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PloS One 2020We investigated the species diversity of Mycobacteriaceae in surface water samples from six environments at the zoological park in São Paulo, Brazil. Three hundred and...
We investigated the species diversity of Mycobacteriaceae in surface water samples from six environments at the zoological park in São Paulo, Brazil. Three hundred and eighty isolates were cultivated and identified by phenotypic characteristics (growth rate and pigmentation) and sequencing of hsp65, rpoB and 16S rRNA genes. The results revealed that almost 48% of the isolates could be identified at the species level; about 50% were classified at the genus level, and only less than 2% of the isolates showed an inconclusive identification. The isolates classified at the genus level and not identified were then evaluated by phylogenetic analyses using the same three concatenated target genes. The results allowed us to identify at the genus level some isolates that previously had inconclusive identification, and they also suggested the presence of putative candidate species within the sample, demonstrating that this zoological park is an important source of diversity.
Topics: Brazil; DNA, Bacterial; Genes, Bacterial; Genomics; Mycobacteriaceae; Parks, Recreational; Phylogeny; RNA, Ribosomal, 16S; Water Microbiology
PubMed: 31935265
DOI: 10.1371/journal.pone.0227759 -
MBio Mar 2021Functional characterization of bacterial proteins lags far behind the identification of new protein families. This is especially true for bacterial species that are more...
Functional characterization of bacterial proteins lags far behind the identification of new protein families. This is especially true for bacterial species that are more difficult to grow and genetically manipulate than model systems such as and To facilitate functional characterization of mycobacterial proteins, we have established a Mycobacterial Systems Resource (MSR) using the model organism This resource focuses specifically on 1,153 highly conserved core genes that are common to many mycobacterial species, including , in order to provide the most relevant information and resources for the mycobacterial research community. The MSR includes both biological and bioinformatic resources. The biological resource includes (i) an expression plasmid library of 1,116 genes fused to a fluorescent protein for determining protein localization; (ii) a library of 569 precise deletions of nonessential genes; and (iii) a set of 843 CRISPR-interference (CRISPRi) plasmids specifically targeted to silence expression of essential core genes and genes for which a precise deletion was not obtained. The bioinformatic resource includes information about individual genes and a detailed assessment of protein localization. We anticipate that integration of these initial functional analyses and the availability of the biological resource will facilitate studies of these core proteins in many species, including the less experimentally tractable pathogens , , , , , , and Diseases caused by mycobacterial species result in millions of deaths per year globally, and present a substantial health and economic burden, especially in immunocompromised patients. Difficulties inherent in working with mycobacterial pathogens have hampered the development and application of high-throughput genetics that can inform genome annotations and subsequent functional assays. To facilitate mycobacterial research, we have created a biological and bioinformatic resource (https://msrdb.org/) using as a model organism. The resource focuses specifically on 1,153 proteins that are highly conserved across the mycobacterial genus and, therefore, likely perform conserved mycobacterial core functions. Thus, functional insights from the MSR will apply to all mycobacterial species. We believe that the availability of this mycobacterial systems resource will accelerate research throughout the mycobacterial research community.
Topics: Computational Biology; Gene Library; Genes, Bacterial; Mycobacterium; Mycobacterium smegmatis; Research
PubMed: 33653882
DOI: 10.1128/mBio.02401-20 -
New Biotechnology Jan 2022Efficient and convenient genetic manipulation of mycobacteria, important microorganisms in human healthcare and the pharmaceutical industry, is limited. In this study,...
Efficient and convenient genetic manipulation of mycobacteria, important microorganisms in human healthcare and the pharmaceutical industry, is limited. In this study, using a model strain Mycolicibacterium neoaurum ATCC 25795, the classical bacterium for the production of valuable steroidal pharmaceuticals, a genome editing system employing CRISPR-Cas12a to achieve efficient and precise genetic manipulation has been developed. Targeted genome mutations could be easily achieved by the CRISPR-Cas12a system without exogenous donor templates, assisted by innate non-homologous end-joining (NHEJ). CRISPR-Cas12a enabled rapid one-step genomic DNA fragment deletions of 1 kb, 5 kb, 10 kb, 15 kb, 20 kb and 24 kb with efficiencies of 70 %, 30 %, 30 %, 20 %, 20 % and 10 %, respectively. Combined with the pNIL/pGOAL system, CRISPR-Cas12a successfully integrated the gene of interest into the targeted genomic site by single crossover and double crossovers with efficiencies of 100 % and 9 %, respectively, using a two-plasmid system. The robust CRISPR systems developed demonstrated strong potential for precise genome editing in M. neoaurum, including targeted deletion of DNA sequences of various lengths and integration of targeted genes into desired sites in the genome.
Topics: CRISPR-Cas Systems; DNA End-Joining Repair; Gene Editing; Mycobacteriaceae; Plasmids
PubMed: 34653700
DOI: 10.1016/j.nbt.2021.10.003 -
Applied Microbiology May 1965The presence in soil of large numbers of a catalase-negative, microaerophilic, coccoid microorganism was demonstrated. Use of media of high nutrient value, without...
The presence in soil of large numbers of a catalase-negative, microaerophilic, coccoid microorganism was demonstrated. Use of media of high nutrient value, without incorporation of inhibitors, and growth in the absence of antagonistic microorganisms were utilized to isolate this organism from soil dilutions greater than those providing growth by other means. The organism described does not grow on soil extract agars and is missed by conventional counting techniques for soil organisms. On the basis of morphological and growth characteristics, this organism appears to have at least some taxonomic relationships to the families Actinomycetaceae and Mycobacteriaceae. It is proposed that this organism makes up much of the coccoid microflora of soil as observed by light and ultraviolet fluorescence microscopy.
Topics: Actinomyces; Actinomycetales; California; Catalase; Classification; Culture Media; Fluorescence; Geraniaceae; Microscopy; Microscopy, Fluorescence; Mycobacterium; Pennsylvania; Research; Soil; Soil Microbiology; Ultraviolet Rays
PubMed: 14325269
DOI: 10.1128/am.13.3.327-334.1965 -
Microbial Genomics Jul 2020Mobile genetic elements (MGEs) are agents of bacterial evolution and adaptation. Genome sequencing provides an unbiased approach that has revealed an abundance of MGEs...
Mobile genetic elements (MGEs) are agents of bacterial evolution and adaptation. Genome sequencing provides an unbiased approach that has revealed an abundance of MGEs in prokaryotes, mainly plasmids and integrative conjugative elements. Nevertheless, many mobilomes, particularly those from environmental bacteria, remain underexplored despite their representing a reservoir of genes that can later emerge in the clinic. Here, we explored the mobilome of the family, focusing on strains from Brazilian Atlantic Forest soil. Novel and strains were identified, with the former ones harbouring linear and circular plasmids encoding the specialized type-VII secretion system (T7SS) and mobility-associated genes. In addition, we also identified a T4SS-mediated integrative conjugative element (ICEMyc226) encoding two T7SSs and a number of xenobiotic degrading genes. Our study uncovers the diversity of the mobilome, providing the evidence of an ICE in this bacterial family. Moreover, the presence of T7SS genes in an ICE, as well as plasmids, highlights the role of these mobile genetic elements in the dispersion of T7SS.
Topics: Brazil; Conjugation, Genetic; Forests; Gene Transfer, Horizontal; Genome, Bacterial; High-Throughput Nucleotide Sequencing; Interspersed Repetitive Sequences; Mycobacteriaceae; Phylogeny; Plasmids; Sequence Analysis, DNA; Soil Microbiology
PubMed: 32496186
DOI: 10.1099/mgen.0.000382 -
Immunological Reviews May 2021Immunity against different Mycobacteria species targeting the lung requires distinctly different pulmonary immune responses for bacterial clearance. Many parameters of... (Review)
Review
Immunity against different Mycobacteria species targeting the lung requires distinctly different pulmonary immune responses for bacterial clearance. Many parameters of acquired and regulatory immune responses differ quantitatively and qualitatively from immunity during infection with Mycobacteria species. Nontuberculosis Mycobacteria species (NTM) Mycobacterium avium- (M avium), Mycobacterium abscessus-(M abscessus), and the Mycobacteria species Mycobacterium tuberculosis-(Mtb). Herein, we discuss the potential implications of acquired and regulatory immune responses in the context of animal and human studies, as well as future directions for efforts to treat Mycobacteria diseases.
Topics: Animals; Humans; Mycobacterium abscessus; Mycobacterium avium; Mycobacterium tuberculosis; Tuberculosis
PubMed: 33713043
DOI: 10.1111/imr.12959 -
Pneumologie (Stuttgart, Germany) Aug 2019The recognition, correct diagnosis and adequate clinical management of infections caused by atypical mycobacteria are challenging tasks in clinical practice. Invasive... (Review)
Review
The recognition, correct diagnosis and adequate clinical management of infections caused by atypical mycobacteria are challenging tasks in clinical practice. Invasive infections caused by , a member of the complex, have been increasingly reported over the past few years. Most infections occurred in patients who had undergone open-chest cardiothoracic surgery. Epidemiological and molecular studies showed that transmission of occurred through intraoperative aerosols derived from contaminated heater-cooler units, i. e. devices that are used to enable the extracardiac circuit in cardiothoracic surgery. Thus far, approximately 120 patient cases have been reported worldwide. The latency between exposure and onset of clinical symptoms may comprise several years. Clinical manifestations of infections include not only endocarditis and implant-associated infections, but also non-cardiac entities such as sarcoidosis-like symptoms, vertebral osteomyelitis and chorioretinitis. The pathogen can be detected in blood culture vials and in surgically obtained specimens from affected tissues, if specific microbiological tests for detection of mycobacteria are employed. There are no simple-to-use screening tests and a high clinical index of suspicion is thus mandatory in patients with previous exposure and compatible signs and symptoms. The successful treatment of infections requires the removal of infected devices and prolonged combination therapy with antimycobacterial drugs. This review summarises the clinical relevance, epidemiology, symptomatology, diagnosis and treatment of infections caused by , with a specific focus on pneumological aspects.
Topics: Humans; Mycobacterium; Mycobacterium Infections, Nontuberculous; Mycobacterium avium Complex; Mycobacterium avium-intracellulare Infection; Nontuberculous Mycobacteria
PubMed: 31075795
DOI: 10.1055/a-0872-8809 -
Clinical Microbiology Reviews Oct 2002The history, taxonomy, geographic distribution, clinical disease, and therapy of the pathogenic nonpigmented or late-pigmenting rapidly growing mycobacteria (RGM) are... (Review)
Review
The history, taxonomy, geographic distribution, clinical disease, and therapy of the pathogenic nonpigmented or late-pigmenting rapidly growing mycobacteria (RGM) are reviewed. Community-acquired disease and health care-associated disease are highlighted for each species. The latter grouping includes health care-associated outbreaks and pseudo-outbreaks as well as sporadic disease cases. Treatment recommendations for each species and type of disease are also described. Special emphasis is on the Mycobacterium fortuitum group, including M. fortuitum, M. peregrinum, and the unnamed third biovariant complex with its recent taxonomic changes and newly recognized species (including M. septicum, M. mageritense, and proposed species M. houstonense and M. bonickei). The clinical and taxonomic status of M. chelonae, M. abscessus, and M. mucogenicum is also detailed, along with that of the closely related new species, M. immunogenum. Additionally, newly recognized species, M. wolinskyi and M. goodii, as well as M. smegmatis sensu stricto, are included in a discussion of the M. smegmatis group. Laboratory diagnosis of RGM using phenotypic methods such as biochemical testing and high-performance liquid chromatography and molecular methods of diagnosis are also discussed. The latter includes PCR-restriction fragment length polymorphism analysis, hybridization, ribotyping, and sequence analysis. Susceptibility testing and antibiotic susceptibility patterns of the RGM are also annotated, along with the current recommendations from the National Committee for Clinical Laboratory Standards (NCCLS) for mycobacterial susceptibility testing.
Topics: Anti-Bacterial Agents; Catheterization; Community-Acquired Infections; Humans; Microbial Sensitivity Tests; Mycobacterium Infections, Nontuberculous; Mycobacterium chelonae; Mycobacterium fortuitum; Mycobacterium smegmatis; Occupational Diseases; Skin Diseases, Infectious; Wound Infection
PubMed: 12364376
DOI: 10.1128/CMR.15.4.716-746.2002 -
Virulence Oct 2017
Topics: Animals; Interferon-beta; Mice; Mycobacterium tuberculosis; Nontuberculous Mycobacteria
PubMed: 28605283
DOI: 10.1080/21505594.2017.1341035 -
Microbial Genomics Mar 2021The mobilome plays a crucial role in bacterial adaptation and is therefore a starting point to understand and establish the gene flow occurring in the process of...
The mobilome plays a crucial role in bacterial adaptation and is therefore a starting point to understand and establish the gene flow occurring in the process of bacterial evolution. This is even more so if we consider that the mobilome of environmental bacteria can be the reservoir of genes that may later appear in the clinic. Recently, new genera have been proposed in the family , including the genus , which encompasses dozens of species of agricultural, biotechnological, clinical and ecological importance, being ubiquitous in several environments. The current scenario in the mobilome has some bias because most of the characterized mycobacteriophages were isolated using a single host strain, and the few plasmids reported mainly relate to the genus . To fill in the gaps in these issues, we performed a systematic study of these mobile elements based on 242 available genomes of the genus . The analyses identified 156 putative plasmids (19 conjugative, 45 mobilizable and 92 non-mobilizable) and 566 prophages in 86 and 229 genomes, respectively. Moreover, a contig was characterized by resembling an actinomycete integrative and conjugative element (AICE). Within this diversity of mobile genetic elements, there is a pool of genes associated with several canonical functions, in addition to adaptive traits, such as virulence and resistance to antibiotics and metals (mercury and arsenic). The type-VII secretion system was a common feature in the predicted plasmids, being associated with genes encoding virulent proteins (EsxA, EsxB, PE and PPE). In addition to the characterization of plasmids and prophages of the family , this study showed an abundance of these genetic elements in a dozen species of the genus .
Topics: Bacterial Proteins; Computer Simulation; Environmental Microbiology; Genetic Variation; Genome, Bacterial; Interspersed Repetitive Sequences; Microbiota; Mycobacteriaceae; Phylogeny; Plasmids; Prophages
PubMed: 33620305
DOI: 10.1099/mgen.0.000533