Systems Microbiology of Intracellular Pathogens
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.
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.
Camilla Ciolli Mattioli
Camilla Ciolli Mattioli studied biotechnology at the University of Florence (Italy) and received her PhD from the Humboldt University of Berlin (Germany) in 2019. During her doctoral research at the Berlin Institute for Medical Systems Biology of the Max Delbrück Center, she focused on the mechanisms driving RNA localization and local translation in eukaryotic cells. She then won a Marie-Curie fellowship and joined the lab of Roi Avraham at the Weizmann Institute of Science (Rehovot, Israel) as a postdoctoral fellow, where she investigated how bacterial phenotypic heterogeneity affects infection outcomes. She has been a research group leader at the Helmholtz Institute for RNA-based Infection Research (HIRI) and a junior professor at the University of Würzburg since February 2026.
Selected Publications
Ciolli Mattioli C, Eisner K, Rosenbaum A, Wang M, Rivalta A, Amir A, Golding I, Avraham R (2023) Physiological stress drives the emergence of a Salmonella subpopulation through ribosomal RNA regulation. Current Biology 33(22):4880-4892.e14 DOI: 10.1016/j.cub.2023.09.064
Heyman O, Yehezkel D, Ciolli Mattioli C, Blumberger N, Rosenberg G, Solomon A, Hoffman D, Bossel Ben-Moshe N, Avraham R (2023) Paired single-cell host profiling with multiplextagged bacterial mutants reveals intracellular virulence-immune networks. PNAS 120(28):e2218812120 DOI: 10.1073/pnas.2218812120
Rosenberg G, Yehezkel D, Hoffman D, Ciolli Mattioli C, Fremder M, Ben-Arosh H, Vainman L, Nissani N, Hen-Avivi S, Brenner S, Itkin M, Malitsky S, Ohana E, Ben-Moshe NB, Avraham R (2021) Host succinate is an activation signal for Salmonella virulence during intracellular infection. Science 371(6527):400-405 DOI: 10.1126/science.aba8026
Ciolli Mattioli C, Rom A, Franke V, Imami K, Arrey G, Teme M, Woehler A, Akalin A, Ulitsky I, Chekulaeva M (2019) Alternative 3' UTRs direct localization of functionally diverse protein isoforms in neuronal compartments. Nucleic Acids Research 47(5):2560-2573 DOI: 10.1093/nar/gky1270
Zappulo A*, Van Den Bruck* D, Ciolli Mattioli C*, Franke V*, Imami K, McShane E, Moreno-Estelles M, Calviello L, Filipchyk A, Peguero-Sanchez E, Müller T, Woehler A, Birchmeier C, Merino E, Rajewsky N, Ohler U, Mazzoni EO, Selbach M, Akalin A, Chekulaeva M (2017) RNA localization is a key determinant of neurite-enriched proteome. Nature Communications 8(1):583 DOI: 10.1038/s41467-017-00690-6
A complete list of publications can be found here.
