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      Non-tuberculous Mycobacteria isolated from Pulmonary samples in sub-Saharan Africa - A Systematic Review and Meta Analyses

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          Abstract

          Pulmonary non-tuberculous mycobacterial (NTM) disease epidemiology in sub-Saharan Africa is not as well described as for pulmonary tuberculosis. Earlier reviews of global NTM epidemiology only included subject-level data from one sub-Saharan Africa country. We systematically reviewed the literature and searched PubMed, Embase, Popline, OVID and Africa Wide Information for articles on prevalence and clinical relevance of NTM detection in pulmonary samples in sub-Saharan Africa. We applied the American Thoracic Society/Infectious Disease Society of America criteria to differentiate between colonisation and disease. Only 37 articles from 373 citations met our inclusion criteria. The prevalence of pulmonary NTM colonization was 7.5% (95% CI: 7.2%–7.8%), and 75.0% (2325 of 3096) occurred in males, 16.5% (512 of 3096) in those previously treated for tuberculosis and Mycobacterium avium complex predominated (27.7% [95% CI: 27.2–28.9%]). In seven eligible studies, 27.9% (266 of 952) of participants had pulmonary NTM disease and M. kansasii with a prevalence of 69.2% [95% CI: 63.2–74.7%] was the most common cause of pulmonary NTM disease. NTM species were unidentifiable in 29.2% [2,623 of 8,980] of isolates. In conclusion, pulmonary NTM disease is a neglected and emerging public health disease and enhanced surveillance is required.

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          Nontuberculous mycobacterial pulmonary infections.

          Pulmonary infections due to nontuberculous mycobacteria (NTM) are increasingly recognized worldwide. Although over 150 different species of NTM have been described, pulmonary infections are most commonly due to Mycobacterium avium complex (MAC), Mycobacterium kansasii, and Mycobacterium abscessus. The identification of these organisms in pulmonary specimens does not always equate with active infection; supportive radiographic and clinical findings are needed to establish the diagnosis. It is difficult to eradicate NTM infections. A prolonged course of therapy with a combination of drugs is required. Unfortunately, recurrent infection with new strains of mycobacteria or a relapse of infection caused by the original organism is not uncommon. Surgical resection is appropriate in selected cases of localized disease or in cases in which the infecting organism is resistant to medical therapy. Additionally, surgery may be required for infections complicated by hemoptysis or abscess formation. This review will summarize the practical aspects of the diagnosis and management of NTM thoracic infections, with emphasis on the indications for surgery and the results of surgical intervention. The management of NTM disease in patients with human immunodeficiency virus (HIV) infections is beyond the scope of this article and, unless otherwise noted, comments apply to hosts without HIV infection.
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            Impact of genotypic studies on mycobacterial taxonomy: the new mycobacteria of the 1990s.

            The advancement of genetic techniques has greatly boosted taxonomic studies in recent years. Within the genus Mycobacterium, 42 new species have been detected since 1990, most of which were grown from clinical samples. Along with species for which relatively large numbers of strains have been reported, some of the new species of mycobacteria have been detected rarely or even only once. From the phenotypic point of view, among the new taxa, chromogens exceed nonchromogens while the numbers of slowly and rapidly growing species are equivalent. Whereas conventional identification tests were usually inconclusive, an important role was played by lipid analyses and in particular by high-performance liquid chromatography. Genotypic investigations based on sequencing of 16S rRNA gene have certainly made the most important contribution. The investigation of genetic relatedness led to the redistribution of the species previously included in the classically known categories of slow and rapid growers into new groupings. Within slow growers, the intermediate branch related to Mycobacterium simiae and the cluster of organisms related to Mycobacterium terrae have been differentiated; among rapid growers, the group of thermotolerant mycobacteria has emerged. The majority of species are resistant to isoniazid and, to a lesser extent, to rifampin. Many of the new species of mycobacteria are potentially pathogenic, and there are numerous reports of their involvement in diseases. Apart from disseminated and localized diseases in immunocompromised patients, the most frequent infections in immunocompetent people involve the lungs, skin, and, in children, cervical lymph nodes. The awareness of such new mycobacteria, far from being a merely speculative exercise, is therefore important for clinicians and microbiologists.
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              Epidemiology of human pulmonary infection with nontuberculous mycobacteria.

              A great deal of study has gone into the assessment of the epidemiology of NTM infection and disease in many different parts of the world. Review of the available studies provides insight into the frequency of this clinical problem as well as important limitations in current data. Study methods have varied greatly, undoubtedly leading to differing biases. In general, reported rates of infection and disease are likely underestimates, with the former probably less accurate than the latter, given that people without significant symptoms are not likely to have intensive investigations to detect infection. Pulmonary NTM is a problem with differing rates in various parts of the world. North American rates of infection and disease have been reported to range from approximately 1-15 per 100,000 and 0.1-2 per 100,000, respectively (see Table 1). Rates have been observed to increase with coincident decreases in TB. MAC has been reported most commonly, followed by rapid growers and M kansasii. Generally similar rates have been reported in European studies, with the exception of extremely high rates in an area of the Czech Republic where mining is the dominant industry (see Table 2). These studies have also shown marked geographic variability in prevalence. The only available population-based studies have been in South Africa and report extremely high rates of infection, three orders of magnitude greater than studies from other parts of the world (see Table 3). This undoubtedly reflects the select population with an extremely high rate of TB and resultant bronchiectasis leading to NTM infection. Rates in Japan and Australia were similar to those reported in Europe and North America and also show significant increases over time (see Table 3). Specific risk factors have been identified in several studies. CF and HIV, mentioned above, are two important high-risk groups. Other important factors include underlying chronic lung disease, work in the mining industry, warm climate, advancing age, and male sex. Aside from HIV and CF, mining with associated high rates of pneumoconiosis and previous TB may be the most important historically, reported in studies worldwide [63]. A recurring observation is the increase in rates of infection and disease. The reason for this is unclear but may be caused by any of several contributing factors. The possibility exists that the apparent increase is either spurious or less significant than studies would suggest. Changes in clinician awareness leading to increased investigations, or laboratory methods leading to isolation and identification of previously unnoticed organisms, could play a role in this trend, and studies have been published that support [67] and refute [31] this argument. We believe such factors may contribute to but do not explain the significant increases that have been observed. A true increase could be related to the host, the pathogen, or some interaction between the two. Host changes leading to increased susceptibility could play an important role, with increased numbers of patients with inadequate defenses from diseases such as HIV infection, malignancy, or simply advanced age [31]. An increase in susceptibility could also relate to the decrease in infection with two other mycobacteria. It has been speculated that infection with TB [29,38] and Bacillus Calmette-Guerin (BCG) [19,68] may provide cross-immunity protecting against NTM infection. Many investigations have observed decreasing rates of TB concomitant with the increases in NTM. In addition, studies from Sweden [68] and the Czech Republic [19] have found that children who were not vaccinated with BCG had a far higher rate of extrapulmonary NTM infection. Potential changes in the pathogens include increases in NTM virulence, and it has been argued that this should be considered as a possible contributing factor [69]. Finally, an interaction between the host and pathogen could involve a major increase in pathogen exposure or potential inoculum size. This may be occurring secondary to the increase in popularity of showering as a form of bathing [66], a habit that greatly increases respiratory exposure to water contaminants. Several limitations of our review should be noted. We reviewed English-language reports and abstracts, probably leading to fewer data from non-English speaking regions, which may explain the paucity of studies from Africa, Eastern Europe, and most Asian nations. The heterogeneity of study methods in identifying cases and the lack of a uniformly applied definition of disease makes it difficult to compare rates between studies. Finally, the lack of systematic reporting of NTM infection in most nations limits the ability to derive accurate estimates of infection and disease. Regardless, there are more than adequate data to conclude that NTM disease rates vary widely depending on population and geographic location. NTM disease is clearly a major problem in certain groups, including patients with underlying lung disease and also in individuals with impaired immunity. The rates of NTM infection and disease are increasing, so the problem will likely continue to grow and become a far more important issue than current rates suggest.
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                Author and article information

                Contributors
                Ifedayo.Adetifa@lshtm.ac.uk
                Journal
                Sci Rep
                Sci Rep
                Scientific Reports
                Nature Publishing Group UK (London )
                2045-2322
                20 September 2017
                20 September 2017
                2017
                : 7
                : 12002
                Affiliations
                [1 ]ISNI 0000 0004 0606 294X, GRID grid.415063.5, Vaccines and Immunity Theme, Medical Research Council Unit, ; Fajara, The Gambia
                [2 ]ISNI 0000 0004 0606 294X, GRID grid.415063.5, Clinical Services Department, Medical Research Council Unit, ; Fajara, The Gambia
                [3 ]ISNI 0000 0000 8809 1613, GRID grid.7372.1, Microbiology and Infection Unit, Warwick Medical School, University of Warwick, ; Coventry, United Kingdom
                [4 ]ISNI 0000 0004 0425 469X, GRID grid.8991.9, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, ; London, United Kingdom
                [5 ]ISNI 0000 0004 0606 294X, GRID grid.415063.5, Disease Control and Elimination Theme, Medical Research Council Unit The Gambia, ; Fajara, The Gambia
                [6 ]ISNI 0000 0001 2153 5088, GRID grid.11505.30, Institute of Tropical Medicine, ; Antwerp, Belgium
                [7 ]ISNI 0000 0004 0425 469X, GRID grid.8991.9, Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, ; London, United Kingdom
                [8 ]ISNI 0000 0001 0155 5938, GRID grid.33058.3d, Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, ; Kilifi, Kenya
                [9 ]ISNI 0000 0004 1803 1817, GRID grid.411782.9, College of Medicine University of Lagos, ; Lagos, Nigeria
                Author information
                http://orcid.org/0000-0003-2556-9407
                Article
                12175
                10.1038/s41598-017-12175-z
                5607231
                28931915
                5c94bef0-6ffd-4538-80a7-8ab76762d3c5
                © The Author(s) 2017

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 6 February 2017
                : 5 September 2017
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