S. Gagneux

Bacterial diversity dominates variable macrophage responses of tuberculosis patients in Tanzania

The study infects macrophages from tuberculosis patients with different MTBC lineages to show that bacterial phylogenetic diversity, not local adaptation, drives variable macrophage responses.

HIV co-infection is associated with reduced Mycobacterium tuberculosis transmissibility in sub-Saharan Africa

This study uses genomic data and a Bayesian phylodynamic model to show HIV co-infection reduces Mycobacterium tuberculosis transmissibility in sub-Saharan Africa.

Leprosy in wild chimpanzees

The paper reports leprosy-like lesions in wild chimpanzees and identifies M. leprae strains with rare genotypes, suggesting multiple introductions from an unknown source.

HIV coinfection is associated with low fitness rpoB variants in rifampicin-resistant Mycobacterium tuberculosis

The paper analyzes drug-resistant Mtb genomes from HIV coinfected and HIV negative patients, finding that HIV coinfected patients have more low fitness rpoB variants in rifampicin-resistant strains.

An African origin for Mycobacterium bovis

The paper traces the origin of Mycobacterium bovis to East Africa and identifies its global dispersal patterns through phylogenetic and phylogeographic analysis.

A sister lineage of the Mycobacterium tuberculosis complex discovered in the African Great Lakes region

The paper identifies a new lineage of Mycobacterium tuberculosis complex, Lineage 8, found in the African Great Lakes region, and shows its evolutionary relationship to known lineages.

Multiple merger genealogies in outbreaks of Mycobacterium tuberculosis

This study uses Approximate Bayesian Computation to show that multiple merger coalescents better fit Mycobacterium tuberculosis outbreak data than the Kingman coalescent.

Interaction between host genes and M. tuberculosis lineage can affect tuberculosis severity: evidence for co-evolution

The paper investigates the interaction between host genetic variants and Mycobacterium tuberculosis lineage to determine their combined effect on TB severity, finding significant interactions that support host-pathogen co-evolution.

The Evolution of Fluoroquinolone-Resistance in Mycobacterium tuberculosis is Modulated by the Genetic Background

This study shows that the genetic background of Mycobacterium tuberculosis significantly affects the evolution of fluoroquinolone resistance in both in vitro experiments and clinical isolates.

Dispersal of Mycobacterium tuberculosis to indigenous populations driven by historical European trade in the South Pacific

This paper traces the dispersal of Mycobacterium tuberculosis lineage 4.4 strains in New Zealand and Canada using genomic data, linking their spread to historical European trade and migration.

The molecular clock of Mycobacterium tuberculosis

This study systematically analyzes the molecular clock of Mycobacterium tuberculosis using 6,285 strains, finding wide variation in clocklike structure and SNP accumulation rates independent of calibration time.

Molecular epidemiology and whole genome sequencing analysis of clinical Mycobacterium bovis from Ghana

This study analyzes Mycobacterium bovis isolates from Ghana using whole-genome sequencing to identify risk factors and genetic characteristics associated with bovine tuberculosis.

Resource misallocation as a mediator of fitness costs in antibiotic resistance.

The paper investigates the fitness cost of rifampicin resistance in Mycobacterium tuberculosis using transcriptomic and proteomic profiling, finding that aberrant gene expression causes the cost and that this burden can be suppressed.

Genomic determinants of sympatric speciation of the Mycobacterium tuberculosis complex across evolutionary timescales.

This study identifies genomic factors driving sympatric speciation in Mycobacterium tuberculosis complex across evolutionary timescales, highlighting the role of phoR in virulence and adaptation.

Transition bias influences the evolution of antibiotic resistance in Mycobacterium tuberculosis

The paper shows transition bias drives antibiotic resistance mutations in Mycobacterium tuberculosis, suggesting mutation supply, not selection, is the cause.

Multiple Introductions of the Mycobacterium tuberculosis Lineage 2 Beijing into Africa over centuries

This study uses whole genome sequences to show that L2-Beijing tuberculosis strains were introduced multiple times into Africa from East and Southeast Asia over the past 300 years, likely due to hypervirulence and transmissibility.

Whole genome sequencing for drug resistance profile prediction in Mycobacterium tuberculosis

This study uses whole genome sequencing to predict drug resistance profiles in M. tuberculosis isolates, achieving high sensitivity and specificity compared to phenotypic testing.

Reference Set of Mycobacterium tuberculosis Clinical Strains: A tool for research and product development

The paper introduces a reference set of 20 genetically characterized Mycobacterium tuberculosis clinical strains to enhance TB research by incorporating phylogenetic diversity beyond the commonly used lab strains.

A New Phylogenetic Framework for the Animal-adapted Mycobacterium tuberculosis Complex

This study analyzes 529 MTBC genomes to reveal the phylogenetic relationships and evolutionary history of animal-adapted MTBC ecotypes, identifying four clades and suggesting host shifts and demographic factors drive host tropism.

Compensatory evolution drives multidrug-resistant tuberculosis in Central Asia

The paper investigates the evolutionary mechanisms behind multidrug-resistant tuberculosis in Central Asia, finding that compensatory mutations enhance resistance and transmission success.