Tuberculosis in the AIDS era

Clearance of persistent SARS-CoV-2 associates with increased neutralizing antibodies in advanced HIV disease post-ART initiation

SARS-CoV-2 clearance requires adaptive immunity but the contribution of neutralizing antibodies and T cells in different immune states is unclear. Here we ask which adaptive immune responses associate with clearance of long-term SARS-CoV-2 infection in HIV-mediated immunosuppression after suppressive antiretroviral therapy (ART) initiation. We assembled a cohort of SARS-CoV-2 infected people in South Africa (n = 994) including participants with advanced HIV disease characterized by immunosuppression due to T cell depletion. Fifty-four percent of participants with advanced HIV disease had prolonged SARS-CoV-2 infection (>1 month). In the five vaccinated participants with advanced HIV disease tested, SARS-CoV-2 clearance associates with emergence of neutralizing antibodies but not SARS-CoV-2 specific CD8 T cells, while CD4 T cell responses were not determined due to low cell numbers. Further, complete HIV suppression is not required for clearance, although it is necessary for an effective vaccine response. Persistent SARS-CoV-2 infection led to SARS-CoV-2 evolution, including virus with extensive neutralization escape in a Delta variant infected participant. The results provide evidence that neutralizing antibodies are required for SARS-CoV-2 clearance in HIV-mediated immunosuppression recovery, and that suppressive ART is necessary to curtail evolution of co-infecting pathogens to reduce individual health consequences as well as public health risk linked with generation of escape mutants.

Tuberculosis and COVID-19 in the elderly: factors driving a higher burden of disease

Mycobacterium tuberculosis (M.tb) and SARS-CoV-2 are both infections that can lead to severe disease in the lower lung. However, these two infections are caused by very different pathogens (Mycobacterium vs. virus), they have different mechanisms of pathogenesis and immune response, and differ in how long the infection lasts. Despite the differences, SARS-CoV-2 and M.tb share a common feature, which is also frequently observed in other respiratory infections: the burden of disease in the elderly is greater. Here, we discuss possible reasons for the higher burden in older adults, including the effect of co-morbidities, deterioration of the lung environment, auto-immunity, and a reduced antibody response. While the answer is likely to be multifactorial, understanding the main drivers across different infections may allow us to design broader interventions that increase the health-span of older people.

Amycolatopsis aidingensis sp. nov., a Halotolerant Actinobacterium, Produces New Secondary Metabolites

A novel actinobacterium, strain YIM 96748T, was isolated from a saline soil sample collected from the south bank of Aiding Lake in Xinjiang Province, Northwest China. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain YIM 96748T is closely related to Amycolatopsis cihanbeyliensis BNT52T (98.9%) and Amycolatopsis jiangsuensis KLBMP 1262T (97.2%). The DNA-DNA relatedness between strain YIM 96748T and its closest type strain A. cihanbeyliensis BNT52T was 59.6%. The average nucleotide identity between strain YIM 96748T and its neighbor strain was 88.97%. Based on the genotypic and phenotypic characteristics, it is concluded that strain YIM 96748T represents a novel species of the genus Amycolatopsis, whose name was proposed as Amycolatopsis aidingensis sp. nov. The type strain is YIM 96748T. To investigate the biosynthetic potential of producing secondary metabolites, the complete genome of YIM 96748T was sequenced and analyzed. The complete genome sequence of YIM 96748T consists of a 7,657,695-bp circular chromosome, comprising 7,162 predicted genes with a DNA G + C content of 70.21 mol%. Fifty-one putative biosynthetic gene clusters of secondary metabolites were found, including the antibacterial/antitumor agent TLN-05220, the antibacterial agent nocardicin A, the antifungal agent nystatin A1, and the osmolyte ectoine. The investigation of the secondary metabolites of A. aidingensis YIM96748T led to the discovery of two new phenylpropyl acetate enantiomers, amycoletates A (1) and B (2), and five known compounds: 4-hydroxy phenethyl acetate (3), 2-p-acetoxyphenylethanol (4), (S)-ethyl indole-3-lactate (5), (R)-ethyl indole-3-lactate (6), and p-hydroxybenzoic acid (7). One of the gene clusters 14, 36, and 43, which contain a single module of polyketide synthase, might be responsible for the biosynthesis of compounds 1 and 2 from compound 7 as a precursor. Further studies, including the one strain many compounds approach (OSMAC) and genetic modification, are needed to explore novel compounds from this talented halophilic Amycolatopsis strain.

Targeted antibiotic discovery through biosynthesis-associated resistance determinants: target directed genome mining

Intense competition between microbes in the environment has directed the evolution of antibiotic production in bacteria. Humans have harnessed these natural molecules for medicinal purposes, magnifying them from environmental concentrations to industrial scale. This increased exposure to antibiotics has amplified antibiotic resistance across bacteria, spurring a global antimicrobial crisis and a search for antibiotics with new modes of action. Genetic insights into these antibiotic-producing microbes reveal that they have evolved several resistance strategies to avoid self-toxicity, including product modification, substrate transport and binding, and target duplication or modification. Of these mechanisms, target duplication or modification will be highlighted in this review, as it uniquely links an antibiotic to its mode of action. We will further discuss and propose a strategy to mine microbial genomes for these genes and their associated biosynthetic gene clusters to discover novel antibiotics using target directed genome mining.

Tuberculosis Patients Who Are A Potential Source for Unprotected Exposure in Health Care Systems: A Multicenter Case Control Study

Setting

Five health care systems in Texas.

Objective

To describe the epidemiology of inadequate isolation for pulmonary tuberculosis leading to tuberculosis (TB) exposures from confirmed TB patients and the patient factors that led to the exposures.

Design

A retrospective cohort and case-control study of adult patients with TB resulting in exposures (cases) vs those TB patients who did not result in exposures (controls) during January 2005 to December 2012.

Results

There were 335 patients with pulmonary TB disease, 199 cases and 136 controls. There was no difference between groups in age (46 ± 14.6 vs 45 ± 17 years; P > .05), race, or substance abuse. Cases were more likely to be transplant recipients (adjusted odds ratio [AOR], 18.90; 95% CI, 1.9-187.76), have typical TB chest radiograph (AOR, 2.23; 95% CI, 1.1-4.51), and have positive acid-fast bacilli stains (AOR, 2.36; 95% CI, 1.31-4.27). Cases were less likely to have extrapulmonary disease (AOR, 0.47; 95% CI, 0.24-0.95).

Conclusions

TB exposure resulting from inadequate isolation is frequent in health care settings. Extrapulmonary involvement resulted in earlier airborne isolation. Being a transplant recipient, having chest radiograph findings typical for TB, and sputum positivity acid-fast bacilli upon staining were associated with increased risk of inadequate isolation.

History of antimicrobial drug discovery: Major classes and health impact

The introduction of antibiotics into clinical practice revolutionized the treatment and management of infectious diseases. Before the introduction of antibiotics, these diseases were the leading cause of morbidity and mortality in human populations. This review presents a brief history of discovery of the main antimicrobial classes (arsphenamines, β-lactams, sulphonamides, polypeptides, aminoglycosides, tetracyclines, amphenicols, lipopeptides, macrolides, oxazolidinones, glycopeptides, streptogramins, ansamycins, quinolones, and lincosamides) that have changed the landscape of contemporary medicine. Given within a historical timeline context, the review discusses how the introduction of certain antimicrobial classes affected the morbidity and mortality rates due to bacterial infectious diseases in human populations. Problems of resistance to antibiotics of different classes are also extensively discussed.

Mycobacteria

The immunocompromised host is at increased risk of Mycobacterium tuberculosis complex and nontuberculous mycobacteria infection. Although Mycobacterium tuberculosis complex is a significant mycobacterial pathogen, nontuberculous mycobacteria causes substantial disease in those with suppressed immune responses. Mycobacterial infections can cause significant morbidity and mortality in this patient population, and rapid identification and susceptibility testing of the mycobacterial species is paramount to patient management and outcomes. Mycobacterial diagnostics has undergone some significant advances in the last two decades with immunodiagnostics (interferon gamma release assay), microscopy (light-emitting diode), culture (automated broth-based systems), identification (direct PCR, sequencing and matrix-assisted laser-desorption ionization–time of flight mass spectrometry) and susceptibility testing (molecular detection of drug resistance from direct specimens or positive cultures). Employing the most rapid and sensitive methods in the mycobacterial laboratory will have a tremendous impact on patient care and, in the case of Mycobacterium tuberculosis complex, in the control of tuberculosis.

Inhibition of Mycobacterium-RmlA by Molecular Modeling, Dynamics Simulation, and Docking

The increasing resistance to anti-tb drugs has enforced strategies for finding new drug targets against Mycobacterium tuberculosis (Mtb). In recent years enzymes associated with the rhamnose pathway in Mtb have attracted attention as drug targets. The present work is on α-D-glucose-1-phosphate thymidylyltransferase (RmlA), the first enzyme involved in the biosynthesis of L-rhamnose, of Mtb cell wall. This study aims to derive a 3D structure of RmlA by using a comparative modeling approach. Structural refinement and energy minimization of the built model have been done with molecular dynamics. The reliability assessment of the built model was carried out with various protein checking tools such as Procheck, Whatif, ProsA, Errat, and Verify 3D. The obtained model investigates the relation between the structure and function. Molecular docking interactions of Mtb-RmlA with modified EMB (ethambutol) ligands and natural substrate have revealed specific key residues Arg13, Lys23, Asn109, and Thr223 which play an important role in ligand binding and selection. Compared to all EMB ligands, EMB-1 has shown better interaction with Mtb-RmlA model. The information thus discussed above will be useful for the rational design of safe and effective inhibitors specific to RmlA enzyme pertaining to the treatment of tuberculosis.

Imaging of the brain in patients with human immunodeficiency virus infection

Neurologic disease in acquired immunodeficiency syndrome (AIDS) patients is related either to opportunistic pathogens or to direct central nervous system (CNS) invasion by the human immunodeficiency virus. Despite the increasing availability of antiretroviral therapy, opportunistic infections continue to afflict patients in the developing world and in other populations with limited access to appropriate treatment. Classic CNS infections in the setting of AIDS include toxoplasmosis, cryptococcosis, progressive multifocal leukoencephalopathy, and cytomegalovirus encephalitis. Additionally, AIDS patients are far more susceptible to acquiring CNS tuberculosis and neurosyphilis, both of which exhibit altered disease characteristics in the setting of immunosuppression. Neuroimaging is a crucial component of the diagnostic work-up of these conditions, and findings include, but are not limited to, intracranial mass lesions, white matter disease, meningoencephalitis, vascular complications, and hydrocephalus. Though various disease processes can produce imaging findings that overlap with one another, certain characteristic patterns may suggest a particular pathogen, and advanced imaging techniques and laboratory tests allow for definitive diagnosis. Knowledge of the imaging patterns seen in the setting of AIDS-related CNS disease is vital to the neuroradiologist, whose interpretation may guide decisions related to treatment and further work-up.

Directly observed therapy for treating tuberculosis

BACKGROUND

Tuberculosis (TB) requires at least six months of treatment. If treatment is incomplete, patients may not be cured and drug resistance may develop. Directly Observed Therapy (DOT) is a specific strategy, endorsed by the World Health Organization, to improve adherence by requiring health workers, community volunteers or family members to observe and record patients taking each dose.

OBJECTIVES

To evaluate DOT compared to self-administered therapy in people on treatment for active TB or on prophylaxis to prevent active disease. We also compared the effects of different forms of DOT.

SEARCH METHODS

We searched the following databases up to 13 January 2015: the Cochrane Infectious Diseases Group Specialized Register; the Cochrane Central Register of Controlled Trials (CENTRAL), published in the Cochrane Library; MEDLINE; EMBASE; LILACS and mRCT. We also checked article reference lists and contacted relevant researchers and organizations.

SELECTION CRITERIA

Randomized controlled trials (RCTs) and quasi-RCTs comparing DOT with routine self-administration of treatment or prophylaxis at home.

DATA COLLECTION AND ANALYSIS

Two review authors independently assessed risk of bias of each included trial and extracted data. We compared interventions using risk ratios (RR) with 95% confidence intervals (CI). We used a random-effects model if meta-analysis was appropriate but heterogeneity present (I(2) statistic > 50%). We assessed the quality of the evidence using the GRADE approach.

MAIN RESULTS

Eleven trials including 5662 participants met the inclusion criteria. DOT was performed by a range of people (nurses, community health workers, family members or former TB patients) in a variety of settings (clinic, the patient's home or the home of a community volunteer). DOT versus self-administered Six trials from South Africa, Thailand, Taiwan, Pakistan and Australia compared DOT with self-administered therapy for treatment. Trials included DOT at home by family members, community health workers (who were usually supervised); DOT at home by health staff; and DOT at health facilities. TB cure was low with self-administration across all studies (range 41% to 67%), and direct observation did not substantially improve this (RR 1.08, 95% CI 0.91 to 1.27; five trials, 1645 participants, moderate quality evidence). In a subgroup analysis stratified by the frequency of contact between health services in the self-treatment arm, daily DOT may improve TB cure when compared to self-administered treatment where patients in the self-administered group only visited the clinic every month (RR 1.15, 95% CI 1.06 to 1.25; two trials, 900 participants); but with contact in the control becoming more frequent, this small effect was not apparent (every two weeks: RR 0.96, 95% CI 0.83 to 1.12; one trial, 497 participants; every week: RR 0.90, 95% CI 0.68 to 1.21; two trials, 248 participants).Treatment completion showed a similar pattern, ranging from 59% to 78% in the self-treatment groups, and direct observation did not improve this (RR 1.07, 95% CI 0.96 to 1.19; six trials, 1839 participants, moderate quality evidence). DOT at home versus DOT at health facility In four trials that compared DOT at home by family members, or community health workers, with DOT by health workers at a health facility there was little or no difference in cure or treatment completion (cure: RR 1.02, 95% CI 0.88 to 1.18, four trials, 1556 participants, moderate quality evidence; treatment completion: RR 1.04, 95% CI 0.91 to 1.17, three trials, 1029 participants, moderate quality evidence). DOT by family member versus DOT by community health workerTwo trials compared DOT at home by family members with DOT at home by community health workers. There was also little or no difference in cure or treatment completion (cure: RR 1.02, 95% CI 0.86 to 1.21; two trials, 1493 participants, moderate quality evidence; completion: RR 1.05, 95% CI 0.90 to 1.22; two trials, 1493 participants, low quality evidence). Specific patient categoriesA trial of 300 intravenous drug users in the USA evaluated direct observation with no observation in TB prophylaxis to prevent active disease and showed little difference in treatment completion (RR 1.00, 95% CI 0.88 to 1.13; one trial, 300 participants, low quality evidence).

AUTHORS' CONCLUSIONS

From the existing trials, DOT did not provide a solution to poor adherence in TB treatment. Given the large resource and cost implications of DOT, policy makers might want to reconsider strategies that depend on direct observation. Other options might take into account financial and logistical barriers to care; approaches that motivate patients and staff; and defaulter follow-up.

Community-acquired intracranial suppurative infections: A 15-year report

Background:

The aim of this study was to retrospectively evaluate the characteristics, treatment, and prognosis of patients with intracranial suppurative infection (ISI) by review of clinical, radiological, and laboratory findings.

Methods:

The data collected from all patients who had been diagnosed with ISI and followed up at the Infectious Diseases and Clinical Microbiology Department of the study site between 1998 and 2013 were reviewed.

Results:

Of the 23 ISI patients identified, the mean age was 38.21 ± 12.61 years (range: 19–67 years, median: 34) and mean symptom duration was 22.25 ± 20.22 days. Headache was the most common symptom, the frontal lobe the most common localization of ISI, and mastoiditis due to chronic suppurative otitis media the most common source of infection causing ISI. Proteus mirabilis, Pseudomonas spp., Peptostreptococcus spp., Enterococcus avium, Mycobacterium tuberculosis complex, and Toxoplasma gondii were isolated from the specimens collected from 6 (37.5%) of the 16 patients who underwent invasive procedures. Of these 16 patients, 2 underwent craniotomy, 12 burr hole aspiration, and 2 stereotactic biopsy. The rate of recurrence was 0% and the rates of sequelae and fatality were both 8%.

Conclusions:

ISI should be considered in male patients presenting with headache and neurological signs and symptoms, whether with or without fever, on admission for early diagnosis and provision of timely, adequate therapy and, if required, surgical intervention to reduce mortality and sequelae rates.

Aphasia secondary to tuberculosis: a review of a nineteenth-century case report by Booth and Curtis (1893)

The topic of aphasia secondary to tuberculosis deserves attention for two reasons: first, for better understanding rare etiologies of aphasia in medical history; and secondly, for initiating a multidisciplinary discussion relevant to aphasiologists, neurologists, pathologists, and clinicians generally. This article will focus on clinical observations of tuberculosis-related aphasia in the nineteenth century, highlighting a noteworthy case report presented by Booth and Curtis (1893).

HIV/AIDS Related Respiratory Diseases

Lungs are the most commonly involved organ by HIV/AIDS related diseases, and pulmonary infections are the main reasons for the increasing death rate from AIDS. Pathogens of HIV related pulmonary infections include parasites, fungi, mycobacteria, viruses, bacteria and toxoplasma gondii. According to international reports, pathogens have different geographical distribution, which is also closely related to the socioeconomic status of the region to produce varied AIDS related diseases spectra. For instance, in the United States, pneumocystis carnii pneumonia (PCP), tuberculosis and recurrent bacterial pneumonia (at least twice within 1 year) occur frequently in HIV infected patients. An international report published 10 years ago indicated that PCP is the most common and serious pulmonary opportunistic infections in HIV infected patients. Now its incidence has dropped with the application of antiretroviral treatment and preventive measures. PCP will continue to occur initially in patients who are aware of their HIV infection. In addition, HIV related viral and parasitic infections have been reported both domestically and internationally. In this section, the clinical manifestations and imaging findings of HIV related pulmonary infections are analyzed and discussed, which provide effective diagnosis basis, so as to reduce the incidence of HIV-related pulmonary infections.

Herbimycins D-F, ansamycin analogues from Streptomyces sp. RM-7-15

Bacterial strains belonging to the class actinomycetes were isolated from the soil near a thermal vent of the Ruth Mullins coal fire (Appalachian Mountains of eastern Kentucky). High-resolution electrospray ionization mass spectrometry and ultraviolet absorption profiles of metabolites from one of the isolates (Streptomyces sp. RM-7-15) revealed the presence of a unique set of metabolites ultimately determined to be herbimycins D-F (1-3). In addition, herbimycin A (4), dihydroherbimycin A (TAN 420E) (7), and the structurally distinct antibiotic bicycylomycin were isolated from the crude extract of Streptomyces sp. RM-7-15. Herbimycins A and D-F (1-3) displayed comparable binding affinities to the Hsp90α. While the new analogues were found to be inactive in cancer cell cytotoxicity and antimicrobial assays, they may offer new insights in the context of nontoxic ansamycin-based Hsp90 inhibitors for the treatment of neurodegenerative disease.

Comparison of 14 molecular assays for detection of Mycobacterium tuberculosis complex in bronchoalveolar lavage fluid

We compared 14 molecular assays for their ability to detect the Mycobacterium tuberculosis complex in bronchoalveolar lavage fluid samples. Three approaches were followed. First, by using DNA from Mycobacterium bovis BCG, we determined the detection limits of the assays using routine molecular methods. Second, in order to determine the analytical sensitivities of the assays, we added one of four M. tuberculosis isolates with various numbers of the insertion sequence IS6110 to N-acetyl-l-cysteine (NALC)-NaOH-treated bronchoalveolar lavage fluid samples in dilutions of 1:10 to 1:10,000,000. Third, intertest variabilities were measured and defined by the standard deviations for the quantitation cycle (Cq) values of three positive test results per dilution per assay. The 14 assays tested had similar analytical sensitivities, except for GeneXpert, which had an analytical sensitivity that was 10- to 100-fold lower than that of the other assays. The MP MTB/NTM test and the in-house TaqMan-10 revealed the best performances for the detection limit and had the highest analytical sensitivities. Most of the tests performed well regarding detection limit and analytical sensitivity for the detection of the M. tuberculosis complex in serial dilutions, and the differences were small. The MP MTB/NTM and the in-house TaqMan-10 assays revealed the best, and GeneXpert the worst, overall performances.

New tuberculosis drug development: targeting the shikimate pathway

BACKGROUND

Tuberculosis (TB) remains a leading cause of morbidity and mortality worldwide, yet no new drugs have been developed in the last 40 years.

OBJECTIVE

The exceedingly lengthy TB chemotherapy and the increasing emergence of drug resistance complicated by HIV co-infection call for the development of new TB drugs. These problems are further compounded by a poor understanding of the biology of persister bacteria.

METHODS

New molecular tools have offered insights into potential new drug targets, particularly the enzymes of the shikimate pathway, which is the focus of this review.

RESULTS/CONCLUSION

Shikimate pathway enzymes, especially shikimate kinase, may offer attractive targets for new TB drug and vaccine development.

Targeting tuberculosis through a small focused library of 1,2,3-triazoles

Looking for new active molecules against Mycobacterium tuberculosis, a small focused library of 1,2,3-triazoles was efficiently prepared by click chemistry. Compounds were subsequently tested against different pathogenic and opportunistic mycobacteria including M. avium and M. tuberculosis. Two of them showed MIC at lower μg/mL concentration for M. avium and even below that for M. tuberculosis, being more potent that control drugs.

Development of balanced medium composition for improved rifamycin B production by isolated Amycolatopsis sp. RSP-3

AIM

To develop optimum fermentation environment for enhanced rifamycin B production by isolated Amycolatopsis sp. RSP-3.

METHODS AND RESULTS

The impact of different fermentation parameters on rifamycin B production by isolated Amycolatopsis sp. RSP-3 was investigated using Taguchi methodology. Controlling fermentation factors were selected based on one variable at a time methodology. The isolated strain revealed more than 25% higher production compared to literature reports. Five different nutritional components (soyabean meal, glucose, potassium nitrate, calcium carbonate and barbital) and inoculum concentration showed impact on rifamycin B production at individual and interactive level. At optimized environment, 65% contribution was observed from selected fermentation parameters.

CONCLUSIONS

Soyabean meal and calcium carbonate were the most significant factors among the selected factors followed by barbital and potassium nitrate. Glucose, however, showed the least significance on rifamycin B production with this strain. A maximum of 5.12 g l(-1) rifamycin B production was achieved with optimized medium containing (g l(-1)) soyabean meal, 27; glucose, 100; potassium nitrate, 4; calcium carbonate, 3 and barbital, 1.2.

SIGNIFICANCE AND IMPACT OF THE STUDY

The present study signifies identification of balanced medium component concentrations for improved rifamycin B production by isolated Amycolatopsis sp. RSP-3. This strain requires organic and inorganic nitrogen sources for effective product yield. Yet at individual level, organic nitrogen source has c. nine-fold higher influence compared to inorganic one.

Mycobacterium tuberculosis cell wall glycolipids directly inhibit CD4+ T-cell activation by interfering with proximal T-cell-receptor signaling

Immune evasion is required for Mycobacterium tuberculosis to survive in the face of robust adaptive CD4(+) T-cell responses. We have previously shown that M. tuberculosis can indirectly inhibit CD4(+) T cells by suppressing the major histocompatibility complex class II antigen-presenting cell function of macrophages. This study was undertaken to determine if M. tuberculosis could directly inhibit CD4(+) T-cell activation. Murine CD4(+) T cells were purified from spleens by negative immunoaffinity selection followed by flow sorting. Purified CD4(+) T cells were activated for 16 to 48 h with CD3 and CD28 monoclonal antibodies in the presence or absence of M. tuberculosis and its subcellular fractions. CD4(+) T-cell activation was measured by interleukin 2 production, proliferation, and expression of activation markers, all of which were decreased in the presence of M. tuberculosis. Fractionation identified that M. tuberculosis cell wall glycolipids, specifically, phosphatidylinositol mannoside and mannose-capped lipoarabinomannan, were potent inhibitors. Glycolipid-mediated inhibition was not dependent on Toll-like receptor signaling and could be bypassed through stimulation with phorbol 12-myristate 13-acetate and ionomycin. ZAP-70 phosphorylation was decreased in the presence of M. tuberculosis glycolipids, indicating that M. tuberculosis glycolipids directly inhibited CD4(+) T-cell activation by interfering with proximal T-cell-receptor signaling.

[Multidrug-resistant tuberculosis]

The emergence and spread of Mycobacterium tuberculosis strains resistant to multiple drugs represent a threat for global tuberculosis control. The World Health Organization (WHO) estimates that almost 500,000 cases of M. tuberculosis resistant to isoniazid and rifampicin (multidrug-resistant, or MDR-TB), at least, emerged in 2006. In addition, new cases of extensively drug-resistant tuberculosis (XDR-TB), defined as MDR-TB with resistance to a fluoroquinolone and at least one second line injectable agent, have been reported in 45 countries in all five continents. Multidrug-resistant tuberculosis is an emerging problem in Spain but the impact of this disease is limited: the WHO estimates that 0.1% of new cases of tuberculosis and 4.3% of previously treated cases are MDR-TB. Treatment of MDR-TB is especially complicated, since this disease requires the use of drugs that are less effective and more toxic, requiring treatment to be administered over longer periods and severely reducing the probability of success. This situation poses a serious problem for low income countries, especially those with a high prevalence of human immunodeficiency virus type 1 (HIV-1) infection. MDR-TB and XDR-TB are also of special concern in wealthy countries, due to mass immigration. Therefore, tuberculosis resistant to multiple drugs should be given high priority in global public health and biomedical research.

Peripheral blood gamma interferon release assays predict lung responses and Mycobacterium tuberculosis disease outcome in mice

Current diagnostic tests for tuberculosis (TB) are not able to distinguish active disease from latent Mycobacterium tuberculosis infection, nor are they able to quantify the risk of a latently infected person progressing to active TB. There is interest, however, in adapting antigen-specific gamma interferon (IFN-gamma) release assays (IGRAs) to predict disease outcome. In this study, we used the differential susceptibilities of inbred mouse strains to M. tuberculosis infection to evaluate the prognostic capabilities of IGRAs. Using lung and blood cultures, we determined that CBA/J, DBA/2, and C3H/HeJ mice (models of heightened risk of progression to active TB) produced less antigen-specific IFN-gamma in response to M. tuberculosis culture filtrate proteins and early secreted antigenic target-6 than the relatively resistant C57BL/6 mouse strain. Additionally, reduced IFN-gamma secretion in supernatants reflected a reduced frequency of IFN-gamma-responding cells in the lung and blood and not a specific defect in IFN-gamma secretion at the single-cell level. Importantly, detection of antigen-specific IFN-gamma from blood cultures accurately reflected lung responses, indicating that blood can be an appropriate test tissue in humans. Furthermore, reduced antigen-specific IFN-gamma production and low frequencies of IFN-gamma-responding cells from peripheral blood predicted increased risk of TB disease progression across genetically diverse TB disease-susceptible mouse strains, suggesting that similar results may occur in humans. The development of efficacious predictive diagnostic tests for humans would lead to targeted therapy prior to progression to active TB, reducing transmission, incidence, and prevalence rates while maximizing the use of public health resources.

Detection of phase shifts in batch fermentation via statistical analysis of the online measurements: A case study with rifamycin B fermentation

Industrial production of antibiotics, biopharmaceuticals and enzymes is typically carried out via a batch or fed-batch fermentation process. These processes go through various phases based on sequential substrate uptake, growth and product formation, which require monitoring due to the potential batch-to-batch variability. The phase shifts can be identified directly by measuring the concentrations of substrates and products or by morphological examinations under microscope. However, such measurements are cumbersome to obtain. We present a method to identify phase transitions in batch fermentation using readily available online measurements. Our approach is based on Dynamic Principal Component Analysis (DPCA), a multivariate statistical approach that can model the dynamics of non-stationary processes. Phase-transitions in fermentation produce distinct patterns in the DPCA scores, which can be identified as singular points. We illustrate the application of the method to detect transitions such as the onset of exponential growth phase, substrate exhaustion and substrate switching for rifamycin B fermentation batches. Further, we analyze the loading vectors of DPCA model to illustrate the mechanism by which the statistical model accounts for process dynamics. The approach can be readily applied to other industrially important processes and may have implications in online monitoring of fermentation batches in a production facility.

Nosocomial Mycobacterium tuberculosis transmission among healthcare students in a high incidence region, in Vitória, State of Espírito Santo

This open comparative study for evaluating hypersensitivity to tuberculin among medical students (n=441), nursing students (n=178) and economics students (n=230) in Vitória, State of Espírito Santo, had the aim of assessing whether the prevalence of positive tuberculin tests among healthcare students could be used as a sentinel event for nosocomial transmission in localities with high endemicity. There was a significant change in the frequency of purified protein derivative reactivity in the nursing students (20. 3%) and medical students (18. 4%), in comparison with the economics students (6%) (p <0. 001). As expected, the medical and nursing students had more knowledge about tuberculosis than did the economics students (p <0. 001). Our data suggest that the incidence of Mycobacterium tuberculosis infection among nursing and medical students in our region, which has high endemicity of tuberculosis, does not differ from what is found in low-incidence countries. These data reinforce the need for implementing biosafety programs for this target population.

New thiopyrazolo[3,4-d]pyrimidine derivatives as anti-mycobacterial agents

The multiple parallel synthesis of a series of N,S-bis-alkylated thiopyrazolo[3,4-d]pyrimidines, based on sequential S- then N-alkylation, is reported. These compounds showed significant anti-mycobacterial activity (MICs down to 2mug/ml) and their potential as significant drug-like leads is substantiated through cytotoxicity evaluation and in silico profiling.

Innate-like gammadelta T cell responses to mycobacterium Bacille Calmette-Guerin using the public V gamma 2 repertoire in Macaca fascicularis

The V gamma 2 V delta 2 T cell subset responds to Bacille Calmette-Guerin (BCG) immunization in macaques and may be a component of protective immunity against tuberculosis. We characterized the effects of BCG on the V gamma 2 V delta 2 T cell receptor repertoire by comparing the starting population of V gamma 2 chains in cynomolgus macaques with the repertoire found after priming or booster immunization with BCG. The starting repertoire was dominated by public V gamma 2 chain sequences that were found repeatedly among unrelated animals. Primary exposure to BCG triggered expansion of cells expressing public V gamma 2 chains and booster immunization was often associated with contraction of these same subsets. Thus, BCG-reactive V gamma 2 chains were present at high frequency in the repertoire of mycobacteria-naïve macaques and they comprised the major response to primary or booster immunization. Normal selection processes that created the naïve V gamma 2 repertoire in macaques, also encoded the capacity for rapid responses to mycobacteria. The unusual composition of a normal V gamma 2 repertoire helps to explain the powerful gammadelta T cell responses to BCG immunization.

Phase shifts in the stoichiometry of rifamycin B fermentation and correlation with the trends in the parameters measured online

Antibiotic fermentation processes are raw material cost intensive and the profitability is greatly dependent on the product yield per unit substrate consumed. In order to reduce costs, industrial processes use organic nitrogen substrates (ONS) such as corn steep liquor and yeast extract. Thus, although the stoichiometric analysis is the first logical step in process development, it is often difficult to achieve due to the ill-defined nature of the medium. Here, we present a black-box stoichiometric model for rifamycin B production via Amycolatopsis mediterranei S699 fermentation in complex multi-substrate medium. The stoichiometric coefficients have been experimentally evaluated for nine different media compositions. The ONS was quantified in terms of the amino acid content that it provides. Note that the black box stoichiometric model is an overall result of the metabolic reactions that occur during growth. Hence, the observed stoichiometric coefficients are liable to change during the batch cycle. To capture the shifts in stoichiometry, we carried out the stoichiometric analysis over short intervals of 8-16 h in a batch cycle of 100-200 h. An error analysis shows that there are no systematic errors in the measurements and that there are no unaccounted products in the process. The growth stoichiometry shows a shift from one substrate combination to another during the batch cycle. The shifts were observed to correlate well with the shifts in the trends of pH and exit carbon dioxide profiles. To exemplify, the ammonia uptake and nitrate uptake phases were marked by a decreasing pH trend and an increasing pH trend, respectively. Further, we find the product yield per unit carbon substrate to be greatly dependent on the nature of the nitrogen substrate. The analysis presented here can be readily applied to other fermentation systems that employ multi-substrate complex media.

Tumor Necrosis Factor Antagonists: Different Kinetics and/or Mechanisms of Action May Explain Differences in the Risk for Developing Granulomatous Infection

OBJECTIVE

Tumor necrosis factor (TNF) antagonists fall into 2 classes:etanercept (ETA) is a soluble TNF receptor, while infliximab (INF) and adalimumab (ADA) are monoclonal antibodies against TNF. All 3 drugs are effective in treating rheumatoid arthritis. However, these agents have been associated with an increased risk of granulomatous infections, such as tuberculosis and histoplasmosis. Several reports indicate that the incidence of granulomatous infections may potentially be higher in individuals treated with INF than ETA.

METHODS

We conducted a comprehensive literature search (1966 to 2004) to review the role of TNF in normal and disease states, and the mechanisms of action of the TNF inhibitors. Specifically, we searched for possible mechanisms for the apparent increase in granulomatous infections associated with TNF inhibitors and for reasons that there may be differences between them.

RESULTS

Infection may result from a number of differences between ETA and INF or ADA. First, binding avidities are different, with ETA binding in a 1:1 ratio and INF/ADA binding in 2 to 3:1 ratios. Second, the clearances of ADA, ETA, and INF are different, being about 13 times higher for ETA than INF or ADA, thus resulting in higher steady-state drug levels for ADA and INF. Also, the methods of administration are different, intravenously (for INF) versus subcutaneously (for ETA and ADA), which results in lower peak concentrations for ETA and ADA, potentially explaining some of the differences in effects on granuloma formation. Third, INF and ADA have somewhat different mechanisms of action from ETA: INF and ADA are associated with antibody-mediated cell lysis, while ETA is not; INF may induce apoptosis in some tissues (eg, gastrointestinal [GI] mucosa) while ETA does not--although this is controversial and may not be true at steady state in synovium, where both drugs seem to cause apoptosis; ETA binds lymphotoxin-alpha while INF does not (ETA may thus be more efficient at preventing granuloma formation by this mechanism than INF); finally, ADA and INF seem to inhibit IFN-gamma expression (probably indirectly), while ETA does not.

CONCLUSIONS

There are significant differences between the 2 classes of TNF antagonists in terms of both their kinetics and mechanisms of action. These differences may help explain the apparent differences in the incidence of granuloma-dependent infections among them.

Hierarchical amino acid utilization and its influence on fermentation dynamics: rifamycin B fermentation using Amycolatopsis mediterranei S699, a case study

Background

Industrial fermentation typically uses complex nitrogen substrates which consist of mixture of amino acids. The uptake of amino acids is known to be mediated by several amino acid transporters with certain preferences. However, models to predict this preferential uptake are not available. We present the stoichiometry for the utilization of amino acids as a sole carbon and nitrogen substrate or along with glucose as an additional carbon source. In the former case, the excess nitrogen provided by the amino acids is excreted by the organism in the form of ammonia. We have developed a cybernetic model to predict the sequence and kinetics of uptake of amino acids. The model is based on the assumption that the growth on a specific substrate is dependent on key enzyme(s) responsible for the uptake and assimilation of the substrates. These enzymes may be regulated by mechanisms of nitrogen catabolite repression. The model hypothesizes that the organism is an optimal strategist and invests resources for the uptake of a substrate that are proportional to the returns.

Results

Stoichiometric coefficients and kinetic parameters of the model were estimated experimentally for Amycolatopsis mediterranei S699, a rifamycin B overproducer. The model was then used to predict the uptake kinetics in a medium containing cas amino acids. In contrast to the other amino acids, the uptake of proline was not affected by the carbon or nitrogen catabolite repression in this strain. The model accurately predicted simultaneous uptake of amino acids at low cas concentrations and sequential uptake at high cas concentrations. The simulated profile of the key enzymes implies the presence of specific transporters for small groups of amino acids.

Conclusion

The work demonstrates utility of the cybernetic model in predicting the sequence and kinetics of amino acid uptake in a case study involving Amycolatopsis mediterranei, an industrially important organism. This work also throws some light on amino acid transporters and their regulation in A. mediterranei .Further, cybernetic model based experimental strategy unravels formation and utilization of ammonia as well as its inhibitory role during amino acid uptake. Our results have implications for model based optimization and monitoring of other industrial fermentation processes involving complex nitrogen substrate.

Molecular epidemiology of tuberculosis: current insights

Molecular epidemiologic studies of tuberculosis (TB) have focused largely on utilizing molecular techniques to address short- and long-term epidemiologic questions, such as in outbreak investigations and in assessing the global dissemination of strains, respectively. This is done primarily by examining the extent of genetic diversity of clinical strains of Mycobacterium tuberculosis. When molecular methods are used in conjunction with classical epidemiology, their utility for TB control has been realized. For instance, molecular epidemiologic studies have added much-needed accuracy and precision in describing transmission dynamics, and they have facilitated investigation of previously unresolved issues, such as estimates of recent-versus-reactive disease and the extent of exogenous reinfection. In addition, there is mounting evidence to suggest that specific strains of M. tuberculosis belonging to discrete phylogenetic clusters (lineages) may differ in virulence, pathogenesis, and epidemiologic characteristics, all of which may significantly impact TB control and vaccine development strategies. Here, we review the current methods, concepts, and applications of molecular approaches used to better understand the epidemiology of TB.

Primary and opportunistic pathogens associated with meningitis in adults in Bangui, Central African Republic, in relation to human immunodeficiency virus serostatus

OBJECTIVE

To determine the causative organisms and characteristics of patients presenting with meningitis in Bangui in order to provide guidance to physicians for case management.

METHODS

Adults with proven or suspected meningitis were enrolled in this prospective study.

LABORATORY TESTS

Full blood count, blood chemistry, and HIV tests were performed. Cerebrospinal fluid (CSF) was submitted for routine microbiology, chemistry (glucose, protein), and hematology testing. When classical microbiology analyses were negative, a broad-range bacterial polymerase chain reaction (BRBPCR) was used.

RESULTS AND CONCLUSIONS

Of the 276 patients enrolled, 215 (77.9%) were HIV positive. In HIV-positive patients cryptococcal meningitis (CM) was the most common cause of meningitis (39.1%) followed by pyogenic meningitis (PM) (30.7%), mononuclear meningitis (MM) (28.8%), and tuberculous meningitis (TM) (1.4%). In HIV-negative patients, PM was the most common cause (60.7%) followed by MM (37.7%) and CM (1.6%, one case). In-hospital mortality was higher in HIV-positive patients (73/128 = 57%) compared to those HIV negative (3/18 = 16.7%) (p = 0.001). Streptococcus pneumoniae (n = 26) was the most common bacterial diagnosis, mainly in HIV-positive patients (n = 22, 10.2%). Meningococcal meningitis (14 Neisseria meningitidis of group A and one W135) was diagnosed in nine (4.2%) HIV-positive and six (9.8%) HIV-negative patients. Gram-negative rods were isolated from five HIV-positive and two HIV-negative patients, respectively. The bacteria and fungi involved in meningitis did not display high levels of in vitro resistance. Conventional microbiology techniques failed to detect the causative agent in 55 (53.4%) PM cases. Broad-range bacterial PCR detected DNA from S. pneumoniae in three samples, N. meningitidis in two, Escherichia coli in one, Listeria monocytogenes in two and Staphylococcus aureus in one sample. In the CSF of five (three HIV negative and two HIV positive), PCR products were not identified with the oligonucleotide probes specific for the usual species of bacteria found in CSF, or genera commonly considered potential contaminants of clinical samples. Among the MM cases, 77 (90.5%) probable viral meningitis (54 HIV positive and 23 HIV negative) and eight TM (HIV positive) were suspected.

Chronic morphine exposure causes pronounced virus replication in cerebral compartment and accelerated onset of AIDS in SIV/SHIV-infected Indian rhesus macaques

Six morphine-exposed and 3 control male Indian rhesus macaques were intravenously inoculated with mixture of SHIV(KU), SHIV(89.6)P and SIV/17E-Fr. These animals were followed for a period of 56 weeks in order to determine CD4 and CD8 profile, viral loads in plasma and cerebrospinal fluid (CSF), relative distribution of 3 pathogenic viruses in blood and brain, binding as well neutralizing antibody levels and cellular immune responses. Both morphine-exposed and control macaques showed a precipitous loss of CD4+ T cells; control animals, however, showed a greater tendency to recover these cells than did their morphine-exposed counterparts. The plasma and CSF viral loads were significantly higher in morphine-exposed group than those in the control group. Four morphine-exposed animals succumbed to SIV/SHIV-induced AIDS at week 18, 19, 20 and 51; post-infection with neurological disorders was found in 3 of the 4 animals. At the end of the 56-week observation period, 2 morphine-exposed and 3 control animals were still alive. All 3 viruses replicated in the blood of both morphine-exposed and control macaques, but the cerebral compartment showed a selection phenomenon; only SIV/17E-Fr and SHIV(KU) successfully crossed the blood brain barrier (BBB). The morphine-exposed macaques further favored viral migration through the blood brain barrier (BBB). SIV/17E-Fr crossed the BBB within 2 weeks in both morphine-exposed and control macaques, whereas SHIV(KU) crossed the BBB more rapidly in morphine-exposed than in control macaques. Three morphine-exposed macaques (euthanized at weeks 18, 19 and 20) did not develop cellular or humoral immune responses, whereas the other 3 morphine-exposed and 3 control macaques developed both cellular and humoral immune responses.

A cybernetic model to predict the effect of freely available nitrogen substrate on rifamycin B production in complex media

It is well-known that secondary metabolite production is repressed by excess nitrogen substrate available in the fermentation media. Although the nitrogen catabolite repression has been known, quantitative process models have not been reported to represent this phenomenon in complex medium. In this paper, we present a cybernetic model for rifamycin B production via Amycolatopsis mediterranei S699 in complex medium, which is typically used in industry. Nitrogen substrate is assumed to be present in two forms in the medium; available nitrogen (S(ANS)) such as free amino acids and unavailable nitrogen (S(UNS)) such as peptides and proteins. The model assumes that an inducible enzyme catalyzes the conversion of S(UNS) to S(ANS). Although S(ANS) is required for growth and product formation, high concentrations were found to inhibit rifamycin production. To experimentally validate the model, five different organic nitrogen sources were used that differ in the ratio of S(ANS)/S (UNS). The model successfully predicts higher rifamycin B productivity for nitrogen sources that contain lower initial S(ANS). The higher productivity is attributed to the sustained availability of S(ANS) at low concentration via conversion of S(UNS) to S(ANS), thereby minimizing the effects of nitrogen catabolite repression on rifamycin production. The model can have applications in model-based optimization of substrate feeding recipe and in monitoring and control of fed batch processes.

Identification of tailoring genes involved in the modification of the polyketide backbone of rifamycin B by Amycolatopsis mediterranei S699

Rifamycin B biosynthesis by Amycolatopsis mediterranei S699 involves a number of unusual modification reactions in the formation of the unique polyketide backbone and decoration of the molecule. A number of genes believed to be involved in the tailoring of rifamycin B were investigated and the results confirmed that the formation of the naphthalene ring moiety of rifamycin takes place during the polyketide chain extension and is catalysed by Rif-Orf19, a 3-(3-hydroxyphenyl)propionate hydroxylase-like protein. The cytochrome P450-dependent monooxygenase encoded by rif-orf5 is required for the conversion of the Delta12, 29 olefinic bond in the polyketide backbone of rifamycin W into the ketal moiety of rifamycin B. Furthermore, Rif-Orf3 may be involved in the regulation of rifamycin B production, as its knock-out mutant produced about 40 % more rifamycin B than the wild-type. The work also revealed that many of the genes located in the cluster are not involved in rifamycin biosynthesis, but might be evolutionary remnants carried over from an ancestral lineage.

Current issues in global tuberculosis control

Despite attempts to standardize tuberculosis (TB) control strategies, there remains wide variation in the selection and implementation of control strategies within and among nations. Some of this variation is appropriate; based on wide variations in the available resources, the prevalence of TB infection, the incidence of TB disease, the relative contribution of reactivation versus recent transmission to incident cases, and the rate of HIV co-infection. This review will discuss three controversial questions relevant to global TB control: (1) What is the role of the treatment of latent TB infection in global TB control? (2) What are successful strategies to control immigrant TB in low incidence countries? (3) What are successful strategies to control TB in persons with HIV infection?

Cloning and characterization of the chromosomal replication origin region of Amycolatopsis mediterranei U32

The chromosomal replication origins (oriC) of gram positive, acid-fast actinomycetes have been investigated in streptomycetes and mycobacteria. A 1339 bp DNA fragment of the putative oriC region from the rifamycin SV producer Amycolatopsis mediterranei U32 was cloned by PCR amplification employing primers designed based on the conserved flanking genes of dnaA and dnaN. The 884 bp sequence of the intergenic region between dnaA and dnaN genes consists of 19 DnaA-boxes and two 13-mer AT-rich sequences, which is similar to the oriC structure of Streptomyces lividans. A mini-chromosome constructed by cloning the putative U32 oriC DNA fragment into an Escherichia coli plasmid was able to replicate autonomously, but was unstable, in A. mediterranei U32 with an estimated copy number of two per cell. Although efficient replication of the mini-chromosome in U32 requires the complete set of DnaA-boxes and AT-rich regions, only one of the AT-rich sequences together with part of the DnaA-boxes is sufficient, suggesting the presence of combinatorial alternatives for a functional oriC region of A. mediterranei U32. Phylogenetic analysis based on definite oriC sequences among eubacteria reflects well the relationship between these species.

Clinical evaluation of the gen-probe amplified mycobacterium tuberculosis direct test for rapid diagnosis of tuberculosis lymphadenitis

This prospective study evaluated the performance of the Amplified Mycobacterium Tuberculosis Direct Test (MTD) for the diagnosis of lymph node tuberculosis in Djibouti, Republic of Djibouti. Of 197 specimens sampled from 153 patients, 123 were from 95 tuberculous patients. The sensitivity and specificity of MTD were 93 and 100%, respectively. The sensitivity of culture was 89%.

Evaluation of a modified gen-probe amplified direct test for detection of Mycobacterium tuberculosis complex organisms in cerebrospinal fluid

Laboratory evidence for tuberculous meningitis is difficult to acquire due to the low numbers of organisms present in cerebrospinal fluid (CSF) and the presence of nucleic acid amplification inhibitors. The Amplified Mycobacterium tuberculosis Direct Test (MTD) is sensitive and specific for the direct detection of M. tuberculosis complex in respiratory samples but has not been approved for CSF. We evaluated a modified version of the current MTD, optimized for use with CSF samples. Samples were prepared by spiking CSF with various numbers of M. tuberculosis complex organisms. The modified MTD performance was compared with results obtained using a purified RNA sample extracted using the Qiagen RNeasy Protect Bacteria Mini Kit. By use of CSF artificially spiked with M. tuberculosis complex, the sensitivity of the modified MTD was 100% (six of six) for CSF samples containing approximately 600 CFU/ml, 78% (seven of nine) for approximately 60 CFU/ml, 50% (three of six) for 6 CFU/ml, and 17% (one of six) for samples with <1 CFU/ml. The specificity of the modified MTD method was 100% (22 of 22). The sensitivity of the Qiagen MTD method was 100% for CSF samples containing approximately 600 CFU/ml (six of six) and approximately 60 CFU/ml (nine of nine), 50% for samples with approximately 6 CFU/ml (three of six), and 50% for samples with <1 CFU/ml (three of six). The specificity of the Qiagen MTD method was 86% (19 of 22). With the Qiagen MTD method, however, initial results were equivocal for 14 of the 27 (52%) positive samples, requiring repeat analysis, whereas with the modified MTD, only 1 of 27 (4%) was equivocal. The modified MTD for CSF samples was less time-consuming and less expensive and resulted in considerably fewer equivocal results than the Qiagen MTD method did.