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Mycobacterium

Mycobacterium is a genus of aerobic, non-spore-forming, rod-shaped bacteria that are well-known for their pathogenic species, including the causative agents of tuberculosis and leprosy.
These bacteria have a unique cell wall structure that contributes to their resilience and ability to persist in host tissues.
Mycobacterial infections can present a significant public health challenge, and research into effective diagnostics, treatments, and prevention strategies is critical.
PubCompare.ai's AI-powered platform can help optimize your Mycobacterium research by easily identifying the most reproducible and accurate findings from scientific literature, preprints, and patents, empowering your work with greater effeciency and confidence.

Most cited protocols related to «Mycobacterium»

We collected 1562 virus RefSeq genomes infecting prokaryotes and 31,986 prokaryotic host RefSeq genomes from NCBI in May 2015. The NCBI accession numbers of the RefSeq sequences are provided in the Additional file 2: Table S2. To mimic fragmented metagenomic sequences, for a given length L = 500, 1000, 3000, 5000, and 10000 bp, viruses were split into non-overlapping fragments of length L and the same number of non-overlapping fragments of length L were randomly subsampled from the prokaryotic genomes. Fragments were generated for virus genomes discovered before 1 January 2014 and after 1 January 2014 and were separately used as training and testing sets, respectively (Table 1). To generate evaluation datasets containing 10, 50, and 90% viral contigs, the number of viral contigs was set as in Table 1 and was combined with 9 times more, equal numbers, or 9-fold less randomly sampled host contigs, respectively.
Highly represented host phyla (Actinobacteria, Cyanobacteria, Firmicutes, Proteobacteria) and genera (Mycobacterium, Escherichia, Pseudomonas, Staphylococcus, Bacillus, Vibrio, and Streptococcus) were selected for the analyses where viruses infecting these taxa were excluded from the training of VirFinder. For evaluation of the different trained VirFinder models, equal numbers of contigs of the excluded viruses and all other viruses were selected and then combined with randomly selected host contigs such that total virus and host contigs were equal in number.
For the analysis of VirFinder trained with 14,722 prokaryotic genomes with or without proviruses removed, these genomes were downloaded from the database cited in [6 (link)]. Likewise, the positions of proviruses predicted by VirSorter in these 14,722 genomes were obtained from the published data of [6 (link)] and were used to remove theses sequence from their corresponding host genomes.
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Publication 2017
Actinomycetes Bacillus Cyanobacteria Escherichia Firmicutes Genome Metagenome Mycobacterium Prokaryotic Cells Proteobacteria Proviruses Pseudomonas Staphylococcus Streptococcus Vibrio Viral Genome Virus
We sequenced isolates of M tuberculosis from an archive of more than 13 000 frozen cultures obtained between 1994 and 2011 that is held at the UK Health Protection Agency (HPA) Regional Mycobacterial Reference Laboratory for the Midlands, South Yorkshire, and Humberside (Heartlands Hospital NHS Foundation Trust, Birmingham, UK).
We selected isolates to estimate genomic diversity within and between hosts and categorised them into four groups. First, we estimated within-host cross-sectional diversity from paired pulmonary and extrapulmonary isolates received within 1 month of each other. Cross-sectional samples were selected at random until 50 pairs had been successfully located, cultured, and prepared for whole-genome sequencing. Second, we measured within-host longitudinal diversity, with two or more pulmonary isolates from the same patient separated by at least 6 months. We intended to select 100 longitudinal isolates, preferentially those from patients with the largest intervals between samples. Third, we estimated between-host diversity in a transmission chain from household outbreaks. We selected all isolates from household outbreaks identified by the reference laboratory. Fourth, we measured diversity within community-based MIRU-VNTR-defined clusters (including school clusters) to specifically investigate what additional benefits whole-genome sequences might provide as compared with MIRU-VTNR. We selected eleven MIRU-VNTR-based community clusters (six to 47 patients) identified by public health teams as containing some cases in which direct case-to-case transmission was supported and others where it was uncertain. These clusters were matched at 15 or 24 MIRU-VTNR loci according to the typing protocol at the time of referral. To relate school clusters to their community, we added local 24-locus MIRU-VNTR matching cases when available. To investigate potential clustering across 24-locus MIRU-VNTR types, some clusters were extended to include isolates that did not match at up to two loci.
In England and Wales, some diseases have to be reported to local authorities (Public Health Act 1984). Public health action taken as a result of notification and surveillance is one of the HPA's key roles and the 2003 HPA Act and the 2002 Statutory Instrument 1438 provide the legislative cover to undertake necessary follow-up. Part of this follow-up is identification of links between cases, which is made possible by increasingly robust methods. A UK Clinical Research Collaboration grant enabled whole-genome sequencing, which offered the potential to detect genetic differences with improved resolution to further identify possible case links or refute such links on the basis of strain divergence. Such methods will increasingly be used in the future and the purpose of the grant was to see how useful such methods would be in practice now. Less robust methods to identify genetic differences were already in routine use in laboratories and it was therefore argued that, as a service-delivery assessment, a research ethics committee application was not warranted for this work.
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Publication 2013
ARID1A protein, human Childbirth Disease Outbreaks Ethics Committees, Research Freezing Genome Households Lung Mycobacterium Mycobacterium tuberculosis Obstetric Delivery Patients Strains Transmission, Communicable Disease Variable Number of Tandem Repeats
Cas9 sequences were identified by Blast42 (link) or obtained from published studies24 (link)–26 . Cas9 nuclease activity was inactivated by making the homologous D10A and H840A (S. pyogenes numbering) mutations in the RuvC and HNH nuclease domains for each Cas9 protein. dcas9 alleles were then codon optimized for mycobacterial expression with Jcat43 (link) and synthesized by Genscript. dCas9 protein sequences used in this study are listed in Supplementary Table 1. Single-plasmid platforms were generated for all dcas9 alleles that contained: 1) the dcas9 allele under the control of a Tet repressor (TetR)-regulated UV15-Tet promoter1 (link) or an optimized, synthetic TetR-regulated promoter (Supplementary Figure 4, Supplementary Table 1); 2) the cognate sgRNA under the control of a minimal synthetic constitutive promoter or an optimized, synthetic TetR-regulated promoter (Supplementary Figure 4, Supplementary Table 1); 3) a Tet repressor; 4) a single-copy L5-integrating backbone44 (link); 5) a pBR322-derived E. coli replication origin; and 6) a kanamycin-selectable marker. sgRNA scaffold sequences were obtained from published studies25 ,26 or engineered by fusing the crRNA direct repeat to the tracrRNA in an analogous manner to the S. pyogenes sgRNA11 (link). We attempted to enrich for highly active dCas9Spy sgRNAs by selecting top-scoring sgRNAs based on the algorithm described in Doench et al.45 (link). All sgRNA scaffold sequences used in this study are listed in Supplementary Table 1.
To clone sgRNA targeting sequences, the sgRNA scaffolds were designed with two unique BsmBI restriction sites immediately 5’ to the sgRNA scaffold sequence. Complementary sgRNA targeting oligos (N20–25) were then annealed and ligated (T4 DNA ligase, NEB) into the BsmBI-digested CRISPRi vector backbone. To clone multiple sgRNAs into the same vector, the CRISPRi vector backbones were designed with a SapI-based Golden Gate cloning site 3’ to the first sgRNA scaffold. sgRNA targeting sequences are listed in Supplementary Table 2.
To construct the Renilla luciferase reporter plasmid, the Renilla gene was cloned downstream of the G13 promoter from Mycobacterium marinum46 (link) with a synthetic 5’ untranslated region (UTR) in a single-copy Giles integrating vector47 (link). The Renilla 5’UTR was engineered such that the optimal PAM for each dCas9 protein could be tested with an identical sgRNA targeting sequence (UTR1) for all dCas9 proteins. The Renilla reporter sequences used for each dCas9 protein are shown in Supplementary Table 1.
Publication 2016
2',5'-oligoadenylate Alleles Amino Acid Sequence Cloning Vectors Codon crRNA, Transactivating Direct Repeat Escherichia coli Genes Kanamycin Luciferases, Renilla Mutation Mycobacterium Plasmids Protein Domain Proteins Replication Origin RNA, CRISPR Guide Sea Pansy Streptococcus pyogenes T4 DNA Ligase tetracycline resistance-encoding transposon repressor protein Untranslated Regions Vertebral Column
MTB H37Rv was used for all experiments with the single exception of one experiment performed in M. smegmatis (Supplementary Fig. 21). This MTB strain was fully sequenced by the Broad Institute (GI:397671778). For Chip-Seq, cells were cultured in Middle brook 7H9 with ADC (Difco), 0.05% Tween 80, and 50 µg ml−1 hygromycin B at 37 °C with constant agitation and induced with 100 ng ml−1 anhydrotetracycline (ATc) during mid-log-phase growth, and ChIP was performed using a protocol optimized for mycobacteria and related Actinomycetes. For the hypoxia and re-aeration time-course, bacilli were cultured in bacteriostatic oxygen-limited conditions (1% aerobic O2 tension) for seven days, followed by re-aeration. Bacteria were cultured in Sauton’s medium without detergent or exogenous lipid source. Profiling samples were collected as described in the Supplementary Text. All data available at http://TBDB.org. Expression data also available at GEO (accession number GSE43466).
Publication 2013
Actinomycetes anhydrotetracycline Bacteria Bacteria, Aerobic Cells Chromatin Immunoprecipitation Sequencing Culture Media Detergents DNA Chips Hygromycin B Hypoxia Lacticaseibacillus casei Lipids Mycobacterium Strains Tween 80
Patients meeting the clinical eligibility criteria were asked to provide three sputum specimens over a 2-day period (two spot samples and one obtained in the morning) (Fig. 1). In a random fashion, two of the three samples were processed with N-acetyl-l-cysteine and sodium hydroxide (NALC–NaOH),14 followed by centrifugation, and then were resuspended in 1.5 ml of phosphate buffer and subjected to microscopy with Ziehl–Neelsen staining, and cultivation on solid medium (egg-based Löwenstein–Jensen15 or 7H11,16 (link) with the latter medium used only in Durban) and liquid medium (BACTECMGIT [mycobacteria growth indicator tube] 960 culture; BD Microbiology Systems), and the MTB/RIF test. The third sputum sample was tested directly by Ziehl–Neelsen microscopy and the MTB/RIF test without NALC–NaOH decontamination.
The first positive culture from each specimen underwent confirmation of M. tuberculosis species by MPT64 antigen detection (Capilia TB, Tauns Laboratories)17 (link) and indirect drug-susceptibility testing with the proportion method on Löwenstein–Jensen medium (for sites in Lima, Durban, and Baku) or MGIT SIRE18 (for sites in Cape Town and Mumbai). For three sites, conventional nucleic acid–amplification testing was carried out on DNA that was extracted from the NALC–NaOH centrifugation pellet of the first sputum sample with the use of Cobas Amplicor MTB (Roche) (in Cape Town and Mumbai) or ProbeTec ET MTB Complex Direct Detection Assay (BD) (in Baku), according to the manufacturer's instructions. At three sites, drug-resistant genotyping was carried out by line-probe assay with the use of the Geno-type MTBDRplus assay (Hain Lifescience) performed from culture isolates (in Baku) or from the NALC–NaOH pellet of the second sputum sample (in Cape Town and Durban), according to the manufacturer's instructions, except that smear-negative specimens were also tested.
All participating laboratories were quality-assured reference laboratories. Study laboratories for four sites were located within 5 km of the enrollment clinic and tested samples within 2 days after collection. Sputum samples from Baku were shipped to the German National Reference Laboratory in Borstel for testing 1 to 5 days after collection.
Repeat tuberculosis analyses (smear, culture, MTB/RIF test, radiography, and clinical workup) were performed in patients who had smear- and culture-negative samples if the MTB/RIF test or other nucleic acid–amplification test was positive or if the patient was selected by the central database as a random control for follow-up. The final diagnosis for patients undergoing repeat analyses was established on the basis of conventional laboratory results and clinical information by clinical review committees composed of three local tuberculosis clinicians. HIV results were obtained by review of clinical records and were available for only a subgroup of patients. Bias was minimized through blinding, since technicians performing molecular and reference tests were not aware of the results of other tests. The interpretation of data from MTB/RIF tests was software-based and independent of the user. Clinical teams and review committees did not have access to nucleic acid–amplification test results. All study coordinators received lists of patients for follow-up but not the reasons for follow-up.
Publication 2010
Acetylcysteine Antigens Biological Assay Buffers Centrifugation Decontamination Diagnosis Eligibility Determination Genotype Microscopy Mycobacterium Mycobacterium tuberculosis Nucleic Acid Amplification Tests Patients Pharmaceutical Preparations Phosphates Sodium Hydroxide Sputum Substance Abuse Detection Susceptibility, Disease Tuberculosis X-Rays, Diagnostic

Most recents protocols related to «Mycobacterium»

Example 4

Composite MTB peptide vaccines induce antibodies that recognize the conserved MTB Alpha Crystallin HSP epitope (designated as TB Pep01) derived from Mycobacterium tuberculosis H37Rv (NC_000962.2).

Serum antibodies from mice 1433-1436 (see FIG. 26) immunized with 50 ug TB Pep01 CRM-conjugated vaccine demonstrated good responses to the conserved MTB epitope (alpha crystallin HSP), TB Pep01. Mouse 1435 (see FIG. 27), selected for fusion, produced hybridomas LD7 I BB2 and CA6 II GA8 that demonstrated good binding activity to TB Pep01 and TB Pep02 epitopes (FIG. 28). Monoclonal antibodies LD7 I BB2 I B9 and CA6 II GA8 I A5 (hereafter referred to as mAb LD7 and CA6) that were developed from the hybridomas not only bound to TB Pep01, but also to live M. smegmatis (see FIG. 29). Importantly, mAbs LD7 and CA6 promoted opsonophagocytic killing of mycobacteria (see FIGS. 30 and 31).

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Patent 2024
alpha-Crystallins Antibodies Epitopes Figs Hybridomas Monoclonal Antibodies Mus Mycobacterium Mycobacterium tuberculosis H37Rv Serum Vaccines, Conjugate Vaccines, Peptide

EXAMPLE 8

Selectivity is a critical requirement when developing novel therapeutics to minimize off-target risk towards mammalian cells or symbiotic bacteria. Dissipating the PMF is an appealing mechanism to combat TB. Although the collapse of the PMF itself is not bactericidal in most species, the survival of both growing and dormant Mtb necessitates a polarized membrane. PMF is composed of two main parameters: Δψ and ΔpH, where the membrane potential (Δψ) plays a greater role in mycobacteria. To measure the Δψ an assay using a potential-sensitive fluorescent dye [i.e., 3,3′-dipropylthiadicarbocyanine iodide, DiSC3(5)] was conducted. As shown in FIG. 13, the self-quenched dye in a hyperpolarized membrane was released to the solution (i.e., fluorescence increase) upon addition of OCG at 2×MIC, indicating that OCG disrupted Δψ, similarly to the positive control, VER (FIG. 13).

Meanwhile, cyanide m-chlorophenyl hydrazone (CCCP), a commonly used protonophore that collapses both of the components of the PMF did not exhibit concentration-dependent potential changes (FIG. 15). This is largely due to the interference on the fluorescence signals of DiSC3 (5) dye quenched by the ionophore.

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Patent 2024
Bacteria Biological Assay Carbonyl Cyanide m-Chlorophenyl Hydrazone Cells Cyanides Fluorescence Fluorescent Dyes Genetic Selection Hydrazones Iodides Ionophores Mammals Membrane Potentials Mycobacterium Shock Symbiosis Therapeutics Tissue, Membrane
A macrolide- and aminoglycoside-resistant (clarithromycin MIC >16 μg/mL and amikacin MIC >64 μg/mL) isolate of M. intracellulare, previously identified by 16S rRNA gene sequence, was prepared for inoculating the marmosets. The clinical isolate was grown on Middlebrook 7H10 agar. After adequate growth was obtained (approximately 7–10 days), several colonies were transferred to 3 mL of sterile distilled water to prepare a suspension with optical density equal to a 0.5 McFarland standard by nephelometer reading. The inoculum was chosen since this turbidity represents the approximate number of organisms (108 CFU/mL) present in the matched turbidity McFarland standard used for antimicrobial susceptibility testing as recommended by the Clinical and Laboratory Standards Institute (CLSI) [17 ]. The suspension was incubated for 7 days at 35°C and 1–3 mL aliquots prepared to be used to inoculate the marmosets.
BAL and tissue samples were processed and cultured for mycobacteria by the Mycobacteria/Nocardia Research Laboratory at the UTHSCT, using standard decontamination procedures, fluorochrome microscopy, solid media culture on a biplate of Middlebrook 7H10 agar with and without antibiotics, and a broth culture (BACTEC 960, Becton Dickinson and Company, Sparks, MD, VersaTrek, Thermofisher, formerly Trek Diagnostic Systems, Cleveland, Ohio) as previously described [18 ]. M. intracullulare isolates were identified using AccuProbe (Hologic-GenProbe, San Diego, CA, as previously described [18 ]. In vitro susceptibility testing of MAC isolates was performed as previously described [17 ]. M. intracellulare growth on broth and solid media was assessed using semi-quantitative scoring: growth on broth medium only = “pos”, growth in broth medium plus 1–49 countable colonies (cc) on solid medium, 50–99 cc on solid medium = 1+, 100–199 cc on solid medium = 2+, 200–299 cc on solid medium = 3+, greater than 300 cc on solid medium = 4+ [19 (link)].
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Publication 2023
Agar Amikacin Aminoglycosides Antibiotics, Antitubercular Callithrix Clarithromycin Clinical Laboratory Services Decontamination Diagnosis Fluorescent Dyes Genes Macrolides Microbicides Microscopy Mycobacterium Nocardia RNA, Ribosomal, 16S Sterility, Reproductive Susceptibility, Disease Tissues
The seven adult marmosets were inoculated endobronchially at the level of the main carina using a special narrow diameter bronchoscope with one mL of a 108 CFU/mL M. intracellulare obtained from the Mycobacteria/Nocardia Research Laboratory at the UTHSCT. All procedures (bronchoscopy, blood draws and euthanasia) were conducted under ketamine anesthesia with the additional use of isoflurane anesthesia with bronchoscopy and bronchoalveolar lavage (BAL) in the presence of veterinary staff. Each animal underwent assessment of serum chemistry, and complete blood count prior to inoculation and on the day of euthanasia. Because there are no previous comparable studies with this primate, we sacrificed a group of animals at 30 days and another group at 60 days to optimize the chance of recovering M. intracelluare as well as to define the time course of an evolving inflammatory response. Cytokine analysis was obtained prior to inoculation with M. intracellualre and on a weekly basis from day 0 to day 30 for all animals and again on day 60 for the animals sacrificed at day 60. All the animals had BAL performed prior to euthanasia at either 30- or 60-days post-inoculation. The animals were then taken directly to necropsy by a primate pathologist.
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Publication 2023
Adult Anesthesia Animals Autopsy Bronchoalveolar Lavage Bronchoscopes Bronchoscopy Callithrix Complete Blood Count Cytokine Euthanasia Inflammation Isoflurane Ketamine Mycobacterium Myeloid Progenitor Cells Nocardia Pathologists Phlebotomy Primates Serum Vaccination
Relevant research articles were searched using two search terms from two different databases, (Google Scholar, Embase, Scopus, PubMed, and Web All of Science) detailed as follow:

Mycobacterium tuberculosis” [MeSH Terms] OR (“mycobacterium” [All Fields] AND “tuberculosis” [All Fields]) OR “Mycobacterium tuberculosis” [All Fields] OR (“tuberculosis” [All Fields] AND “mycobacterium” [All Fields]) OR “tuberculosis mycobacterium” [All Fields]) AND (“tuberculosis” [All Fields] OR “tuberculosis” [MeSH Terms] OR “tuberculosis” [All Fields] OR “tuberculoses” [All Fields] OR “tuberculosis” [All Fields]) AND (“Schistosoma mansoni” [MeSH Terms] OR (“schistosoma” [All Fields] AND “mansoni” [All Fields]) OR “Schistosoma mansoni” [All Fields]) AND (“co-infect” [All Fields] OR “co-infected” [All Fields] OR “co-infecting” [All Fields] OR “co-infection” [MeS Terms] OR “co-infection” [All Fields] OR “co-infections” [All Fields] OR “co-infects” [All Fields]).

All full-text articles found throughout this database search were assessed and all those eligible with an abstract in English were included in this study regardless of the language of the full article.
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Publication 2023
Coinfection Mycobacterium Mycobacterium tuberculosis Schistosoma Schistosoma mansoni Tuberculosis

Top products related to «Mycobacterium»

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Tween 80 is a non-ionic surfactant and emulsifier. It is a viscous, yellow liquid that is commonly used in laboratory settings to solubilize and stabilize various compounds and formulations.
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Middlebrook 7H9 broth is a type of culture media used for the growth and maintenance of mycobacteria, such as Mycobacterium tuberculosis. It provides essential nutrients and growth factors required by these bacteria.
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The BACTEC MGIT 960 is a fully automated mycobacterial detection system that utilizes liquid culture technology to facilitate the rapid detection of mycobacteria, including Mycobacterium tuberculosis, in clinical specimens. The system employs fluorescence-based technology to continuously monitor the growth of mycobacteria in culture tubes, providing timely and accurate results.
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The MGIT 960 is a laboratory instrument designed for the automated detection and identification of mycobacteria in clinical samples. It utilizes liquid culture technology to rapidly detect the presence of mycobacteria, including Mycobacterium tuberculosis, in a controlled and efficient manner.
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Glycerol is a colorless, odorless, and viscous liquid used in various laboratory applications. It is a basic chemical compound with the molecular formula C₃H₈O₃. Glycerol is commonly used as a solvent, humectant, and stabilizer in many laboratory procedures.
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The Xpert MTB/RIF is a molecular diagnostic test developed by Cepheid. It is designed to detect the presence of Mycobacterium tuberculosis (MTB) and identify resistance to the antibiotic rifampicin (RIF) directly from sputum samples. The test utilizes real-time PCR technology to provide rapid and accurate results.
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The BACTEC MGIT 960 system is a fully automated mycobacterial growth indicator tube (MGIT) system designed for the detection and identification of mycobacteria in clinical specimens. The system utilizes fluorescent technology to continuously monitor for bacterial growth in liquid culture media.
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The MGIT 960 system is a fully automated, high-throughput diagnostic instrument designed for the detection and identification of mycobacteria from clinical specimens. The system utilizes fluorescent technology to monitor the growth of mycobacteria in liquid culture, providing a rapid and efficient method for the diagnosis of tuberculosis and other mycobacterial infections.
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Kanamycin is a broad-spectrum antibiotic derived from the bacterium Streptomyces kanamyceticus. It is commonly used as a selective agent in molecular biology and microbiology laboratories for the growth and selection of bacteria that have been genetically modified to express a gene of interest.
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Middlebrook 7H9 medium is a nutrient-rich growth medium used for the cultivation of mycobacteria, including Mycobacterium tuberculosis. It provides the necessary nutrients and supplements to support the growth of these bacteria in a laboratory setting.

More about "Mycobacterium"

Mycobacterium is a genus of aerobic, non-spore-forming, rod-shaped bacteria that are well-known for their pathogenic species, including the causative agents of tuberculosis (TB) and leprosy.
These bacteria have a unique cell wall structure that contributes to their resilience and ability to persist in host tissues.
Mycobacterial infections, caused by species like Mycobacterium tuberculosis and Mycobacterium leprae, can present a significant public health challenge globally.
Effective diagnosis, treatment, and prevention strategies are critical for managing these infections.
In the laboratory, Mycobacterium species are often cultured using specialized media like Middlebrook 7H9 broth, which may contain additives like Tween 80 and glycerol to support growth.
Diagnostic techniques like the BACTEC MGIT 960 system and the Xpert MTB/RIF assay are commonly used to detect and identify Mycobacterium infections.
Research into Mycobacterium is an active area of study, with scientists exploring various aspects such as drug resistance, pathogenesis, and vaccine development.
PubCompare.ai's AI-powered platform can help optimize this research by identifying the most reproducible and accurate findings from scientific literature, preprints, and patents, empowering researchers with greater efficiency and confidence in their work.