Tuberculosis Research and Epidemiology

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.

A convolutional neural network highlights mutations relevant to antimicrobial resistance in Mycobacterium tuberculosis

This paper presents a deep convolutional neural network to predict antibiotic resistance in M. tuberculosis isolates, achieving state-of-the-art accuracy and enabling interpretable feature analysis.

Higher Native Peruvian ancestry proportion is associated with tuberculosis progression risk

This study finds that higher Native Peruvian ancestry is associated with increased tuberculosis progression risk, independent of socio-demographic and environmental factors.

The discovery of genome-wide mutational dependence in naturally evolving populations

The paper identifies genome-wide mutational dependencies in Mycobacterium tuberculosis evolution, showing how mutations interact to confer antibiotic resistance and detect environmental pressures.

More than Mycobacterium tuberculosis: specific site-of-disease microbial communities, functional capacities, and their distinct clinical profiles in tuberculous lymphadenitis

The paper identifies distinct microbial community clusters in tuberculosis lymphadenitis linked to clinical features and immune responses.

Identification of mutations associated with Macozinone-resistant in Mycobacterium Tuberculosis

The paper identifies mutations conferring resistance to Macozinone in Mycobacterium tuberculosis through in vitro selection and whole genome sequencing.

Relationship between common polymorphisms of NRAMP1 gene and pulmonary tuberculosis in Lorestan LUR population

This study examines the association between NRAMP1 gene polymorphisms and susceptibility to pulmonary tuberculosis in the LUR population of Lorestan, finding significant links for the D543N polymorphism.

Machine learning of all Mycobacterium Tuberculosis H37Rv RNA-seq data reveals complex interplay between metabolism, stress response, and infection

The paper uses machine learning to analyze M. tuberculosis RNA-seq data, identifying gene modules and their roles in metabolism, stress response, and infection.

Experimental Evolution Reveals Redox State Modulates Mycobacterial Pathogenicity

The paper shows that redox state modulates mycobacterial pathogenicity through genetic mutations and gene expression changes in M. smegmatis.

Genomics epidemiology analysis reveals hidden signatures of drug resistance in Mycobacterium tuberculosis

This study analyzes Mtb genomes from Mexico to identify drug resistance signatures and introduces a functional networking tool for exploring resistance mechanisms.

Human alveolar macrophage response to Mycobacterium tuberculosis: immune characteristics underlying large inter-individual variability

The paper examines inter-individual variability in human alveolar macrophage responses to Mycobacterium tuberculosis by analyzing gene and protein expression over time.

Host-pathogen genetic interactions underlie tuberculosis susceptibility

This study identifies host-pathogen genetic interactions influencing tuberculosis susceptibility using a genetically diverse mouse panel and Mtb mutants.

A virtual host model of Mycobacterium tuberculosis infection identifies early immune events as predictive of infection outcomes

The paper develops a whole-host model of Mtb infection to predict immune outcomes and shows blood biomarkers may only reflect early lung events.

Host- and age-dependent transcriptional changes in Mycobacterium tuberculosis cell envelope biosynthesis genes after exposure to human alveolar lining fluid

This study shows that Mycobacterium tuberculosis alters its cell envelope gene expression in response to human alveolar lining fluid, with differences observed between young and elderly donors.

Comparing transmission reconstruction models with Mycobacterium tuberculosis whole genome sequence data

This study compares seven transmission reconstruction tools for Mycobacterium tuberculosis using simulated and real-world data, finding that some tools better identify true transmission events than others.

Connection between two historical tuberculosis outbreak sites in Japan, Honshu, due to a new ancestral L2 sublineage

The paper identifies a new ancestral L2 sublineage of Mycobacterium tuberculosis in Japan, linking historical tuberculosis outbreaks through genetic analysis.

Inferring Mycobacterium bovis transmission between cattle and badgers using isolates from the Randomised Badger Culling Trial

The paper uses whole genome sequences and movement data to infer M. bovis transmission routes between cattle and badgers, finding higher cattle-to-cattle and badger-to-badger transmission rates than between species.

Rare alternative second line injectable drug resistance markers identified by gene-wise genome wide association in M. tuberculosis with unexplained resistance

The paper identifies rare alternative resistance markers in M. tuberculosis using gene-wise genome-wide association, uncovering novel associations with second-line injectable drug resistance.