S. Niemann

Phylogenomic and genomic analysis reveals unique and shared genetic signatures of Mycobacterium kansasii complex species

This study analyzes 665 Mycobacterium kansasii complex strains to identify unique and shared genomic signatures, revealing lineage splits, virulence factors, and drug resistance mechanisms.

Phylogroup-specific variation shapes the clustering of antimicrobial resistance genes and defence systems across regions of genome plasticity

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.

High potency of sequential therapy with only beta-lactam antibiotics

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

Deciphering Bedaquiline and Clofazimine Resistance in Tuberculosis: An Evolutionary Medicine Approach

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

Improving tuberculosis surveillance by detecting international transmission using publicly available whole-genome sequencing data

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

Population structure, biogeography and transmissibility of Mycobacterium tuberculosis

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.

Global genomic population structure of Clostridioides difficile

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

WNT6-ACC2-induced accumulation of triacylglycerol rich lipid droplets is exploited by Mycobacterium tuberculosis

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.

Characterization of genomic variants associated with resistance to bedaquiline and delamanid in naïve Mycobacterium tuberculosis clinical strains

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

Insertion and deletion evolution reflects antibiotics selection pressure in a Mycobacterium tuberculosis outbreak.

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.

Isoniazid resistance in Mycobacterium tuberculosis is a heterogeneous phenotype comprised of overlapping MIC distributions with different underlying resistance mechanisms

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

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.

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.

A novel multi SNP based method for the identification of subspecies and associated lineages and sub-lineages of the Mycobacterium tuberculosis complex by whole genome sequencing

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.