S. Niemann

This study examines phylogroup-specific evolutionary dynamics in Pseudomonas aeruginosa genomes, revealing distinct pangenome characteristics and distribution patterns of antimicrobial resistance genes and defence systems.

This study shows that sequential therapy with only beta-lactam antibiotics can increase bacterial population extinction by reducing spontaneous resistance and cross-resistance.

This study identifies 230 genomic variants associated with resistance to bedaquiline and clofazimine in tuberculosis using experimental evolution, genome sequencing, and structural modeling.

This study uses global whole-genome sequencing data to identify international tuberculosis transmission clusters, improving surveillance by connecting cases across countries.

This study analyzes the population structure, biogeography, and transmissibility of Mycobacterium tuberculosis using genomic data from thousands of strains, identifying new clades and sub-lineages.

This study introduces EnteroBase, a database for C. difficile genomic data, showing it can identify related genomes with 89% consistency between cgMLST and SNPs.

This study shows that the WNT6-ACC2 pathway promotes lipid droplet accumulation in macrophages, which Mycobacterium tuberculosis exploits for growth, and that inhibiting this pathway enhances anti-tuberculosis treatment.

This study identifies genetic mutations associated with resistance to bedaquiline and delamanid in Mycobacterium tuberculosis strains using whole genome sequencing and in silico analysis.

This study identifies that insertions and deletions (indels) contribute to antibiotic resistance evolution in Mycobacterium tuberculosis during an outbreak, with indels showing a slower evolutionary rate than substitutions.

The paper analyzes isoniazid resistance in M. tuberculosis strains, finding overlapping MIC distributions and showing that whole-genome sequencing can explain most resistance levels.

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.

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

This paper introduces SNP-IT, a method using whole genome sequencing to identify subspecies and lineages of Mycobacterium tuberculosis complex, revealing high prevalence of M. orygis in UK clinical isolates.