Stefan Niemann

This study identifies niche-specific metabolic differences in non-typeable Haemophilus influenzae (NTHi) isolates from ear, pharynx, and lung sites, revealing site-specific metabolic profiles.

This study identifies Serratia sp. as a dominant genus in the lung microbiome of TB and NTM-LD patients, with specific ASVs associated with disease states.

This study investigates sex differences in immune response to TB vaccines in mice, finding that male mice show poorer BCG vaccine efficacy and specific CD8 T cell deficiencies compared to females.

This study shows that C1q from the classical complement pathway, along with MBL from the lectin pathway, recognizes MTBC strains, with C1q playing a key role in complement activation.

The paper updates the EnteroBase platform with new data and tools for genomic epidemiology of bacterial pathogens, including antimicrobial resistance detection and visualization features.

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

This study quantifies antibiotic resistance in tuberculosis using genomic data and MIC measurements to identify genetic determinants of resistance and hypersensitivity across multiple drugs.

The paper demonstrates epistatic interactions in Mycobacterium tuberculosis complex that can reverse antibiotic resistance, specifically showing that eis promoter mutations cannot confer resistance if paired with LoF mutations in the eis coding region.

The paper identifies high within-lineage genomic diversity and gene content differences in Mycobacterium tuberculosis complex lineage 5 compared to H37Rv, affecting transmission analysis and suggesting the need for alternative reference genomes.

The paper predicts the secretomes of M. abscessus isolates and identifies antigenic differences between subspecies and colony morphotypes.

This study performs a genome-wide association analysis of host genetic variants and MTBC strain infection in two cohorts, identifying 32 SNPs significantly associated with infection risk in the Ghanaian cohort.

The paper analyzes whole genome sequencing data from tuberculosis strains in Mumbai to identify factors driving the pre-XDR and XDR-TB epidemic, finding lineage 2 strains are strongly associated with these resistant forms.

The paper analyzes genomes of Mycobacterium africanum strains to identify a new lineage and explore their evolutionary history and phylogeography.

The paper analyzes global S. maltophilia strains to show genetic diversity and intra-hospital transmission.

GenomegaMap estimates genome-wide dN/dS ratios across 10,209 tuberculosis genomes to identify selection pressures shaping the pathogen's evolution.

The paper compares the genomes of Mycobacterium africanum Lineage 5 and 6 from Ghana, finding genomic diversity and selection pressure differences suggesting distinct ecological niches.

This paper develops a tool to predict antibiotic resistance in S. aureus and M. tuberculosis from genome sequences with high accuracy and speed.