Tuberculosis Research and Epidemiology

Rescue of Mycobacterium bovis DNA obtained from cultured strains during official surveillance of animal TB: key steps for robust whole genome sequence data generation

The paper describes methods to recover whole genome sequence data from challenging M. bovis DNA samples, improving the success rate of genome recovery from archived cultures.

Drug resistance prediction for Mycobacterium tuberculosis with reference graphs

This paper develops DrPRG, a tool for predicting drug resistance in Mycobacterium tuberculosis using reference graphs, showing improved sensitivity and specificity compared to existing methods.

A Versatile Tool for Precise Variant Calling in Mycobacterium tuberculosis Genetic Polymorphisms

The paper introduces MTB-VCF, a variant calling pipeline for Mycobacterium tuberculosis that identifies sequence variations in resistance genes with high specificity and sensitivity.

Establishment of Tuberculosis Meningitis Mouse Model Using Aerosol Route of W. Beijing HN878 strain

This study establishes a tuberculosis meningitis mouse model using the aerosol route with the HN878 strain, showing reduced bacterial dissemination in BCG-vaccinated mice.

Genome-wide screen identifies host loci that modulate M. tuberculosis fitness in immunodivergent mice

The paper uses transposon mutagenesis and QTL mapping to identify host-pathogen genetic interactions affecting Mtb fitness in immunodivergent mice.

Single nucleotide variation catalogue from clinical isolates mapped on tertiary and quaternary structures of ESX-1 related proteins reveals critical regions as putative Mtb therapeutic targets

The paper identifies conserved regions in ESX-1 related proteins by mapping SNVs from MTB isolates onto protein structures, highlighting potential therapeutic targets.

Diagnostic Accuracy of FluoroCycler XT MTBDR Assay for Detection of Rifampicin and Isoniazid Resistant Mycobacteria tuberculosis in Clinical Isolates from Kenya

This study evaluates the FluoroCycler XT MTBDR assay for detecting rifampicin and isoniazid resistance in Mycobacterium tuberculosis, finding high sensitivity and specificity compared to GenoType MTBDRplus.

The mutational signatures of poor treatment outcomes on the drug-susceptible Mycobacterium tuberculosis genome

The paper identifies bacterial genomic variants and a mutational signature associated with poor treatment outcomes in drug-susceptible tuberculosis, while showing host factors are more important in prediction models.

Mycobacterium tuberculosis-Macrophage Interactome: Molecular Network Structure and Resilience against Antibiotics

The paper analyzes the gene regulatory network and interactome of Mycobacterium tuberculosis to identify structural features contributing to antibiotic resistance.

Altered neutrophil extracellular traps in response to Mycobacterium tuberculosis in persons living with HIV with no previous TB and negative TST and IGRA

The paper compares the neutrophil response to Mycobacterium tuberculosis infection between HIV+ individuals with and without TB history, finding distinct gene expression and NETosis patterns in those without TB.

Proteomic characterization of the Mycobacterium marinum-containing vacuole in Dictyostelium discoideum

The paper characterizes the proteomic composition of Mycobacterium marinum-containing vacuoles in Dictyostelium discoideum at different infection stages and compares them to other mycobacterial compartments.

Tuberculosis severity associates with variants and eQTLs related to vascular biology and infection-induced inflammation

This paper identifies genetic variants and eQTLs associated with TB severity, linking them to vascular biology and inflammation, using GWAS and eQTL analyses in TB patients.

Using a Whole Genome Co-expression Network to Inform the Functional Characterisation of Predicted Genomic Elements from Mycobacterium tuberculosis Transcriptomic Data

The paper constructs a whole genome co-expression network from Mycobacterium tuberculosis transcriptomic data to identify and prioritize unannotated expressed transcripts for functional analysis.

In silico agent-based modeling approach to characterize multiple in vitro tuberculosis infection models

This paper introduces an agent-based model to simulate and compare traditional and spheroid in vitro tuberculosis infection models, showing heterogeneous outputs and predictive capabilities.

Circularization of rv0678 for genotypic bedaquiline resistance testing of Mycobacterium tuberculosis

The paper presents streamlined methods for generating circular DNA from the rv0678 gene to improve genotypic bedaquiline resistance testing in Mycobacterium tuberculosis.

Performances of bioinformatics tools for the analysis of sequencing data of Mycobacterium tuberculosis complex strains

This study evaluates two bioinformatics tools for analyzing MTBC sequencing data, finding high concordance with phenotypic testing and high agreement in lineage determination.

Transcriptome and chromatin accessibility mapping reveals a type I interferon response triggered by Mycobacterium tuberculosis infection

The paper shows Mtb infection triggers a type I interferon response through chromatin remodeling, with PPM1A affecting chromatin accessibility and gene expression.

Laboratory evolution of Mycobacterium smegmatis in the presence of a fluoroquinolone leads to extreme drug resistance phenotype through the over-expression of Msmeg_5659-61 efflux pump.

This study shows that laboratory evolution of Mycobacterium smegmatis under fluoroquinolone pressure leads to extreme drug resistance through overexpression of an efflux pump, without mutations in drug target genes.

Evaluation of Mycobacterium Tuberculosis enrichment in metagenomic samples using ONT adaptive sequencing and amplicon sequencing for identification and variant calling

This study compares Oxford Nanopore adaptive sequencing and PCR amplicon sequencing for detecting Mycobacterium Tuberculosis in metagenomic samples and calls variants, with an open-source analysis framework.

Neutrophil degranulation, NETosis and platelet degranulation pathway genes are co-induced in whole blood up to six months before tuberculosis diagnosis

The paper identifies gene pathways associated with neutrophil and platelet responses that are activated up to six months before TB diagnosis in whole blood.

Common gene signature model discovery and systematic validation for TB prognosis and response to treatment

The paper develops a gene signature model for TB prognosis and treatment response using network-based meta-analysis and machine learning, validated across 57 studies with high predictive accuracy.

An updated evolutionary history and taxonomy of Mycobacterium tuberculosis lineage 5, also called M. africanum

This study improves understanding of Mycobacterium tuberculosis lineage 5 diversity and phylogeography using new genomic data and a novel bioinformatics pipeline.

High Throughput Chromosome Conformation Capture identifies differential genome organization in virulent and avirulent strains of Mycobacterium tuberculosis

This study uses Hi-C to compare genome organization between virulent and avirulent Mycobacterium tuberculosis strains, finding differences in Chromosome Interacting Domain (CID) size and gene distribution.

Characterising indel diversity in a large Mycobacterium tuberculosis outbreak - implications for transmission reconstruction

This study shows that including indels improves transmission reconstruction in a large Mtb outbreak by reducing clonal clusters and altering transmission networks.

Mycobacterium tuberculosis transcriptional regulator Rv1019 is upregulated in hypoxia and negatively regulates Rv3230c-Rv3229c operon encoding enzymes in the oleic acid biosynthetic pathway

This study shows that Rv1019, a transcriptional regulator in M. tuberculosis, is upregulated under hypoxia and negatively regulates an operon involved in oleic acid biosynthesis.

Detection of rifampicin resistance in sputum samples by PCR-ELISA

This study optimizes a PCR-ELISA method to detect rifampicin resistance mutations in sputum samples, showing high specificity and agreement with a commercial test.

Large Registry Based Analysis of Genetic Predisposition to Tuberculosis Identifies Genetic Risk Factors at HLA

The paper identifies genetic risk factors for tuberculosis, including HLA alleles and INPP5A variants, and shows smoking as a lifestyle risk factor.

High-resolution transcriptomics of bovine purified protein derivative-stimulated peripheral blood from cattle infected with Mycobacterium bovis across an experimental time course

The paper identifies a 170-gene transcriptional signature in bovine peripheral blood post-M. bovis infection following PPD-b stimulation, suggesting potential biomarkers for bTB diagnostics.

Quantitative Systems Pharmacology Modeling Framework of Autophagy in Tuberculosis: Application to Adjunctive Metformin Host-Directed Therapy

This paper develops a QSP framework to evaluate metformin's effect on autophagy in tuberculosis, showing limited but dose-dependent benefits in reducing bacterial load and inflammation.

Unravelling the population structure and transmission patterns of Mycobacterium tuberculosis in Mozambique, a high TB/HIV burden country

The paper uses whole-genome sequencing to analyze Mycobacterium tuberculosis population structure and transmission patterns in Mozambique, finding recent transmission and endemic clades linked to HIV/TB coinfected patients.