Electron micrograph of Salmonella typhimurium on a COS7 cell
© HZI / Rohde
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Systems Microbiology of Intracellular Pathogens

Bacterial and Viral Pathogens
HIRI
Junior group
Research group of the HZI

The research group led by Camilla Ciolli Mattioli decodes how intracellular bacteria, like Salmonella, survive, persist, and evade destruction within host cells. By revealing the molecular mechanisms that determine infection outcomes, the team aims to develop new strategies to combat antibiotic-resistant infections. This group is located at the Helmholtz Institute for RNA-based Infection Research (HIRI).

Jun Prof Dr Camilla Ciolli Mattioli

Head

Jun Prof Dr Camilla Ciolli Mattioli
Research Group Leader

Our Research

Antibiotic-resistant intracellular pathogens pose a critical threat: they hide inside our cells, evading both immune defenses and antibiotics. Understanding how these bacteria adapt and survive requires capturing the full picture of host-pathogen interactions at single-cell resolution in physiologically-relevant infection models—something current technologies cannot achieve.

Camilla Ciolli Mattioli’s group develops innovative platforms that simultaneously capture host and pathogen gene expression at single-cell resolution during infection. The researchers complement this with spatial transcriptomics to map interactions within native tissue architectures and CRISPR-based molecular recording systems to trace bacterial transcriptional histories. 

By integrating spatial, temporal, and phenotypic dimensions—using image-enabled cell sorting to isolate specific infection outcomes—the group identifies molecular switches that determine whether bacteria persist, replicate, or face elimination. Its goal is to discover vulnerabilities in bacterial survival strategies and reveal therapeutic targets that redirect infections toward pathogen clearance, advancing the fight against antimicrobial resistance.

Newsroom

Further information:

A current overview of the team and further information about the research group can be found in the HIRI page