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Longhi G, Argentini C, Fontana F, Tarracchini C, Mancabelli L, Lugli GA, Alessandri G, Lahner E, Pivetta G, Turroni F, Ventura M, Milani C. Saponin treatment for eukaryotic DNA depletion alters the microbial DNA profiles by reducing the abundance of Gram-negative bacteria in metagenomics analyses. MICROBIOME RESEARCH REPORTS 2023; 3:4. [PMID: 38455080 PMCID: PMC10917613 DOI: 10.20517/mrr.2023.02] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 11/01/2023] [Accepted: 11/10/2023] [Indexed: 03/09/2024]
Abstract
Background: Recent advances in microbiome sequencing techniques have provided new insights into the role of the microbiome on human health with potential diagnostic implications. However, these developments are often hampered by the presence of a large amount of human DNA interfering with the analysis of the bacterial content. Nowadays, extensive scientific literature focuses on eukaryotic DNA depletion methods, which successfully remove host DNA in microbiome studies, even if a precise assessment of the impact on bacterial DNA is often missing. Methods: Here, we have investigated a saponin-based DNA isolation protocol commonly applied to different biological matrices to deplete the released host DNA. Results: The bacterial DNA obtained was used to assess the relative abundance of bacterial and human DNA, revealing that the inclusion of 2.5% wt/vol saponin allowed the depletion of most of the host's DNA in favor of bacterial DNA enrichment. However, shotgun metagenomic sequencing showed inaccurate microbial profiles of the DNA samples, highlighting an erroneous increase in Gram-positive DNA. Even the application of 0.0125% wt/vol saponin altered the bacterial profile by depleting Gram-negative bacteria, resulting in an overall increase of Gram-positive bacterial DNA. Conclusion: The application of the saponin-based protocol drastically changes the detection of the microbial composition of human-related biological specimens. In this context, we revealed that saponin targets not only host cells but also specific bacterial cells, thus inducing a drastic reduction in the profiling of Gram-negative bacterial DNA.
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Affiliation(s)
- Giulia Longhi
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma 43124, Italy
- GenProbio Srl, Parma 43124, Italy
| | - Chiara Argentini
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma 43124, Italy
| | - Federico Fontana
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma 43124, Italy
- GenProbio Srl, Parma 43124, Italy
| | - Chiara Tarracchini
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma 43124, Italy
| | - Leonardo Mancabelli
- Department of Medicine and Surgery, University of Parma, Parma 43124, Italy
- Microbiome Research Hub, University of Parma, Parma 43124, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma 43124, Italy
| | - Giulia Alessandri
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma 43124, Italy
| | - Edith Lahner
- Medical-Surgical Department of Clinical Sciences and Translational Medicine, Sant’Andrea Hospital, School of Medicine, University Sapienza, Rome 00185, Italy
| | - Giulia Pivetta
- Medical-Surgical Department of Clinical Sciences and Translational Medicine, Sant’Andrea Hospital, School of Medicine, University Sapienza, Rome 00185, Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma 43124, Italy
- Microbiome Research Hub, University of Parma, Parma 43124, Italy
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma 43124, Italy
- Microbiome Research Hub, University of Parma, Parma 43124, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma 43124, Italy
- Microbiome Research Hub, University of Parma, Parma 43124, Italy
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Jaafar J, Hitam WHW, Noor RAM. Bilateral atypical optic neuritis associated with tuberculosis in an immunocompromised patient. Asian Pac J Trop Biomed 2015; 2:586-8. [PMID: 23569976 DOI: 10.1016/s2221-1691(12)60102-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Revised: 12/02/2011] [Accepted: 02/23/2011] [Indexed: 11/29/2022] Open
Abstract
A 27 year-old lady, presented with sudden loss of vision in the right eye for a week. It was followed by poor vision in the left eye after 3 days. It involved the whole entire visual field and was associated with pain on eye movement. She was diagnosed to have miliary tuberculosis and retroviral disease 4 months ago. She was started on anti-TB since then but defaulted highly active anti-retroviral therapy (HAART). On examination, her visual acuity was no perception of light in the right eye and 6/120 (pinhole 3/60) in the left eye. Anterior segment in both eyes was unremarkable. Funduscopy showed bilateral optic disc swelling with presence of multiple foci of choroiditis in the peripheral retina. The vitreous and retinal vessels were normal. Chest radiography was normal. CT scan of orbit and brain revealed bilateral enhancement of the optic nerve sheath that suggest the diagnosis of bilateral atypical optic neuritis. This patient was managed with infectious disease team. She was started on HAART and anti-TB treatment was continued. She completed anti-TB treatment after 9 months without any serious side effects. During follow up the visual acuity in both eyes was not improved. However, funduscopy showed resolving of disc swelling and choroiditis following treatment.
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Affiliation(s)
- Juanarita Jaafar
- Department of Ophthalmology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kota Bharu, Kelantan, Malaysia
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3
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Abstract
Endobronchial tuberculosis is defined as tuberculous infection of the tracheobronchial tree. Although clinical features differ between various types and stages of endobronchial tuberculosis, common symptoms are cough, hemoptysis, sputum production, wheezing, chest pain, fever and dyspnea. Endobronchial tuberculosis is difficult to diagnose, because the lesion is not evident in the chest radiograph. Computerized tomography is very useful in evaluating bronchial lesions such as stenosis or obstruction. The most important goal of treatment in active endobronchial tuberculosis is the eradication of tubercle bacilli. The second most important goal is prevention of bronchial stenosis. Corticosteroid therapy for prevention of bronchial stenosis in endobronchial tuberculosis remains controversial, but the best results are associated with minimal delay in the initiation of steroid treatment. In inactive disease, treatment to restore full patency is appropriate. As steroids or other medication are unable to reverse stenosis from fibrous disease, airway patency must be restored mechanically by surgery or endobronchial intervention. Aerosol therapy with streptomycin and corticosteroids is useful in treatment against active endobronchial tuberculosis. Time to healing of ulcerous lesions is shorter, and bronchial stenosis is less severe in patients on aerosol therapy. Progression to bronchial stenosis may be prevented if the therapy is initiated as soon as possible.
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Affiliation(s)
- Toru Rikimaru
- The First Department of Medicine, Kurume University, School of Medicine, 67 Asahi-machi, Kurume 830, Japan.
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4
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Abstract
Endobronchial tuberculosis (EBTB) is defined as tuberculous infection of the tracheobronchial tree. Common symptoms are cough, haemoptysis, sputum production, wheezing, chest pain and fever in active disease and dyspnoea and wheezing in the fibrous stage. This form of tuberculosis is difficult to diagnose because the lesion is not evident in the chest radiograph, frequently delaying treatment. Computed tomography is very useful in evaluating bronchial lesions such as stenosis or obstruction. The most important goal of treatment in active EBTB is eradication of tubercle bacilli. The second most important goal is prevention of bronchial stenosis. Corticosteroid therapy for the prevention of bronchial stenosis in EBTB remains controversial. However, the healing time of ulcerous lesions was shorter and bronchial stenosis was less severe, in patients treated with aerosol therapy, consisting of streptomycin 100 mg, a corticosteroid (dexamethasone 0.5 mg) and naphazoline 0.1 mg administered twice-daily along with conventional oral therapy. In inactive disease, treatment to restore full patency is appropriate. As steroids or other medications are unable to reverse stenosis from fibrous disease, airway patency must be restored mechanically by surgery or endobronchial intervention. Effectiveness and complications remain important issues with the mechanical techniques as use and evaluation continue. Corticosteroid therapy for prevention of bronchial stenosis in EBTB remains controversial. Our observations suggest that progression of bronchial stenosis can be prevented in patients who are treated with aerosol therapy with corticosteroids.
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Affiliation(s)
- Toru Rikimaru
- Kurume University School of Medicine, The First Department of Medicine, 67 Asahi-machi, Kurume 830, Japan.
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5
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Egeli E, Oghan F, Alper M, Harputluoglu U, Bulut I. Epiglottic Tuberculosis in a Patient Treated with Steroids for Addison's Disease. TOHOKU J EXP MED 2003; 201:119-25. [PMID: 14626513 DOI: 10.1620/tjem.201.119] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Isolated epiglottic tuberculosis (TBC) is uncommon and has rarely been described. We report the case of a 40-year-old man with tuberculous involvement of the epiglottis and primary adrenal insufficiency. Endoscopic examination showed a severely swollen epiglottis with granulomatous and partially necrotic mucosa. The patient has been treated with glucocorticoids for four years due to primary adrenocortical insufficiency. We therefore assume that tuferculous involvement of epiglottis is due to the reactivation of pulmonary TBC. We also discuss differential diagnosis and management of epiglottic TBC and Addison's disease.
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Affiliation(s)
- Erol Egeli
- Department of Otorhinolaryngology, Düzce Faculty of Medicine, University of Abant Izzet Baysal, Konuralp, Duzce, Turkey
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Mínguez C, Roca B, González-Miño C, Simón E. Superior vena cava syndrome during the treatment of pulmonary tuberculosis in an HIV-1 infected patient. J Infect 2000; 40:187-9. [PMID: 10841098 DOI: 10.1016/s0163-4453(00)80015-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Tuberculosis is nowadays an uncommon cause of superior vena cava syndrome (SVCS). We report the case of an HIV-infected patient who presented with respiratory symptoms accompanied by cervical and mediastinal lymphadenopathy. Sputum examination showed acid-fast bacilli, and treatment was instituted with isoniazid, rifampicin, pyrazinamide and ethambutol. A few days later SVCS developed, presumably as a consequence of inflammatory lymphadenitis. With corticosteroids, all symptoms disappeared. To our knowledge, no cases of SVCS provoked by this kind of paradoxical reaction have been described previously.
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Affiliation(s)
- C Mínguez
- Department of Medicine, Hospital General de Castellón, Spain
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Werneck-Barroso E, Bonecini-de-Almeida MD, Vieira MA, Carvalho CE, Teixeira AK, Kritski AL, Ho JL. Preferential recruitment of phagocytes into the lung of patients with advanced acquired immunodeficiency syndrome and tuberculosis. Respir Med 2000; 94:64-70. [PMID: 10714481 DOI: 10.1053/rmed.1999.0669] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Limited data are available on the cellular and immunocytological characteristics of bronchoalveolar lavage (BAL) fluid in individuals infected with the human immunodeficiency virus (HIV) and pulmonary tuberculosis (TB). The immune host response against tuberculosis in early HIV-infection may differ from that in later stages of HIV disease, as is strongly suggested by different clinical and radiographic patterns. We studied the cellular elements in the lungs of 15 HIV-infected patients with advanced immunosuppression and pulmonary tuberculosis (TB/AIDS). The findings were compared with data from four other groups: 1) 15 HIV-seronegative patients with pulmonary TB; 2) 12 HIV-seropositive TB patients without previous AIDS-defining illnesses and with CD4+ >200 cells mm(-3); 3) five AIDS patients without pulmonary lesions; and 4) five healthy controls. BAL fluid and differential cell counts, as well as lymphocyte subsets, were determined. Despite a low CD4/CD8 ratio, the TB/AIDS group had a higher absolute number of CD8+ lymphocytes in the BAL fluid than the other groups. Alveolar macrophages and neutrophils were significantly increased in TB/AIDS patients compared to control groups. The number of eosinophils was increased in TB/HIV--patients but not in TB/AIDS patients. We conclude that tuberculosis in late stage HIV-infected patients has a distinct inflammatory cell profile, suggesting an enhanced compensatory mechanism that amplifies the unspecific inflammatory reaction.
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Affiliation(s)
- E Werneck-Barroso
- Thorax Disease Institute, Federal University of Rio de Janeiro, RJ, Brazil.
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8
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Vignes S, Wechsler B. [Role of corticosteroid therapy in non-malignant diseases]. Rev Med Interne 1998; 19:799-810. [PMID: 9864778 DOI: 10.1016/s0248-8663(98)80384-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
INTRODUCTION As short-term corticosteroid therapy is widely used in clinical practice, it is important to determine its precise indications and limits of use. CURRENT KNOWLEDGE AND KEY POINTS Duration of short-term corticosteroid therapy is arbitrarily considered to be up to 21 days. Anti-inflammatory, antiproliferative or analgesic actions represent the main pharmacological features of steroids. They are related to the interactions of steroids with cytokines and immune cells. Results of randomized double-blind and uncontrolled clinical studies were included in this review. Furthermore, clearly demonstrated results that were obtained more particularly in neurology, otorhinolaryngology, pneumology, infectious diseases, rheumatologic and traumatic processes are summarized. FUTURE PROSPECTS AND PROJECTS Indications for short-term corticosteroid therapy are well established. However, further clinical studies are required, as current prescription of corticosteroid is still empirical in the management of most diseases.
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Affiliation(s)
- S Vignes
- Service de médecine interne, hôpital Saint-Louis, Paris, France
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10
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Abstract
In the last decade, sub-Saharan Africa has experienced an explosive increase in tuberculosis (TB) cases, largely as a result of the co-epidemic of human immunodeficiency virus (HIV) infection. This article reviews the essential background epidemiology of TB in sub-Saharan Africa. The clinical features and diagnostic problems of pulmonary/extrapulmonary TB in adults and children are discussed, particularly in relation to HIV infection. Different treatment regimens, their cost, adverse reactions, the ways in which HIV infection influences treatment response and the extent of drug resistance are reviewed. The recommended approaches to TB control in Africa, including methods used to prevent TB through Bacillus Calmette-Guerin and chemoprophylaxis are examined. The success achieved by good National TB Control Programmes in some African countries allows cautious optimism that this epidemic can be controlled.
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Affiliation(s)
- A D Harries
- Department of Medicine, College of Medicine, Malawi, Central Africa
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11
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Abstract
OBJECTIVE To examine the effects of corticosteroids used for concomitant disease states in patients with latent or active tuberculosis (TB). The role of corticosteroids in the treatment of extrapulmonary TB is also discussed. DATA SOURCES A MEDLINE search was conducted for the years 1953-1995. The International Pharmaceutical Abstracts service was also used to conduct an extensive literature review. In addition, relevant articles were cross-referenced to screen for additional information. STUDY SELECTION/DATA EXTRACTION During the literature review, emphasis was placed on human studies and individual case reports. DATA SYNTHESIS The resurgence of TB in this decade has affected many populations, especially immunocompromised patients. These patients may need corticosteroid therapy for various concomitant diseases that might predispose a patient to develop primary TB infection or reactivate latent TB infection. In appropriate patients, prophylaxis with isoniazid is recommended. Corticosteroid therapy may benefit patients with some forms of extrapulmonary TB. After steroid therapy, improved survival and more rapid reduction of tuberculous symptoms have been noted in cases of tuberculous pleurisy, endobronchial TB, tuberculous meningitis, and tuberculous pericarditis. Corticosteroids may also be useful in controlling both fever and hypersensitivity reactions in pulmonary and extrapulmonary TB, although not routinely used for this purpose. CONCLUSIONS Corticosteroids may play an important role in TB infection by promoting reactivation of latent infection. Corticosteroids may modify symptoms of some forms of extrapulmonary TB, although randomized, placebo-controlled studies are needed before corticosteroids will have a definitive place in the standard therapy of TB.
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Affiliation(s)
- J R Cisneros
- Department of Pharmaceutical Services, Morton Plant Mease Healthcare, Clearwater, FL 34617, USA
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12
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Mofredj A, Guérin JM, Leibinger F, Masmoudi R. Paradoxical worsening in tuberculosis during therapy in an HIV-infected patient. Infection 1996; 24:390-1. [PMID: 8923052 PMCID: PMC7102111 DOI: 10.1007/bf01716088] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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13
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Muthuswamy P, Hu TC, Carasso B, Antonio M, Dandamudi N. Prednisone as adjunctive therapy in the management of pulmonary tuberculosis. Report of 12 cases and review of the literature. Chest 1995; 107:1621-30. [PMID: 7781357 DOI: 10.1378/chest.107.6.1621] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
A retrospective chart review was conducted over a 5-year period (1988 to 1993) in a tertiary inpatient care center on the effects of the addition of prednisone to the treatment regimens of 12 patients with pulmonary tuberculosis who continued to spike high temperatures and lose weight while showing bacteriologic response to effective antituberculosis therapy. After exclusion of other causes of fever, all patients were treated with 20 to 60 mg of prednisone daily until normalization of temperature and clinical improvement. Analyzed data included twice weekly sputum bacillary count, temperature record every 4 h, weekly patient weight, serum albumin level, liver function tests, and chest roentgenogram. The patients continued to spike temperatures of 38.3 degrees C to 40.5 degrees C (mean +/- SD = 39.6 degrees C +/- 0.6 degrees C) even after 18 to 53 days (mean +/- SD = 33.9 +/- 9.8 days) of antituberculosis therapy. Within 24 h after the addition of oral prednisone, temperature decreased in all 12 patients from a daily highest spike mean of 39.6 degrees C +/- 0.6 degrees C (SD) to 38.1 degrees C +/- 0.6 degrees C (SD) (p = 0.0022). The duration of required prednisone therapy was 20.1 +/- 9 days (mean +/- SD). During this period patients' appetites improved, and their weight increased from a mean (+/- SD) of 53.6 +/- 5.7 kg to 58.1 +/- 6.4 kg (p = 0.0022). The serum albumin level increased from a mean (+/- SD) of 2.51 +/- 0.4 g/dL to 3.21 +/- 0.4 g/dL (p = 0.0033). All the patients also showed clinical evidence of a decrease in toxic reactions associated with tuberculosis. There were no side effects from the addition of prednisone. This study shows the need for randomized controlled clinical trials to clarify the role of prednisone as adjunctive therapy in the management of pulmonary tuberculosis.
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Affiliation(s)
- P Muthuswamy
- Division of Pulmonary Diseases and Critical Care Medicine, Cook County Hospital, Chicago, IL 60612, USA
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14
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Abstract
Common for all older studies is the use of less potent anti-tuberculosis chemotherapy as compared with the present. The results of these studies cannot without reservation be used in the present setting. The newer, prospective, randomized placebo-controlled trials include rather few patients and their number is limited. The results must be interpreted carefully. There is no reason to give prophylactic isoniazide treatment to Mantoux-positive patients or patients with earlier tuberculosis who start treatment with corticosteroids. If allergic reactions to one of the antituberculous drugs emerge during therapy, the treatment can, if necessary, be continued if corticosteroids are added. Pericardial tuberculosis and atelectasis in children with endobronchial tuberculosis should be treated with corticosteroids, as can pleural disease with prolonged fever and exudation. Cases of severe pulmonary tuberculosis may be treated with supplementary steroids. The effect seems modest. Patients with tuberculous meningitis, stages II and III seem to benefit from corticosteroid-treatment.
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Affiliation(s)
- T Senderovitz
- Department of Pulmonary Medicine P, Bispebjerg Hospital, Copenhagen, Denmark
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15
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Abstract
The impact of the acquired immunodeficiency syndrome (AIDS) pandemic has made tuberculosis an increasing worldwide problem, and the effectiveness of modern chemotherapy has been blunted by the high incidence of primary drug resistance, especially in developing countries. The prospect of finding new and highly effective drugs similar to isoniazid or rifampicin is dim, yet the maximum benefits from the existing drugs which are highly effective have not been received. A 6-month regimen of isoniazid plus rifampicin, supplemented by pyrazinamide during the first 2 months, for treatment of uncomplicated tuberculosis is highly effective and the regimen of choice. Ethambutol should be added if the risk of isoniazid resistance is increased. A regimen of isoniazid, rifampicin, pyrazinamide and streptomycin for 4 months provides effective defence against smear-negative pulmonary tuberculosis. Re-treatment of multiple drug-resistant tuberculosis remains a difficult therapeutic problem. At least 3 drugs that the patient has never previously received, and that are effective according to laboratory susceptibility testing, must be used. Preventive therapy against tuberculosis is accomplished with isoniazid for 6 to 12 months, although rifampicin plus isoniazid for 3 months has been used in the United Kingdom with success. In a mouse model, rifampicin plus pyrazinamide for 2 months is more effective than isoniazid for 6 months as preventive treatment. Patient noncompliance with medication remains the biggest problem in tuberculosis control, and is a complex issue. It can only be resolved by multiple approaches. Intermittent directly observed short course chemotherapy is a major, but not the only, possible solution.
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Affiliation(s)
- P T Davidson
- Department of Tuberculosis Control, Los Angeles County Department of Health Services, California
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Affiliation(s)
- M Parsons
- Department of Neurology, General Infirmary, Leeds, UK
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