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Bioinformatics Training

 

I am a Senior Research Associate at the Department of Veterinary Medicine of the University of Cambridge and a visiting scientist at the Victor Phillip Dahdaleh Heart & Lung Research Institute (HLRI) where I study Antimicrobial Resistance and Host-pathogen Interactions in Gram negative human pathogens, especially Salmonella Typhimurium, Klebsiella pneumoniae and Mycobacterium abscessus.
I use several Next Generation Sequencing techniques in the field of functional genomics such as deep transcriptome sequencing (RNA-seq) and transposon directed insertion sequencing (TraDIS), Illumina and Oxford nanopore based whole genome sequencing (WGS) and genome wide association studies (GWAS) as well as wet-lab methods like flow cytometry (FACS) and confocal fluorescence microscopy.

Biography

After graduating from the Technical University of Braunschweig/Germany, I joined to lab of Susanne Häussler at the Helmholtz Centre for Infection Research. During my PhD I used deep transcriptomic sequencing (RNA-seq) to study Antimicrobial Resistance in Pseudomonas aeruginosa and Klebsiella pneumoniae. Followed by a short post-doc in the same group where I developed rapid molecular diagnostics to detect hospital outbreaks and antibiotic resistance in several different bacterial species (mainly, Pseudomonas aeruginosa, Klebsiella pneumoniae, Escherichia coli and Clostridium difficile). In 2017, I took up a post as a postdoctoral fellow in the Parkhill group at the Wellcome Sanger Institute using Functional Genomics (RNA-sequencing and transposon-directed insertion site sequencing, TraDIS) to understand the antimicrobial stress response in the Enterobacteriaceae species Klebsiella, Salmonella and Enterobacter.

Publications

Key publications: 

 

Identifying virulence determinants of multidrug-resistant Klebsiella pneumoniae in Galleria mellonella
S Bruchmann, T Feltwell, J Parkhill, FL Short
Pathogens and disease 79 (3), ftab009


Deep transcriptome profiling of clinical Klebsiella pneumoniae isolates reveals strain and sequence type‐specific adaptation
S Bruchmann, U Muthukumarasamy, S Pohl, M Preusse, A Bielecka, ...
Environmental microbiology 17 (11), 4690-4710


Discordant bioinformatic predictions of antimicrobial resistance from whole-genome sequencing data of bacterial isolates: an inter-laboratory study
RM Doyle, DM O'sullivan, SD Aller, S Bruchmann, T Clark, AC Pelegrin, ...
Microbial genomics 6 (2)


Spatiotemporal control of FlgZ activity impacts Pseudomonas aeruginosa flagellar motility
S Bense, S Bruchmann, A Steffen, TEB Stradal, S Häussler, J Düvel
Molecular Microbiology 111 (6), 1544-1557


Importance of flagella in acute and chronic Pseudomonas aeruginosa infections
A Lorenz, M Preuße, S Bruchmann, V Pawar, N Grahl, MC Pils, LM Nolan, ...
Environmental microbiology 21 (3), 883-897


BACTOME—a reference database to explore the sequence- and gene expression-variation landscape of Pseudomonas aeruginosa clinical isolates
K Hornischer, A Khaledi, S Pohl, M Schniederjans, L Pezoldt, F Casilag, ...
Nucleic acids research 47 (D1), D716-D720


Transcriptome profiling of antimicrobial resistance in Pseudomonas aeruginosa
A Khaledi, M Schniederjans, S Pohl, R Rainer, U Bodenhofer, B Xia, ...
Antimicrobial agents and chemotherapy 60 (8), 4722-4733

Teaching and Supervisions

Teaching: 

 

2023/2024:

  • Cholera Genomics - Training Lead
  • Working with Bacterial Genomes - Trainer