Tuberculosis Research and Epidemiology

Comprehensive and accurate genetic variant identification from contaminated and low coverage Mycobacterium tuberculosis whole genome sequencing data.

This paper introduces XBS, a bioinformatics pipeline that improves variant detection in contaminated and low coverage Mycobacterium tuberculosis sequencing data, outperforming existing methods in complex genomic regions and low-depth samples.

Silencing of an efflux pump coding gene decreases the efflux rate of pyrazinoic acid in Mycobacterium smegmatis

The paper silences efflux pump genes in Mycobacterium smegmatis and finds that silencing MSMEG_0250 reduces POA efflux rate by 5-fold.

Mycobacteria-host interactions in human bronchiolar airway organoids

This study uses human airway organoids to model tuberculosis infection, showing mycobacteria infect epithelial cells with low efficiency and the organoid microenvironment controls but does not eliminate the pathogen.

Genome-wide association studies of global Mycobacterium tuberculosis resistance to thirteen antimicrobials in 10,228 genomes

This study performs genome-wide association analyses on 10,228 Mycobacterium tuberculosis genomes to identify genetic variants linked to resistance against 13 antimicrobials.

AbmR is a mycobacterial dual-function transcription factor and ribonucleoprotein with distinct DNA and RNA-binding determinants

This study identifies AbmR as a dual-function transcription factor and ribonucleoprotein in Mtb that binds DNA and RNA with distinct determinants, affecting gene regulation and RNA stability.

Epigenetic impairment and blunted transcriptional response to Mycobacterium tuberculosis of alveolar macrophages from persons living with HIV

The paper investigates how HIV and antiretroviral therapy affect the transcriptional and epigenetic response of alveolar macrophages to Mycobacterium tuberculosis.

In Silico analysis of PE_PGRS20 (Rv1068c) protein in Mycobacterium tuberculosis H37Rv

This study analyzes the PE_PGRS20 protein in M. tuberculosis H37Rv using bioinformatics tools to explore its potential role in virulence and drug resistance.

GenTB: A user-friendly genome-based predictor for tuberculosis resistance powered by machine learning

GenTB predicts tuberculosis drug resistance from genomic data using machine learning, achieving higher sensitivity than existing tools with slightly lower specificity.

The role of epistasis in amikacin, kanamycin, bedaquiline, and clofazimine resistance in Mycobacterium tuberculosis complex

The paper demonstrates epistatic interactions in Mycobacterium tuberculosis complex that can reverse antibiotic resistance, specifically showing that eis promoter mutations cannot confer resistance if paired with LoF mutations in the eis coding region.

Genetic composition and evolution of the prevalent Mycobacterium tuberculosis lineages 2 and 4 in the Chinese and Zhejiang Province populations

The paper analyzes whole-genome sequencing data of Mycobacterium tuberculosis isolates to study lineage evolution and antigenic diversity in China and Zhejiang Province.

An interpretable classification method for predicting drug resistance in M. tuberculosis

This paper introduces an interpretable classification method for predicting drug resistance in M. tuberculosis, achieving high accuracy and flexibility.

CRISPR interference identifies vulnerable cellular pathways with bactericidal phenotypes in Mycobacterium tuberculosis

This study uses CRISPR interference to assess the vulnerability and lethality of 96 target genes in Mycobacterium tuberculosis, identifying bactericidal and bacteriostatic effects across different cellular pathways.

Mycobacterium tuberculosis complex lineage 5 exhibits high levels of within-lineage genomic diversity and differing gene content compared to the type strain H37Rv

The paper identifies high within-lineage genomic diversity and gene content differences in Mycobacterium tuberculosis complex lineage 5 compared to H37Rv, affecting transmission analysis and suggesting the need for alternative reference genomes.

Structure-aware M. tuberculosis functional annotation uncloaks resistance, metabolic, and virulence genes

The paper updates functional annotations for Mycobacterium tuberculosis genes using literature curation and structural modeling, identifying resistance, metabolic, and virulence genes.

Comparative proteome analysis revealed the differences in responses of bovine alveolar macrophages to both M.tb and Mb infection

The paper compares the proteomic responses of bovine alveolar macrophages to Mycobacterium tuberculosis and Mycobacterium bovis infections, finding greater sensitivity to MB and distinct activation of autophagy and inflammatory pathways.

Integrative genomics of the mammalian alveolar macrophage response to intracellular mycobacteria

The paper integrates multi-omics data with genome-wide association results to identify infection response pathways and genomic variants associated with resistance to bovine tuberculosis.

Population structure and transmission of Mycobacterium bovis in Ethiopia

This study uses whole genome sequencing to analyze the population structure and transmission patterns of Mycobacterium bovis in Ethiopia, identifying two distinct introductions of the Eu3 clonal complex from Europe.

Phylogenomics Sheds Light on the population structure of Mycobacterium bovis from a Multi-Host Tuberculosis System

The paper uses whole genome sequencing to analyze M. bovis isolates from Portugal, revealing genetic clades and transmission networks in a multi-host tuberculosis system.

Whole genome sequencing based differentiation between re-infection and relapse in Indian patients with tuberculosis recurrence, with and without HIV co-infection

This study uses whole genome sequencing to differentiate between TB relapse and re-infection in HIV-positive and negative patients, finding 95% relapse in HIV-negative and 75% re-infection in HIV-positive cases.

Association of NRAMP1-INT4 gene with Susceptibility to Tuberculosis in the Sudanese Population: A Case-Control Study

The paper investigates the association between NRAMP1-INT4 polymorphism and TB susceptibility in Sudanese patients, finding a significant link with heterozygosity for the variant.

A multi-scale pipeline linking drug transcriptomics with pharmacokinetics predicts in vivo interactions of tuberculosis drugs

This paper links drug transcriptomics with pharmacokinetics to predict in vivo drug interactions for tuberculosis treatments.

Genome-wide association study of resistance to Mycobacterium tuberculosis infection identifies a locus at 10q26.2 in three distinct populations

Identification of reduced host transcriptomic signatures for tuberculosis and digital PCR-based validation and quantification

The paper identifies reduced host transcriptomic signatures for tuberculosis using microarray data and validates them with digital PCR, showing high accuracy in distinguishing TB from other conditions and latent TB.

MtrA regulation of essential peptidoglycan cleavage in Mycobacterium tuberculosis during infection

This study identifies MtrA as a critical regulator of peptidoglycan cleavage in Mtb, essential for survival under acidic stress and a potential drug target.

Transmission of pre-XDR and XDR-TB in the Mumbai Metropolitan Region, India

The paper analyzes whole genome sequencing data from tuberculosis strains in Mumbai to identify factors driving the pre-XDR and XDR-TB epidemic, finding lineage 2 strains are strongly associated with these resistant forms.

Phylogenomics of Mycobacterium africanum reveals a new lineage and a complex evolutionary history

The paper analyzes genomes of Mycobacterium africanum strains to identify a new lineage and explore their evolutionary history and phylogeography.

Local adaptation in populations of Mycobacterium tuberculosis endemic to the Indian Ocean Rim

The paper analyzes whole genome sequences of Mycobacterium tuberculosis lineages L1 and L3 to show South Asia's role in their dispersion and identify local adaptation at the esxH locus.

Multi-omic regulatory networks capture downstream effects of kinase inhibition in Mycobacterium tuberculosis

The paper shows that kinase inhibition in Mtb affects regulatory networks, altering cell wall integrity, stress response, and energy production through transcription factor activity changes.

Metabolic flux partitioning between the TCA cycle and glyoxylate shunt combined with a reversible methyl citrate cycle provide nutritional flexibility for Mycobacterium tuberculosis

This paper identifies the metabolic flux partitioning between the TCA cycle, glyoxylate shunt, and reversible methyl citrate cycle in Mtb as critical for its nutritional flexibility when co-metabolizing carbon substrates.

Quantitative prediction of conditional vulnerabilities in regulatory and metabolic networks of Mycobacterium tuberculosis

This paper introduces PRIME, a model predicting environment-specific vulnerabilities in Mtb's regulatory and metabolic networks, validated through genome-wide fitness screens.