Tuberculosis Research and Epidemiology

The paper introduces a phylogeny-related parallelism score to improve machine learning prediction of antibiotic resistance in M. tuberculosis by incorporating evolutionary relationships.

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.

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.

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

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

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

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

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 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.

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

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.

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.

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.

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

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.

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

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

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

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.

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.

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

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.

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

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.

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

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.

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

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

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.

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.