Andrea Fossati

Patients with cystic fibrosis are at risk of developing infections caused by Pseudomonas aeruginosa. Normally, these infections are challenging to treat and require intravenous treatment for two weeks. Moreover, the patients frequently remain colonized with P. aeruginosa and with time the strains accumulate antimicrobial resistance mechanisms, thus compromising future treatment. Despite recent emergence of novel antimicrobials, development of resistance is observed already before the new antimicrobials are introduced on the market. Novel strategies are urgently needed for the management of these infections, and it has been proposed to combine traditional antimicrobials with bacteriophages, viruses that selectively infect and kill bacteria with very high specificity. Herein, we describe a multidisciplinary approach with isolation and characterization of bacteriophages and evaluation of their properties in lung organoid models, murine pneumonia models, and finally in a clinical trial where combination of bacteriophages and antimicrobials is compared to standard of care treatment. The infection models described herein simulate acute-on-chronic infections, and we will use multi-omics strategies to assess the immune responses. Phages that will be used in the project have largely been isolated and their detailed bioinformatical characterization is ongoing. Discussions are also ongoing with regulatory agencies on clinical trial design to allow for rapid clinical translation.

I aim to use genetics and proteomics to discover how bacteria combat bacteriophage lysis. Driving this goal is the desire to combat phage resistance mechanisms to make bacteria more susceptible to phage predation. My group will first tackle the problem by employing genetic methods to interrogate the role of M tuberculosis (Mtb) genes in limiting phage replication and bacterial lysis. Using CRISPRi, my group will conduct the first study in the Mtb to determine whether gene knockdown can positively impact phage replication. To increase our understanding of the physical underpinnings of phage resistance, we will create a physical map of the protein-protein interactions between the phage and the bacterium using whole cell fractionation proteomics. This is critical as many phage proteins are of unknown function might interact with essential bacterial complexes. Lastly, I suspect that phage “accessory genes” represent a treasure trove of modulators of host processes, which could be useful genetic fodder for enhancing future phage therapeutics. Using conventional affinity-purification MS, my group will identify the interactor partners of the phage accessory proteins and validate their phenotype with phage replication assays. My goal is to shift the paradigm of phage therapy by identifying essential pathways and complexes in the host that can be inhibited with small molecules or phage engineering to boost lysis and retard the emergence of resistant bacteria during phage therapy.