis, histology and microbiological cultures. Five patients (11%) were finally diagnosed by BM study (three had an infectious disease and two were found to have haematological malignancies), all of whom were immunocompetent patients. Histology was the most useful study (diagnosis was obtained in 4/5 patients), while BM cultures did not establish the final diagnosis in any patient. Flow cytometry established the diagnosis in one patient, although this patient was also diagnosed by histology. In conclusion, BM study is useful for establishing the aetiology of FUO. BM biopsy for histological examination should be always mandatory if a BM examination is performed.

Evaluation of hsp65 nested PCR-restriction analysis (PRA) for diagnosing tuberculosis in a high burden country.

Current study evaluated the hsp65 Nested PCR Restriction Fragment Length Polymorphism Analysis (hsp65 Nested PCR-PRA) to detect and identify Mycobacterium tuberculosis complex directly in clinical samples for a rapid and specific diagnosis of tuberculosis (TB). hsp65 Nested PCR-PRA was applied directly to 218 clinical samples obtained from 127 patients suspected of TB or another mycobacterial infection from July 2009 to July 2010. The hsp65 Nested PCR-PRA showed 100% sensitivity and 95.0 and 93.1% specificity in comparison with culture and microscopy (acid fast bacillus smear), respectively. hsp65 Nested PCR-PRA was shown to be a fast and reliable assay for diagnosing TB, which may contribute towards a fast diagnosis that could help the selection of appropriate chemotherapeutic and early epidemiological management of the cases which are of paramount importance in a high TB burden country.

Tuberculosis and tuberculosis/HIV/AIDS-associated mortality in Africa: the urgent need to expand and invest in routine and research autopsies.

Frequently quoted statistics that tuberculosis and human immunodeficiency virus (HIV)/AIDS are the most important infectious causes of death in high-burden countries are based on clinical records, death certificates, and verbal autopsy studies. Causes of death ascertained through these methods are known to be grossly inaccurate. Most data from Africa on mortality and causes of death currently used by international agencies have come from verbal autopsy studies, which only provide inaccurate estimates of causes of death. Autopsy rates in most sub-Saharan African countries have declined over the years, and actual causes of deaths in the community and in hospitals in most sub-Saharan African countries remain unknown. The quality of cause-specific mortality statistics remains poor. The effect of various interventions to reduce mortality rates can only be evaluated accurately if cause-specific mortality data are available. Autopsy studies could have particular relevance to direct public health interventions, such as vaccination programs or preventive therapy, and could also allow for study of background levels of subclinical tuberculosis disease, Mycobacterium tuberculosis-HIV coinfection, and other infectious and noncommunicable diseases not yet clinically manifest. Autopsies performed soon after death may represent a unique opportunity to understand the pathogenesis of M. tuberculosis and the pathogenesis of early deaths after initiation of antiretroviral therapy. The few autopsies performed so far for research purposes have yielded invaluable information and insights into tuberculosis, HIV/AIDS, and other opportunistic infections. Accurate cause-specific mortality data are essential for prioritization of governmental and donor investments into health services to reduce morbidity and mortality from deadly infectious diseases such as tuberculosis and HIV/AIDS. There is an urgent need for reviving routine and research autopsies in sub-Saharan African countries.

Establishing a serologic decision tree model of extrapulmonary tuberculosis by MALDI-TOF MS analysis.

Matrix-assisted laser desorption-ionization time of flight mass spectrometry (MALDI-TOF MS) combined with weak cationic exchange (WCX) magnetic beads was used to establish a decision tree model that distinguished extrapulmonary tuberculosis (EPTB) from non-EPTB individuals. Eight-one patients with EPTB and 112 non-EPTB individuals (72 disease controls and 40 healthy controls) were involved in this study. The model was set up by 5 of 19 differentially expressed peaks (P < 0.05), m/z 4100, 4310, 6093, 8605, and 14,019. This model can discriminate patients with EPTB from non-EPTB with a sensitivity of 97.7% and a specificity of 84.1%. The test set verified that this model had good sensitivity and specificity: 94.4% and 83.6%, respectively. In conclusion, MALDI-TOF MS combined with WCX magnetic beads is a powerful technology for constructing a decision tree model and the model we built could serve as a potential diagnostic tool for EPTB.

Assessment of antemortem tests used in the control of an outbreak of tuberculosis in llamas (Lama glama).

An outbreak of tuberculosis (TB) caused by Mycobacterium bovis in a llama herd is described. Over a 25-month period, a total of 70 llamas were selected for postmortem examination using four distinct criteria: clinical suspicion of disease (15 animals), positive tuberculin skin test result (three animals), antibody positive using a novel serological test (Rapid Test, 54 animals) and elective cull (five animals). Some animals qualified on more than one criterion. Gross lesions of TB were detected in 15 animals, with lung and lymph node lesions consistently observed. Samples were collected from 14 of 15 animals with visible lesions as well as those with no visible lesions, for histopathology and mycobacterial culture. All 14 llamas with visible lesions had caseonecrotic granulomatous lesions associated with acid-fast bacteria and variable mineralisation, and M bovis was isolated from 13. There were no histopathological lesions of TB in llamas with no grossly visible lesions, and M bovis was not isolated from any of these. The predictive value of suspicious gross lesions at postmortem examination was therefore high in the herd. Molecular typing results indicated that the outbreak was caused by a single strain likely to have originated from a local reservoir, probably cattle or wildlife. Antemortem indicators of infection assisted control of the outbreak, but no single test accurately identified all TB cases. Visible lesions were detected in nine of 15 llamas with clinical suspicion of disease, in two of three that had positive tuberculin skin test results and in 10 of 54 that were antibody positive; there was none (zero out of five) in llamas that were electively culled.

[Tuberculosis epidemiology in Mayotte Island]. / Epidémiologie de la tuberculose à Mayotte.

Mayotte is a French territory island, part of the Comoros Archipelago in the Indian Ocean with 200,000 inhabitants. The tuberculosis control program started in 1976, although available epidemiological data remains incomplete. We conducted a retrospective hospital-based survey in 202 outpatients and hospital medical records from the Hospital Centre of the main city to contribute to the epidemiological evaluation of tuberculosis patterns. The tuberculosis frequency remains unchanged since 2000. It affects a young population partly coming from the other neighbouring Comoro Islands (69%) with illegal immigrate status (53% in 2004). The systematic diagnostic screening efficiency of the condition appears marginal. Pulmonary involvement is the most frequent clinical manifestation (78%), although severe extrapulmonary manifestations are not exceptional. Co-infection with HIV and multi resistance to antituberculosis agents are not frequent. Up to 60% of cases have been proven to be bacteriologically linked. The notification rate remains critically low with an estimate of 39% of notifications to the local sanitary authorities in charge of secondary cases screening. The case coverage seems limited both by low socio-economical status and poor health facility accessibility The loss of follow up is dramatically high, 41% on the overall period, and up to 51% in 2004. Our results make mandatory the reinforcement of a tuberculosis survey and control involvement within the context of this French territory. Screening, care and follow up are to be implemented particularly for vulnerable and precarious groups and for patients.

The changing pattern of "smart" flow cytometry (S-FC) to assist the cost-effective diagnosis of HIV, tuberculosis, and leukemias in resource-restricted conditions.

There is a need to introduce cytometry into areas of the globe that have remained virtually untouched by modern laboratory medicine. With the demand to carry out tests on 100,000 s of individuals requiring antiretroviral therapy (ART), flow cytometry must remain simple and cost-effective - while being sustainable and industry supported as well as proven by quality assessment (QA). This outlook is referred to as "smart flow cytometry" (S-FC). There are five main areas where the power of S-FC is demonstrated. These are: (i) the use of CD45 to assist precise cell counting in blood and tissue samples; (ii) the primary CD4 gating to count CD4+ T cells in patients waiting for ART, including the combination (i) and (ii) in the panleucogating (PLG) protocol; (iii) monitoring of human immunodeficiency virus (HIV+) patients during ART by the decreasing levels of lymphocyte activation in a CD8/CD38 test - leading to economies of viral-load assays; (iv) in tuberculosis and HIV-TB coinfections the use of TB-antigen-stimulated cytokine-synthetic CD4+ T cells to identify active disease; and (v) the utilization of "minimal residual disease (MRD)-Lite" technology in patients 19 days after the start of antileukemic therapy to detect MRD. These methods of S-FC have been successfully introduced in "resource-restricted" countries with international and local QA.