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Related Concept Videos

Pulmonary Tuberculosis IV01:26

Pulmonary Tuberculosis IV

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Tuberculosis, more commonly referred to as TB, is an infectious disease stemming from Mycobacterium tuberculosis. While it primarily impacts the lungs, TB can also affect other body areas. Given its severity and global impact, timely and accurate diagnosis is crucial for controlling its spread and improving patient outcomes.
Several diagnostic approaches are used to detect TB. The conventional method is the Tuberculin Skin Test (TST), also known as the Mantoux test. However, this method has...
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Pulmonary Tuberculosis V01:28

Pulmonary Tuberculosis V

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Medical management of tuberculosis (TB) patients involves a comprehensive approach that includes diagnosis, treatment, and monitoring. The specific strategies can vary depending on the type of tuberculosis (latent or active), the patient's overall health status, and other considerations.
Latent tuberculosis infection occurs when TB bacteria are present in a person's body, but are not causing illness or symptoms. It is not contagious, and preventive treatment is crucial to avoid the...
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Pulmonary Tuberculosis III01:31

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Tuberculosis (TB) is a contagious infection primarily affecting the lung parenchyma but which can also affect other body parts. TB can be classified based on disease development, presentation, and the affected anatomical site.
The first classification is based on the development of the disease, and it includes the following categories:
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Pulmonary Tuberculosis I01:29

Pulmonary Tuberculosis I

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Tuberculosis, often called TB, is a contagious illness primarily caused by Mycobacterium tuberculosis. It mainly affects the lung parenchyma but can also impact other body parts.
Causative Organism
The primary infectious agent causing tuberculosis is Mycobacterium tuberculosis, a slow-growing, acid-fast, aerobic rod that exhibits sensitivity to heat and ultraviolet light. Instances of Mycobacterium bovis and Mycobacterium avium contributing to the development of TB infection are rare.
Mode of...
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Pulmonary Tuberculosis II01:28

Pulmonary Tuberculosis II

681
Tuberculosis, or TB, is a bacterial infectious disease caused by Mycobacterium tuberculosis. While its primary impact is on the lungs, leading to pulmonary tuberculosis, it can also affect various other organs, a condition referred to as extrapulmonary tuberculosis.
Here is a detailed explanation of its pathophysiology:
Transmission: The process begins when a person inhales droplet nuclei containing M. tuberculosis. These are typically released into the air when an individual with pulmonary or...
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Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

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Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
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Matrix-based DNA Extraction for Targeted Next-Generation Sequencing on Decontaminated Sputum Samples
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GenTB: A user-friendly genome-based predictor for tuberculosis resistance powered by machine learning.

Matthias I Gröschel1, Martin Owens1, Luca Freschi1

  • 1Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.

Genome Medicine
|August 31, 2021
PubMed
Summary

GenTB, a new web tool, accurately predicts multidrug-resistant tuberculosis (MDR-TB) from DNA sequences, offering a faster alternative to traditional testing. This aids clinicians in diagnosing drug resistance and tailoring patient treatment plans effectively.

Keywords:
DiagnosticsDrug resistanceDrug-susceptibility testingMDR-TBMachine learningTuberculosisWhole genome sequencingXDR-TB

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Area of Science:

  • Genomics
  • Computational Biology
  • Infectious Disease

Background:

  • Multidrug-resistant tuberculosis (MDR-TB) poses a significant global health challenge.
  • Genotypic resistance prediction from Mycobacterium tuberculosis (Mtb) DNA sequences offers a promising alternative to conventional drug-susceptibility testing.
  • There is a critical need for user-friendly and accurate tools to facilitate rapid diagnosis and inform treatment decisions.

Purpose of the Study:

  • To introduce the Translational Genomics platform for Tuberculosis (GenTB), a free, open-access web application.
  • To enable prediction of antibiotic resistance in Mtb using next-generation sequencing data.
  • To provide users with a choice between Random Forest (RF) and Wide and Deep Neural Network (WDNN) prediction models.

Main Methods:

  • GenTB was developed as a web-based application utilizing RF and WDNN classifiers.
  • Predictive performance was benchmarked against leading tools (Mykrobe, TB-Profiler) using a dataset of 20,408 Mtb isolates with known drug susceptibility.
  • Sensitivity and specificity metrics were evaluated for predicting resistance to multiple anti-tuberculosis drugs.

Main Results:

  • GenTB demonstrated reliable prediction of first-line drug resistance, with competitive performance for second-line drugs.
  • GenTB-RF and GenTB-WDNN showed mean sensitivities of 77.6% and 75.4% respectively across nine shared drugs, slightly outperforming TB-Profiler and Mykrobe.
  • Lower sequence data quality (depth < 10×) negatively impacted genotypic resistance sensitivity for key drugs like isoniazid and rifampicin.

Conclusions:

  • GenTB is an accessible and effective online tool for rapid and accurate prediction of anti-tuberculosis drug resistance.
  • The platform aids public health and clinical practitioners in managing MDR-TB.
  • GenTB is available online with its source code publicly accessible for further development and application.